Citrus Sinensis ID: 017573

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------37
Protein Sequence
MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPSNVADLL
Secondary Structure (PSIPRED)
ccccHHHHHHHHHcccccccHHHHHHHHHHHccccEEEEcccccHHHHHHHHHHHHccccccccEEEEEEcccHHHHHHHHHHHHHHHcccccEEEEEEccccHHHHHHHHcccccEEEcccHHHHHHHcccccccccccEEEEEccHHccccccHHHHHHHHHHcccccEEEEEEccccHHHHHHHHHHccccEEEEEEccccccccEEEEEEEEccccHHHHHHHHHHHHcccccEEEEEcccccHHHHHHHHHHcccEEEEEccccccHHHHHHHHHHHcccccEEEEccccccccccccccEEEEccccccccccEEccccccccccccEEEEcccHHHHHHHHHHHHHHccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccHHHHHHHHHcccccccccHHHHHHHHHccccEEEEccccHHHHHHHHHHHHHHcccccccccEEEEcccHHHHHHHHHHHHHHcccccccEEEEcccccHHHHHHHHHHccEEEEEcHHHHHHHHcccccccccccEEEEccHHHHHccccHHHHHHHHHccccccEEEEEEccccHHHHHHHHHHccccEEEEcEcccccccccEEEEEEEccHHHHHHHHHHHHHcccccEEEEEEccHHHHHHHHHHHHHcccEEEEEcccccHHHHHHHHHHHHccccEEEEEEEHHHccccccccEEEEEEcccccccHcEEEEccccccccccEEEEEEcHHHHHHHHHHHHHHHHHHccccccHHHHc
Coil and Loop (DISEMBL)
MGLQENLLRGIYAygfekpsaiqqrgivpfckgLDVIQQaqsgtgktatfCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHAcvggtsvreDQRILQAGVHVVVGTPGRVFDMLRrqslrpdyikMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQvgvfsatmppeALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDwltdkmrsrdhtvsathgdmdqntRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVInydlptqpenylhrigrsgrfgrkgvainfvtrdderMLFDIQKFYNVVIEELpsnvadll
Flexible Loop (DISEMBL)
MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGvhvvvgtpgrvfDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMPPEALeitrkfmnkpvRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLaitqsvifvntrrkvdwltdkmrsrdhtvsathgdmdqntrDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYlhrigrsgrfgrkGVAINfvtrddermLFDIQKFYNVVIEELPSNVADLL
Low Complexity Region (SEG)
MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPSNVADLL
Disordered region (IsUnstruct)
******LLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDK********************DIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEEL********
Disordered Region (DISOPRED)
*GLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPSNV*DLL
Disordered Region (DISEMBL)
MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPSNVADLL
Disordered Region (DISPRO)
MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPSNV****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPSNVADLL
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	369	2.2.26 [Sep-21-2011]
P41381	413	Eukaryotic initiation fac	N/A	no	1.0	0.893	0.970	0.0
P35683	414	Eukaryotic initiation fac	yes	no	1.0	0.891	0.970	0.0
P41379	413	Eukaryotic initiation fac	N/A	no	1.0	0.893	0.970	0.0
Q6Z2Z4	414	Eukaryotic initiation fac	yes	no	1.0	0.891	0.967	0.0
Q40467	413	Eukaryotic initiation fac	N/A	no	1.0	0.893	0.964	0.0
P41376	412	Eukaryotic initiation fac	yes	no	1.0	0.895	0.967	0.0
P41382	413	Eukaryotic initiation fac	N/A	no	1.0	0.893	0.964	0.0
Q40465	413	Eukaryotic initiation fac	N/A	no	1.0	0.893	0.967	0.0
P41378	414	Eukaryotic initiation fac	N/A	no	1.0	0.891	0.964	0.0
Q41741	410	Eukaryotic initiation fac	N/A	no	1.0	0.9	0.953	0.0

>sp|P41381|IF4A8_TOBAC Eukaryotic initiation factor 4A-8 OS=Nicotiana tabacum PE=2 SV=1

 Score =  745 bits (1923), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 358/369 (97%), Positives = 366/369 (99%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
           MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY
Sbjct: 45  MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 104

Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG 120
           GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL AGVHV+VG
Sbjct: 105 GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILAAGVHVIVG 164

Query: 121 TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMP 180
           TPGRVFDMLRRQSLRPDY++MFVLDEADEMLSRGFKDQIYDIFQ+LP KVQVGVFSATMP
Sbjct: 165 TPGRVFDMLRRQSLRPDYLRMFVLDEADEMLSRGFKDQIYDIFQMLPTKVQVGVFSATMP 224

Query: 181 PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVI 240
           PEAL+ITRKFMNKPVRILVKRDELTLEGIKQFYVNV+KEEWKLETLCDLYETLAITQSVI
Sbjct: 225 PEALDITRKFMNKPVRILVKRDELTLEGIKQFYVNVDKEEWKLETLCDLYETLAITQSVI 284

Query: 241 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 300
           FVNTRRKVDWLTDKMR+RDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID
Sbjct: 285 FVNTRRKVDWLTDKMRTRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 344

Query: 301 VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEE 360
           VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVT DDERMLFDIQKFYNV+IEE
Sbjct: 345 VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTTDDERMLFDIQKFYNVIIEE 404

Query: 361 LPSNVADLL 369
           LPSNVADLL
Sbjct: 405 LPSNVADLL 413

ATP-dependent RNA helicase which is a subunit of the eIF4F complex involved in cap recognition and is required for mRNA binding to ribosome. In the current model of translation initiation, eIF4A unwinds RNA secondary structures in the 5'-UTR of mRNAs which is necessary to allow efficient binding of the small ribosomal subunit, and subsequent scanning for the initiator codon.
Nicotiana tabacum (taxid: 4097)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 3

>sp|P35683|IF4A1_ORYSJ Eukaryotic initiation factor 4A-1 OS=Oryza sativa subsp. japonica GN=Os06g0701100 PE=2 SV=2

 Score =  744 bits (1920), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 358/369 (97%), Positives = 366/369 (99%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
           MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY
Sbjct: 46  MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 105

Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG 120
            +V+CQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL +GVHVVVG
Sbjct: 106 AVVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILASGVHVVVG 165

Query: 121 TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMP 180
           TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLP+K+QVGVFSATMP
Sbjct: 166 TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPSKIQVGVFSATMP 225

Query: 181 PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVI 240
           PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKL+TLCDLYETLAITQSVI
Sbjct: 226 PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLDTLCDLYETLAITQSVI 285

Query: 241 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 300
           FVNTRRKVDWLTDKMR RDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID
Sbjct: 286 FVNTRRKVDWLTDKMRGRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 345

Query: 301 VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEE 360
           VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQ+FYNVVIEE
Sbjct: 346 VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQRFYNVVIEE 405

Query: 361 LPSNVADLL 369
           LP+NVADLL
Sbjct: 406 LPANVADLL 414

ATP-dependent RNA helicase which is a subunit of the eIF4F complex involved in cap recognition and is required for mRNA binding to ribosome. In the current model of translation initiation, eIF4A unwinds RNA secondary structures in the 5'-UTR of mRNAs which is necessary to allow efficient binding of the small ribosomal subunit, and subsequent scanning for the initiator codon.

Oryza sativa subsp. japonica (taxid: 39947)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|P41379|IF4A2_NICPL Eukaryotic initiation factor 4A-2 OS=Nicotiana plumbaginifolia PE=2 SV=1

 Score =  743 bits (1919), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 358/369 (97%), Positives = 366/369 (99%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
           MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSG+LQQLDY
Sbjct: 45  MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGVLQQLDY 104

Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG 120
            LV+CQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQ+GVHVVVG
Sbjct: 105 SLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQSGVHVVVG 164

Query: 121 TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMP 180
           TPGRVFDMLRRQSLRPD+IKMFVLDEADEMLSRGFKDQIYDIFQLLP K+QVGVFSATMP
Sbjct: 165 TPGRVFDMLRRQSLRPDHIKMFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMP 224

Query: 181 PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVI 240
           PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNV+KEEWKLETLCDLYETLAITQSVI
Sbjct: 225 PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVDKEEWKLETLCDLYETLAITQSVI 284

Query: 241 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 300
           FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID
Sbjct: 285 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 344

Query: 301 VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEE 360
           VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAIN VT+DDERMLFDIQKFYNVVIEE
Sbjct: 345 VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINSVTKDDERMLFDIQKFYNVVIEE 404

Query: 361 LPSNVADLL 369
           LP+NVADLL
Sbjct: 405 LPANVADLL 413

ATP-dependent RNA helicase which is a subunit of the eIF4F complex involved in cap recognition and is required for mRNA binding to ribosome. In the current model of translation initiation, eIF4A unwinds RNA secondary structures in the 5'-UTR of mRNAs which is necessary to allow efficient binding of the small ribosomal subunit, and subsequent scanning for the initiator codon.

Nicotiana plumbaginifolia (taxid: 4092)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q6Z2Z4|IF4A3_ORYSJ Eukaryotic initiation factor 4A-3 OS=Oryza sativa subsp. japonica GN=Os02g0146600 PE=2 SV=1

 Score =  742 bits (1915), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 357/369 (96%), Positives = 366/369 (99%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
           MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY
Sbjct: 46  MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 105

Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG 120
           GLV+CQ+LVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL +GVHVVVG
Sbjct: 106 GLVECQSLVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILASGVHVVVG 165

Query: 121 TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMP 180
           TPGRVFDMLRRQSLRPD+IKMFVLDEADEMLSRGFKDQIYDIFQLLP K+QVGVFSATMP
Sbjct: 166 TPGRVFDMLRRQSLRPDHIKMFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMP 225

Query: 181 PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVI 240
           PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKE+WKL+TLCDLYETLAITQSVI
Sbjct: 226 PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEDWKLDTLCDLYETLAITQSVI 285

Query: 241 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 300
           FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID
Sbjct: 286 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 345

Query: 301 VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEE 360
           VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQ+FYNV IEE
Sbjct: 346 VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQRFYNVTIEE 405

Query: 361 LPSNVADLL 369
           LP+NVADLL
Sbjct: 406 LPANVADLL 414

ATP-dependent RNA helicase which is a subunit of the eIF4F complex involved in cap recognition and is required for mRNA binding to ribosome. In the current model of translation initiation, eIF4A unwinds RNA secondary structures in the 5'-UTR of mRNAs which is necessary to allow efficient binding of the small ribosomal subunit, and subsequent scanning for the initiator codon.

Oryza sativa subsp. japonica (taxid: 39947)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q40467|IF414_TOBAC Eukaryotic initiation factor 4A-14 OS=Nicotiana tabacum PE=2 SV=1

 Score =  741 bits (1913), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 356/369 (96%), Positives = 367/369 (99%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
           MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSG+LQQLDY
Sbjct: 45  MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGVLQQLDY 104

Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG 120
            LV+CQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQ+GVHVVVG
Sbjct: 105 SLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQSGVHVVVG 164

Query: 121 TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMP 180
           TPGRVFDMLRRQSLRPD+IKMFVLDEADEMLSRGFKDQIYDIFQLLP K+QVGVFSATMP
Sbjct: 165 TPGRVFDMLRRQSLRPDHIKMFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMP 224

Query: 181 PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVI 240
           PEALEITRKFM+KPVRILVKRD++TLEGIKQFYVNV+KEEWKLETLCDLYETLAITQSVI
Sbjct: 225 PEALEITRKFMSKPVRILVKRDDVTLEGIKQFYVNVDKEEWKLETLCDLYETLAITQSVI 284

Query: 241 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 300
           FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID
Sbjct: 285 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 344

Query: 301 VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEE 360
           VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVT+DDERMLFDIQKFYNVVIEE
Sbjct: 345 VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTKDDERMLFDIQKFYNVVIEE 404

Query: 361 LPSNVADLL 369
           LP+NVADLL
Sbjct: 405 LPANVADLL 413

ATP-dependent RNA helicase which is a subunit of the eIF4F complex involved in cap recognition and is required for mRNA binding to ribosome. In the current model of translation initiation, eIF4A unwinds RNA secondary structures in the 5'-UTR of mRNAs which is necessary to allow efficient binding of the small ribosomal subunit, and subsequent scanning for the initiator codon.

Nicotiana tabacum (taxid: 4097)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|P41376|IF4A1_ARATH Eukaryotic initiation factor 4A-1 OS=Arabidopsis thaliana GN=TIF4A-1 PE=1 SV=1

 Score =  741 bits (1912), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 357/369 (96%), Positives = 365/369 (98%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
           MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSG+LQQLD+
Sbjct: 44  MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGVLQQLDF 103

Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG 120
            L+QCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG
Sbjct: 104 SLIQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG 163

Query: 121 TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMP 180
           TPGRVFDML+RQSLR D IKMFVLDEADEMLSRGFKDQIYDIFQLLP K+QVGVFSATMP
Sbjct: 164 TPGRVFDMLKRQSLRADNIKMFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMP 223

Query: 181 PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVI 240
           PEALEITRKFM+KPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVI
Sbjct: 224 PEALEITRKFMSKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVI 283

Query: 241 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 300
           FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID
Sbjct: 284 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 343

Query: 301 VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEE 360
           VQQVSLVIN+DLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVV+EE
Sbjct: 344 VQQVSLVINFDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVVEE 403

Query: 361 LPSNVADLL 369
           LPSNVADLL
Sbjct: 404 LPSNVADLL 412

ATP-dependent RNA helicase which is a subunit of the eIF4F complex involved in cap recognition and is required for mRNA binding to ribosome. In the current model of translation initiation, eIF4A unwinds RNA secondary structures in the 5'-UTR of mRNAs which is necessary to allow efficient binding of the small ribosomal subunit, and subsequent scanning for the initiator codon.

Arabidopsis thaliana (taxid: 3702)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|P41382|IF410_TOBAC Eukaryotic initiation factor 4A-10 OS=Nicotiana tabacum PE=2 SV=1

 Score =  740 bits (1910), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 356/369 (96%), Positives = 366/369 (99%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
           MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSG+LQQLDY
Sbjct: 45  MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGVLQQLDY 104

Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG 120
            LV+CQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQ+GVHVVVG
Sbjct: 105 SLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQSGVHVVVG 164

Query: 121 TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMP 180
           TPGRVFDMLRRQSLRPD+IKMFVLDEADEMLSRGFKDQIYDIFQLLP K+QVGVFSATMP
Sbjct: 165 TPGRVFDMLRRQSLRPDHIKMFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMP 224

Query: 181 PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVI 240
           PEALEITRKFMNKPVRILVKRD++TLEGIKQFYVNV+KEEWKLETLCDLYETLAITQSVI
Sbjct: 225 PEALEITRKFMNKPVRILVKRDDVTLEGIKQFYVNVDKEEWKLETLCDLYETLAITQSVI 284

Query: 241 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 300
           FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID
Sbjct: 285 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 344

Query: 301 VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEE 360
           VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVT+DDERML DIQKFYNVVIEE
Sbjct: 345 VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTKDDERMLSDIQKFYNVVIEE 404

Query: 361 LPSNVADLL 369
           LP+NVADLL
Sbjct: 405 LPANVADLL 413

ATP-dependent RNA helicase which is a subunit of the eIF4F complex involved in cap recognition and is required for mRNA binding to ribosome. In the current model of translation initiation, eIF4A unwinds RNA secondary structures in the 5'-UTR of mRNAs which is necessary to allow efficient binding of the small ribosomal subunit, and subsequent scanning for the initiator codon.

Nicotiana tabacum (taxid: 4097)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q40465|IF411_TOBAC Eukaryotic initiation factor 4A-11 OS=Nicotiana tabacum PE=2 SV=1

 Score =  740 bits (1910), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 357/369 (96%), Positives = 364/369 (98%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
           MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY
Sbjct: 45  MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 104

Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG 120
            LV+CQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQ+GVHVVVG
Sbjct: 105 SLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQSGVHVVVG 164

Query: 121 TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMP 180
           TPGRVFDMLRRQSLRPD IKMFVLDEADEMLSRGFKDQIYDIFQLLP K+QVGVFSATMP
Sbjct: 165 TPGRVFDMLRRQSLRPDNIKMFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMP 224

Query: 181 PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVI 240
           PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNV+KEEWKLETLCDLYETLAITQSVI
Sbjct: 225 PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVDKEEWKLETLCDLYETLAITQSVI 284

Query: 241 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 300
           FVNTRRKVDWLTDKMR RDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID
Sbjct: 285 FVNTRRKVDWLTDKMRGRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 344

Query: 301 VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEE 360
           VQQVSLVINYDLPTQPENYLHRIG SGRFGRKGV+INFVT+DDERMLFDIQKFYNVVIEE
Sbjct: 345 VQQVSLVINYDLPTQPENYLHRIGHSGRFGRKGVSINFVTKDDERMLFDIQKFYNVVIEE 404

Query: 361 LPSNVADLL 369
           LP+NVADLL
Sbjct: 405 LPANVADLL 413

ATP-dependent RNA helicase which is a subunit of the eIF4F complex involved in cap recognition and is required for mRNA binding to ribosome. In the current model of translation initiation, eIF4A unwinds RNA secondary structures in the 5'-UTR of mRNAs which is necessary to allow efficient binding of the small ribosomal subunit, and subsequent scanning for the initiator codon.

Nicotiana tabacum (taxid: 4097)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|P41378|IF4A_WHEAT Eukaryotic initiation factor 4A OS=Triticum aestivum PE=2 SV=1

 Score =  738 bits (1905), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 356/369 (96%), Positives = 364/369 (98%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
           MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY
Sbjct: 46  MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 105

Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG 120
           GLV+CQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL +GVHVVVG
Sbjct: 106 GLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILASGVHVVVG 165

Query: 121 TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMP 180
           TPGRVFD++RRQSLRPD IKMFVLDEADEMLSRGFKDQIYDIFQLLP K+QVGVFSATMP
Sbjct: 166 TPGRVFDIVRRQSLRPDNIKMFVLDEADEMLSRGFKDQIYDIFQLLPGKIQVGVFSATMP 225

Query: 181 PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVI 240
           PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKL+TLCDLYETLAITQSVI
Sbjct: 226 PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLDTLCDLYETLAITQSVI 285

Query: 241 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 300
           FVNTRRKVDWLTDKMR RDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID
Sbjct: 286 FVNTRRKVDWLTDKMRGRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 345

Query: 301 VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEE 360
           VQQVSLVINYDLPTQPENY HRIGRSGRFGRKGVAINFVTR+DERMLFDIQKFYNVVIEE
Sbjct: 346 VQQVSLVINYDLPTQPENYQHRIGRSGRFGRKGVAINFVTREDERMLFDIQKFYNVVIEE 405

Query: 361 LPSNVADLL 369
           LP+NVADLL
Sbjct: 406 LPANVADLL 414

ATP-dependent RNA helicase which is a subunit of the eIF4F complex involved in cap recognition and is required for mRNA binding to ribosome. In the current model of translation initiation, eIF4A unwinds RNA secondary structures in the 5'-UTR of mRNAs which is necessary to allow efficient binding of the small ribosomal subunit, and subsequent scanning for the initiator codon.

Triticum aestivum (taxid: 4565)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q41741|IF4A_MAIZE Eukaryotic initiation factor 4A OS=Zea mays PE=2 SV=1

 Score =  736 bits (1899), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 352/369 (95%), Positives = 366/369 (99%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
           MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY
Sbjct: 42  MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 101

Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG 120
           GLV+CQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL +GVHVVVG
Sbjct: 102 GLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILASGVHVVVG 161

Query: 121 TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMP 180
           TPGRVFDMLRRQSLRPD IKMFVLDEADEMLSRGFKDQIYDIFQLLP+K+QVGVFSATMP
Sbjct: 162 TPGRVFDMLRRQSLRPDNIKMFVLDEADEMLSRGFKDQIYDIFQLLPSKIQVGVFSATMP 221

Query: 181 PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVI 240
           PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVN++KE+WKL+TLCDLYETLAITQSVI
Sbjct: 222 PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNIDKEDWKLDTLCDLYETLAITQSVI 281

Query: 241 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 300
           FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID
Sbjct: 282 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 341

Query: 301 VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEE 360
           VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDER++FD+Q+FYNV +EE
Sbjct: 342 VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERIVFDVQRFYNVTVEE 401

Query: 361 LPSNVADLL 369
           LP+NVADLL
Sbjct: 402 LPANVADLL 410

ATP-dependent RNA helicase which is a subunit of the eIF4F complex involved in cap recognition and is required for mRNA binding to ribosome. In the current model of translation initiation, eIF4A unwinds RNA secondary structures in the 5'-UTR of mRNAs which is necessary to allow efficient binding of the small ribosomal subunit, and subsequent scanning for the initiator codon.

Zea mays (taxid: 4577)

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	369
255560725	413	dead box ATP-dependent RNA helicase, put	1.0	0.893	0.997	0.0
224073500	413	predicted protein [Populus trichocarpa]	1.0	0.893	0.989	0.0
283049400	413	DEAD-box RNA helicase-like protein [Prun	1.0	0.893	0.983	0.0
359484301	803	PREDICTED: eukaryotic initiation factor	1.0	0.459	0.981	0.0
297738640	413	unnamed protein product [Vitis vinifera]	1.0	0.893	0.981	0.0
224153793	390	predicted protein [Populus trichocarpa]	1.0	0.946	0.983	0.0
449447868	413	PREDICTED: eukaryotic initiation factor	1.0	0.893	0.981	0.0
449458151	413	PREDICTED: eukaryotic initiation factor	1.0	0.893	0.978	0.0
307135861	413	helicase [Cucumis melo subsp. melo]	1.0	0.893	0.975	0.0
224128550	413	predicted protein [Populus trichocarpa]	1.0	0.893	0.981	0.0

>gi|255560725|ref|XP_002521376.1| dead box ATP-dependent RNA helicase, putative [Ricinus communis] gi|223539454|gb|EEF41044.1| dead box ATP-dependent RNA helicase, putative [Ricinus communis]

 Score =  758 bits (1956), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 368/369 (99%), Positives = 368/369 (99%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
           MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY
Sbjct: 45  MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 104

Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG 120
           GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG
Sbjct: 105 GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG 164

Query: 121 TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMP 180
           TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMP
Sbjct: 165 TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMP 224

Query: 181 PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVI 240
           PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVI
Sbjct: 225 PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVI 284

Query: 241 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 300
           FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID
Sbjct: 285 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 344

Query: 301 VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEE 360
           VQQVSLVINYDLPTQPENYLHRIGR GRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEE
Sbjct: 345 VQQVSLVINYDLPTQPENYLHRIGRGGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEE 404

Query: 361 LPSNVADLL 369
           LPSNVADLL
Sbjct: 405 LPSNVADLL 413

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224073500|ref|XP_002304104.1| predicted protein [Populus trichocarpa] gi|118484805|gb|ABK94270.1| unknown [Populus trichocarpa] gi|222841536|gb|EEE79083.1| predicted protein [Populus trichocarpa]

 Score =  753 bits (1944), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 365/369 (98%), Positives = 369/369 (100%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
           MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY
Sbjct: 45  MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 104

Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG 120
           GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG
Sbjct: 105 GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG 164

Query: 121 TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMP 180
           TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLP+KVQVGVFSATMP
Sbjct: 165 TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPSKVQVGVFSATMP 224

Query: 181 PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVI 240
           PEALEITRKFMNKPVRILVKRDELTLEGIKQF+VNV+KEEWKLETLCDLYETLAITQSVI
Sbjct: 225 PEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVDKEEWKLETLCDLYETLAITQSVI 284

Query: 241 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 300
           FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID
Sbjct: 285 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 344

Query: 301 VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEE 360
           VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDD+RMLFDIQKFYNVVIEE
Sbjct: 345 VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDDRMLFDIQKFYNVVIEE 404

Query: 361 LPSNVADLL 369
           LPSNVADLL
Sbjct: 405 LPSNVADLL 413

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|283049400|gb|ADB07168.1| DEAD-box RNA helicase-like protein [Prunus persica] gi|283049402|gb|ADB07169.1| DEAD-box RNA helicase-like protein [Prunus persica]

 Score =  751 bits (1939), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 363/369 (98%), Positives = 368/369 (99%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
           MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY
Sbjct: 45  MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 104

Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG 120
            +VQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG
Sbjct: 105 AVVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG 164

Query: 121 TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMP 180
           TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLP+KVQVGVFSATMP
Sbjct: 165 TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPSKVQVGVFSATMP 224

Query: 181 PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVI 240
           PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNV+KEEWKLETLCDLYETLAITQSVI
Sbjct: 225 PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVDKEEWKLETLCDLYETLAITQSVI 284

Query: 241 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 300
           FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID
Sbjct: 285 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 344

Query: 301 VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEE 360
           VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERML+DIQ+FYNVVIEE
Sbjct: 345 VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLYDIQRFYNVVIEE 404

Query: 361 LPSNVADLL 369
           LPSNVADLL
Sbjct: 405 LPSNVADLL 413

Source: Prunus persica

Species: Prunus persica

Genus: Prunus

Family: Rosaceae

Order: Rosales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359484301|ref|XP_002281247.2| PREDICTED: eukaryotic initiation factor 4A-15-like [Vitis vinifera]

 Score =  750 bits (1936), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 362/369 (98%), Positives = 368/369 (99%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
           MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY
Sbjct: 435 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 494

Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG 120
           GLV+CQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL +GVHVVVG
Sbjct: 495 GLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVG 554

Query: 121 TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMP 180
           TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLP+KVQVGVFSATMP
Sbjct: 555 TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPSKVQVGVFSATMP 614

Query: 181 PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVI 240
           PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNV+KEEWKLETLCDLYETLAITQSVI
Sbjct: 615 PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVDKEEWKLETLCDLYETLAITQSVI 674

Query: 241 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 300
           FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID
Sbjct: 675 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 734

Query: 301 VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEE 360
           VQQVSLVIN+DLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQ+FYNVVIEE
Sbjct: 735 VQQVSLVINFDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQRFYNVVIEE 794

Query: 361 LPSNVADLL 369
           LPSNVADLL
Sbjct: 795 LPSNVADLL 803

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297738640|emb|CBI27885.3| unnamed protein product [Vitis vinifera]

 Score =  749 bits (1935), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 362/369 (98%), Positives = 368/369 (99%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
           MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY
Sbjct: 45  MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 104

Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG 120
           GLV+CQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL +GVHVVVG
Sbjct: 105 GLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVG 164

Query: 121 TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMP 180
           TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLP+KVQVGVFSATMP
Sbjct: 165 TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPSKVQVGVFSATMP 224

Query: 181 PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVI 240
           PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNV+KEEWKLETLCDLYETLAITQSVI
Sbjct: 225 PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVDKEEWKLETLCDLYETLAITQSVI 284

Query: 241 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 300
           FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID
Sbjct: 285 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 344

Query: 301 VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEE 360
           VQQVSLVIN+DLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQ+FYNVVIEE
Sbjct: 345 VQQVSLVINFDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQRFYNVVIEE 404

Query: 361 LPSNVADLL 369
           LPSNVADLL
Sbjct: 405 LPSNVADLL 413

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224153793|ref|XP_002337398.1| predicted protein [Populus trichocarpa] gi|222838972|gb|EEE77323.1| predicted protein [Populus trichocarpa]

 Score =  749 bits (1935), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 363/369 (98%), Positives = 367/369 (99%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
           MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY
Sbjct: 22  MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 81

Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG 120
           GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG
Sbjct: 82  GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG 141

Query: 121 TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMP 180
           TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLP+KVQVGVFSATMP
Sbjct: 142 TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPSKVQVGVFSATMP 201

Query: 181 PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVI 240
           PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNV+KEEWKLETLCDLYETLAITQSVI
Sbjct: 202 PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVDKEEWKLETLCDLYETLAITQSVI 261

Query: 241 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 300
           FVNTRRKVDWLTDKMR RDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID
Sbjct: 262 FVNTRRKVDWLTDKMRGRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 321

Query: 301 VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEE 360
           VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVT DD+RMLFDIQKFYNVV+EE
Sbjct: 322 VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTSDDDRMLFDIQKFYNVVVEE 381

Query: 361 LPSNVADLL 369
           LPSNVADLL
Sbjct: 382 LPSNVADLL 390

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449447868|ref|XP_004141688.1| PREDICTED: eukaryotic initiation factor 4A-11-like [Cucumis sativus] gi|449480559|ref|XP_004155930.1| PREDICTED: eukaryotic initiation factor 4A-11-like [Cucumis sativus]

 Score =  748 bits (1932), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 362/369 (98%), Positives = 367/369 (99%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
           MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY
Sbjct: 45  MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 104

Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG 120
           GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG
Sbjct: 105 GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG 164

Query: 121 TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMP 180
           TPGRVFDMLRRQSLRPD IKMFVLDEADEMLSRGFKDQIYDIFQLLP+K+QVGVFSATMP
Sbjct: 165 TPGRVFDMLRRQSLRPDCIKMFVLDEADEMLSRGFKDQIYDIFQLLPSKIQVGVFSATMP 224

Query: 181 PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVI 240
           PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNV+KE+WKLETLCDLYETLAITQSVI
Sbjct: 225 PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVDKEDWKLETLCDLYETLAITQSVI 284

Query: 241 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 300
           FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID
Sbjct: 285 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 344

Query: 301 VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEE 360
           VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVT DDERMLFDIQKFYNVVIEE
Sbjct: 345 VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTNDDERMLFDIQKFYNVVIEE 404

Query: 361 LPSNVADLL 369
           LP+NVADLL
Sbjct: 405 LPANVADLL 413

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449458151|ref|XP_004146811.1| PREDICTED: eukaryotic initiation factor 4A-8-like [Cucumis sativus] gi|449476633|ref|XP_004154791.1| PREDICTED: eukaryotic initiation factor 4A-8-like [Cucumis sativus]

 Score =  748 bits (1931), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 361/369 (97%), Positives = 368/369 (99%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
           MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY
Sbjct: 45  MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 104

Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG 120
           GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG
Sbjct: 105 GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG 164

Query: 121 TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMP 180
           TPGRVFDMLRRQSLRPDYI+MFVLDEADEMLSRGFKDQIYDIFQLLP+K+QVGVFSATMP
Sbjct: 165 TPGRVFDMLRRQSLRPDYIRMFVLDEADEMLSRGFKDQIYDIFQLLPSKIQVGVFSATMP 224

Query: 181 PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVI 240
           PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNV+KE+WKLETLCDLYETLAITQSVI
Sbjct: 225 PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVDKEDWKLETLCDLYETLAITQSVI 284

Query: 241 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 300
           FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID
Sbjct: 285 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 344

Query: 301 VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEE 360
           VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVT +DERMLFDIQKFYNVVIEE
Sbjct: 345 VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTTEDERMLFDIQKFYNVVIEE 404

Query: 361 LPSNVADLL 369
           LP+NVADLL
Sbjct: 405 LPANVADLL 413

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|307135861|gb|ADN33729.1| helicase [Cucumis melo subsp. melo]

 Score =  748 bits (1930), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 360/369 (97%), Positives = 368/369 (99%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
           MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY
Sbjct: 45  MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 104

Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG 120
           GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG
Sbjct: 105 GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG 164

Query: 121 TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMP 180
           TPGRVFDMLRRQSLRPDYI+MFVLDEADEMLSRGFKDQIYDIFQLLP+K+QVGVFSATMP
Sbjct: 165 TPGRVFDMLRRQSLRPDYIRMFVLDEADEMLSRGFKDQIYDIFQLLPSKIQVGVFSATMP 224

Query: 181 PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVI 240
           PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNV+KE+WKLETLCDLYETLAITQSVI
Sbjct: 225 PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVDKEDWKLETLCDLYETLAITQSVI 284

Query: 241 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 300
           FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID
Sbjct: 285 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 344

Query: 301 VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEE 360
           VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVT +DERMLFDIQKFYNV+IEE
Sbjct: 345 VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTTEDERMLFDIQKFYNVIIEE 404

Query: 361 LPSNVADLL 369
           LP+NVADLL
Sbjct: 405 LPANVADLL 413

Source: Cucumis melo subsp. melo

Species: Cucumis melo

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224128550|ref|XP_002329031.1| predicted protein [Populus trichocarpa] gi|118482674|gb|ABK93256.1| unknown [Populus trichocarpa] gi|222839702|gb|EEE78025.1| predicted protein [Populus trichocarpa]

 Score =  747 bits (1929), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 362/369 (98%), Positives = 366/369 (99%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
           MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY
Sbjct: 45  MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 104

Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG 120
           GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG
Sbjct: 105 GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG 164

Query: 121 TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMP 180
           TPGRVFDMLRRQSLR DYIKMFVLDEADEMLSRGFKDQIYDIFQLLP+KVQVGVFSATMP
Sbjct: 165 TPGRVFDMLRRQSLRQDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPSKVQVGVFSATMP 224

Query: 181 PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVI 240
           PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNV+KEEWKLETLCDLYETLAITQSVI
Sbjct: 225 PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVDKEEWKLETLCDLYETLAITQSVI 284

Query: 241 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 300
           FVNTRRKVDWLTDKMR RDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID
Sbjct: 285 FVNTRRKVDWLTDKMRGRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 344

Query: 301 VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEE 360
           VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVT DD+RMLFDIQKFYNVV+EE
Sbjct: 345 VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTSDDDRMLFDIQKFYNVVVEE 404

Query: 361 LPSNVADLL 369
           LPSNVADLL
Sbjct: 405 LPSNVADLL 413

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

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	369
TAIR|locus:2020078	412	EIF4A-2 "eif4a-2" [Arabidopsis	1.0	0.895	0.964	1.1e-188
TAIR|locus:2030285	414	AT1G72730 [Arabidopsis thalian	1.0	0.891	0.934	6e-183
TAIR|locus:2088237	415	EIF4A1 "eukaryotic translation	0.940	0.836	0.968	9.3e-178
UNIPROTKB|Q8JFP1	407	EIF4A2 "Eukaryotic initiation	1.0	0.906	0.751	7.1e-148
UNIPROTKB|Q3SZ65	407	EIF4A2 "Eukaryotic initiation	1.0	0.906	0.748	3.9e-147
UNIPROTKB|E2R3J1	407	EIF4A2 "Uncharacterized protei	1.0	0.906	0.748	3.9e-147
UNIPROTKB|Q14240	407	EIF4A2 "Eukaryotic initiation	1.0	0.906	0.748	3.9e-147
UNIPROTKB|A6M930	407	EIF4A2 "Eukaryotic translation	1.0	0.906	0.748	3.9e-147
MGI|MGI:106906	407	Eif4a2 "eukaryotic translation	1.0	0.906	0.748	3.9e-147
RGD|1309225	407	Eif4a2 "eukaryotic translation	1.0	0.906	0.748	3.9e-147

TAIR|locus:2020078 EIF4A-2 "eif4a-2" [Arabidopsis thaliana (taxid:3702)]

 Score = 1829 (648.9 bits), Expect = 1.1e-188, P = 1.1e-188
 Identities = 356/369 (96%), Positives = 364/369 (98%)

Query:     1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
             MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSG+LQQLDY
Sbjct:    44 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGVLQQLDY 103

Query:    61 GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG 120
              L+QCQALVLAPTRELAQQIEKVMRALGDY GVKVHACVGGTSVREDQRILQAGVHVVVG
Sbjct:   104 ALLQCQALVLAPTRELAQQIEKVMRALGDYQGVKVHACVGGTSVREDQRILQAGVHVVVG 163

Query:   121 TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMP 180
             TPGRVFDMLRRQSLRPD IKMFVLDEADEMLSRGFKDQIYDIFQLLP K+QVGVFSATMP
Sbjct:   164 TPGRVFDMLRRQSLRPDCIKMFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMP 223

Query:   181 PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVI 240
             PEALEITRKFM+KPVRILVKRDELTLEGIKQFYVNVEKE+WKLETLCDLYETLAITQSVI
Sbjct:   224 PEALEITRKFMSKPVRILVKRDELTLEGIKQFYVNVEKEDWKLETLCDLYETLAITQSVI 283

Query:   241 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 300
             FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID
Sbjct:   284 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 343

Query:   301 VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEE 360
             VQQVSLVIN+DLPTQPENYLHRIGRSGRFGRKGVAINFVT DD+RMLFDIQKFYNVV+EE
Sbjct:   344 VQQVSLVINFDLPTQPENYLHRIGRSGRFGRKGVAINFVTLDDQRMLFDIQKFYNVVVEE 403

Query:   361 LPSNVADLL 369
             LPSNVADLL
Sbjct:   404 LPSNVADLL 412

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003743 "translation initiation factor activity" evidence=ISS

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

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

GO:0046686 "response to cadmium ion" evidence=IEP;RCA

GO:0005774 "vacuolar membrane" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0009506 "plasmodesma" evidence=IDA

GO:0005794 "Golgi apparatus" evidence=RCA

GO:0006094 "gluconeogenesis" evidence=RCA

GO:0006096 "glycolysis" evidence=RCA

GO:0009651 "response to salt stress" evidence=RCA

TAIR|locus:2030285 AT1G72730 [Arabidopsis thaliana (taxid:3702)]

 Score = 1775 (629.9 bits), Expect = 6.0e-183, P = 6.0e-183
 Identities = 345/369 (93%), Positives = 359/369 (97%)

Query:     1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
             M LQ +LLRGIYAYGFEKPSAIQQRGI+PFCKGLDVIQQAQSGTGKTATFCSG+LQQLD 
Sbjct:    46 MELQPDLLRGIYAYGFEKPSAIQQRGIIPFCKGLDVIQQAQSGTGKTATFCSGVLQQLDI 105

Query:    61 GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG 120
              LVQCQALVLAPTRELAQQIEKVMRALGDYLGVK  ACVGGTSVREDQR+LQ+GVHVVVG
Sbjct:   106 SLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKAQACVGGTSVREDQRVLQSGVHVVVG 165

Query:   121 TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMP 180
             TPGRVFD+LRRQSLR D IKMFVLDEADEMLSRGFKDQIYDIFQLLP+KVQVGVFSATMP
Sbjct:   166 TPGRVFDLLRRQSLRADAIKMFVLDEADEMLSRGFKDQIYDIFQLLPSKVQVGVFSATMP 225

Query:   181 PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVI 240
             PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNV+KEEWKLETLCDLYETLAITQSVI
Sbjct:   226 PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVDKEEWKLETLCDLYETLAITQSVI 285

Query:   241 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 300
             FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID
Sbjct:   286 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 345

Query:   301 VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEE 360
             VQQVSLVIN+DLPTQPENYLHRIGRSGRFGRKGVAINF+T +DERM+ DIQ+FYNVV+EE
Sbjct:   346 VQQVSLVINFDLPTQPENYLHRIGRSGRFGRKGVAINFMTSEDERMMADIQRFYNVVVEE 405

Query:   361 LPSNVADLL 369
             LPSNVADLL
Sbjct:   406 LPSNVADLL 414

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

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

GO:0009505 "plant-type cell wall" evidence=IDA

GO:0005774 "vacuolar membrane" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0005794 "Golgi apparatus" evidence=RCA

GO:0009744 "response to sucrose stimulus" evidence=RCA

GO:0009749 "response to glucose stimulus" evidence=RCA

GO:0009750 "response to fructose stimulus" evidence=RCA

TAIR|locus:2088237 EIF4A1 "eukaryotic translation initiation factor 4A1" [Arabidopsis thaliana (taxid:3702)]

 Score = 1726 (612.6 bits), Expect = 9.3e-178, P = 9.3e-178
 Identities = 336/347 (96%), Positives = 343/347 (98%)

Query:     1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
             MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSG+LQQLD+
Sbjct:    44 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGVLQQLDF 103

Query:    61 GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG 120
              L+QCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG
Sbjct:   104 SLIQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG 163

Query:   121 TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMP 180
             TPGRVFDML+RQSLR D IKMFVLDEADEMLSRGFKDQIYDIFQLLP K+QVGVFSATMP
Sbjct:   164 TPGRVFDMLKRQSLRADNIKMFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMP 223

Query:   181 PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVI 240
             PEALEITRKFM+KPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVI
Sbjct:   224 PEALEITRKFMSKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVI 283

Query:   241 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 300
             FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID
Sbjct:   284 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 343

Query:   301 VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERML 347
             VQQVSLVIN+DLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERML
Sbjct:   344 VQQVSLVINFDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERML 390

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003743 "translation initiation factor activity" evidence=ISS

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0005737 "cytoplasm" evidence=ISM

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

GO:0006413 "translational initiation" evidence=ISS

GO:0005515 "protein binding" evidence=IPI

GO:0005730 "nucleolus" evidence=IDA

GO:0005618 "cell wall" evidence=IDA

GO:0046686 "response to cadmium ion" evidence=IEP;RCA

GO:0016020 "membrane" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0009506 "plasmodesma" evidence=IDA

GO:0048046 "apoplast" evidence=IDA

GO:0005794 "Golgi apparatus" evidence=RCA

GO:0006094 "gluconeogenesis" evidence=RCA

GO:0006096 "glycolysis" evidence=RCA

GO:0009651 "response to salt stress" evidence=RCA

UNIPROTKB|Q8JFP1 EIF4A2 "Eukaryotic initiation factor 4A-II" [Gallus gallus (taxid:9031)]

 Score = 1444 (513.4 bits), Expect = 7.1e-148, P = 7.1e-148
 Identities = 278/370 (75%), Positives = 319/370 (86%)

Query:     1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
             M L+E+LLRGIYAYGFEKPSAIQQR I+P  KG DVI QAQSGTGKTATF   ILQQL+ 
Sbjct:    38 MNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQLEI 97

Query:    61 GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGV-HVVV 119
              L + QALVLAPTRELAQQI+KV+ ALGDY+G   HAC+GGT+VR + + LQA   H+VV
Sbjct:    98 DLKETQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRNEMQKLQAEAPHIVV 157

Query:   120 GTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATM 179
             GTPGRVFDML R+ L P +IKMFVLDEADEMLSRGFKDQIY+IFQ L   +QV + SATM
Sbjct:   158 GTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSRGFKDQIYEIFQKLSTNIQVVLLSATM 217

Query:   180 PPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSV 239
             P + LE+T+KFM +P+RILVK++ELTLEGIKQFY+NVE+EEWKL+TLCDLYETL ITQ+V
Sbjct:   218 PMDVLEVTKKFMREPIRILVKKEELTLEGIKQFYINVEREEWKLDTLCDLYETLTITQAV 277

Query:   240 IFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGI 299
             IF+NTRRKVDWLT+KM +RD TVSA HGDMDQ  RD+IMREFRSGSSRVLITTDLLARGI
Sbjct:   278 IFLNTRRKVDWLTEKMHARDFTVSALHGDMDQKERDVIMREFRSGSSRVLITTDLLARGI 337

Query:   300 DVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIE 359
             DVQQVSLVINYDLPT  ENY+HRIGR GRFGRKGVAINFVT +D+R+L DI+ FYN  +E
Sbjct:   338 DVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINFVTEEDKRILRDIETFYNTTVE 397

Query:   360 ELPSNVADLL 369
             E+P NVADL+
Sbjct:   398 EMPMNVADLI 407

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

GO:0003743 "translation initiation factor activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|Q3SZ65 EIF4A2 "Eukaryotic initiation factor 4A-II" [Bos taurus (taxid:9913)]

 Score = 1437 (510.9 bits), Expect = 3.9e-147, P = 3.9e-147
 Identities = 277/370 (74%), Positives = 317/370 (85%)

Query:     1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
             M L+E+LLRGIYAYGFEKPSAIQQR I+P  KG DVI QAQSGTGKTATF   ILQQL+ 
Sbjct:    38 MNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQLEI 97

Query:    61 GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGV-HVVV 119
                + QALVLAPTRELAQQI+KV+ ALGDY+G   HAC+GGT+VR + + LQA   H+VV
Sbjct:    98 EFKETQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRNEMQKLQAEAPHIVV 157

Query:   120 GTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATM 179
             GTPGRVFDML R+ L P +IKMFVLDEADEMLSRGFKDQIY+IFQ L   +QV + SATM
Sbjct:   158 GTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSRGFKDQIYEIFQKLNTSIQVVLLSATM 217

Query:   180 PPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSV 239
             P + LE+T+KFM  P+RILVK++ELTLEGIKQFY+NVE+EEWKL+TLCDLYETL ITQ+V
Sbjct:   218 PTDVLEVTKKFMRDPIRILVKKEELTLEGIKQFYINVEREEWKLDTLCDLYETLTITQAV 277

Query:   240 IFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGI 299
             IF+NTRRKVDWLT+KM +RD TVSA HGDMDQ  RD+IMREFRSGSSRVLITTDLLARGI
Sbjct:   278 IFLNTRRKVDWLTEKMHARDFTVSALHGDMDQKERDVIMREFRSGSSRVLITTDLLARGI 337

Query:   300 DVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIE 359
             DVQQVSLVINYDLPT  ENY+HRIGR GRFGRKGVAINFVT +D+R+L DI+ FYN  +E
Sbjct:   338 DVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINFVTEEDKRILRDIETFYNTTVE 397

Query:   360 ELPSNVADLL 369
             E+P NVADL+
Sbjct:   398 EMPMNVADLI 407

GO:0005524 "ATP binding" evidence=IEA

GO:0003743 "translation initiation factor activity" evidence=IEA

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

UNIPROTKB|E2R3J1 EIF4A2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 1437 (510.9 bits), Expect = 3.9e-147, P = 3.9e-147
 Identities = 277/370 (74%), Positives = 317/370 (85%)

Query:     1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
             M L+E+LLRGIYAYGFEKPSAIQQR I+P  KG DVI QAQSGTGKTATF   ILQQL+ 
Sbjct:    38 MNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQLEI 97

Query:    61 GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGV-HVVV 119
                + QALVLAPTRELAQQI+KV+ ALGDY+G   HAC+GGT+VR + + LQA   H+VV
Sbjct:    98 EFKETQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRNEMQKLQAEAPHIVV 157

Query:   120 GTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATM 179
             GTPGRVFDML R+ L P +IKMFVLDEADEMLSRGFKDQIY+IFQ L   +QV + SATM
Sbjct:   158 GTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSRGFKDQIYEIFQKLNTSIQVVLLSATM 217

Query:   180 PPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSV 239
             P + LE+T+KFM  P+RILVK++ELTLEGIKQFY+NVE+EEWKL+TLCDLYETL ITQ+V
Sbjct:   218 PTDVLEVTKKFMRDPIRILVKKEELTLEGIKQFYINVEREEWKLDTLCDLYETLTITQAV 277

Query:   240 IFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGI 299
             IF+NTRRKVDWLT+KM +RD TVSA HGDMDQ  RD+IMREFRSGSSRVLITTDLLARGI
Sbjct:   278 IFLNTRRKVDWLTEKMHARDFTVSALHGDMDQKERDVIMREFRSGSSRVLITTDLLARGI 337

Query:   300 DVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIE 359
             DVQQVSLVINYDLPT  ENY+HRIGR GRFGRKGVAINFVT +D+R+L DI+ FYN  +E
Sbjct:   338 DVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINFVTEEDKRILRDIETFYNTTVE 397

Query:   360 ELPSNVADLL 369
             E+P NVADL+
Sbjct:   398 EMPMNVADLI 407

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|Q14240 EIF4A2 "Eukaryotic initiation factor 4A-II" [Homo sapiens (taxid:9606)]

 Score = 1437 (510.9 bits), Expect = 3.9e-147, P = 3.9e-147
 Identities = 277/370 (74%), Positives = 317/370 (85%)

Query:     1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
             M L+E+LLRGIYAYGFEKPSAIQQR I+P  KG DVI QAQSGTGKTATF   ILQQL+ 
Sbjct:    38 MNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQLEI 97

Query:    61 GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGV-HVVV 119
                + QALVLAPTRELAQQI+KV+ ALGDY+G   HAC+GGT+VR + + LQA   H+VV
Sbjct:    98 EFKETQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRNEMQKLQAEAPHIVV 157

Query:   120 GTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATM 179
             GTPGRVFDML R+ L P +IKMFVLDEADEMLSRGFKDQIY+IFQ L   +QV + SATM
Sbjct:   158 GTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSRGFKDQIYEIFQKLNTSIQVVLLSATM 217

Query:   180 PPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSV 239
             P + LE+T+KFM  P+RILVK++ELTLEGIKQFY+NVE+EEWKL+TLCDLYETL ITQ+V
Sbjct:   218 PTDVLEVTKKFMRDPIRILVKKEELTLEGIKQFYINVEREEWKLDTLCDLYETLTITQAV 277

Query:   240 IFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGI 299
             IF+NTRRKVDWLT+KM +RD TVSA HGDMDQ  RD+IMREFRSGSSRVLITTDLLARGI
Sbjct:   278 IFLNTRRKVDWLTEKMHARDFTVSALHGDMDQKERDVIMREFRSGSSRVLITTDLLARGI 337

Query:   300 DVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIE 359
             DVQQVSLVINYDLPT  ENY+HRIGR GRFGRKGVAINFVT +D+R+L DI+ FYN  +E
Sbjct:   338 DVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINFVTEEDKRILRDIETFYNTTVE 397

Query:   360 ELPSNVADLL 369
             E+P NVADL+
Sbjct:   398 EMPMNVADLI 407

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

GO:0003743 "translation initiation factor activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0019048 "virus-host interaction" evidence=IEA

GO:0004386 "helicase activity" evidence=TAS

GO:0006446 "regulation of translational initiation" evidence=TAS

GO:0016281 "eukaryotic translation initiation factor 4F complex" evidence=TAS

GO:0000288 "nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay" evidence=TAS

GO:0000289 "nuclear-transcribed mRNA poly(A) tail shortening" evidence=TAS

GO:0005829 "cytosol" evidence=TAS

GO:0006412 "translation" evidence=TAS

GO:0006413 "translational initiation" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0016071 "mRNA metabolic process" evidence=TAS

GO:0019221 "cytokine-mediated signaling pathway" evidence=TAS

GO:0044267 "cellular protein metabolic process" evidence=TAS

GO:0005515 "protein binding" evidence=IPI

UNIPROTKB|A6M930 EIF4A2 "Eukaryotic translation initiation factor 4A isoform 2" [Sus scrofa (taxid:9823)]

 Score = 1437 (510.9 bits), Expect = 3.9e-147, P = 3.9e-147
 Identities = 277/370 (74%), Positives = 317/370 (85%)

Query:     1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
             M L+E+LLRGIYAYGFEKPSAIQQR I+P  KG DVI QAQSGTGKTATF   ILQQL+ 
Sbjct:    38 MNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQLEI 97

Query:    61 GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGV-HVVV 119
                + QALVLAPTRELAQQI+KV+ ALGDY+G   HAC+GGT+VR + + LQA   H+VV
Sbjct:    98 EFKETQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRNEMQKLQAEAPHIVV 157

Query:   120 GTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATM 179
             GTPGRVFDML R+ L P +IKMFVLDEADEMLSRGFKDQIY+IFQ L   +QV + SATM
Sbjct:   158 GTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSRGFKDQIYEIFQKLNTSIQVVLLSATM 217

Query:   180 PPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSV 239
             P + LE+T+KFM  P+RILVK++ELTLEGIKQFY+NVE+EEWKL+TLCDLYETL ITQ+V
Sbjct:   218 PTDVLEVTKKFMRDPIRILVKKEELTLEGIKQFYINVEREEWKLDTLCDLYETLTITQAV 277

Query:   240 IFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGI 299
             IF+NTRRKVDWLT+KM +RD TVSA HGDMDQ  RD+IMREFRSGSSRVLITTDLLARGI
Sbjct:   278 IFLNTRRKVDWLTEKMHARDFTVSALHGDMDQKERDVIMREFRSGSSRVLITTDLLARGI 337

Query:   300 DVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIE 359
             DVQQVSLVINYDLPT  ENY+HRIGR GRFGRKGVAINFVT +D+R+L DI+ FYN  +E
Sbjct:   338 DVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINFVTEEDKRILRDIETFYNTTVE 397

Query:   360 ELPSNVADLL 369
             E+P NVADL+
Sbjct:   398 EMPMNVADLI 407

GO:0005524 "ATP binding" evidence=IEA

GO:0003743 "translation initiation factor activity" evidence=IEA

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

MGI|MGI:106906 Eif4a2 "eukaryotic translation initiation factor 4A2" [Mus musculus (taxid:10090)]

 Score = 1437 (510.9 bits), Expect = 3.9e-147, P = 3.9e-147
 Identities = 277/370 (74%), Positives = 317/370 (85%)

Query:     1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
             M L+E+LLRGIYAYGFEKPSAIQQR I+P  KG DVI QAQSGTGKTATF   ILQQL+ 
Sbjct:    38 MNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQLEI 97

Query:    61 GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGV-HVVV 119
                + QALVLAPTRELAQQI+KV+ ALGDY+G   HAC+GGT+VR + + LQA   H+VV
Sbjct:    98 EFKETQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRNEMQKLQAEAPHIVV 157

Query:   120 GTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATM 179
             GTPGRVFDML R+ L P +IKMFVLDEADEMLSRGFKDQIY+IFQ L   +QV + SATM
Sbjct:   158 GTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSRGFKDQIYEIFQKLNTSIQVVLLSATM 217

Query:   180 PPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSV 239
             P + LE+T+KFM  P+RILVK++ELTLEGIKQFY+NVE+EEWKL+TLCDLYETL ITQ+V
Sbjct:   218 PTDVLEVTKKFMRDPIRILVKKEELTLEGIKQFYINVEREEWKLDTLCDLYETLTITQAV 277

Query:   240 IFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGI 299
             IF+NTRRKVDWLT+KM +RD TVSA HGDMDQ  RD+IMREFRSGSSRVLITTDLLARGI
Sbjct:   278 IFLNTRRKVDWLTEKMHARDFTVSALHGDMDQKERDVIMREFRSGSSRVLITTDLLARGI 337

Query:   300 DVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIE 359
             DVQQVSLVINYDLPT  ENY+HRIGR GRFGRKGVAINFVT +D+R+L DI+ FYN  +E
Sbjct:   338 DVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINFVTEEDKRILRDIETFYNTTVE 397

Query:   360 ELPSNVADLL 369
             E+P NVADL+
Sbjct:   398 EMPMNVADLI 407

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0003743 "translation initiation factor activity" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0006412 "translation" evidence=IEA

GO:0006413 "translational initiation" evidence=IEA

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

GO:0016787 "hydrolase activity" evidence=IEA

RGD|1309225 Eif4a2 "eukaryotic translation initiation factor 4A2" [Rattus norvegicus (taxid:10116)]

 Score = 1437 (510.9 bits), Expect = 3.9e-147, P = 3.9e-147
 Identities = 277/370 (74%), Positives = 317/370 (85%)

Query:     1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
             M L+E+LLRGIYAYGFEKPSAIQQR I+P  KG DVI QAQSGTGKTATF   ILQQL+ 
Sbjct:    38 MNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQLEI 97

Query:    61 GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGV-HVVV 119
                + QALVLAPTRELAQQI+KV+ ALGDY+G   HAC+GGT+VR + + LQA   H+VV
Sbjct:    98 EFKETQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRNEMQKLQAEAPHIVV 157

Query:   120 GTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATM 179
             GTPGRVFDML R+ L P +IKMFVLDEADEMLSRGFKDQIY+IFQ L   +QV + SATM
Sbjct:   158 GTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSRGFKDQIYEIFQKLNTSIQVVLLSATM 217

Query:   180 PPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSV 239
             P + LE+T+KFM  P+RILVK++ELTLEGIKQFY+NVE+EEWKL+TLCDLYETL ITQ+V
Sbjct:   218 PTDVLEVTKKFMRDPIRILVKKEELTLEGIKQFYINVEREEWKLDTLCDLYETLTITQAV 277

Query:   240 IFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGI 299
             IF+NTRRKVDWLT+KM +RD TVSA HGDMDQ  RD+IMREFRSGSSRVLITTDLLARGI
Sbjct:   278 IFLNTRRKVDWLTEKMHARDFTVSALHGDMDQKERDVIMREFRSGSSRVLITTDLLARGI 337

Query:   300 DVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIE 359
             DVQQVSLVINYDLPT  ENY+HRIGR GRFGRKGVAINFVT +D+R+L DI+ FYN  +E
Sbjct:   338 DVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINFVTEEDKRILRDIETFYNTTVE 397

Query:   360 ELPSNVADLL 369
             E+P NVADL+
Sbjct:   398 EMPMNVADLI 407

GO:0003743 "translation initiation factor activity" evidence=IEA

GO:0005524 "ATP 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)
Q0UU86	IF4A_PHANO	3, ., 6, ., 4, ., 1, 3	0.7208	1.0	0.9318	N/A	no
Q40470	IF4A7_TOBAC	3, ., 6, ., 4, ., 1, 3	0.9566	1.0	0.8934	N/A	no
Q6Z2Z4	IF4A3_ORYSJ	3, ., 6, ., 4, ., 1, 3	0.9674	1.0	0.8913	yes	no
P0CQ73	FAL1_CRYNB	3, ., 6, ., 4, ., 1, 3	0.6983	0.9972	0.9292	N/A	no
P0CQ72	FAL1_CRYNJ	3, ., 6, ., 4, ., 1, 3	0.6983	0.9972	0.9292	yes	no
P10630	IF4A2_MOUSE	3, ., 6, ., 4, ., 1, 3	0.7486	1.0	0.9066	yes	no
P35683	IF4A1_ORYSJ	3, ., 6, ., 4, ., 1, 3	0.9701	1.0	0.8913	yes	no
Q4R4Y9	IF4A2_MACFA	3, ., 6, ., 4, ., 1, 3	0.7459	1.0	0.9044	N/A	no
A1CJT5	IF4A_ASPCL	3, ., 6, ., 4, ., 1, 3	0.7181	1.0	0.9271	N/A	no
Q4WEB4	FAL1_ASPFU	3, ., 6, ., 4, ., 1, 3	0.6802	1.0	0.9271	yes	no
Q41741	IF4A_MAIZE	3, ., 6, ., 4, ., 1, 3	0.9539	1.0	0.9	N/A	no
O42226	I4A3B_XENLA	3, ., 6, ., 4, ., 1, 3	0.6802	1.0	0.8913	N/A	no
A4QVP2	IF4A_MAGO7	3, ., 6, ., 4, ., 1, 3	0.7262	1.0	0.9318	N/A	no
Q40471	IF4A9_TOBAC	3, ., 6, ., 4, ., 1, 3	0.9593	1.0	0.8934	N/A	no
Q4P331	IF4A_USTMA	3, ., 6, ., 4, ., 1, 3	0.7235	1.0	0.8978	N/A	no
Q3SZ54	IF4A1_BOVIN	3, ., 6, ., 4, ., 1, 3	0.7459	1.0	0.9088	no	no
P41382	IF410_TOBAC	3, ., 6, ., 4, ., 1, 3	0.9647	1.0	0.8934	N/A	no
Q7RV88	IF4A_NEUCR	3, ., 6, ., 4, ., 1, 3	0.7262	1.0	0.9294	N/A	no
P41381	IF4A8_TOBAC	3, ., 6, ., 4, ., 1, 3	0.9701	1.0	0.8934	N/A	no
P47943	IF4A_SCHPO	3, ., 6, ., 4, ., 1, 3	0.7181	1.0	0.9413	yes	no
A7EGL7	IF4A_SCLS1	3, ., 6, ., 4, ., 1, 3	0.7208	1.0	0.9271	N/A	no
B5DG42	IF4A3_SALSA	3, ., 6, ., 4, ., 1, 3	0.6829	1.0	0.9088	N/A	no
Q5R4X1	IF4A2_PONAB	3, ., 6, ., 4, ., 1, 3	0.7486	1.0	0.9066	yes	no
Q14240	IF4A2_HUMAN	3, ., 6, ., 4, ., 1, 3	0.7486	1.0	0.9066	yes	no
P41377	IF4A2_ARATH	3, ., 6, ., 4, ., 1, 3	0.9647	1.0	0.8956	yes	no
P41376	IF4A1_ARATH	3, ., 6, ., 4, ., 1, 3	0.9674	1.0	0.8956	yes	no
A5A6N4	IF4A1_PANTR	3, ., 6, ., 4, ., 1, 3	0.7432	1.0	0.9088	no	no
Q40467	IF414_TOBAC	3, ., 6, ., 4, ., 1, 3	0.9647	1.0	0.8934	N/A	no
Q40466	IF413_TOBAC	3, ., 6, ., 4, ., 1, 3	0.9646	0.8428	0.8760	N/A	no
Q40465	IF411_TOBAC	3, ., 6, ., 4, ., 1, 3	0.9674	1.0	0.8934	N/A	no
O02494	IF4A_CRYPV	3, ., 6, ., 4, ., 1, 3	0.6883	1.0	0.9111	yes	no
Q40468	IF415_TOBAC	3, ., 6, ., 4, ., 1, 3	0.9566	1.0	0.8934	N/A	no
Q02748	IF4A_DROME	3, ., 6, ., 4, ., 1, 3	0.7127	1.0	0.9156	yes	no
P41379	IF4A2_NICPL	3, ., 6, ., 4, ., 1, 3	0.9701	1.0	0.8934	N/A	no
Q5RKI1	IF4A2_RAT	3, ., 6, ., 4, ., 1, 3	0.7486	1.0	0.9066	yes	no
Q9CAI7	IF4A3_ARATH	3, ., 6, ., 4, ., 1, 3	0.9349	1.0	0.8913	no	no
Q5R5F5	IF4A1_PONAB	3, ., 6, ., 4, ., 1, 3	0.7432	1.0	0.9088	yes	no
Q4R8K5	IF4A1_MACFA	3, ., 6, ., 4, ., 1, 3	0.7432	1.0	0.9088	N/A	no
Q2HFP1	IF4A_CHAGB	3, ., 6, ., 4, ., 1, 3	0.7181	1.0	0.9294	N/A	no
P41378	IF4A_WHEAT	3, ., 6, ., 4, ., 1, 3	0.9647	1.0	0.8913	N/A	no
P27639	IF4A_CAEEL	3, ., 6, ., 4, ., 1, 3	0.6910	1.0	0.9179	yes	no
A1D7N3	IF4A_NEOFI	3, ., 6, ., 4, ., 1, 3	0.7208	1.0	0.9271	N/A	no
Q3SZ65	IF4A2_BOVIN	3, ., 6, ., 4, ., 1, 3	0.7486	1.0	0.9066	yes	no
P29562	IF4A1_RABIT	3, ., 6, ., 4, ., 1, 3	0.7459	1.0	0.9271	no	no
Q8JFP1	IF4A2_CHICK	3, ., 6, ., 4, ., 1, 3	0.7513	1.0	0.9066	yes	no
A6RJ45	IF4A_BOTFB	3, ., 6, ., 4, ., 1, 3	0.7235	1.0	0.9271	N/A	no
P60842	IF4A1_HUMAN	3, ., 6, ., 4, ., 1, 3	0.7459	1.0	0.9088	no	no
P60843	IF4A1_MOUSE	3, ., 6, ., 4, ., 1, 3	0.7459	1.0	0.9088	no	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.6.4.13	0.994
3rd Layer	3.6.4	0.998

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	369
PTZ00424	401	PTZ00424, PTZ00424, helicase 45; Provisional	0.0
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	1e-138
cd00268	203	cd00268, DEADc, DEAD-box helicases	1e-100
PRK11776	460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	3e-95
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	1e-78
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	1e-72
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	1e-71
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	3e-64
PRK01297	475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	1e-63
PLN00206	518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	6e-59
PRK04837	423	PRK04837, PRK04837, ATP-dependent RNA helicase Rhl	6e-59
PRK04537	572	PRK04537, PRK04537, ATP-dependent RNA helicase Rhl	6e-55
pfam00270	169	pfam00270, DEAD, DEAD/DEAH box helicase	2e-54
smart00487	201	smart00487, DEXDc, DEAD-like helicases superfamily	3e-50
cd00079	131	cd00079, HELICc, Helicase superfamily c-terminal d	1e-42
cd00046	144	cd00046, DEXDc, DEAD-like helicases superfamily	9e-40
pfam00271	78	pfam00271, Helicase_C, Helicase conserved C-termin	1e-27
smart00490	82	smart00490, HELICc, helicase superfamily c-termina	7e-27
COG1201	814	COG1201, Lhr, Lhr-like helicases [General function	2e-16
COG0514	590	COG0514, RecQ, Superfamily II DNA helicase [DNA re	7e-15
COG1205	851	COG1205, COG1205, Distinct helicase family with a	5e-14
TIGR00614	470	TIGR00614, recQ_fam, ATP-dependent DNA helicase, R	6e-10
TIGR01389	591	TIGR01389, recQ, ATP-dependent DNA helicase RecQ	2e-09
COG1202	830	COG1202, COG1202, Superfamily II helicase, archaea	4e-09
COG1204	766	COG1204, COG1204, Superfamily II helicase [General	1e-08
PRK11057	607	PRK11057, PRK11057, ATP-dependent DNA helicase Rec	1e-08
COG1061	442	COG1061, SSL2, DNA or RNA helicases of superfamily	2e-08
TIGR04121	803	TIGR04121, DEXH_lig_assoc, DEXH box helicase, DNA	1e-06
TIGR00643	630	TIGR00643, recG, ATP-dependent DNA helicase RecG	2e-06
COG1111	542	COG1111, MPH1, ERCC4-like helicases [DNA replicati	1e-05
PLN03137	1195	PLN03137, PLN03137, ATP-dependent DNA helicase; Q4	4e-05
PRK09751	1490	PRK09751, PRK09751, putative ATP-dependent helicas	2e-04
TIGR00631	655	TIGR00631, uvrb, excinuclease ABC, B subunit	0.002

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

 Score =  615 bits (1587), Expect = 0.0
 Identities = 269/369 (72%), Positives = 305/369 (82%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
           + L E+LLRGIY+YGFEKPSAIQQRGI P   G D I QAQSGTGKTATF    LQ +DY
Sbjct: 33  LKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQLIDY 92

Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG 120
            L  CQAL+LAPTRELAQQI+KV+ ALGDYL V+ HACVGGT VR+D   L+AGVH+VVG
Sbjct: 93  DLNACQALILAPTRELAQQIQKVVLALGDYLKVRCHACVGGTVVRDDINKLKAGVHMVVG 152

Query: 121 TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMP 180
           TPGRV+DM+ ++ LR D +K+F+LDEADEMLSRGFK QIYD+F+ LP  VQV +FSATMP
Sbjct: 153 TPGRVYDMIDKRHLRVDDLKLFILDEADEMLSRGFKGQIYDVFKKLPPDVQVALFSATMP 212

Query: 181 PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVI 240
            E LE+T KFM  P RILVK+DELTLEGI+QFYV VEKEEWK +TLCDLYETL ITQ++I
Sbjct: 213 NEILELTTKFMRDPKRILVKKDELTLEGIRQFYVAVEKEEWKFDTLCDLYETLTITQAII 272

Query: 241 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 300
           + NTRRKVD+LT KM  RD TVS  HGDMDQ  RD+IMREFRSGS+RVLITTDLLARGID
Sbjct: 273 YCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGID 332

Query: 301 VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEE 360
           VQQVSLVINYDLP  PENY+HRIGRSGRFGRKGVAINFVT DD   L +I++ YN  IEE
Sbjct: 333 VQQVSLVINYDLPASPENYIHRIGRSGRFGRKGVAINFVTPDDIEQLKEIERHYNTQIEE 392

Query: 361 LPSNVADLL 369
           +P  VAD L
Sbjct: 393 MPMEVADYL 401

Length = 401

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

 Score =  401 bits (1033), Expect = e-138
 Identities = 165/366 (45%), Positives = 227/366 (62%), Gaps = 6/366 (1%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLD- 59
           +GL   LL+ +   GFE+P+ IQ   I     G DV+ QAQ+GTGKTA F   +LQ++  
Sbjct: 34  LGLSPELLQALKDLGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFLLPLLQKILK 93

Query: 60  -YGLVQCQALVLAPTRELAQQIEKVMRALGDYL-GVKVHACVGGTSVREDQRILQAGVHV 117
                   AL+LAPTRELA QI + +R LG  L G++V    GG S+R+    L+ GV +
Sbjct: 94  SVERKYVSALILAPTRELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQIEALKRGVDI 153

Query: 118 VVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSA 177
           VV TPGR+ D+++R  L    ++  VLDEAD ML  GF D I  I + LP   Q  +FSA
Sbjct: 154 VVATPGRLLDLIKRGKLDLSGVETLVLDEADRMLDMGFIDDIEKILKALPPDRQTLLFSA 213

Query: 178 TMPPEALEITRKFMNKPVRILVKRDEL--TLEGIKQFYVNVEKEEWKLETLCDLYETLAI 235
           TMP +  E+ R+++N PV I V  ++L  TL+ IKQFY+ VE EE KLE L  L +    
Sbjct: 214 TMPDDIRELARRYLNDPVEIEVSVEKLERTLKKIKQFYLEVESEEEKLELLLKLLKDEDE 273

Query: 236 TQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLL 295
            + ++FV T+R V+ L + +R R   V+A HGD+ Q  RD  + +F+ G  RVL+ TD+ 
Sbjct: 274 GRVIVFVRTKRLVEELAESLRKRGFKVAALHGDLPQEERDRALEKFKDGELRVLVATDVA 333

Query: 296 ARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVT-RDDERMLFDIQKFY 354
           ARG+D+  VS VINYDLP  PE+Y+HRIGR+GR GRKGVAI+FVT  ++ + L  I+K  
Sbjct: 334 ARGLDIPDVSHVINYDLPLDPEDYVHRIGRTGRAGRKGVAISFVTEEEEVKKLKRIEKRL 393

Query: 355 NVVIEE 360
              +  
Sbjct: 394 ERKLPS 399

Length = 513

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

 Score =  295 bits (757), Expect = e-100
 Identities = 107/200 (53%), Positives = 131/200 (65%), Gaps = 2/200 (1%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
           +GL   LLRGIYA GFEKP+ IQ R I P   G DVI QAQ+G+GKTA F   IL++LD 
Sbjct: 4   LGLSPELLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEKLDP 63

Query: 61  --GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVV 118
                  QAL+LAPTRELA QI +V R LG +  +KV    GGTS+ +  R L+ G H+V
Sbjct: 64  SPKKDGPQALILAPTRELALQIAEVARKLGKHTNLKVVVIYGGTSIDKQIRKLKRGPHIV 123

Query: 119 VGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSAT 178
           V TPGR+ D+L R  L    +K  VLDEAD ML  GF+DQI +I +LLP   Q  +FSAT
Sbjct: 124 VATPGRLLDLLERGKLDLSKVKYLVLDEADRMLDMGFEDQIREILKLLPKDRQTLLFSAT 183

Query: 179 MPPEALEITRKFMNKPVRIL 198
           MP E  ++ RKF+  PVRIL
Sbjct: 184 MPKEVRDLARKFLRNPVRIL 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|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional

 Score =  290 bits (746), Expect = 3e-95
 Identities = 136/362 (37%), Positives = 207/362 (57%), Gaps = 9/362 (2%)

Query: 7   LLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQ 66
           LL  +   G+ + + IQ + +     G DVI QA++G+GKTA F  G+LQ+LD    + Q
Sbjct: 15  LLANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQKLDVKRFRVQ 74

Query: 67  ALVLAPTRELAQQIEKVMRALGDYL-GVKVHACVGGTSVREDQRILQAGVHVVVGTPGRV 125
           ALVL PTRELA Q+ K +R L  ++  +KV    GG  +      L+ G H++VGTPGR+
Sbjct: 75  ALVLCPTRELADQVAKEIRRLARFIPNIKVLTLCGGVPMGPQIDSLEHGAHIIVGTPGRI 134

Query: 126 FDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMPPEALE 185
            D LR+ +L  D +   VLDEAD ML  GF+D I  I +  PA+ Q  +FSAT P     
Sbjct: 135 LDHLRKGTLDLDALNTLVLDEADRMLDMGFQDAIDAIIRQAPARRQTLLFSATYPEGIAA 194

Query: 186 ITRKFMNKPVRILV--KRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVN 243
           I+++F   PV + V    D   +E  ++FY  V  +E +L  L  L         V+F N
Sbjct: 195 ISQRFQRDPVEVKVESTHDLPAIE--QRFY-EVSPDE-RLPALQRLLLHHQPESCVVFCN 250

Query: 244 TRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQ 303
           T+++   + D + ++  +  A HGD++Q  RD ++  F + S  VL+ TD+ ARG+D++ 
Sbjct: 251 TKKECQEVADALNAQGFSALALHGDLEQRDRDQVLVRFANRSCSVLVATDVAARGLDIKA 310

Query: 304 VSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYN--VVIEEL 361
           +  VINY+L   PE ++HRIGR+GR G KG+A++ V  ++ +    I+ +    +  E L
Sbjct: 311 LEAVINYELARDPEVHVHRIGRTGRAGSKGLALSLVAPEEMQRANAIEDYLGRKLNWEPL 370

Query: 362 PS 363
           PS
Sbjct: 371 PS 372

Length = 460

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

 Score =  253 bits (647), Expect = 1e-78
 Identities = 144/370 (38%), Positives = 205/370 (55%), Gaps = 2/370 (0%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
           +GL+  +L  +   G+EKPS IQ   I     G DV+  AQ+G+GKTA F   +L  LD 
Sbjct: 11  LGLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLHNLDP 70

Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYL-GVKVHACVGGTSVREDQRILQAGVHVVV 119
            L   Q LVLAPTRELA Q+ + M     ++ GV V A  GG       R L+ G  +VV
Sbjct: 71  ELKAPQILVLAPTRELAVQVAEAMTDFSKHMRGVNVVALYGGQRYDVQLRALRQGPQIVV 130

Query: 120 GTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATM 179
           GTPGR+ D L+R +L    +   VLDEADEML  GF + +  I   +P   Q  +FSATM
Sbjct: 131 GTPGRLLDHLKRGTLDLSKLSGLVLDEADEMLRMGFIEDVETIMAQIPEGHQTALFSATM 190

Query: 180 PPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSV 239
           P     ITR+FM +P  + ++    T   I Q Y  V     K E L    E      ++
Sbjct: 191 PEAIRRITRRFMKEPQEVRIQSSVTTRPDISQSYWTVWGMR-KNEALVRFLEAEDFDAAI 249

Query: 240 IFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGI 299
           IFV T+     + + +    +  +A +GDM+Q  R+  +   + G   +LI TD+ ARG+
Sbjct: 250 IFVRTKNATLEVAEALERNGYNSAALNGDMNQALREQTLERLKDGRLDILIATDVAARGL 309

Query: 300 DVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIE 359
           DV+++SLV+NYD+P   E+Y+HRIGR+GR GR G A+ FV   + R+L +I++   + I 
Sbjct: 310 DVERISLVVNYDIPMDSESYVHRIGRTGRAGRAGRALLFVENRERRLLRNIERTMKLTIP 369

Query: 360 ELPSNVADLL 369
           E+    A+LL
Sbjct: 370 EVELPNAELL 379

Length = 629

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

 Score =  232 bits (593), Expect = 1e-72
 Identities = 127/371 (34%), Positives = 189/371 (50%), Gaps = 14/371 (3%)

Query: 3   LQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQL-DY- 60
           L E+LL  +   G+ +P+AIQ   I P   G DV+  A +GTGKTA F    LQ L D+ 
Sbjct: 8   LDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQHLLDFP 67

Query: 61  ----GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVH 116
               G    + L+L PTRELA Q+    R L  +  + +    GG +      +      
Sbjct: 68  RRKSG--PPRILILTPTRELAMQVADQARELAKHTHLDIATITGGVAYMNHAEVFSENQD 125

Query: 117 VVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFS 176
           +VV TPGR+   ++ ++     ++  +LDEAD ML  GF   I  I      + Q  +FS
Sbjct: 126 IVVATPGRLLQYIKEENFDCRAVETLILDEADRMLDMGFAQDIETIAAETRWRKQTLLFS 185

Query: 177 ATMPPEALE-ITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAI 235
           AT+  +A++    + +N PV +  +      + I Q+Y   +  E K   LC L +   +
Sbjct: 186 ATLEGDAVQDFAERLLNDPVEVEAEPSRRERKKIHQWYYRADDLEHKTALLCHLLKQPEV 245

Query: 236 TQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLL 295
           T+S++FV TR +V  L   +R          G+M Q  R+  ++    G   VL+ TD+ 
Sbjct: 246 TRSIVFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATDVA 305

Query: 296 ARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYN 355
           ARGID+  VS VIN+D+P   + YLHRIGR+GR GRKG AI+ V   D  +L  I+++  
Sbjct: 306 ARGIDIDDVSHVINFDMPRSADTYLHRIGRTGRAGRKGTAISLVEAHDHLLLGKIERYIE 365

Query: 356 V-----VIEEL 361
                 VI+EL
Sbjct: 366 EPLKARVIDEL 376

Length = 434

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

 Score =  230 bits (588), Expect = 1e-71
 Identities = 129/358 (36%), Positives = 201/358 (56%), Gaps = 7/358 (1%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
           +GL  ++LR +   G+ +P+ IQQ+ I    +G D++  AQ+GTGKTA F   +LQ L  
Sbjct: 6   LGLSPDILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQHLIT 65

Query: 61  ------GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAG 114
                 G    +AL+L PTRELA QI + +R    YL ++     GG S+      L+ G
Sbjct: 66  RQPHAKGRRPVRALILTPTRELAAQIGENVRDYSKYLNIRSLVVFGGVSINPQMMKLRGG 125

Query: 115 VHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGV 174
           V V+V TPGR+ D+  + +++ D +++ VLDEAD ML  GF   I  +   LPAK Q  +
Sbjct: 126 VDVLVATPGRLLDLEHQNAVKLDQVEILVLDEADRMLDMGFIHDIRRVLAKLPAKRQNLL 185

Query: 175 FSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLA 234
           FSAT   +   +  K ++ P+ I V R     E + Q    V+K+  K E L  +     
Sbjct: 186 FSATFSDDIKALAEKLLHNPLEIEVARRNTASEQVTQHVHFVDKKR-KRELLSQMIGKGN 244

Query: 235 ITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDL 294
             Q ++F  T+   + L +++       +A HG+  Q  R   + +F+SG  RVL+ TD+
Sbjct: 245 WQQVLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALADFKSGDIRVLVATDI 304

Query: 295 LARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQK 352
            ARG+D++++  V+NY+LP  PE+Y+HRIGR+GR    G A++ V  D+ ++L DI+K
Sbjct: 305 AARGLDIEELPHVVNYELPNVPEDYVHRIGRTGRAAATGEALSLVCVDEHKLLRDIEK 362

Length = 456

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

 Score =  213 bits (544), Expect = 3e-64
 Identities = 131/360 (36%), Positives = 188/360 (52%), Gaps = 20/360 (5%)

Query: 7   LLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFC----SGILQQ--LDY 60
           +L+ +   GF +P+ IQ +G      G D+I  A++G+GKT  F       I  Q  L Y
Sbjct: 141 ILKSLKNAGFTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLPAIVHINAQPLLRY 200

Query: 61  G---LVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHV 117
           G   +V    LVLAPTRELA+QI +     G    ++     GG   R     L+ GV +
Sbjct: 201 GDGPIV----LVLAPTRELAEQIREQCNKFGASSKIRNTVAYGGVPKRGQIYALRRGVEI 256

Query: 118 VVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIF-QLLPAKVQVGVFS 176
           ++  PGR+ D L         +   VLDEAD ML  GF+ QI  I  Q+ P + Q  ++S
Sbjct: 257 LIACPGRLIDFLESNVTNLRRVTYLVLDEADRMLDMGFEPQIRKIVSQIRPDR-QTLMWS 315

Query: 177 ATMPPEALEITRKFM-NKPVRILVKRDELTL-EGIKQFYVNVEKEEWKLETLCDLYETLA 234
           AT P E   + R     +PV + V   +LT    IKQ  V V +E  K   L  L + + 
Sbjct: 316 ATWPKEVQSLARDLCKEEPVHVNVGSLDLTACHNIKQ-EVFVVEEHEKRGKLKMLLQRIM 374

Query: 235 ITQS--VIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITT 292
                 +IFV T++  D+LT ++R         HGD  Q  R  ++ EF++G S ++I T
Sbjct: 375 RDGDKILIFVETKKGADFLTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKSPIMIAT 434

Query: 293 DLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQK 352
           D+ +RG+DV+ V  VIN+D P Q E+Y+HRIGR+GR G KG +  F+T D  R+  D+ K
Sbjct: 435 DVASRGLDVKDVKYVINFDFPNQIEDYVHRIGRTGRAGAKGASYTFLTPDKYRLARDLVK 494

Length = 545

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

 Score =  209 bits (534), Expect = 1e-63
 Identities = 119/361 (32%), Positives = 190/361 (52%), Gaps = 13/361 (3%)

Query: 3   LQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGL 62
           L   L+  I+  GF   + IQ + +     G D I +AQ+GTGKTA F   I+ QL    
Sbjct: 94  LAPELMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQLLQTP 153

Query: 63  VQCQ-------ALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAG- 114
              +       AL++APTREL  QI K   AL  Y G+ V   VGG    +  + L+A  
Sbjct: 154 PPKERYMGEPRALIIAPTRELVVQIAKDAAALTKYTGLNVMTFVGGMDFDKQLKQLEARF 213

Query: 115 VHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKV--QV 172
             ++V TPGR+ D  +R  +  D +++ VLDEAD ML  GF  Q+  I +  P K   Q 
Sbjct: 214 CDILVATPGRLLDFNQRGEVHLDMVEVMVLDEADRMLDMGFIPQVRQIIRQTPRKEERQT 273

Query: 173 GVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQ-FYVNVEKEEWKLETLCDLYE 231
            +FSAT   + + + +++   P  + ++ + +  + ++Q  Y     +++KL  L +L  
Sbjct: 274 LLFSATFTDDVMNLAKQWTTDPAIVEIEPENVASDTVEQHVYAVAGSDKYKL--LYNLVT 331

Query: 232 TLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLIT 291
                + ++F N + +V  + +++       +   GD+ Q+ R   +  FR G  RVL+ 
Sbjct: 332 QNPWERVMVFANRKDEVRRIEERLVKDGINAAQLSGDVPQHKRIKTLEGFREGKIRVLVA 391

Query: 292 TDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQ 351
           TD+  RGI +  +S VIN+ LP  P++Y+HRIGR+GR G  GV+I+F   DD   L +I+
Sbjct: 392 TDVAGRGIHIDGISHVINFTLPEDPDDYVHRIGRTGRAGASGVSISFAGEDDAFQLPEIE 451

Query: 352 K 352
           +
Sbjct: 452 E 452

Length = 475

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

 Score =  198 bits (506), Expect = 6e-59
 Identities = 121/360 (33%), Positives = 187/360 (51%), Gaps = 19/360 (5%)

Query: 2   GLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATF-------CSGI 54
           GL   LL  +   G+E P+ IQ + I     G  ++  A +G+GKTA+F       C  I
Sbjct: 127 GLPPKLLLNLETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPIISRCCTI 186

Query: 55  LQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAG 114
                       A+VL PTREL  Q+E   + LG  L  K    VGG ++ +    +Q G
Sbjct: 187 RSGHPSEQRNPLAMVLTPTRELCVQVEDQAKVLGKGLPFKTALVVGGDAMPQQLYRIQQG 246

Query: 115 VHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGV 174
           V ++VGTPGR+ D+L +  +  D + + VLDE D ML RGF+DQ+  IFQ L  + QV +
Sbjct: 247 VELIVGTPGRLIDLLSKHDIELDNVSVLVLDEVDCMLERGFRDQVMQIFQALS-QPQVLL 305

Query: 175 FSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLA 234
           FSAT+ PE  +         + I +       + +KQ  + VE ++ K +    L++ L 
Sbjct: 306 FSATVSPEVEKFASSLAKDIILISIGNPNRPNKAVKQLAIWVETKQKKQK----LFDILK 361

Query: 235 ITQ-----SVIFVNTRRKVDWLTDKMRSRDHTVSAT-HGDMDQNTRDIIMREFRSGSSRV 288
             Q     +V+FV++R   D L + +       + + HG+     R  +M+ F  G   V
Sbjct: 362 SKQHFKPPAVVFVSSRLGADLLANAITVVTGLKALSIHGEKSMKERREVMKSFLVGEVPV 421

Query: 289 LITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLF 348
           ++ T +L RG+D+ +V  VI +D+P   + Y+H+IGR+ R G KG AI FV  +++R LF
Sbjct: 422 IVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQIGRASRMGEKGTAIVFVN-EEDRNLF 480

Length = 518

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

 Score =  196 bits (500), Expect = 6e-59
 Identities = 116/349 (33%), Positives = 180/349 (51%), Gaps = 14/349 (4%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQL-- 58
             L   ++  +   GF   + IQ   +     G DV  QAQ+GTGKT  F +     L  
Sbjct: 13  FALHPQVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHYLLS 72

Query: 59  -----DYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQA 113
                D  + Q +AL++APTRELA QI      L    G+K+    GG    +  ++L++
Sbjct: 73  HPAPEDRKVNQPRALIMAPTRELAVQIHADAEPLAQATGLKLGLAYGGDGYDKQLKVLES 132

Query: 114 GVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQ-- 171
           GV +++GT GR+ D  ++  +    I++ VLDEAD M   GF   I  +F+ +P   Q  
Sbjct: 133 GVDILIGTTGRLIDYAKQNHINLGAIQVVVLDEADRMFDLGFIKDIRWLFRRMPPANQRL 192

Query: 172 VGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQ--FYVNVEKEEWKLETLCDL 229
             +FSAT+     E+  + MN P  + V+ ++ T   IK+  FY + E+   K+  L  L
Sbjct: 193 NMLFSATLSYRVRELAFEHMNNPEYVEVEPEQKTGHRIKEELFYPSNEE---KMRLLQTL 249

Query: 230 YETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVL 289
            E     +++IF NT+ + + +   + +  H V    GD+ Q  R  I+ EF  G   +L
Sbjct: 250 IEEEWPDRAIIFANTKHRCEEIWGHLAADGHRVGLLTGDVAQKKRLRILEEFTRGDLDIL 309

Query: 290 ITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINF 338
           + TD+ ARG+ +  V+ V NYDLP   E+Y+HRIGR+GR G  G +I+ 
Sbjct: 310 VATDVAARGLHIPAVTHVFNYDLPDDCEDYVHRIGRTGRAGASGHSISL 358

Length = 423

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

 Score =  189 bits (480), Expect = 6e-55
 Identities = 122/364 (33%), Positives = 191/364 (52%), Gaps = 17/364 (4%)

Query: 3   LQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQL---- 58
           L   LL G+ + GF + + IQ   +     G DV  QAQ+GTGKT  F   ++ +L    
Sbjct: 16  LHPALLAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMNRLLSRP 75

Query: 59  ---DYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGV 115
              D      +AL+LAPTRELA QI K     G  LG++     GG    + + +LQ GV
Sbjct: 76  ALADRKPEDPRALILAPTRELAIQIHKDAVKFGADLGLRFALVYGGVDYDKQRELLQQGV 135

Query: 116 HVVVGTPGRVFDMLRRQ---SLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKV-- 170
            V++ TPGR+ D +++    SL     ++ VLDEAD M   GF   I  + + +P +   
Sbjct: 136 DVIIATPGRLIDYVKQHKVVSLHA--CEICVLDEADRMFDLGFIKDIRFLLRRMPERGTR 193

Query: 171 QVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQ-FYVNVEKEEWKLETLCDL 229
           Q  +FSAT+    LE+  + MN+P +++V+ + +T   ++Q  Y   ++E  K   L  L
Sbjct: 194 QTLLFSATLSHRVLELAYEHMNEPEKLVVETETITAARVRQRIYFPADEE--KQTLLLGL 251

Query: 230 YETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVL 289
                  ++++FVNT+  V+ +   +    + V    GD+ Q  R+ ++  F+ G   +L
Sbjct: 252 LSRSEGARTMVFVNTKAFVERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQKGQLEIL 311

Query: 290 ITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFD 349
           + TD+ ARG+ +  V  V NYDLP   E+Y+HRIGR+ R G +G AI+F        L D
Sbjct: 312 VATDVAARGLHIDGVKYVYNYDLPFDAEDYVHRIGRTARLGEEGDAISFACERYAMSLPD 371

Query: 350 IQKF 353
           I+ +
Sbjct: 372 IEAY 375

Length = 572

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

 Score =  176 bits (449), Expect = 2e-54
 Identities = 72/169 (42%), Positives = 101/169 (59%), Gaps = 2/169 (1%)

Query: 20  SAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQ 79
           + IQ + I     G DV+ QA +G+GKT  F   ILQ L       QALVLAPTRELA+Q
Sbjct: 1   TPIQAQAIPAILSGKDVLVQAPTGSGKTLAFLLPILQALLPKKGGPQALVLAPTRELAEQ 60

Query: 80  IEKVMRALGDYLGVKVHACVGGTSVREDQRILQAG-VHVVVGTPGRVFDMLRRQSLRP-D 137
           I + ++ L   LG++V    GGTS++E  R L+ G   ++VGTPGR+ D+LRR  L+   
Sbjct: 61  IYEELKKLFKILGLRVALLTGGTSLKEQARKLKKGKADILVGTPGRLLDLLRRGKLKLLK 120

Query: 138 YIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMPPEALEI 186
            +K+ VLDEA  +L  GF D + +I   LP   Q+ + SAT+P    ++
Sbjct: 121 NLKLLVLDEAHRLLDMGFGDDLEEILSRLPPDRQILLLSATLPRNLEDL 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 =  166 bits (423), Expect = 3e-50
 Identities = 81/204 (39%), Positives = 110/204 (53%), Gaps = 5/204 (2%)

Query: 11  IYAYGFEKPSAIQQRGIVPFCKGL-DVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALV 69
           I  +GFE     Q+  I     GL DVI  A +G+GKT       L+ L  G    + LV
Sbjct: 1   IEKFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGK-GGRVLV 59

Query: 70  LAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGV-HVVVGTPGRVFDM 128
           L PTRELA+Q  + ++ LG  LG+KV    GG S RE  R L++G   ++V TPGR+ D+
Sbjct: 60  LVPTRELAEQWAEELKKLGPSLGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDL 119

Query: 129 LRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMPPEALEITR 188
           L    L    + + +LDEA  +L  GF DQ+  + +LLP  VQ+ + SAT P E   +  
Sbjct: 120 LENDKLSLSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNVQLLLLSATPPEEIENLLE 179

Query: 189 KFMNKPVRILVKRDELTLEGIKQF 212
            F+N PV I V      LE I+QF
Sbjct: 180 LFLNDPVFIDVGF--TPLEPIEQF 201

Length = 201

>gnl|CDD|238034 cd00079, HELICc, Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process

 Score =  144 bits (365), Expect = 1e-42
 Identities = 57/132 (43%), Positives = 84/132 (63%), Gaps = 4/132 (3%)

Query: 209 IKQFYVNVEKEEWKLETLCDLYETLAIT--QSVIFVNTRRKVDWLTDKMRSRDHTVSATH 266
           IKQ+ + VE  + KLE L +L +       + +IF  +++ +D L + +R     V+A H
Sbjct: 2   IKQYVLPVE--DEKLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAALH 59

Query: 267 GDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRS 326
           GD  Q  R+ ++++FR G   VL+ TD++ARGID+  VS+VINYDLP  P +YL RIGR+
Sbjct: 60  GDGSQEEREEVLKDFREGEIVVLVATDVIARGIDLPNVSVVINYDLPWSPSSYLQRIGRA 119

Query: 327 GRFGRKGVAINF 338
           GR G+KG AI  
Sbjct: 120 GRAGQKGTAILL 131

Length = 131

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

 Score =  137 bits (347), Expect = 9e-40
 Identities = 59/145 (40%), Positives = 84/145 (57%), Gaps = 2/145 (1%)

Query: 35  DVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVK 94
           DV+  A +G+GKT      IL+ LD  L   Q LVLAPTRELA Q+ + ++ L    G+K
Sbjct: 2   DVLLAAPTGSGKTLAALLPILELLDS-LKGGQVLVLAPTRELANQVAERLKELFGE-GIK 59

Query: 95  VHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRG 154
           V   +GGTS+++ +++L     +VVGTPGR+ D L R  L    + + +LDEA  +L++G
Sbjct: 60  VGYLIGGTSIKQQEKLLSGKTDIVVGTPGRLLDELERLKLSLKKLDLLILDEAHRLLNQG 119

Query: 155 FKDQIYDIFQLLPAKVQVGVFSATM 179
           F      I   LP   QV + SAT 
Sbjct: 120 FGLLGLKILLKLPKDRQVLLLSATP 144

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

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

 Score =  103 bits (260), Expect = 1e-27
 Identities = 37/78 (47%), Positives = 52/78 (66%)

Query: 253 DKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDL 312
             +R     V+  HG + Q  R+ I+ +FR+G S+VL+ TD+  RGID+  V+LVINYDL
Sbjct: 1   KLLRKPGIKVARLHGGLSQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNLVINYDL 60

Query: 313 PTQPENYLHRIGRSGRFG 330
           P  P +Y+ RIGR+GR G
Sbjct: 61  PWNPASYIQRIGRAGRAG 78

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

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

 Score =  101 bits (254), Expect = 7e-27
 Identities = 33/82 (40%), Positives = 51/82 (62%)

Query: 249 DWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVI 308
           + L + ++     V+  HG + Q  R+ I+ +F +G  +VL+ TD+  RG+D+  V LVI
Sbjct: 1   EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVI 60

Query: 309 NYDLPTQPENYLHRIGRSGRFG 330
            YDLP  P +Y+ RIGR+GR G
Sbjct: 61  IYDLPWSPASYIQRIGRAGRAG 82

Length = 82

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

 Score = 80.8 bits (200), Expect = 2e-16
 Identities = 83/354 (23%), Positives = 143/354 (40%), Gaps = 34/354 (9%)

Query: 16  FEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQL-------DYGLVQCQAL 68
           F   +  Q+  I     G +V+  A +G+GKT      ++ +L           +    L
Sbjct: 20  FTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLSLGKGKLEDGIYA--L 77

Query: 69  VLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDM 128
            ++P + L   I + +      LG++V    G T   E Q++L+   H+++ TP  +  +
Sbjct: 78  YISPLKALNNDIRRRLEEPLRELGIEVAVRHGDTPQSEKQKMLKNPPHILITTPESLAIL 137

Query: 129 LRRQSLRPDY--IKMFVLDEADEMLS--RGFKDQI---YDIFQLLPAKVQ-VGVFSATMP 180
           L     R     ++  ++DE   +    RG   Q+    +  + L    Q +G+ SAT+ 
Sbjct: 138 LNSPKFRELLRDVRYVIVDEIHALAESKRG--VQLALSLERLRELAGDFQRIGL-SATVG 194

Query: 181 PEALEITRKFM---NKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLA--I 235
           P   E   KF+     P  I+       LE IK      +   +  E    LYE +A  +
Sbjct: 195 P--PEEVAKFLVGFGDPCEIVDVSAAKKLE-IKVISPVEDLI-YDEELWAALYERIAELV 250

Query: 236 TQSV---IFVNTRRKVDWLTDKMRSR-DHTVSATHGDMDQNTRDIIMREFRSGSSRVLIT 291
            +     IF NTR   + L  +++      +   HG + +  R  +    + G  + ++ 
Sbjct: 251 KKHRTTLIFTNTRSGAERLAFRLKKLGPDIIEVHHGSLSRELRLEVEERLKEGELKAVVA 310

Query: 292 TDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSG-RFGRKGVAINFVTRDDE 344
           T  L  GID+  + LVI    P     +L RIGR+G R G     I      D+
Sbjct: 311 TSSLELGIDIGDIDLVIQLGSPKSVNRFLQRIGRAGHRLGEVSKGIIIAEDRDD 364

Length = 814

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

 Score = 75.4 bits (186), Expect = 7e-15
 Identities = 54/235 (22%), Positives = 98/235 (41%), Gaps = 23/235 (9%)

Query: 123 GRVFDMLRRQSLRPDYIKMFVLDEADEMLSR---GFK---DQIYDIFQLLPAKVQVGVFS 176
            R  ++L+R       I +  +DEA   +S+    F+    ++  +   LP    V   +
Sbjct: 121 PRFLELLKRLP-----ISLVAIDEA-HCISQWGHDFRPDYRRLGRLRAGLP-NPPVLALT 173

Query: 177 ATMPPEALE--ITRKFMNKPVRIL--VKRDELTLEGIKQFYVNVEKEEWKLETLCDLYET 232
           AT  P   +    +  +           R  L L+ + +     ++  +    L  L ++
Sbjct: 174 ATATPRVRDDIREQLGLQDANIFRGSFDRPNLALK-VVEKGEPSDQLAFLATVLPQLSKS 232

Query: 233 LAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITT 292
                 +I+  TR+KV+ L + +R    +  A H  +    R+ + + F +   +V++ T
Sbjct: 233 -----GIIYCLTRKKVEELAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKVMVAT 287

Query: 293 DLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERML 347
           +    GID   V  VI+YDLP   E+Y    GR+GR G    AI   + +D R  
Sbjct: 288 NAFGMGIDKPDVRFVIHYDLPGSIESYYQETGRAGRDGLPAEAILLYSPEDIRWQ 342

Length = 590

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

 Score = 73.2 bits (180), Expect = 5e-14
 Identities = 78/352 (22%), Positives = 129/352 (36%), Gaps = 52/352 (14%)

Query: 32  KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYL 91
           +G +V+    +G+GKT +F   IL  L       +AL+L PT  LA    + +R L   L
Sbjct: 84  EGRNVVVTTGTGSGKTESFLLPILDHLLRDP-SARALLLYPTNALANDQAERLRELISDL 142

Query: 92  GVKVHACV--GGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRP--------DYIKM 141
             KV      G T   E + I++    +++  P    DML    LR           +K 
Sbjct: 143 PGKVTFGRYTGDTPPEERRAIIRNPPDILLTNP----DMLHYLLLRNHDAWLWLLRNLKY 198

Query: 142 FVLDEAD----------EMLSRGFKDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFM 191
            V+DE             +L R          +   + +Q+   SAT+     E   +  
Sbjct: 199 LVVDELHTYRGVQGSEVALLLRRLLR----RLRRYGSPLQIICTSATLA-NPGEFAEELF 253

Query: 192 NKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLA---ITQSV-------IF 241
            +   + V  D     G++ F           E++               V       +F
Sbjct: 254 GRDFEVPVDEDGSP-RGLRYFVRREPPIRELAESIRRSALAELATLAALLVRNGIQTLVF 312

Query: 242 VNTRRKV--DWLTDKMRSRD------HTVSATHGDMDQNTRDIIMREFRSGSSRVLITTD 293
             +R++V   +L+ + R           VS     + +  R  I  EF+ G    +I T+
Sbjct: 313 FRSRKQVELLYLSPRRRLVREGGKLLDAVSTYRAGLHREERRRIEAEFKEGELLGVIATN 372

Query: 294 LLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKG-VAINFVTRDDE 344
            L  GID+  +  VI Y  P        +  R+GR GR+G  ++  V    +
Sbjct: 373 ALELGIDIGSLDAVIAYGYPGVSVLSFRQ--RAGRAGRRGQESLVLVVLRSD 422

Length = 851

>gnl|CDD|129701 TIGR00614, recQ_fam, ATP-dependent DNA helicase, RecQ family

 Score = 60.2 bits (146), Expect = 6e-10
 Identities = 28/105 (26%), Positives = 50/105 (47%)

Query: 239 VIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARG 298
           +I+  +R+K + +T  +++      A H  ++ + RD +  +F+    +V++ T     G
Sbjct: 230 IIYCPSRKKSEQVTASLQNLGIAAGAYHAGLEISARDDVHHKFQRDEIQVVVATVAFGMG 289

Query: 299 IDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDD 343
           I+   V  VI+Y LP   E+Y    GR+GR G       F    D
Sbjct: 290 INKPDVRFVIHYSLPKSMESYYQESGRAGRDGLPSECHLFYAPAD 334

All proteins in this family for which functions are known are 3'-5' DNA-DNA helicases. These proteins are used for recombination, recombinational repair, and possibly maintenance of chromosome stability. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 470

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

 Score = 58.5 bits (142), Expect = 2e-09
 Identities = 30/98 (30%), Positives = 51/98 (52%)

Query: 239 VIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARG 298
           +I+ ++R+KV+ L +++ S+  +  A H  +    R     +F     +V++ T+    G
Sbjct: 228 IIYASSRKKVEELAERLESQGISALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMG 287

Query: 299 IDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAI 336
           ID   V  VI+YD+P   E+Y    GR+GR G    AI
Sbjct: 288 IDKPNVRFVIHYDMPGNLESYYQEAGRAGRDGLPAEAI 325

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

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

 Score = 57.9 bits (140), Expect = 4e-09
 Identities = 80/318 (25%), Positives = 132/318 (41%), Gaps = 32/318 (10%)

Query: 32  KGLDVIQQAQSGTGKTATF-CSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDY 90
           +G +++  + + +GKT     +GI + L  G    + L L P   LA Q  +  +     
Sbjct: 231 EGENLLVVSATASGKTLIGELAGIPRLLSGGK---KMLFLVPLVALANQKYEDFKERYSK 287

Query: 91  LGVKVHACVGGTSVREDQRILQA----GVHVVVGT-PGRVFDMLRRQSLRPDYIKMFVLD 145
           LG+KV   VG + ++  +  +         ++VGT  G   D L R       I   V+D
Sbjct: 288 LGLKVAIRVGMSRIKTREEPVVVDTSPDADIIVGTYEG--IDYLLRTGKDLGDIGTVVID 345

Query: 146 EAD--EMLSRGFK-DQIYDIFQLLPAKVQVGVFSATMP-PEALEITRKFMNKPVRILVKR 201
           E    E   RG + D +    + L    Q    SAT+  PE  E+ +K   K V  L   
Sbjct: 346 EIHTLEDEERGPRLDGLIGRLRYLFPGAQFIYLSATVGNPE--ELAKKLGAKLV--LYDE 401

Query: 202 DELTLEGIKQFYVNVEKEEWKLE-TLCDL-YETLAIT----QSVIFVNTRRKVDWLTDKM 255
             + LE    F  N E E+W +   L    + T +      Q+++F  +RR+   L D +
Sbjct: 402 RPVPLERHLVFARN-ESEKWDIIARLVKREFSTESSKGYRGQTIVFTYSRRRCHELADAL 460

Query: 256 RSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID--VQQV---SLVINY 310
             +    +  H  +    R  + R F +     ++TT  LA G+D    QV   SL +  
Sbjct: 461 TGKGLKAAPYHAGLPYKERKSVERAFAAQELAAVVTTAALAAGVDFPASQVIFESLAMGI 520

Query: 311 DLPTQPENYLHRIGRSGR 328
           +  +    +   +GR+GR
Sbjct: 521 EWLS-VREFQQMLGRAGR 537

Length = 830

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

 Score = 56.2 bits (136), Expect = 1e-08
 Identities = 67/319 (21%), Positives = 127/319 (39%), Gaps = 61/319 (19%)

Query: 32  KGLDVIQQAQSGTGKTATFCSGILQQL-DYGLVQCQALVLAPTRELAQQIEKVMRALGDY 90
              +V+  A +G+GKT      IL  L + G    + + + P + LA++  +    L + 
Sbjct: 46  SDENVLISAPTGSGKTLIALLAILSTLLEGGG---KVVYIVPLKALAEEKYEEFSRLEEL 102

Query: 91  LGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEM 150
            G++V     G    +D+R+  A   V+V TP ++  + R++    + + + V+DE   +
Sbjct: 103 -GIRV-GISTGDYDLDDERL--ARYDVIVTTPEKLDSLTRKRPSWIEEVDLVVIDEI-HL 157

Query: 151 LS---RG-FKDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMN-KPVRILVKRDEL- 204
           L    RG   + I    + L   +++   SAT+ P A E+   ++N K V    +   L 
Sbjct: 158 LGDRTRGPVLESIVARMRRLNELIRIVGLSATL-PNAEEVA-DWLNAKLVESDWRPVPLR 215

Query: 205 --TLEGIKQFYVNVEKEEWKLE----TLCDLYETLA-ITQSVIFVNTRR----------- 246
                       + +K+ W L      L  + E+LA   Q ++FV++R+           
Sbjct: 216 RGVPYVGAFLGADGKKKTWPLLIDNLALELVLESLAEGGQVLVFVHSRKEAEKTAKKLRI 275

Query: 247 ------------KVDWLTDKMRSRDHTVSAT--------------HGDMDQNTRDIIMRE 280
                        +D     +   +   S                H  + +  R ++   
Sbjct: 276 KMSATLSDDEKIVLDEGASPILIPETPTSEDEELAELVLRGVAFHHAGLPREDRQLVEDA 335

Query: 281 FRSGSSRVLITTDLLARGI 299
           FR G  +VL++T  LA G+
Sbjct: 336 FRKGKIKVLVSTPTLAAGV 354

Length = 766

>gnl|CDD|182933 PRK11057, PRK11057, ATP-dependent DNA helicase RecQ; Provisional

 Score = 55.9 bits (135), Expect = 1e-08
 Identities = 28/100 (28%), Positives = 53/100 (53%)

Query: 239 VIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARG 298
           +I+ N+R KV+    +++SR  + +A H  +D + R  +   F+    ++++ T     G
Sbjct: 240 IIYCNSRAKVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMG 299

Query: 299 IDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINF 338
           I+   V  V+++D+P   E+Y    GR+GR G    A+ F
Sbjct: 300 INKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLF 339

Length = 607

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

 Score = 55.1 bits (133), Expect = 2e-08
 Identities = 64/332 (19%), Positives = 112/332 (33%), Gaps = 73/332 (21%)

Query: 43  GTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQ-IEKVMRALGDYLGVKVHACVGG 101
           G GKT               ++   LVL PT+EL  Q  E + + L     + +    GG
Sbjct: 65  GAGKTVVAA------EAIAELKRSTLVLVPTKELLDQWAEALKKFLLLNDEIGI---YGG 115

Query: 102 TSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLR---PDYIKMFVLDEADEMLSRGFKDQ 158
                +         V V T   V  + RRQ L     +   + + DE   + +  ++  
Sbjct: 116 GEKELE------PAKVTVAT---VQTLARRQLLDEFLGNEFGLIIFDEVHHLPAPSYRR- 165

Query: 159 IYDIFQLLPAKVQVGVFSATMP---------------PEALEITRKFMNK-----PVRIL 198
              I +LL A       +AT                 P   E++ K +       P + +
Sbjct: 166 ---ILELLSAAYPRLGLTATPEREDGGRIGDLFDLIGPIVYEVSLKELIDEGYLAPYKYV 222

Query: 199 VKRDELTLEGIKQ---FYVNVEKEEWKLETLCDLYETLAIT------------------- 236
             +  LT +  ++         +      TL    E   I                    
Sbjct: 223 EIKVTLTEDEEREYAKESARFRELLRARGTLRAENEARRIAIASERKIAAVRGLLLKHAR 282

Query: 237 --QSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDL 294
             +++IF +       +          V A  G+  +  R+ I+  FR+G  +VL+T  +
Sbjct: 283 GDKTLIFASDVEHAYEIAKLFL-APGIVEAITGETPKEEREAILERFRTGGIKVLVTVKV 341

Query: 295 LARGIDVQQVSLVINYDLPTQ-PENYLHRIGR 325
           L  G+D+    ++I    PT     ++ R+GR
Sbjct: 342 LDEGVDIPDADVLI-ILRPTGSRRLFIQRLGR 372

Length = 442

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

 Score = 50.2 bits (121), Expect = 1e-06
 Identities = 84/341 (24%), Positives = 132/341 (38%), Gaps = 64/341 (18%)

Query: 39  QAQSGTGKT-ATFCSGILQQLDY------GLVQCQALVLAPTRELAQQIEKVMRALGDYL 91
            A +G+GKT A F    L  L        GL     L + P R LA  I + ++A  + L
Sbjct: 34  IAPTGSGKTLAGFL-PSLIDLAGPEKPKKGL---HTLYITPLRALAVDIARNLQAPIEEL 89

Query: 92  GVKVHACV--GGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSL-----RPDYIKMF-- 142
           G+ +      G TS  E  R  +    +++ TP         +SL      PD  ++F  
Sbjct: 90  GLPIRVETRTGDTSSSERARQRKKPPDILLTTP---------ESLALLLSYPDAARLFKD 140

Query: 143 ----VLDEADEMLS--RGFKDQ----IYDIFQLLPAKVQVGVFSATM--PPEALEITRKF 190
               V+DE  E+    RG  DQ    +  + +L P   + G+ SAT+    EA  +    
Sbjct: 141 LRCVVVDEWHELAGSKRG--DQLELALARLRRLAPGLRRWGL-SATIGNLEEARRVLLGV 197

Query: 191 MNKPVRILVKRDELTLEGIKQFYVNVEKEEWK----LETLCDLYETLAITQSV-IFVNTR 245
              P  ++  +    +  I     + E+  W     L  L ++Y  +   ++  +F NTR
Sbjct: 198 GGAPAVLVRGKLPKAIPVISLLPESEERFPWAGHLGLRALPEVYAEIDQARTTLVFTNTR 257

Query: 246 RKVD-WLTDKMRSRD--------HTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLA 296
            + + W      +          H     HG +D+  R  +     +G  R ++ T  L 
Sbjct: 258 SQAELWFQALWEANPEFALPIALH-----HGSLDREQRRWVEAAMAAGRLRAVVCTSSLD 312

Query: 297 RGIDVQQVSLVINYDLPTQPENYLHRIGRSG-RFGRKGVAI 336
            G+D   V LVI    P      L R GRS  R G    A+
Sbjct: 313 LGVDFGPVDLVIQIGSPKGVARLLQRAGRSNHRPGEPSRAL 353

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

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

 Score = 49.3 bits (118), Expect = 2e-06
 Identities = 75/326 (23%), Positives = 131/326 (40%), Gaps = 55/326 (16%)

Query: 39  QAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHAC 98
           Q   G+GKT      +L  ++ G    Q  ++APT  LA+Q    +R L   LG++V   
Sbjct: 262 QGDVGSGKTLVAALAMLAAIEAGY---QVALMAPTEILAEQHYNSLRNLLAPLGIEVALL 318

Query: 99  VGGTSVREDQRIL---QAG-VHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEA------- 147
            G    +  + +L    +G +H+VVGT   + + +  + L      + ++DE        
Sbjct: 319 TGSLKGKRRKELLETIASGQIHLVVGTHALIQEKVEFKRLA-----LVIIDEQHRFGVEQ 373

Query: 148 -DEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTL 206
             ++  +G                 V V SAT  P  L +T  + +    I+   DEL  
Sbjct: 374 RKKLREKGQGGF----------TPHVLVMSATPIPRTLALT-VYGDLDTSII---DELPP 419

Query: 207 EGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTR----RKVD-------WLTDKM 255
            G K     + K + K      + E +A  +    V        K+D       +   K 
Sbjct: 420 -GRKPITTVLIKHDEKDIVYEFIEEEIAKGRQAYVVYPLIEESEKLDLKAAEALYERLKK 478

Query: 256 RSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQ 315
               + V   HG M  + ++ +M EFR G   +L+ T ++  G+DV   ++++  D    
Sbjct: 479 AFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPNATVMVIED---- 534

Query: 316 PENY----LHRI-GRSGRFGRKGVAI 336
            E +    LH++ GR GR   +   +
Sbjct: 535 AERFGLSQLHQLRGRVGRGDHQSYCL 560

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

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

 Score = 46.6 bits (111), Expect = 1e-05
 Identities = 26/78 (33%), Positives = 38/78 (48%), Gaps = 1/78 (1%)

Query: 269 MDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGR 328
           M Q  +  I+ +FR G   VL+ T +   G+D+ +V LVI Y+        + R GR+GR
Sbjct: 409 MSQKEQKEIIDQFRKGEYNVLVATSVGEEGLDIPEVDLVIFYEPVPSEIRSIQRKGRTGR 468

Query: 329 FGRKGVAINFVTRDDERM 346
             RKG  +  VT      
Sbjct: 469 -KRKGRVVVLVTEGTRDE 485

Length = 542

>gnl|CDD|215597 PLN03137, PLN03137, ATP-dependent DNA helicase; Q4-like; Provisional

 Score = 45.7 bits (108), Expect = 4e-05
 Identities = 23/94 (24%), Positives = 45/94 (47%)

Query: 239 VIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARG 298
           +I+  +R   + + ++++   H  +  HG MD   R  + +++      ++  T     G
Sbjct: 684 IIYCLSRMDCEKVAERLQEFGHKAAFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGMG 743

Query: 299 IDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRK 332
           I+   V  VI++ LP   E Y    GR+GR G++
Sbjct: 744 INKPDVRFVIHHSLPKSIEGYHQECGRAGRDGQR 777

Length = 1195

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

 Score = 43.4 bits (102), Expect = 2e-04
 Identities = 23/62 (37%), Positives = 32/62 (51%)

Query: 266 HGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGR 325
           HG + +  R I  +  +SG  R ++ T  L  GID+  V LVI    P    + L RIGR
Sbjct: 308 HGSVSKEQRAITEQALKSGELRCVVATSSLELGIDMGAVDLVIQVATPLSVASGLQRIGR 367

Query: 326 SG 327
           +G
Sbjct: 368 AG 369

Length = 1490

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

 Score = 39.6 bits (93), Expect = 0.002
 Identities = 22/64 (34%), Positives = 36/64 (56%)

Query: 244 TRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQ 303
           T++  + LTD ++     V   H ++D   R  I+R+ R G   VL+  +LL  G+D+ +
Sbjct: 451 TKKMAEDLTDYLKELGIKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPE 510

Query: 304 VSLV 307
           VSLV
Sbjct: 511 VSLV 514

All proteins in this family for wich functions are known are DNA helicases that function in the nucleotide excision repair and are endonucleases that make the 3' incision next to DNA damage. They are part of a pathway requiring UvrA, UvrB, UvrC, and UvrD homologs. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 655

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	369
KOG0328	400	consensus Predicted ATP-dependent RNA helicase FAL	100.0
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	100.0
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	100.0
PTZ00110	545	helicase; Provisional	100.0
KOG0330	476	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0331	519	consensus ATP-dependent RNA helicase [RNA processi	100.0
PTZ00424	401	helicase 45; Provisional	100.0
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	100.0
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	100.0
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	100.0
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	100.0
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	100.0
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	100.0
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	100.0
KOG0333	673	consensus U5 snRNP-like RNA helicase subunit [RNA	100.0
KOG0345	567	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0338	691	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0326	459	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0340	442	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0335	482	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0342	543	consensus ATP-dependent RNA helicase pitchoune [RN	100.0
KOG0327	397	consensus Translation initiation factor 4F, helica	100.0
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	100.0
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	100.0
KOG0343	758	consensus RNA Helicase [RNA processing and modific	100.0
KOG0346	569	consensus RNA helicase [RNA processing and modific	100.0
KOG0339	731	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0332	477	consensus ATP-dependent RNA helicase [RNA processi	100.0
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	100.0
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	100.0
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	100.0
KOG0341	610	consensus DEAD-box protein abstrakt [RNA processin	100.0
KOG0348	708	consensus ATP-dependent RNA helicase [RNA processi	100.0
PRK02362	737	ski2-like helicase; Provisional	100.0
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	100.0
KOG0347	731	consensus RNA helicase [RNA processing and modific	100.0
KOG0334	997	consensus RNA helicase [RNA processing and modific	100.0
KOG4284	980	consensus DEAD box protein [Transcription]	100.0
PRK00254	720	ski2-like helicase; Provisional	100.0
KOG0337	529	consensus ATP-dependent RNA helicase [RNA processi	100.0
PRK13767	876	ATP-dependent helicase; Provisional	100.0
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	100.0
COG1201	814	Lhr Lhr-like helicases [General function predictio	100.0
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	100.0
PRK01172	674	ski2-like helicase; Provisional	100.0
KOG0350	620	consensus DEAD-box ATP-dependent RNA helicase [RNA	100.0
KOG0344	593	consensus ATP-dependent RNA helicase [RNA processi	100.0
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	100.0
PRK10689	1147	transcription-repair coupling factor; Provisional	100.0
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	100.0
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	100.0
PHA02558	501	uvsW UvsW helicase; Provisional	100.0
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	100.0
COG1202	830	Superfamily II helicase, archaea-specific [General	100.0
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	100.0
PRK09401	1176	reverse gyrase; Reviewed	100.0
COG1204	766	Superfamily II helicase [General function predicti	100.0
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	100.0
KOG0354	746	consensus DEAD-box like helicase [General function	100.0
PRK13766	773	Hef nuclease; Provisional	100.0
COG1205	851	Distinct helicase family with a unique C-terminal	100.0
KOG0329	387	consensus ATP-dependent RNA helicase [RNA processi	100.0
PHA02653	675	RNA helicase NPH-II; Provisional	100.0
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	100.0
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	100.0
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	100.0
PRK14701	1638	reverse gyrase; Provisional	100.0
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	100.0
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	100.0
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	100.0
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	100.0
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	100.0
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	100.0
KOG0952	1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	100.0
PRK04914	956	ATP-dependent helicase HepA; Validated	100.0
PRK09200	790	preprotein translocase subunit SecA; Reviewed	100.0
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	100.0
KOG0351	941	consensus ATP-dependent DNA helicase [Replication,	100.0
KOG0352	641	consensus ATP-dependent DNA helicase [Replication,	100.0
KOG0353	695	consensus ATP-dependent DNA helicase [General func	100.0
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	100.0
KOG0349	725	consensus Putative DEAD-box RNA helicase DDX1 [RNA	100.0
PRK05580	679	primosome assembly protein PriA; Validated	100.0
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	100.0
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	100.0
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	100.0
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	100.0
PRK09694	878	helicase Cas3; Provisional	100.0
TIGR00595	505	priA primosomal protein N'. All proteins in this f	100.0
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	100.0
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	100.0
KOG0947	1248	consensus Cytoplasmic exosomal RNA helicase SKI2,	99.97
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	99.97
KOG0948	1041	consensus Nuclear exosomal RNA helicase MTR4, DEAD	99.97
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	99.97
PRK12904	830	preprotein translocase subunit SecA; Reviewed	99.97
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	99.97
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	99.97
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	99.96
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	99.96
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	99.96
KOG0387	923	consensus Transcription-coupled repair protein CSB	99.96
KOG0950	1008	consensus DNA polymerase theta/eta, DEAD-box super	99.95
KOG0385	971	consensus Chromatin remodeling complex WSTF-ISWI,	99.95
PRK13107	908	preprotein translocase subunit SecA; Reviewed	99.95
COG4096	875	HsdR Type I site-specific restriction-modification	99.95
KOG0390	776	consensus DNA repair protein, SNF2 family [Replica	99.95
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	99.95
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	99.94
KOG1123	776	consensus RNA polymerase II transcription initiati	99.94
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	99.94
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	99.93
KOG1000	689	consensus Chromatin remodeling protein HARP/SMARCA	99.93
COG1198	730	PriA Primosomal protein N' (replication factor Y)	99.93
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	99.93
KOG0392	1549	consensus SNF2 family DNA-dependent ATPase domain-	99.93
KOG0922	674	consensus DEAH-box RNA helicase [RNA processing an	99.92
PRK12326	764	preprotein translocase subunit SecA; Reviewed	99.92
KOG0389	941	consensus SNF2 family DNA-dependent ATPase [Chroma	99.92
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	99.91
COG4889	1518	Predicted helicase [General function prediction on	99.91
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	99.91
smart00487	201	DEXDc DEAD-like helicases superfamily.	99.9
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	99.9
KOG0384	1373	consensus Chromodomain-helicase DNA-binding protei	99.9
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	99.88
KOG0923	902	consensus mRNA splicing factor ATP-dependent RNA h	99.88
KOG0949	1330	consensus Predicted helicase, DEAD-box superfamily	99.88
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	99.87
KOG0920	924	consensus ATP-dependent RNA helicase A [RNA proces	99.87
PRK05298	652	excinuclease ABC subunit B; Provisional	99.87
KOG0926	1172	consensus DEAH-box RNA helicase [RNA processing an	99.86
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	99.85
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	99.85
KOG0924	1042	consensus mRNA splicing factor ATP-dependent RNA h	99.84
CHL00122	870	secA preprotein translocase subunit SecA; Validate	99.84
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	99.84
KOG4439	901	consensus RNA polymerase II transcription terminat	99.84
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	99.83
KOG0386	1157	consensus Chromatin remodeling complex SWI/SNF, co	99.82
KOG4150	1034	consensus Predicted ATP-dependent RNA helicase [RN	99.82
cd00079	131	HELICc Helicase superfamily c-terminal domain; ass	99.82
KOG0391	1958	consensus SNF2 family DNA-dependent ATPase [Genera	99.82
KOG0953	700	consensus Mitochondrial RNA helicase SUV3, DEAD-bo	99.82
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	99.8
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	99.79
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	99.78
KOG0388	1185	consensus SNF2 family DNA-dependent ATPase [Replic	99.78
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	99.78
KOG1002	791	consensus Nucleotide excision repair protein RAD16	99.77
COG0610	962	Type I site-specific restriction-modification syst	99.77
PF00271	78	Helicase_C: Helicase conserved C-terminal domain;	99.77
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	99.76
KOG0925	699	consensus mRNA splicing factor ATP-dependent RNA h	99.76
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	99.74
KOG1015	1567	consensus Transcription regulator XNP/ATRX, DEAD-b	99.74
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	99.71
PRK14873	665	primosome assembly protein PriA; Provisional	99.7
TIGR02562	1110	cas3_yersinia CRISPR-associated helicase Cas3. The	99.69
COG0553	866	HepA Superfamily II DNA/RNA helicases, SNF2 family	99.65
smart00490	82	HELICc helicase superfamily c-terminal domain.	99.64
PF06862	442	DUF1253: Protein of unknown function (DUF1253); In	99.64
PF00176	299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	99.63
PF07652	148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	99.59
COG0653	822	SecA Preprotein translocase subunit SecA (ATPase,	99.53
KOG1016	1387	consensus Predicted DNA helicase, DEAD-box superfa	99.48
PRK15483	986	type III restriction-modification system StyLTI en	99.43
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	99.39
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	99.39
KOG2340	698	consensus Uncharacterized conserved protein [Funct	99.27
PF07517	266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	99.24
KOG1133	821	consensus Helicase of the DEAD superfamily [Replic	99.24
KOG1001	674	consensus Helicase-like transcription factor HLTF/	99.16
COG3587	985	Restriction endonuclease [Defense mechanisms]	99.15
PF13872	303	AAA_34: P-loop containing NTP hydrolase pore-1	99.07
KOG0952	1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	98.95
COG3421	812	Uncharacterized protein conserved in bacteria [Fun	98.95
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	98.89
PF13307	167	Helicase_C_2: Helicase C-terminal domain; PDB: 4A1	98.86
KOG1802	935	consensus RNA helicase nonsense mRNA reducing fact	98.85
KOG0921	1282	consensus Dosage compensation complex, subunit MLE	98.82
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	98.8
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	98.76
KOG1131	755	consensus RNA polymerase II transcription initiati	98.68
TIGR00596	814	rad1 DNA repair protein (rad1). This family is bas	98.66
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	98.56
PRK10536	262	hypothetical protein; Provisional	98.51
KOG1132	945	consensus Helicase of the DEAD superfamily [Replic	98.5
PF13245	76	AAA_19: Part of AAA domain	98.48
KOG1803	649	consensus DNA helicase [Replication, recombination	98.45
TIGR00376	637	DNA helicase, putative. The gene product may repre	98.43
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	98.41
PRK10875	615	recD exonuclease V subunit alpha; Provisional	98.38
TIGR01447	586	recD exodeoxyribonuclease V, alpha subunit. This f	98.38
PF00580	315	UvrD-helicase: UvrD/REP helicase N-terminal domain	98.3
smart00492	141	HELICc3 helicase superfamily c-terminal domain.	98.24
PF12340	229	DUF3638: Protein of unknown function (DUF3638); In	98.2
smart00491	142	HELICc2 helicase superfamily c-terminal domain.	98.19
KOG0298	1394	consensus DEAD box-containing helicase-like transc	98.19
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	98.16
PRK06526	254	transposase; Provisional	98.12
PRK04296	190	thymidine kinase; Provisional	98.09
PRK08181	269	transposase; Validated	98.08
KOG0383	696	consensus Predicted helicase [General function pre	98.06
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	98.01
COG1875	436	NYN ribonuclease and ATPase of PhoH family domains	97.98
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	97.93
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	97.85
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	97.84
PRK13889	988	conjugal transfer relaxase TraA; Provisional	97.78
PF13871	278	Helicase_C_4: Helicase_C-like	97.77
KOG1805	1100	consensus DNA replication helicase [Replication, r	97.76
PRK13826	1102	Dtr system oriT relaxase; Provisional	97.73
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	97.73
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	97.73
smart00382	148	AAA ATPases associated with a variety of cellular	97.7
PRK14974	336	cell division protein FtsY; Provisional	97.68
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	97.66
PRK06835	329	DNA replication protein DnaC; Validated	97.6
PRK11054	684	helD DNA helicase IV; Provisional	97.58
PRK10919	672	ATP-dependent DNA helicase Rep; Provisional	97.56
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	97.55
PRK05642	234	DNA replication initiation factor; Validated	97.52
PRK06921	266	hypothetical protein; Provisional	97.51
PRK05707	328	DNA polymerase III subunit delta'; Validated	97.51
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	97.48
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	97.47
PHA02533	534	17 large terminase protein; Provisional	97.45
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	97.44
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	97.42
PRK06893	229	DNA replication initiation factor; Validated	97.41
PRK08769	319	DNA polymerase III subunit delta'; Validated	97.4
TIGR02785	1232	addA_Gpos recombination helicase AddA, Firmicutes	97.4
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	97.4
KOG1513	1300	consensus Nuclear helicase MOP-3/SNO (DEAD-box sup	97.39
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	97.38
PRK08903	227	DnaA regulatory inactivator Hda; Validated	97.38
PRK14087	450	dnaA chromosomal replication initiation protein; P	97.38
PRK08084	235	DNA replication initiation factor; Provisional	97.37
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	97.37
PRK12377	248	putative replication protein; Provisional	97.37
PF03354	477	Terminase_1: Phage Terminase ; InterPro: IPR005021	97.37
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	97.36
TIGR01075	715	uvrD DNA helicase II. Designed to identify uvrD me	97.36
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	97.34
PRK08727	233	hypothetical protein; Validated	97.34
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	97.32
PRK00149	450	dnaA chromosomal replication initiation protein; R	97.31
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	97.3
TIGR01074	664	rep ATP-dependent DNA helicase Rep. Designed to id	97.3
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	97.3
PRK11773	721	uvrD DNA-dependent helicase II; Provisional	97.28
PRK07952	244	DNA replication protein DnaC; Validated	97.26
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	97.24
PF05127	177	Helicase_RecD: Helicase; InterPro: IPR007807 This	97.24
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	97.23
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	97.23
PRK06871	325	DNA polymerase III subunit delta'; Validated	97.21
COG2256	436	MGS1 ATPase related to the helicase subunit of the	97.19
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	97.17
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	97.17
PRK09183	259	transposase/IS protein; Provisional	97.16
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	97.14
COG1435	201	Tdk Thymidine kinase [Nucleotide transport and met	97.14
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	97.12
PRK08116	268	hypothetical protein; Validated	97.1
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	97.08
PRK12402	337	replication factor C small subunit 2; Reviewed	97.06
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	97.06
PTZ00293	211	thymidine kinase; Provisional	97.04
PLN03025	319	replication factor C subunit; Provisional	97.03
PRK12422	445	chromosomal replication initiation protein; Provis	97.03
PRK07993	334	DNA polymerase III subunit delta'; Validated	97.03
PRK08533	230	flagellar accessory protein FlaH; Reviewed	97.02
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	97.0
PRK00411	394	cdc6 cell division control protein 6; Reviewed	96.99
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	96.99
TIGR01547	396	phage_term_2 phage terminase, large subunit, PBSX	96.98
PHA03368	738	DNA packaging terminase subunit 1; Provisional	96.95
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	96.95
KOG0739	439	consensus AAA+-type ATPase [Posttranslational modi	96.93
PRK14712	1623	conjugal transfer nickase/helicase TraI; Provision	96.93
PRK00771	437	signal recognition particle protein Srp54; Provisi	96.92
CHL00181	287	cbbX CbbX; Provisional	96.92
TIGR01073	726	pcrA ATP-dependent DNA helicase PcrA. Designed to	96.91
PF05876	557	Terminase_GpA: Phage terminase large subunit (GpA)	96.9
PRK13709	1747	conjugal transfer nickase/helicase TraI; Provision	96.89
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	96.89
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	96.89
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	96.88
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	96.87
COG4626	546	Phage terminase-like protein, large subunit [Gener	96.86
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	96.86
PRK14088	440	dnaA chromosomal replication initiation protein; P	96.85
PRK05986	191	cob(I)alamin adenolsyltransferase/cobinamide ATP-d	96.84
PRK14086	617	dnaA chromosomal replication initiation protein; P	96.84
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	96.84
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	96.83
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	96.82
PHA02544	316	44 clamp loader, small subunit; Provisional	96.81
PF13173	128	AAA_14: AAA domain	96.8
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	96.79
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	96.79
COG3973	747	Superfamily I DNA and RNA helicases [General funct	96.78
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	96.77
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	96.76
PF00004	132	AAA: ATPase family associated with various cellula	96.76
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	96.75
PHA00729	226	NTP-binding motif containing protein	96.75
PRK06964	342	DNA polymerase III subunit delta'; Validated	96.74
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	96.74
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	96.74
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	96.73
PRK11823	446	DNA repair protein RadA; Provisional	96.73
PHA03333	752	putative ATPase subunit of terminase; Provisional	96.72
PRK06731	270	flhF flagellar biosynthesis regulator FlhF; Valida	96.71
COG0593	408	DnaA ATPase involved in DNA replication initiation	96.71
PRK06067	234	flagellar accessory protein FlaH; Validated	96.69
PTZ00112	1164	origin recognition complex 1 protein; Provisional	96.68
PRK06090	319	DNA polymerase III subunit delta'; Validated	96.68
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	96.66
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	96.66
COG1484	254	DnaC DNA replication protein [DNA replication, rec	96.65
PF02572	172	CobA_CobO_BtuR: ATP:corrinoid adenosyltransferase	96.64
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	96.63
PRK08939	306	primosomal protein DnaI; Reviewed	96.63
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	96.61
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	96.59
PRK00440	319	rfc replication factor C small subunit; Reviewed	96.57
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	96.56
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	96.54
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	96.53
PRK10867	433	signal recognition particle protein; Provisional	96.52
PRK05973	237	replicative DNA helicase; Provisional	96.5
TIGR00708	173	cobA cob(I)alamin adenosyltransferase. Alternate n	96.5
PF14617	252	CMS1: U3-containing 90S pre-ribosomal complex subu	96.48
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	96.47
COG2805	353	PilT Tfp pilus assembly protein, pilus retraction	96.47
TIGR00064	272	ftsY signal recognition particle-docking protein F	96.46
PRK09112	351	DNA polymerase III subunit delta'; Validated	96.46
cd03115	173	SRP The signal recognition particle (SRP) mediates	96.46
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	96.43
PRK07940	394	DNA polymerase III subunit delta'; Validated	96.41
PRK07471	365	DNA polymerase III subunit delta'; Validated	96.41
KOG2028	554	consensus ATPase related to the helicase subunit o	96.41
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	96.4
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	96.39
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	96.39
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	96.38
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	96.34
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	96.33
PF02456	369	Adeno_IVa2: Adenovirus IVa2 protein; InterPro: IPR	96.33
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	96.32
TIGR00959	428	ffh signal recognition particle protein. This mode	96.32
COG2109	198	BtuR ATP:corrinoid adenosyltransferase [Coenzyme m	96.32
PRK07414	178	cob(I)yrinic acid a,c-diamide adenosyltransferase;	96.31
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	96.3
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	96.29
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	96.26
PF00265	176	TK: Thymidine kinase; InterPro: IPR001267 Thymidin	96.19
COG1444	758	Predicted P-loop ATPase fused to an acetyltransfer	96.17
TIGR00767	415	rho transcription termination factor Rho. Members	96.16
COG2874	235	FlaH Predicted ATPases involved in biogenesis of a	96.16
PRK04195	482	replication factor C large subunit; Provisional	96.15
PRK09376	416	rho transcription termination factor Rho; Provisio	96.11
PRK08699	325	DNA polymerase III subunit delta'; Validated	96.1
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	96.1
KOG0738	491	consensus AAA+-type ATPase [Posttranslational modi	96.1
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	96.06
PRK06620	214	hypothetical protein; Validated	96.06
PRK13342	413	recombination factor protein RarA; Reviewed	96.05
TIGR02237	209	recomb_radB DNA repair and recombination protein R	96.05
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	96.01
COG3972	660	Superfamily I DNA and RNA helicases [General funct	96.01
TIGR03600	421	phage_DnaB phage replicative helicase, DnaB family	96.0
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	96.0
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	95.98
PRK13833	323	conjugal transfer protein TrbB; Provisional	95.97
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	95.95
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	95.95
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	95.93
PRK06904	472	replicative DNA helicase; Validated	95.91
PF03796	259	DnaB_C: DnaB-like helicase C terminal domain; Inte	95.9
PF05729	166	NACHT: NACHT domain	95.89
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	95.88
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	95.87
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	95.85
PRK08058	329	DNA polymerase III subunit delta'; Validated	95.84
KOG0298	1394	consensus DEAD box-containing helicase-like transc	95.83
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	95.83
PRK07399	314	DNA polymerase III subunit delta'; Validated	95.81
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	95.79
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	95.77
COG4962	355	CpaF Flp pilus assembly protein, ATPase CpaF [Intr	95.74
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	95.72
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	95.71
PRK13341	725	recombination factor protein RarA/unknown domain f	95.69
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	95.68
PRK08506	472	replicative DNA helicase; Provisional	95.67
PRK10416	318	signal recognition particle-docking protein FtsY;	95.65
COG0210	655	UvrD Superfamily I DNA and RNA helicases [DNA repl	95.65
PRK04328	249	hypothetical protein; Provisional	95.64
PF03237	384	Terminase_6: Terminase-like family; InterPro: IPR0	95.62
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	95.6
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	95.58
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	95.54
PF01443	234	Viral_helicase1: Viral (Superfamily 1) RNA helicas	95.52
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	95.49
PRK08006	471	replicative DNA helicase; Provisional	95.42
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	95.41
PRK14873	665	primosome assembly protein PriA; Provisional	95.31
cd01128	249	rho_factor Transcription termination factor rho is	95.3
PRK08840	464	replicative DNA helicase; Provisional	95.3
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	95.29
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	95.28
KOG0742	630	consensus AAA+-type ATPase [Posttranslational modi	95.28
PRK05580	679	primosome assembly protein PriA; Validated	95.25
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	95.24
PRK13851	344	type IV secretion system protein VirB11; Provision	95.24
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	95.23
CHL00176	638	ftsH cell division protein; Validated	95.22
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	95.2
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	95.2
COG0552	340	FtsY Signal recognition particle GTPase [Intracell	95.2
PRK07004	460	replicative DNA helicase; Provisional	95.19
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	95.15
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	95.15
PRK03992	389	proteasome-activating nucleotidase; Provisional	95.11
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	95.09
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	95.02
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	95.01
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	94.96
TIGR00665	434	DnaB replicative DNA helicase. This model describe	94.96
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	94.93
PRK12608	380	transcription termination factor Rho; Provisional	94.91
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	94.88
TIGR03880	224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	94.88
TIGR02688	449	conserved hypothetical protein TIGR02688. Members	94.85
PRK05748	448	replicative DNA helicase; Provisional	94.84
TIGR00595	505	priA primosomal protein N'. All proteins in this f	94.82
PF06733	174	DEAD_2: DEAD_2; InterPro: IPR010614 This represent	94.81
PF12846	304	AAA_10: AAA-like domain	94.79
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	94.73
PHA00012	361	I assembly protein	94.71
TIGR02784	1141	addA_alphas double-strand break repair helicase Ad	94.65
PRK08760	476	replicative DNA helicase; Provisional	94.64
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	94.62
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	94.62
PF03969	362	AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654	94.56
COG1198	730	PriA Primosomal protein N' (replication factor Y)	94.5
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	94.48
PRK09087	226	hypothetical protein; Validated	94.47
KOG1807	1025	consensus Helicases [Replication, recombination an	94.45
KOG0737	386	consensus AAA+-type ATPase [Posttranslational modi	94.44
PRK05917	290	DNA polymerase III subunit delta'; Validated	94.44
) proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia [].; GO: 0005524 ATP binding, 0051085 chaperone mediated protein folding requiring cofactor" target="_blank" href="http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PF06309">PF06309	127	Torsin: Torsin; InterPro: IPR010448 This family co	94.44
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	94.41
PRK04841	903	transcriptional regulator MalT; Provisional	94.39
PF03266	168	NTPase_1: NTPase; InterPro: IPR004948 This entry r	94.39
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	94.37
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	94.35
COG0541	451	Ffh Signal recognition particle GTPase [Intracellu	94.32
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	94.25
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	94.24
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	94.24
PHA03372	668	DNA packaging terminase subunit 1; Provisional	94.22
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	94.22
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	94.18
PHA00350	399	putative assembly protein	94.13
KOG0729	435	consensus 26S proteasome regulatory complex, ATPas	94.13
KOG1513	1300	consensus Nuclear helicase MOP-3/SNO (DEAD-box sup	94.05
KOG0780	483	consensus Signal recognition particle, subunit Srp	94.01
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	93.99
PF13555	62	AAA_29: P-loop containing region of AAA domain	93.97
COG1132	567	MdlB ABC-type multidrug transport system, ATPase a	93.96
KOG0740	428	consensus AAA+-type ATPase [Posttranslational modi	93.94
PRK09165	497	replicative DNA helicase; Provisional	93.94
KOG0732	1080	consensus AAA+-type ATPase containing the bromodom	93.93
cd01394	218	radB RadB. The archaeal protein radB shares simila	93.89
PRK05595	444	replicative DNA helicase; Provisional	93.83
cd00983	325	recA RecA is a bacterial enzyme which has roles in	93.82
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	93.8
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	93.8
CHL00095	821	clpC Clp protease ATP binding subunit	93.8
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	93.79
COG1074	1139	RecB ATP-dependent exoDNAse (exonuclease V) beta s	93.74
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	93.73
PRK05564	313	DNA polymerase III subunit delta'; Validated	93.72
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	93.69
PRK10436	462	hypothetical protein; Provisional	93.68
PRK05636	505	replicative DNA helicase; Provisional	93.67
PRK10865	857	protein disaggregation chaperone; Provisional	93.65
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	93.58
KOG1132	945	consensus Helicase of the DEAD superfamily [Replic	93.57
PF08423	256	Rad51: Rad51; InterPro: IPR013632 This domain is f	93.56
PRK06321	472	replicative DNA helicase; Provisional	93.53
cd01125	239	repA Hexameric Replicative Helicase RepA. RepA is	93.51
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	93.41
KOG0701	1606	consensus dsRNA-specific nuclease Dicer and relate	93.32
KOG2228	408	consensus Origin recognition complex, subunit 4 [R	93.28

>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=7.9e-65  Score=396.77  Aligned_cols=369  Identities=69%  Similarity=1.079  Sum_probs=357.3

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQI   80 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~   80 (369)
                      |||.+++.+.+.+.||+.|+.+|+.|++++++|++++.++..|+|||.++.+.++..+.-+.+..++++++|+++|+.|.
T Consensus        32 Mgl~edlLrgiY~yGfekPS~IQqrAi~~IlkGrdViaQaqSGTGKTa~~si~vlq~~d~~~r~tQ~lilsPTRELa~Qi  111 (400)
T KOG0328|consen   32 MGLKEDLLRGIYAYGFEKPSAIQQRAIPQILKGRDVIAQAQSGTGKTATFSISVLQSLDISVRETQALILSPTRELAVQI  111 (400)
T ss_pred             cCchHHHHHHHHHhccCCchHHHhhhhhhhhcccceEEEecCCCCceEEEEeeeeeecccccceeeEEEecChHHHHHHH
Confidence            79999999999999999999999999999999999999999999999988888888877766666899999999999999


Q ss_pred             HHHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHH
Q 017573           81 EKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIY  160 (369)
Q Consensus        81 ~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~  160 (369)
                      .+.+..+....++++..+.|+.+..++.+.+..+.+++.+||.+.+.+.++..+....+.++|+||++.+.+.++..++.
T Consensus       112 ~~vi~alg~~mnvq~hacigg~n~gedikkld~G~hvVsGtPGrv~dmikr~~L~tr~vkmlVLDEaDemL~kgfk~Qiy  191 (400)
T KOG0328|consen  112 QKVILALGDYMNVQCHACIGGKNLGEDIKKLDYGQHVVSGTPGRVLDMIKRRSLRTRAVKMLVLDEADEMLNKGFKEQIY  191 (400)
T ss_pred             HHHHHHhcccccceEEEEecCCccchhhhhhcccceEeeCCCchHHHHHHhccccccceeEEEeccHHHHHHhhHHHHHH
Confidence            99999999999999999999999888888888889999999999999999999999999999999999999999999999


Q ss_pred             HHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHHHhccCCCeEE
Q 017573          161 DIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVI  240 (369)
Q Consensus       161 ~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lv  240 (369)
                      .+++.+|+..|++++|||++.+..+..+.++.+|+.+.+.+++.+.+.+.++++....++++.+.+..+........++|
T Consensus       192 diyr~lp~~~Qvv~~SATlp~eilemt~kfmtdpvrilvkrdeltlEgIKqf~v~ve~EewKfdtLcdLYd~LtItQavI  271 (400)
T KOG0328|consen  192 DIYRYLPPGAQVVLVSATLPHEILEMTEKFMTDPVRILVKRDELTLEGIKQFFVAVEKEEWKFDTLCDLYDTLTITQAVI  271 (400)
T ss_pred             HHHHhCCCCceEEEEeccCcHHHHHHHHHhcCCceeEEEecCCCchhhhhhheeeechhhhhHhHHHHHhhhhehheEEE
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999988889999


Q ss_pred             EeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCCCCccchh
Q 017573          241 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYL  320 (369)
Q Consensus       241 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~  320 (369)
                      ||+++..+.++.+.++..+..+...||+|+.++|++++++|++|+.+||++|+...+|+|+|.++.||.+++|.+...|+
T Consensus       272 FcnTk~kVdwLtekm~~~nftVssmHGDm~qkERd~im~dFRsg~SrvLitTDVwaRGiDv~qVslviNYDLP~nre~YI  351 (400)
T KOG0328|consen  272 FCNTKRKVDWLTEKMREANFTVSSMHGDMEQKERDKIMNDFRSGKSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYI  351 (400)
T ss_pred             EecccchhhHHHHHHHhhCceeeeccCCcchhHHHHHHHHhhcCCceEEEEechhhccCCcceeEEEEecCCCccHHHHh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhcccccCCCceeEEEEeccccHHHHHHHHHHhccccccCCcchhhcC
Q 017573          321 HRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPSNVADLL  369 (369)
Q Consensus       321 Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  369 (369)
                      +|+||.||.|++|.++-|+...|.+.+..++++|...+.++|-++.+++
T Consensus       352 HRIGRSGRFGRkGvainFVk~~d~~~lrdieq~yst~i~emp~nvad~i  400 (400)
T KOG0328|consen  352 HRIGRSGRFGRKGVAINFVKSDDLRILRDIEQYYSTQIDEMPMNVADLI  400 (400)
T ss_pred             hhhccccccCCcceEEEEecHHHHHHHHHHHHHHhhhcccccchhhhcC
Confidence            9999999999999999999999999999999999999999999998875

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=3.1e-60  Score=424.97  Aligned_cols=360  Identities=32%  Similarity=0.478  Sum_probs=321.2

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhcc-------CCCccEEEEcCC
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYG-------LVQCQALVLAPT   73 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~-------~~~~~~liv~P~   73 (369)
                      +||++.+.++|..+||..|+|+|.++++.+++|++++++||||||||+++++++++.+...       ..++++||++|+
T Consensus        13 ~~l~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvi~~ApTGsGKTla~llp~l~~l~~~~~~~~~~~~~~~~lil~Pt   92 (423)
T PRK04837         13 FALHPQVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHYLLSHPAPEDRKVNQPRALIMAPT   92 (423)
T ss_pred             CCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCcEEEECCCCchHHHHHHHHHHHHHHhcccccccccCCceEEEECCc
Confidence            6899999999999999999999999999999999999999999999999999999877532       123579999999


Q ss_pred             HHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhcc
Q 017573           74 RELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSR  153 (369)
Q Consensus        74 ~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~  153 (369)
                      ++|+.|+.+.+..+....++++..+.|+.....+...+..+++|+|+||+.+..++....+....++++|+||||++.+.
T Consensus        93 reLa~Qi~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~l~~~~~IlV~TP~~l~~~l~~~~~~l~~v~~lViDEad~l~~~  172 (423)
T PRK04837         93 RELAVQIHADAEPLAQATGLKLGLAYGGDGYDKQLKVLESGVDILIGTTGRLIDYAKQNHINLGAIQVVVLDEADRMFDL  172 (423)
T ss_pred             HHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHhcCCCCEEEECHHHHHHHHHcCCcccccccEEEEecHHHHhhc
Confidence            99999999999999888899999999988877776667778899999999999999988888999999999999999999


Q ss_pred             CcHHHHHHHHhhCCc--cCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHHH
Q 017573          154 GFKDQIYDIFQLLPA--KVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYE  231 (369)
Q Consensus       154 ~~~~~~~~~~~~~~~--~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  231 (369)
                      ++...+..++..++.  ..+.+++|||++..........+..+..+...........+.+.+... ....+...+..++.
T Consensus       173 ~f~~~i~~i~~~~~~~~~~~~~l~SAT~~~~~~~~~~~~~~~p~~i~v~~~~~~~~~i~~~~~~~-~~~~k~~~l~~ll~  251 (423)
T PRK04837        173 GFIKDIRWLFRRMPPANQRLNMLFSATLSYRVRELAFEHMNNPEYVEVEPEQKTGHRIKEELFYP-SNEEKMRLLQTLIE  251 (423)
T ss_pred             ccHHHHHHHHHhCCCccceeEEEEeccCCHHHHHHHHHHCCCCEEEEEcCCCcCCCceeEEEEeC-CHHHHHHHHHHHHH
Confidence            999999999988875  455788999999888888888888887777665555445555544433 34557778888887


Q ss_pred             hccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEec
Q 017573          232 TLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYD  311 (369)
Q Consensus       232 ~~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~  311 (369)
                      .....++||||++.+.++.+++.|...+.++..+||+++.++|.++++.|++|+++|||||+++++|+|+|++++||+++
T Consensus       252 ~~~~~~~lVF~~t~~~~~~l~~~L~~~g~~v~~lhg~~~~~~R~~~l~~F~~g~~~vLVaTdv~~rGiDip~v~~VI~~d  331 (423)
T PRK04837        252 EEWPDRAIIFANTKHRCEEIWGHLAADGHRVGLLTGDVAQKKRLRILEEFTRGDLDILVATDVAARGLHIPAVTHVFNYD  331 (423)
T ss_pred             hcCCCeEEEEECCHHHHHHHHHHHHhCCCcEEEecCCCChhHHHHHHHHHHcCCCcEEEEechhhcCCCccccCEEEEeC
Confidence            77778999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCccchhhhhcccccCCCceeEEEEeccccHHHHHHHHHHhccccccC
Q 017573          312 LPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEEL  361 (369)
Q Consensus       312 ~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  361 (369)
                      +|.+..+|.||+||+||.|+.|.+++|+.+.+...+..+++++...+...
T Consensus       332 ~P~s~~~yiqR~GR~gR~G~~G~ai~~~~~~~~~~~~~i~~~~~~~~~~~  381 (423)
T PRK04837        332 LPDDCEDYVHRIGRTGRAGASGHSISLACEEYALNLPAIETYIGHSIPVS  381 (423)
T ss_pred             CCCchhheEeccccccCCCCCeeEEEEeCHHHHHHHHHHHHHhCCCCCCc
Confidence            99999999999999999999999999999999999999999888876543

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=100.00  E-value=6.8e-60  Score=427.26  Aligned_cols=357  Identities=37%  Similarity=0.619  Sum_probs=326.5

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQI   80 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~   80 (369)
                      |||++.+.++|.++||.+|+|+|+++++.+.++++++++||||+|||+++++++++.+.......+++|++|+++|+.|+
T Consensus         9 l~l~~~l~~~l~~~g~~~~t~iQ~~ai~~~l~g~dvi~~a~TGsGKT~a~~lpil~~l~~~~~~~~~lil~PtreLa~Q~   88 (460)
T PRK11776          9 LPLPPALLANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQKLDVKRFRVQALVLCPTRELADQV   88 (460)
T ss_pred             cCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHhhhccCCceEEEEeCCHHHHHHH
Confidence            68999999999999999999999999999999999999999999999999999999987665555899999999999999


Q ss_pred             HHHHHHhcccc-CcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHH
Q 017573           81 EKVMRALGDYL-GVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQI  159 (369)
Q Consensus        81 ~~~~~~~~~~~-~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~  159 (369)
                      .++++.+.... +.++..++|+.....+...+...++|+|+||+.+..++.++.....+++++|+||||++.+.++...+
T Consensus        89 ~~~~~~~~~~~~~~~v~~~~Gg~~~~~~~~~l~~~~~IvV~Tp~rl~~~l~~~~~~l~~l~~lViDEad~~l~~g~~~~l  168 (460)
T PRK11776         89 AKEIRRLARFIPNIKVLTLCGGVPMGPQIDSLEHGAHIIVGTPGRILDHLRKGTLDLDALNTLVLDEADRMLDMGFQDAI  168 (460)
T ss_pred             HHHHHHHHhhCCCcEEEEEECCCChHHHHHHhcCCCCEEEEChHHHHHHHHcCCccHHHCCEEEEECHHHHhCcCcHHHH
Confidence            99999886644 68899999999887777777788999999999999999998888889999999999999999999999


Q ss_pred             HHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHHHhccCCCeE
Q 017573          160 YDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSV  239 (369)
Q Consensus       160 ~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~l  239 (369)
                      ..++..+++..|++++|||+++....+...++..+..+...... ....+.+.++...... +.+.+..++.....+++|
T Consensus       169 ~~i~~~~~~~~q~ll~SAT~~~~~~~l~~~~~~~~~~i~~~~~~-~~~~i~~~~~~~~~~~-k~~~l~~ll~~~~~~~~l  246 (460)
T PRK11776        169 DAIIRQAPARRQTLLFSATYPEGIAAISQRFQRDPVEVKVESTH-DLPAIEQRFYEVSPDE-RLPALQRLLLHHQPESCV  246 (460)
T ss_pred             HHHHHhCCcccEEEEEEecCcHHHHHHHHHhcCCCEEEEECcCC-CCCCeeEEEEEeCcHH-HHHHHHHHHHhcCCCceE
Confidence            99999999999999999999999889999999988877765544 3445677777666544 788888888887778999


Q ss_pred             EEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCCCCccch
Q 017573          240 IFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENY  319 (369)
Q Consensus       240 v~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~  319 (369)
                      |||++++.++.+++.|...+..+..+||++++.+|..+++.|++|+.+|||||+++++|+|+|++++||+++.|.+...|
T Consensus       247 VF~~t~~~~~~l~~~L~~~~~~v~~~hg~~~~~eR~~~l~~F~~g~~~vLVaTdv~~rGiDi~~v~~VI~~d~p~~~~~y  326 (460)
T PRK11776        247 VFCNTKKECQEVADALNAQGFSALALHGDLEQRDRDQVLVRFANRSCSVLVATDVAARGLDIKALEAVINYELARDPEVH  326 (460)
T ss_pred             EEECCHHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHHcCCCcEEEEecccccccchhcCCeEEEecCCCCHhHh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhcccccCCCceeEEEEeccccHHHHHHHHHHhccccc
Q 017573          320 LHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIE  359 (369)
Q Consensus       320 ~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  359 (369)
                      .||+||+||.|+.|.+++++.+.+...+..+.++++..++
T Consensus       327 iqR~GRtGR~g~~G~ai~l~~~~e~~~~~~i~~~~~~~~~  366 (460)
T PRK11776        327 VHRIGRTGRAGSKGLALSLVAPEEMQRANAIEDYLGRKLN  366 (460)
T ss_pred             hhhcccccCCCCcceEEEEEchhHHHHHHHHHHHhCCCCc
Confidence            9999999999999999999999999999999998887654

>PTZ00110 helicase; Provisional

Probab=100.00  E-value=5.3e-60  Score=431.51  Aligned_cols=367  Identities=33%  Similarity=0.521  Sum_probs=324.0

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhcc-----CCCccEEEEcCCHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYG-----LVQCQALVLAPTRE   75 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~-----~~~~~~liv~P~~~   75 (369)
                      ++||+++.++|.++||.+|+++|.++++.++.|+++++++|||||||++++++++..+...     ..++.+||++|+++
T Consensus       135 ~~l~~~l~~~l~~~g~~~pt~iQ~~aip~~l~G~dvI~~ApTGSGKTlaylLP~l~~i~~~~~~~~~~gp~~LIL~PTre  214 (545)
T PTZ00110        135 TSFPDYILKSLKNAGFTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLPAIVHINAQPLLRYGDGPIVLVLAPTRE  214 (545)
T ss_pred             cCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEEeCCCChHHHHHHHHHHHHHHhcccccCCCCcEEEEECChHH
Confidence            4799999999999999999999999999999999999999999999999999888765432     23457999999999


Q ss_pred             HHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCc
Q 017573           76 LAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGF  155 (369)
Q Consensus        76 l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~  155 (369)
                      |+.|+.+.+.++....++++....++.....+...+...++|+|+||+.|..++.+....+.+++++|+||||++.+.++
T Consensus       215 La~Qi~~~~~~~~~~~~i~~~~~~gg~~~~~q~~~l~~~~~IlVaTPgrL~d~l~~~~~~l~~v~~lViDEAd~mld~gf  294 (545)
T PTZ00110        215 LAEQIREQCNKFGASSKIRNTVAYGGVPKRGQIYALRRGVEILIACPGRLIDFLESNVTNLRRVTYLVLDEADRMLDMGF  294 (545)
T ss_pred             HHHHHHHHHHHHhcccCccEEEEeCCCCHHHHHHHHHcCCCEEEECHHHHHHHHHcCCCChhhCcEEEeehHHhhhhcch
Confidence            99999999999988888899899998887776666777899999999999999998888888999999999999999999


Q ss_pred             HHHHHHHHhhCCccCcEEEEEeeCChhHHHHHHHhcC-CCEEEEecCcc-ccccceeEEEEEccchhhhHHHHHHHHHhc
Q 017573          156 KDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMN-KPVRILVKRDE-LTLEGIKQFYVNVEKEEWKLETLCDLYETL  233 (369)
Q Consensus       156 ~~~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~-~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  233 (369)
                      ...+..++..+++..|++++|||++.....+...++. .++.+...... .....+.+.+..... ..+...+..++...
T Consensus       295 ~~~i~~il~~~~~~~q~l~~SAT~p~~v~~l~~~l~~~~~v~i~vg~~~l~~~~~i~q~~~~~~~-~~k~~~L~~ll~~~  373 (545)
T PTZ00110        295 EPQIRKIVSQIRPDRQTLMWSATWPKEVQSLARDLCKEEPVHVNVGSLDLTACHNIKQEVFVVEE-HEKRGKLKMLLQRI  373 (545)
T ss_pred             HHHHHHHHHhCCCCCeEEEEEeCCCHHHHHHHHHHhccCCEEEEECCCccccCCCeeEEEEEEec-hhHHHHHHHHHHHh
Confidence            9999999999999999999999999888888887775 46655544332 223344554444433 34566666666554


Q ss_pred             --cCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEec
Q 017573          234 --AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYD  311 (369)
Q Consensus       234 --~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~  311 (369)
                        ...++||||++++.++.+++.|...++.+..+||+++.++|.++++.|++|+.+|||||+++++|+|+|++++||+++
T Consensus       374 ~~~~~k~LIF~~t~~~a~~l~~~L~~~g~~~~~ihg~~~~~eR~~il~~F~~G~~~ILVaTdv~~rGIDi~~v~~VI~~d  453 (545)
T PTZ00110        374 MRDGDKILIFVETKKGADFLTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKSPIMIATDVASRGLDVKDVKYVINFD  453 (545)
T ss_pred             cccCCeEEEEecChHHHHHHHHHHHHcCCcEEEEECCCcHHHHHHHHHHHhcCCCcEEEEcchhhcCCCcccCCEEEEeC
Confidence              457999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCccchhhhhcccccCCCceeEEEEeccccHHHHHHHHHHhccccccCCcchhhc
Q 017573          312 LPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPSNVADL  368 (369)
Q Consensus       312 ~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  368 (369)
                      .|.+..+|.||+||+||.|+.|.+++|+++.+...+..+.+.++...+++|++|.++
T Consensus       454 ~P~s~~~yvqRiGRtGR~G~~G~ai~~~~~~~~~~~~~l~~~l~~~~q~vp~~l~~~  510 (545)
T PTZ00110        454 FPNQIEDYVHRIGRTGRAGAKGASYTFLTPDKYRLARDLVKVLREAKQPVPPELEKL  510 (545)
T ss_pred             CCCCHHHHHHHhcccccCCCCceEEEEECcchHHHHHHHHHHHHHccCCCCHHHHHH
Confidence            999999999999999999999999999999999999999999999999999998764

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

Probab=100.00  E-value=7.8e-61  Score=390.23  Aligned_cols=359  Identities=35%  Similarity=0.552  Sum_probs=340.8

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQI   80 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~   80 (369)
                      ||+.|.+..+++..++..|+++|+++++.++.|++++..|.||||||.++++++++++...+..+.++|++|+++|+.|.
T Consensus        66 Lgv~~~L~~ac~~l~~~~PT~IQ~~aiP~~L~g~dvIglAeTGSGKT~afaLPIl~~LL~~p~~~~~lVLtPtRELA~QI  145 (476)
T KOG0330|consen   66 LGVHPELLEACQELGWKKPTKIQSEAIPVALGGRDVIGLAETGSGKTGAFALPILQRLLQEPKLFFALVLTPTRELAQQI  145 (476)
T ss_pred             cCcCHHHHHHHHHhCcCCCchhhhhhcchhhCCCcEEEEeccCCCchhhhHHHHHHHHHcCCCCceEEEecCcHHHHHHH
Confidence            68999999999999999999999999999999999999999999999999999999998888778999999999999999


Q ss_pred             HHHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHH-cCCCCCCCccEEEEechhHhhccCcHHHH
Q 017573           81 EKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLR-RQSLRPDYIKMFVLDEADEMLSRGFKDQI  159 (369)
Q Consensus        81 ~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~-~~~~~~~~~~~viiDE~H~~~~~~~~~~~  159 (369)
                      .+.+..++...|+++..+.|+.....+...+.++++|+|+||..|..++. -+.+++..++++|+|||+++.+..|...+
T Consensus       146 ~e~fe~Lg~~iglr~~~lvGG~~m~~q~~~L~kkPhilVaTPGrL~dhl~~Tkgf~le~lk~LVlDEADrlLd~dF~~~l  225 (476)
T KOG0330|consen  146 AEQFEALGSGIGLRVAVLVGGMDMMLQANQLSKKPHILVATPGRLWDHLENTKGFSLEQLKFLVLDEADRLLDMDFEEEL  225 (476)
T ss_pred             HHHHHHhccccCeEEEEEecCchHHHHHHHhhcCCCEEEeCcHHHHHHHHhccCccHHHhHHHhhchHHhhhhhhhHHHH
Confidence            99999999999999999999999888888888899999999999999998 67788888999999999999999999999


Q ss_pred             HHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHHHhccCCCeE
Q 017573          160 YDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSV  239 (369)
Q Consensus       160 ~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~l  239 (369)
                      ..++..+|...|.+++|||++.....+....+..|..+.+.......+.+.+.|..++. .++...+..+++...+..+|
T Consensus       226 d~ILk~ip~erqt~LfsATMt~kv~kL~rasl~~p~~v~~s~ky~tv~~lkQ~ylfv~~-k~K~~yLV~ll~e~~g~s~i  304 (476)
T KOG0330|consen  226 DYILKVIPRERQTFLFSATMTKKVRKLQRASLDNPVKVAVSSKYQTVDHLKQTYLFVPG-KDKDTYLVYLLNELAGNSVI  304 (476)
T ss_pred             HHHHHhcCccceEEEEEeecchhhHHHHhhccCCCeEEeccchhcchHHhhhheEeccc-cccchhHHHHHHhhcCCcEE
Confidence            99999999999999999999999999998889999999988888888888898888876 44677788888888889999


Q ss_pred             EEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCCCCccch
Q 017573          240 IFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENY  319 (369)
Q Consensus       240 v~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~  319 (369)
                      |||++...+..++-.|+..|+.+..+||+|+.+.|...+++|++|..+||+||++.++|+|+|.+++||.||.|.+..+|
T Consensus       305 VF~~t~~tt~~la~~L~~lg~~a~~LhGqmsq~~Rlg~l~~Fk~~~r~iLv~TDVaSRGLDip~Vd~VVNyDiP~~skDY  384 (476)
T KOG0330|consen  305 VFCNTCNTTRFLALLLRNLGFQAIPLHGQMSQSKRLGALNKFKAGARSILVCTDVASRGLDIPHVDVVVNYDIPTHSKDY  384 (476)
T ss_pred             EEEeccchHHHHHHHHHhcCcceecccchhhHHHHHHHHHHHhccCCcEEEecchhcccCCCCCceEEEecCCCCcHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhcccccCCCceeEEEEeccccHHHHHHHHHHhcccccc
Q 017573          320 LHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEE  360 (369)
Q Consensus       320 ~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  360 (369)
                      ++|+||++|.|..|.++.+++..|.+.++.|+-..+....+
T Consensus       385 IHRvGRtaRaGrsG~~ItlVtqyDve~~qrIE~~~gkkl~~  425 (476)
T KOG0330|consen  385 IHRVGRTARAGRSGKAITLVTQYDVELVQRIEHALGKKLPE  425 (476)
T ss_pred             HHHcccccccCCCcceEEEEehhhhHHHHHHHHHHhcCCCc
Confidence            99999999999999999999999999999999999887755

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

Probab=100.00  E-value=3.4e-60  Score=410.95  Aligned_cols=367  Identities=37%  Similarity=0.597  Sum_probs=338.5

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhc------cCCCccEEEEcCCH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY------GLVQCQALVLAPTR   74 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~------~~~~~~~liv~P~~   74 (369)
                      ++|++.+.++|...||..|+|+|.+.|+.++.|++++..|.||||||++++++++.++..      ...++.+|+++||+
T Consensus        96 ~~ls~~~~~~lk~~g~~~PtpIQaq~wp~~l~GrD~v~iA~TGSGKTLay~lP~i~~l~~~~~~~~~~~~P~vLVL~PTR  175 (519)
T KOG0331|consen   96 LGLSEELMKALKEQGFEKPTPIQAQGWPIALSGRDLVGIARTGSGKTLAYLLPAIVHLNNEQGKLSRGDGPIVLVLAPTR  175 (519)
T ss_pred             ccccHHHHHHHHhcCCCCCchhhhcccceeccCCceEEEeccCCcchhhhhhHHHHHHHhccccccCCCCCeEEEEcCcH
Confidence            589999999999999999999999999999999999999999999999999999998876      34456899999999


Q ss_pred             HHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccC
Q 017573           75 ELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRG  154 (369)
Q Consensus        75 ~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~  154 (369)
                      +|+.|..+.+.++...++++..+++|+.+...+.+.+.++.+|+|+||..+..+++....+++++.++|+||+|+|.+.+
T Consensus       176 ELA~QV~~~~~~~~~~~~~~~~cvyGG~~~~~Q~~~l~~gvdiviaTPGRl~d~le~g~~~l~~v~ylVLDEADrMldmG  255 (519)
T KOG0331|consen  176 ELAVQVQAEAREFGKSLRLRSTCVYGGAPKGPQLRDLERGVDVVIATPGRLIDLLEEGSLNLSRVTYLVLDEADRMLDMG  255 (519)
T ss_pred             HHHHHHHHHHHHHcCCCCccEEEEeCCCCccHHHHHHhcCCcEEEeCChHHHHHHHcCCccccceeEEEeccHHhhhccc
Confidence            99999999999999999999999999999888888899999999999999999999999999999999999999999999


Q ss_pred             cHHHHHHHHhhC-CccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCc--cccccceeEEEEEccchhhhHHHHHHHHH
Q 017573          155 FKDQIYDIFQLL-PAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRD--ELTLEGIKQFYVNVEKEEWKLETLCDLYE  231 (369)
Q Consensus       155 ~~~~~~~~~~~~-~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  231 (369)
                      |...+..++..+ ++..|.+..|||.+.....+...++..+..+.....  ......+.++...+. ...+...+..++.
T Consensus       256 Fe~qI~~Il~~i~~~~rQtlm~saTwp~~v~~lA~~fl~~~~~i~ig~~~~~~a~~~i~qive~~~-~~~K~~~l~~lL~  334 (519)
T KOG0331|consen  256 FEPQIRKILSQIPRPDRQTLMFSATWPKEVRQLAEDFLNNPIQINVGNKKELKANHNIRQIVEVCD-ETAKLRKLGKLLE  334 (519)
T ss_pred             cHHHHHHHHHhcCCCcccEEEEeeeccHHHHHHHHHHhcCceEEEecchhhhhhhcchhhhhhhcC-HHHHHHHHHHHHH
Confidence            999999999999 555589999999999999999999999888876543  345566777776666 4556777777776


Q ss_pred             hc---cCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEE
Q 017573          232 TL---AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVI  308 (369)
Q Consensus       232 ~~---~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi  308 (369)
                      ..   ..+|+||||++++.|..+...++..++++..+||+.++.+|..+++.|++|+..|||||+++++|+|+|++++||
T Consensus       335 ~~~~~~~~KvIIFc~tkr~~~~l~~~l~~~~~~a~~iHGd~sQ~eR~~~L~~FreG~~~vLVATdVAaRGLDi~dV~lVI  414 (519)
T KOG0331|consen  335 DISSDSEGKVIIFCETKRTCDELARNLRRKGWPAVAIHGDKSQSERDWVLKGFREGKSPVLVATDVAARGLDVPDVDLVI  414 (519)
T ss_pred             HHhccCCCcEEEEecchhhHHHHHHHHHhcCcceeeecccccHHHHHHHHHhcccCCcceEEEcccccccCCCccccEEE
Confidence            55   456999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EecCCCCccchhhhhcccccCCCceeEEEEeccccHHHHHHHHHHhccccccCCcchhhc
Q 017573          309 NYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPSNVADL  368 (369)
Q Consensus       309 ~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  368 (369)
                      .+++|.+..+|+||+||+||.|+.|.+++|++..+......+.+.++...+.+++.+.++
T Consensus       415 nydfP~~vEdYVHRiGRTGRa~~~G~A~tfft~~~~~~a~~l~~~l~e~~q~v~~~l~~~  474 (519)
T KOG0331|consen  415 NYDFPNNVEDYVHRIGRTGRAGKKGTAITFFTSDNAKLARELIKVLREAGQTVPPDLLEY  474 (519)
T ss_pred             eCCCCCCHHHHHhhcCccccCCCCceEEEEEeHHHHHHHHHHHHHHHHccCCCChHHHHH
Confidence            999999999999999999999999999999999999999999999999999999887543

>PTZ00424 helicase 45; Provisional

Probab=100.00  E-value=3.9e-59  Score=417.56  Aligned_cols=369  Identities=73%  Similarity=1.133  Sum_probs=333.9

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQI   80 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~   80 (369)
                      +||++.+.+++.++||..|+|+|.++++.+.+++++++++|||+|||++++++++..+.....++++||++|+++|+.|+
T Consensus        33 l~l~~~~~~~l~~~~~~~~~~~Q~~ai~~i~~~~d~ii~apTGsGKT~~~~l~~l~~~~~~~~~~~~lil~Pt~~L~~Q~  112 (401)
T PTZ00424         33 LKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQLIDYDLNACQALILAPTRELAQQI  112 (401)
T ss_pred             CCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhcCCCCCceEEEECCCHHHHHHH
Confidence            58999999999999999999999999999999999999999999999999999998876555556899999999999999


Q ss_pred             HHHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHH
Q 017573           81 EKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIY  160 (369)
Q Consensus        81 ~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~  160 (369)
                      .+.+..+....+..+..+.|+.....+.......++|+|+||+.+...+........+++++|+||+|++.+.++...+.
T Consensus       113 ~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~l~~i~lvViDEah~~~~~~~~~~~~  192 (401)
T PTZ00424        113 QKVVLALGDYLKVRCHACVGGTVVRDDINKLKAGVHMVVGTPGRVYDMIDKRHLRVDDLKLFILDEADEMLSRGFKGQIY  192 (401)
T ss_pred             HHHHHHHhhhcCceEEEEECCcCHHHHHHHHcCCCCEEEECcHHHHHHHHhCCcccccccEEEEecHHHHHhcchHHHHH
Confidence            99999988777788888888877666655566678999999999999988887888889999999999999888888889


Q ss_pred             HHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHHHhccCCCeEE
Q 017573          161 DIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVI  240 (369)
Q Consensus       161 ~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lv  240 (369)
                      .++..+++..|++++|||++.........+...+..+...........+..++........+...+..++......++||
T Consensus       193 ~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~iv  272 (401)
T PTZ00424        193 DVFKKLPPDVQVALFSATMPNEILELTTKFMRDPKRILVKKDELTLEGIRQFYVAVEKEEWKFDTLCDLYETLTITQAII  272 (401)
T ss_pred             HHHhhCCCCcEEEEEEecCCHHHHHHHHHHcCCCEEEEeCCCCcccCCceEEEEecChHHHHHHHHHHHHHhcCCCeEEE
Confidence            99999999999999999999888888888888887776666666666777777777766667777888887777789999


Q ss_pred             EeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCCCCccchh
Q 017573          241 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYL  320 (369)
Q Consensus       241 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~  320 (369)
                      ||++++.++.+++.|...+..+..+||+++.++|..+++.|++|+++|||+|+++++|+|+|++++||+++.|.+..+|.
T Consensus       273 F~~t~~~~~~l~~~l~~~~~~~~~~h~~~~~~~R~~i~~~f~~g~~~vLvaT~~l~~GiDip~v~~VI~~~~p~s~~~y~  352 (401)
T PTZ00424        273 YCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDLPASPENYI  352 (401)
T ss_pred             EecCcHHHHHHHHHHHHCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEEcccccCCcCcccCCEEEEECCCCCHHHEe
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhcccccCCCceeEEEEeccccHHHHHHHHHHhccccccCCcchhhcC
Q 017573          321 HRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPSNVADLL  369 (369)
Q Consensus       321 Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  369 (369)
                      ||+||+||.|+.|.+++++++.+.+.++.+++.+..++++.+....+.|
T Consensus       353 qr~GRagR~g~~G~~i~l~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~  401 (401)
T PTZ00424        353 HRIGRSGRFGRKGVAINFVTPDDIEQLKEIERHYNTQIEEMPMEVADYL  401 (401)
T ss_pred             ecccccccCCCCceEEEEEcHHHHHHHHHHHHHHCCcccccCcchhhcC
Confidence            9999999999999999999999999999999999999999888876654

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=100.00  E-value=2.7e-59  Score=421.30  Aligned_cols=358  Identities=36%  Similarity=0.604  Sum_probs=322.5

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccC------CCccEEEEcCCH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGL------VQCQALVLAPTR   74 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~------~~~~~liv~P~~   74 (369)
                      |||++.+.+.|.++||..|+++|+++++.+++++++++++|||+|||+++++++++.+....      ...++||++|++
T Consensus         6 l~l~~~l~~~l~~~g~~~pt~iQ~~ai~~il~g~dvlv~apTGsGKTla~~lpil~~l~~~~~~~~~~~~~~aLil~Ptr   85 (456)
T PRK10590          6 LGLSPDILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQHLITRQPHAKGRRPVRALILTPTR   85 (456)
T ss_pred             cCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHhhhcccccccCCCceEEEEeCcH
Confidence            68999999999999999999999999999999999999999999999999999998875432      123799999999


Q ss_pred             HHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccC
Q 017573           75 ELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRG  154 (369)
Q Consensus        75 ~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~  154 (369)
                      +|+.|+.+.+.++....++.+..+.++.....+...+...++|+|+||+.|..++......++.++++|+||+|++.+.+
T Consensus        86 eLa~Qi~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~IiV~TP~rL~~~~~~~~~~l~~v~~lViDEah~ll~~~  165 (456)
T PRK10590         86 ELAAQIGENVRDYSKYLNIRSLVVFGGVSINPQMMKLRGGVDVLVATPGRLLDLEHQNAVKLDQVEILVLDEADRMLDMG  165 (456)
T ss_pred             HHHHHHHHHHHHHhccCCCEEEEEECCcCHHHHHHHHcCCCcEEEEChHHHHHHHHcCCcccccceEEEeecHHHHhccc
Confidence            99999999999998888899999999888777666667788999999999999998888888999999999999999999


Q ss_pred             cHHHHHHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHHHhcc
Q 017573          155 FKDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLA  234 (369)
Q Consensus       155 ~~~~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  234 (369)
                      +...+..++..++...|++++|||++.+...+...++.++..+...........+.+.+..... ..+...+..++....
T Consensus       166 ~~~~i~~il~~l~~~~q~l~~SAT~~~~~~~l~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~-~~k~~~l~~l~~~~~  244 (456)
T PRK10590        166 FIHDIRRVLAKLPAKRQNLLFSATFSDDIKALAEKLLHNPLEIEVARRNTASEQVTQHVHFVDK-KRKRELLSQMIGKGN  244 (456)
T ss_pred             cHHHHHHHHHhCCccCeEEEEeCCCcHHHHHHHHHHcCCCeEEEEecccccccceeEEEEEcCH-HHHHHHHHHHHHcCC
Confidence            9999999999999999999999999988888888888888877766555555566666655543 345666777777666


Q ss_pred             CCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCCC
Q 017573          235 ITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPT  314 (369)
Q Consensus       235 ~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~  314 (369)
                      ..++||||++++.++.+++.|...+..+..+||+++.++|.++++.|++|+++|||||+++++|+|+|++++||++++|.
T Consensus       245 ~~~~lVF~~t~~~~~~l~~~L~~~g~~~~~lhg~~~~~~R~~~l~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~~~~P~  324 (456)
T PRK10590        245 WQQVLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALADFKSGDIRVLVATDIAARGLDIEELPHVVNYELPN  324 (456)
T ss_pred             CCcEEEEcCcHHHHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHcCCCcEEEEccHHhcCCCcccCCEEEEeCCCC
Confidence            67999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CccchhhhhcccccCCCceeEEEEeccccHHHHHHHHHHhccccc
Q 017573          315 QPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIE  359 (369)
Q Consensus       315 ~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  359 (369)
                      +..+|.||+||+||.|..|.+++++...+...++.+++.++.++.
T Consensus       325 ~~~~yvqR~GRaGR~g~~G~ai~l~~~~d~~~~~~ie~~l~~~~~  369 (456)
T PRK10590        325 VPEDYVHRIGRTGRAAATGEALSLVCVDEHKLLRDIEKLLKKEIP  369 (456)
T ss_pred             CHHHhhhhccccccCCCCeeEEEEecHHHHHHHHHHHHHhcCCCc
Confidence            999999999999999999999999999999999999999888774

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=100.00  E-value=8.5e-59  Score=417.76  Aligned_cols=359  Identities=33%  Similarity=0.541  Sum_probs=326.8

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhcc----CCCccEEEEcCCHHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYG----LVQCQALVLAPTREL   76 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~----~~~~~~liv~P~~~l   76 (369)
                      |+|++.+.+.|.++||.+|+++|+++++.+.+++++++++|||+|||+++++++++.+...    ...+++||++|+++|
T Consensus         6 l~l~~~l~~~l~~~g~~~p~~iQ~~ai~~~~~g~d~l~~apTGsGKT~~~~lp~l~~l~~~~~~~~~~~~~lil~Pt~eL   85 (434)
T PRK11192          6 LELDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQHLLDFPRRKSGPPRILILTPTREL   85 (434)
T ss_pred             cCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhhccccCCCCceEEEECCcHHH
Confidence            6899999999999999999999999999999999999999999999999999999877432    123489999999999


Q ss_pred             HHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcH
Q 017573           77 AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFK  156 (369)
Q Consensus        77 ~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~  156 (369)
                      +.|+.+.+..+....++++..+.|+.........+...++|+|+||+.|.+.+....+....++++|+||||++.+.++.
T Consensus        86 a~Q~~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~l~~~~~IlV~Tp~rl~~~~~~~~~~~~~v~~lViDEah~~l~~~~~  165 (434)
T PRK11192         86 AMQVADQARELAKHTHLDIATITGGVAYMNHAEVFSENQDIVVATPGRLLQYIKEENFDCRAVETLILDEADRMLDMGFA  165 (434)
T ss_pred             HHHHHHHHHHHHccCCcEEEEEECCCCHHHHHHHhcCCCCEEEEChHHHHHHHHcCCcCcccCCEEEEECHHHHhCCCcH
Confidence            99999999999888899999999998887777777778899999999999999988888888999999999999999999


Q ss_pred             HHHHHHHhhCCccCcEEEEEeeCCh-hHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHHHhccC
Q 017573          157 DQIYDIFQLLPAKVQVGVFSATMPP-EALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAI  235 (369)
Q Consensus       157 ~~~~~~~~~~~~~~~~i~~saT~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  235 (369)
                      ..+..+...++...|++++|||++. ....+...++..+..+...........+.+.+........+.+.+..++.....
T Consensus       166 ~~~~~i~~~~~~~~q~~~~SAT~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~~~~~  245 (434)
T PRK11192        166 QDIETIAAETRWRKQTLLFSATLEGDAVQDFAERLLNDPVEVEAEPSRRERKKIHQWYYRADDLEHKTALLCHLLKQPEV  245 (434)
T ss_pred             HHHHHHHHhCccccEEEEEEeecCHHHHHHHHHHHccCCEEEEecCCcccccCceEEEEEeCCHHHHHHHHHHHHhcCCC
Confidence            9999999999888999999999975 466777778888888777666666667777777777667788888888887677


Q ss_pred             CCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCCCC
Q 017573          236 TQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQ  315 (369)
Q Consensus       236 ~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~~  315 (369)
                      .++||||++++.++.+++.|...+..+..+||+++..+|..+++.|++|+++|||||+++++|+|+|++++||+++.|.+
T Consensus       246 ~~~lVF~~s~~~~~~l~~~L~~~~~~~~~l~g~~~~~~R~~~l~~f~~G~~~vLVaTd~~~~GiDip~v~~VI~~d~p~s  325 (434)
T PRK11192        246 TRSIVFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATDVAARGIDIDDVSHVINFDMPRS  325 (434)
T ss_pred             CeEEEEeCChHHHHHHHHHHHhCCCCEEEecCCCCHHHHHHHHHHHhCCCCcEEEEccccccCccCCCCCEEEEECCCCC
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccchhhhhcccccCCCceeEEEEeccccHHHHHHHHHHhccccc
Q 017573          316 PENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIE  359 (369)
Q Consensus       316 ~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  359 (369)
                      ...|.||+||+||.|+.|.++++++..|...+..+++++...+.
T Consensus       326 ~~~yiqr~GR~gR~g~~g~ai~l~~~~d~~~~~~i~~~~~~~~~  369 (434)
T PRK11192        326 ADTYLHRIGRTGRAGRKGTAISLVEAHDHLLLGKIERYIEEPLK  369 (434)
T ss_pred             HHHHhhcccccccCCCCceEEEEecHHHHHHHHHHHHHHhcccc
Confidence            99999999999999999999999999999999999998887664

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=100.00  E-value=4.5e-59  Score=428.77  Aligned_cols=361  Identities=39%  Similarity=0.615  Sum_probs=328.7

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQI   80 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~   80 (369)
                      |+|++.+.++|+++||.+|+|+|.++++.+.++++++++||||+|||.++.+++++.+......+++||++|+++|+.|+
T Consensus        11 l~L~~~ll~al~~~G~~~ptpiQ~~ai~~ll~g~dvl~~ApTGsGKT~af~lpll~~l~~~~~~~~~LIL~PTreLa~Qv   90 (629)
T PRK11634         11 LGLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLHNLDPELKAPQILVLAPTRELAVQV   90 (629)
T ss_pred             cCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHHHhhhccCCCeEEEEeCcHHHHHHH
Confidence            58999999999999999999999999999999999999999999999999999998887665556899999999999999


Q ss_pred             HHHHHHhcccc-CcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHH
Q 017573           81 EKVMRALGDYL-GVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQI  159 (369)
Q Consensus        81 ~~~~~~~~~~~-~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~  159 (369)
                      .+.+.++.... ++.+..++++.....+...+...++|+|+||+.+..++.+..+.+++++++|+||+|.+.+.++...+
T Consensus        91 ~~~l~~~~~~~~~i~v~~~~gG~~~~~q~~~l~~~~~IVVgTPgrl~d~l~r~~l~l~~l~~lVlDEAd~ml~~gf~~di  170 (629)
T PRK11634         91 AEAMTDFSKHMRGVNVVALYGGQRYDVQLRALRQGPQIVVGTPGRLLDHLKRGTLDLSKLSGLVLDEADEMLRMGFIEDV  170 (629)
T ss_pred             HHHHHHHHhhcCCceEEEEECCcCHHHHHHHhcCCCCEEEECHHHHHHHHHcCCcchhhceEEEeccHHHHhhcccHHHH
Confidence            99999887654 78899999998877777777778999999999999999998888899999999999999999999999


Q ss_pred             HHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHHHhccCCCeE
Q 017573          160 YDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSV  239 (369)
Q Consensus       160 ~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~l  239 (369)
                      ..++..++...|++++|||++.....+...++..+..+...........+.+.+..... ..+...+..++......++|
T Consensus       171 ~~Il~~lp~~~q~llfSAT~p~~i~~i~~~~l~~~~~i~i~~~~~~~~~i~q~~~~v~~-~~k~~~L~~~L~~~~~~~~I  249 (629)
T PRK11634        171 ETIMAQIPEGHQTALFSATMPEAIRRITRRFMKEPQEVRIQSSVTTRPDISQSYWTVWG-MRKNEALVRFLEAEDFDAAI  249 (629)
T ss_pred             HHHHHhCCCCCeEEEEEccCChhHHHHHHHHcCCCeEEEccCccccCCceEEEEEEech-hhHHHHHHHHHHhcCCCCEE
Confidence            99999999999999999999988888899999988887776666666666666665543 34677788888777778999


Q ss_pred             EEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCCCCccch
Q 017573          240 IFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENY  319 (369)
Q Consensus       240 v~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~  319 (369)
                      |||+++..++.+++.|...++.+..+||++++.+|..+++.|++|+++|||||+++++|+|+|++++||+++.|.+...|
T Consensus       250 VF~~tk~~a~~l~~~L~~~g~~~~~lhgd~~q~~R~~il~~Fr~G~~~ILVATdv~arGIDip~V~~VI~~d~P~~~e~y  329 (629)
T PRK11634        250 IFVRTKNATLEVAEALERNGYNSAALNGDMNQALREQTLERLKDGRLDILIATDVAARGLDVERISLVVNYDIPMDSESY  329 (629)
T ss_pred             EEeccHHHHHHHHHHHHhCCCCEEEeeCCCCHHHHHHHHHHHhCCCCCEEEEcchHhcCCCcccCCEEEEeCCCCCHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhcccccCCCceeEEEEeccccHHHHHHHHHHhccccccCC
Q 017573          320 LHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELP  362 (369)
Q Consensus       320 ~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  362 (369)
                      .|++||+||.|+.|.+++++++.+...++.+++.++..+.+++
T Consensus       330 vqRiGRtGRaGr~G~ai~~v~~~e~~~l~~ie~~~~~~i~~~~  372 (629)
T PRK11634        330 VHRIGRTGRAGRAGRALLFVENRERRLLRNIERTMKLTIPEVE  372 (629)
T ss_pred             HHHhccccCCCCcceEEEEechHHHHHHHHHHHHhCCCcceec
Confidence            9999999999999999999999999999999999888876654

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

Probab=100.00  E-value=1.2e-58  Score=421.74  Aligned_cols=365  Identities=33%  Similarity=0.542  Sum_probs=322.4

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhc-------cCCCccEEEEcCC
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY-------GLVQCQALVLAPT   73 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~-------~~~~~~~liv~P~   73 (369)
                      +|||+.+.++|...||..|+|+|.++++.++.|+++++.+|||||||++++++++.++..       ...++.+||++|+
T Consensus       126 ~~l~~~l~~~L~~~g~~~ptpiQ~~aip~il~g~dviv~ApTGSGKTlayllPil~~l~~~~~~~~~~~~~~~aLIL~PT  205 (518)
T PLN00206        126 CGLPPKLLLNLETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPIISRCCTIRSGHPSEQRNPLAMVLTPT  205 (518)
T ss_pred             CCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEEecCCCCccHHHHHHHHHHHHhhccccccccCCceEEEEeCC
Confidence            589999999999999999999999999999999999999999999999999999877532       1234589999999


Q ss_pred             HHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhcc
Q 017573           74 RELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSR  153 (369)
Q Consensus        74 ~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~  153 (369)
                      ++|+.|+.+.++.+....++.+..+.++.....+...+..+++|+|+||+.|..++.+.....++++++|+||+|.+.+.
T Consensus       206 reLa~Qi~~~~~~l~~~~~~~~~~~~gG~~~~~q~~~l~~~~~IiV~TPgrL~~~l~~~~~~l~~v~~lViDEad~ml~~  285 (518)
T PLN00206        206 RELCVQVEDQAKVLGKGLPFKTALVVGGDAMPQQLYRIQQGVELIVGTPGRLIDLLSKHDIELDNVSVLVLDEVDCMLER  285 (518)
T ss_pred             HHHHHHHHHHHHHHhCCCCceEEEEECCcchHHHHHHhcCCCCEEEECHHHHHHHHHcCCccchheeEEEeecHHHHhhc
Confidence            99999999999998888888888888888776666666778899999999999999988888899999999999999999


Q ss_pred             CcHHHHHHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHHHhc
Q 017573          154 GFKDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETL  233 (369)
Q Consensus       154 ~~~~~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  233 (369)
                      ++...+..++..++ ..|++++|||++.....+...+...+..+...........+.+........ .+...+.+++...
T Consensus       286 gf~~~i~~i~~~l~-~~q~l~~SATl~~~v~~l~~~~~~~~~~i~~~~~~~~~~~v~q~~~~~~~~-~k~~~l~~~l~~~  363 (518)
T PLN00206        286 GFRDQVMQIFQALS-QPQVLLFSATVSPEVEKFASSLAKDIILISIGNPNRPNKAVKQLAIWVETK-QKKQKLFDILKSK  363 (518)
T ss_pred             chHHHHHHHHHhCC-CCcEEEEEeeCCHHHHHHHHHhCCCCEEEEeCCCCCCCcceeEEEEeccch-hHHHHHHHHHHhh
Confidence            99999988888875 679999999999988888888888888777766555555566666555443 3445566666543


Q ss_pred             c--CCCeEEEeCCHhhHHHHHHHHhh-CCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEe
Q 017573          234 A--ITQSVIFVNTRRKVDWLTDKMRS-RDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINY  310 (369)
Q Consensus       234 ~--~~k~lv~~~~~~~~~~~~~~l~~-~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~  310 (369)
                      .  ..++||||+++..++.+++.|.. .+..+..+||+++.++|..+++.|++|+.+|||||+++++|+|+|++++||++
T Consensus       364 ~~~~~~~iVFv~s~~~a~~l~~~L~~~~g~~~~~~Hg~~~~~eR~~il~~Fr~G~~~ILVaTdvl~rGiDip~v~~VI~~  443 (518)
T PLN00206        364 QHFKPPAVVFVSSRLGADLLANAITVVTGLKALSIHGEKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIF  443 (518)
T ss_pred             cccCCCEEEEcCCchhHHHHHHHHhhccCcceEEeeCCCCHHHHHHHHHHHHCCCCCEEEEecHhhccCCcccCCEEEEe
Confidence            2  35899999999999999999975 58899999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCccchhhhhcccccCCCceeEEEEeccccHHHHHHHHHHhccccccCCcchhh
Q 017573          311 DLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPSNVAD  367 (369)
Q Consensus       311 ~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  367 (369)
                      ++|.+..+|.||+||+||.|+.|.+++|+++.+...+..+.+.++....++|++|.+
T Consensus       444 d~P~s~~~yihRiGRaGR~g~~G~ai~f~~~~~~~~~~~l~~~l~~~~~~vp~~l~~  500 (518)
T PLN00206        444 DMPNTIKEYIHQIGRASRMGEKGTAIVFVNEEDRNLFPELVALLKSSGAAIPRELAN  500 (518)
T ss_pred             CCCCCHHHHHHhccccccCCCCeEEEEEEchhHHHHHHHHHHHHHHcCCCCCHHHHh
Confidence            999999999999999999999999999999999999999999999999999998865

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=2e-58  Score=422.36  Aligned_cols=358  Identities=33%  Similarity=0.523  Sum_probs=319.6

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccC-------CCccEEEEcCC
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGL-------VQCQALVLAPT   73 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~-------~~~~~liv~P~   73 (369)
                      |+|++.+.++|.++||..|+++|.++++.+++++++++++|||+|||+++++++++.+....       ..+++||++|+
T Consensus        14 l~l~~~l~~~L~~~g~~~ptpiQ~~~ip~~l~G~Dvi~~ApTGSGKTlafllpil~~l~~~~~~~~~~~~~~raLIl~PT   93 (572)
T PRK04537         14 FDLHPALLAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMNRLLSRPALADRKPEDPRALILAPT   93 (572)
T ss_pred             cCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEEcCCCCcHHHHHHHHHHHHHHhcccccccccCCceEEEEeCc
Confidence            58999999999999999999999999999999999999999999999999999998774321       23589999999


Q ss_pred             HHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcC-CCCCCCccEEEEechhHhhc
Q 017573           74 RELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQ-SLRPDYIKMFVLDEADEMLS  152 (369)
Q Consensus        74 ~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~-~~~~~~~~~viiDE~H~~~~  152 (369)
                      ++|+.|+.+.+.++....++++..++|+.....+...+...++|+|+||+.|..++.+. .+.+..++++|+||+|++.+
T Consensus        94 reLa~Qi~~~~~~l~~~~~i~v~~l~Gg~~~~~q~~~l~~~~dIiV~TP~rL~~~l~~~~~~~l~~v~~lViDEAh~lld  173 (572)
T PRK04537         94 RELAIQIHKDAVKFGADLGLRFALVYGGVDYDKQRELLQQGVDVIIATPGRLIDYVKQHKVVSLHACEICVLDEADRMFD  173 (572)
T ss_pred             HHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHHhCCCCEEEECHHHHHHHHHhccccchhheeeeEecCHHHHhh
Confidence            99999999999999988899999999999887777777778899999999999988765 35677789999999999999


Q ss_pred             cCcHHHHHHHHhhCCc--cCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHH
Q 017573          153 RGFKDQIYDIFQLLPA--KVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLY  230 (369)
Q Consensus       153 ~~~~~~~~~~~~~~~~--~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~  230 (369)
                      .++...+..++..++.  ..|++++|||++.....+...++..+..+...........+.+.+.... ...+...+..++
T Consensus       174 ~gf~~~i~~il~~lp~~~~~q~ll~SATl~~~v~~l~~~~l~~p~~i~v~~~~~~~~~i~q~~~~~~-~~~k~~~L~~ll  252 (572)
T PRK04537        174 LGFIKDIRFLLRRMPERGTRQTLLFSATLSHRVLELAYEHMNEPEKLVVETETITAARVRQRIYFPA-DEEKQTLLLGLL  252 (572)
T ss_pred             cchHHHHHHHHHhcccccCceEEEEeCCccHHHHHHHHHHhcCCcEEEeccccccccceeEEEEecC-HHHHHHHHHHHH
Confidence            9999999999998886  6789999999998888888888888877666555555555555555443 345677777787


Q ss_pred             HhccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEe
Q 017573          231 ETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINY  310 (369)
Q Consensus       231 ~~~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~  310 (369)
                      ......++||||++++.++.+++.|...+..+..+||+++..+|.++++.|++|+.+|||+|+++++|+|+|++++||++
T Consensus       253 ~~~~~~k~LVF~nt~~~ae~l~~~L~~~g~~v~~lhg~l~~~eR~~il~~Fr~G~~~VLVaTdv~arGIDip~V~~VIny  332 (572)
T PRK04537        253 SRSEGARTMVFVNTKAFVERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQKGQLEILVATDVAARGLHIDGVKYVYNY  332 (572)
T ss_pred             hcccCCcEEEEeCCHHHHHHHHHHHHHcCCCEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEehhhhcCCCccCCCEEEEc
Confidence            77777899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCccchhhhhcccccCCCceeEEEEeccccHHHHHHHHHHhccccc
Q 017573          311 DLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIE  359 (369)
Q Consensus       311 ~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  359 (369)
                      +.|.+..+|.||+||+||.|+.|.+++|+.+.+...+..+++++...+.
T Consensus       333 d~P~s~~~yvqRiGRaGR~G~~G~ai~~~~~~~~~~l~~i~~~~~~~~~  381 (572)
T PRK04537        333 DLPFDAEDYVHRIGRTARLGEEGDAISFACERYAMSLPDIEAYIEQKIP  381 (572)
T ss_pred             CCCCCHHHHhhhhcccccCCCCceEEEEecHHHHHHHHHHHHHHcCCCC
Confidence            9999999999999999999999999999999999999999998887664

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

Probab=100.00  E-value=3.3e-58  Score=415.70  Aligned_cols=359  Identities=46%  Similarity=0.720  Sum_probs=334.9

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhc-cCCCcc-EEEEcCCHHHHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY-GLVQCQ-ALVLAPTRELAQ   78 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~-~~~~~~-~liv~P~~~l~~   78 (369)
                      ++|++.+.+++.+.||..|+|+|.++++.++.|++++..|+||||||.++++++++.+.. ...... +||++||++|+.
T Consensus        34 l~l~~~ll~~l~~~gf~~pt~IQ~~~IP~~l~g~Dvi~~A~TGsGKT~Af~lP~l~~l~~~~~~~~~~aLil~PTRELA~  113 (513)
T COG0513          34 LGLSPELLQALKDLGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFLLPLLQKILKSVERKYVSALILAPTRELAV  113 (513)
T ss_pred             cCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhcccccCCCceEEECCCHHHHH
Confidence            579999999999999999999999999999999999999999999999999999999774 222212 999999999999


Q ss_pred             HHHHHHHHhcccc-CcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHH
Q 017573           79 QIEKVMRALGDYL-GVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKD  157 (369)
Q Consensus        79 q~~~~~~~~~~~~-~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~  157 (369)
                      |..+.+.++.... ++.+..++|+.....+...+..+++|+|+||..+.+++.+..+.++.+.++|+||++++.+.+|..
T Consensus       114 Qi~~~~~~~~~~~~~~~~~~i~GG~~~~~q~~~l~~~~~ivVaTPGRllD~i~~~~l~l~~v~~lVlDEADrmLd~Gf~~  193 (513)
T COG0513         114 QIAEELRKLGKNLGGLRVAVVYGGVSIRKQIEALKRGVDIVVATPGRLLDLIKRGKLDLSGVETLVLDEADRMLDMGFID  193 (513)
T ss_pred             HHHHHHHHHHhhcCCccEEEEECCCCHHHHHHHHhcCCCEEEECccHHHHHHHcCCcchhhcCEEEeccHhhhhcCCCHH
Confidence            9999999999888 799999999998888877777779999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccc--cccceeEEEEEccchhhhHHHHHHHHHhccC
Q 017573          158 QIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDEL--TLEGIKQFYVNVEKEEWKLETLCDLYETLAI  235 (369)
Q Consensus       158 ~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  235 (369)
                      .+..+...++...|++++|||++.....+...++.+|..+.......  ....+.+.++.+.....+...+..++.....
T Consensus       194 ~i~~I~~~~p~~~qtllfSAT~~~~i~~l~~~~l~~p~~i~v~~~~~~~~~~~i~q~~~~v~~~~~k~~~L~~ll~~~~~  273 (513)
T COG0513         194 DIEKILKALPPDRQTLLFSATMPDDIRELARRYLNDPVEIEVSVEKLERTLKKIKQFYLEVESEEEKLELLLKLLKDEDE  273 (513)
T ss_pred             HHHHHHHhCCcccEEEEEecCCCHHHHHHHHHHccCCcEEEEccccccccccCceEEEEEeCCHHHHHHHHHHHHhcCCC
Confidence            99999999999999999999999999999999999998887775555  7889999999998876799999999998888


Q ss_pred             CCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCCCC
Q 017573          236 TQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQ  315 (369)
Q Consensus       236 ~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~~  315 (369)
                      .++||||++.+.++.++..|...|+++..+||++++++|.+.++.|++|+.+|||||+++++|+|+|++++||.++.|.+
T Consensus       274 ~~~IVF~~tk~~~~~l~~~l~~~g~~~~~lhG~l~q~~R~~~l~~F~~g~~~vLVaTDvaaRGiDi~~v~~VinyD~p~~  353 (513)
T COG0513         274 GRVIVFVRTKRLVEELAESLRKRGFKVAALHGDLPQEERDRALEKFKDGELRVLVATDVAARGLDIPDVSHVINYDLPLD  353 (513)
T ss_pred             CeEEEEeCcHHHHHHHHHHHHHCCCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEEechhhccCCccccceeEEccCCCC
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccchhhhhcccccCCCceeEEEEeccc-cHHHHHHHHHHhccccc
Q 017573          316 PENYLHRIGRSGRFGRKGVAINFVTRD-DERMLFDIQKFYNVVIE  359 (369)
Q Consensus       316 ~~~~~Q~~GR~~R~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~  359 (369)
                      ...|+||+||+||.|..|.++.|+.+. +...+..+++.+.....
T Consensus       354 ~e~yvHRiGRTgRaG~~G~ai~fv~~~~e~~~l~~ie~~~~~~~~  398 (513)
T COG0513         354 PEDYVHRIGRTGRAGRKGVAISFVTEEEEVKKLKRIEKRLERKLP  398 (513)
T ss_pred             HHHheeccCccccCCCCCeEEEEeCcHHHHHHHHHHHHHHhcccc
Confidence            999999999999999999999999986 89999999998866633

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=4.7e-57  Score=409.62  Aligned_cols=358  Identities=33%  Similarity=0.526  Sum_probs=317.1

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCC-------CccEEEEcCC
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLV-------QCQALVLAPT   73 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~-------~~~~liv~P~   73 (369)
                      ++|++.+.++|.++||.+|+++|.++++.+.+|+++++.+|||||||+++++++++.+.....       .+++||++|+
T Consensus        92 ~~l~~~l~~~l~~~g~~~~~~iQ~~ai~~~~~G~dvi~~apTGSGKTlay~lpil~~l~~~~~~~~~~~~~~~aLil~Pt  171 (475)
T PRK01297         92 FNLAPELMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQLLQTPPPKERYMGEPRALIIAPT  171 (475)
T ss_pred             CCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhcCcccccccCCceEEEEeCc
Confidence            589999999999999999999999999999999999999999999999999999988765421       3489999999


Q ss_pred             HHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHH-ccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhc
Q 017573           74 RELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL-QAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLS  152 (369)
Q Consensus        74 ~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~-~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~  152 (369)
                      ++|+.|+.+.+..+....++.+..+.|+.......+.+ ...++|+|+||++|..+...+...+++++++|+||+|.+.+
T Consensus       172 reLa~Q~~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~~~~~~~~Iiv~TP~~Ll~~~~~~~~~l~~l~~lViDEah~l~~  251 (475)
T PRK01297        172 RELVVQIAKDAAALTKYTGLNVMTFVGGMDFDKQLKQLEARFCDILVATPGRLLDFNQRGEVHLDMVEVMVLDEADRMLD  251 (475)
T ss_pred             HHHHHHHHHHHHHhhccCCCEEEEEEccCChHHHHHHHhCCCCCEEEECHHHHHHHHHcCCcccccCceEEechHHHHHh
Confidence            99999999999999888889999888887655544433 45689999999999999988888889999999999999999


Q ss_pred             cCcHHHHHHHHhhCCc--cCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHH
Q 017573          153 RGFKDQIYDIFQLLPA--KVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLY  230 (369)
Q Consensus       153 ~~~~~~~~~~~~~~~~--~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~  230 (369)
                      .++...+..++..++.  ..|++++|||.+.+.......+...+..+...........+.+.+..... ..+...+..++
T Consensus       252 ~~~~~~l~~i~~~~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~-~~k~~~l~~ll  330 (475)
T PRK01297        252 MGFIPQVRQIIRQTPRKEERQTLLFSATFTDDVMNLAKQWTTDPAIVEIEPENVASDTVEQHVYAVAG-SDKYKLLYNLV  330 (475)
T ss_pred             cccHHHHHHHHHhCCCCCCceEEEEEeecCHHHHHHHHHhccCCEEEEeccCcCCCCcccEEEEEecc-hhHHHHHHHHH
Confidence            9988889899888864  56899999999988888888998888877666555555555555554433 34667777777


Q ss_pred             HhccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEe
Q 017573          231 ETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINY  310 (369)
Q Consensus       231 ~~~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~  310 (369)
                      ......++||||++++.++.+++.|.+.+..+..+||+++.++|.++++.|++|++++||+|+++++|+|+|++++||++
T Consensus       331 ~~~~~~~~IVF~~s~~~~~~l~~~L~~~~~~~~~~~g~~~~~~R~~~~~~Fr~G~~~vLvaT~~l~~GIDi~~v~~VI~~  410 (475)
T PRK01297        331 TQNPWERVMVFANRKDEVRRIEERLVKDGINAAQLSGDVPQHKRIKTLEGFREGKIRVLVATDVAGRGIHIDGISHVINF  410 (475)
T ss_pred             HhcCCCeEEEEeCCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHhCCCCcEEEEccccccCCcccCCCEEEEe
Confidence            77777899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCccchhhhhcccccCCCceeEEEEeccccHHHHHHHHHHhccccc
Q 017573          311 DLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIE  359 (369)
Q Consensus       311 ~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  359 (369)
                      +.|.+..+|.||+||+||.|++|.+++|+++.|...+..++++++..+.
T Consensus       411 ~~P~s~~~y~Qr~GRaGR~g~~g~~i~~~~~~d~~~~~~~~~~~~~~~~  459 (475)
T PRK01297        411 TLPEDPDDYVHRIGRTGRAGASGVSISFAGEDDAFQLPEIEELLGRKIS  459 (475)
T ss_pred             CCCCCHHHHHHhhCccCCCCCCceEEEEecHHHHHHHHHHHHHhCCCCc
Confidence            9999999999999999999999999999999999999999999988763

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

Probab=100.00  E-value=3.7e-55  Score=369.76  Aligned_cols=365  Identities=35%  Similarity=0.558  Sum_probs=336.2

Q ss_pred             CCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccC---------CCccEEEEcC
Q 017573            2 GLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGL---------VQCQALVLAP   72 (369)
Q Consensus         2 ~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~---------~~~~~liv~P   72 (369)
                      |||.++++.+...||..|+|+|+.+++..++.+++|-.|.||||||.+++++++..+...+         .++.++++.|
T Consensus       251 ~~P~e~l~~I~~~~y~eptpIqR~aipl~lQ~rD~igvaETgsGktaaf~ipLl~~IsslP~~~~~en~~~gpyaiilap  330 (673)
T KOG0333|consen  251 GFPLELLSVIKKPGYKEPTPIQRQAIPLGLQNRDPIGVAETGSGKTAAFLIPLLIWISSLPPMARLENNIEGPYAIILAP  330 (673)
T ss_pred             CCCHHHHHHHHhcCCCCCchHHHhhccchhccCCeeeEEeccCCccccchhhHHHHHHcCCCcchhhhcccCceeeeech
Confidence            7999999999999999999999999999999999999999999999999888887663322         3458999999


Q ss_pred             CHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhc
Q 017573           73 TRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLS  152 (369)
Q Consensus        73 ~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~  152 (369)
                      +++|++|..++-.+|...+++++..+.|+...+++.-.+...|+|+|+||..|...+.+.++.++.+.++|+||++++.+
T Consensus       331 tReLaqqIeeEt~kf~~~lg~r~vsvigg~s~EEq~fqls~gceiviatPgrLid~Lenr~lvl~qctyvvldeadrmiD  410 (673)
T KOG0333|consen  331 TRELAQQIEEETNKFGKPLGIRTVSVIGGLSFEEQGFQLSMGCEIVIATPGRLIDSLENRYLVLNQCTYVVLDEADRMID  410 (673)
T ss_pred             HHHHHHHHHHHHHHhcccccceEEEEecccchhhhhhhhhccceeeecCchHHHHHHHHHHHHhccCceEeccchhhhhc
Confidence            99999999999999999999999999999998888777888999999999999999999999999999999999999999


Q ss_pred             cCcHHHHHHHHhhCCcc-------------------------CcEEEEEeeCChhHHHHHHHhcCCCEEEEecCcccccc
Q 017573          153 RGFKDQIYDIFQLLPAK-------------------------VQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLE  207 (369)
Q Consensus       153 ~~~~~~~~~~~~~~~~~-------------------------~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  207 (369)
                      .+|...+..++..+|..                         .|.+.+|||+++....++..++..|+.+.........+
T Consensus       411 mgfE~dv~~iL~~mPssn~k~~tde~~~~~~~~~~~~~~k~yrqT~mftatm~p~verlar~ylr~pv~vtig~~gk~~~  490 (673)
T KOG0333|consen  411 MGFEPDVQKILEQMPSSNAKPDTDEKEGEERVRKNFSSSKKYRQTVMFTATMPPAVERLARSYLRRPVVVTIGSAGKPTP  490 (673)
T ss_pred             ccccHHHHHHHHhCCccccCCCccchhhHHHHHhhcccccceeEEEEEecCCChHHHHHHHHHhhCCeEEEeccCCCCcc
Confidence            99999999999988642                         57889999999999999999999999999988888888


Q ss_pred             ceeEEEEEccchhhhHHHHHHHHHhccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCc
Q 017573          208 GIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSR  287 (369)
Q Consensus       208 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~  287 (369)
                      .+.+.+......+ +...|.+++......++|||+|..+.++.+++.|.+.++++..+||+-++++|+.+++.|++|..+
T Consensus       491 rveQ~v~m~~ed~-k~kkL~eil~~~~~ppiIIFvN~kk~~d~lAk~LeK~g~~~~tlHg~k~qeQRe~aL~~fr~~t~d  569 (673)
T KOG0333|consen  491 RVEQKVEMVSEDE-KRKKLIEILESNFDPPIIIFVNTKKGADALAKILEKAGYKVTTLHGGKSQEQRENALADFREGTGD  569 (673)
T ss_pred             chheEEEEecchH-HHHHHHHHHHhCCCCCEEEEEechhhHHHHHHHHhhccceEEEeeCCccHHHHHHHHHHHHhcCCC
Confidence            8999988887755 588899999888778999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEecCCcCCCCCCCCcEEEEecCCCCccchhhhhcccccCCCceeEEEEeccccHHHHHHHHHHhcc-ccccCCcchh
Q 017573          288 VLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNV-VIEELPSNVA  366 (369)
Q Consensus       288 vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~  366 (369)
                      |||||+++++|+|+|++++||.++.+++..+|.+||||+||.|+.|.++.|+++.|...++.+.+.+.. .....|+++.
T Consensus       570 IlVaTDvAgRGIDIpnVSlVinydmaksieDYtHRIGRTgRAGk~GtaiSflt~~dt~v~ydLkq~l~es~~s~~P~Ela  649 (673)
T KOG0333|consen  570 ILVATDVAGRGIDIPNVSLVINYDMAKSIEDYTHRIGRTGRAGKSGTAISFLTPADTAVFYDLKQALRESVKSHCPPELA  649 (673)
T ss_pred             EEEEecccccCCCCCccceeeecchhhhHHHHHHHhccccccccCceeEEEeccchhHHHHHHHHHHHHhhhccCChhhc
Confidence            999999999999999999999999999999999999999999999999999999999999888887764 4445666654


Q ss_pred             h
Q 017573          367 D  367 (369)
Q Consensus       367 ~  367 (369)
                      +
T Consensus       650 ~  650 (673)
T KOG0333|consen  650 N  650 (673)
T ss_pred             c
Confidence            3

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

Probab=100.00  E-value=1.2e-54  Score=362.13  Aligned_cols=344  Identities=33%  Similarity=0.548  Sum_probs=308.3

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhcc--CCC---ccEEEEcCCHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYG--LVQ---CQALVLAPTRE   75 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~--~~~---~~~liv~P~~~   75 (369)
                      ++|++++..++..+||..++|.|..+++.++.++++.+.++||||||+++++++++.+...  ...   -.++||+||++
T Consensus        11 ~~L~~~l~~~l~~~GF~~mTpVQa~tIPlll~~KDVvveavTGSGKTlAFllP~le~i~rr~~~~~~~~vgalIIsPTRE   90 (567)
T KOG0345|consen   11 PPLSPWLLEALDESGFEKMTPVQAATIPLLLKNKDVVVEAVTGSGKTLAFLLPMLEIIYRREAKTPPGQVGALIISPTRE   90 (567)
T ss_pred             CCccHHHHHHHHhcCCcccCHHHHhhhHHHhcCCceEEEcCCCCCchhhHHHHHHHHHHhhccCCCccceeEEEecCcHH
Confidence            3678999999999999999999999999999999999999999999999999999998322  111   14899999999


Q ss_pred             HHHHHHHHHHHhccc-cCcEEEEEECCcchHHHHHHHc-cCCcEEEeccHHHHHHHHcCCCCCC--CccEEEEechhHhh
Q 017573           76 LAQQIEKVMRALGDY-LGVKVHACVGGTSVREDQRILQ-AGVHVVVGTPGRVFDMLRRQSLRPD--YIKMFVLDEADEML  151 (369)
Q Consensus        76 l~~q~~~~~~~~~~~-~~~~v~~~~~~~~~~~~~~~~~-~~~~iiv~t~~~l~~~~~~~~~~~~--~~~~viiDE~H~~~  151 (369)
                      |+.|..+....|... .++++..+.|+.+..++...+. ..++|+|+||..|.+++.+....++  .+.++|+|||+++.
T Consensus        91 La~QI~~V~~~F~~~l~~l~~~l~vGG~~v~~Di~~fkee~~nIlVgTPGRL~di~~~~~~~l~~rsLe~LVLDEADrLl  170 (567)
T KOG0345|consen   91 LARQIREVAQPFLEHLPNLNCELLVGGRSVEEDIKTFKEEGPNILVGTPGRLLDILQREAEKLSFRSLEILVLDEADRLL  170 (567)
T ss_pred             HHHHHHHHHHHHHHhhhccceEEEecCccHHHHHHHHHHhCCcEEEeCchhHHHHHhchhhhccccccceEEecchHhHh
Confidence            999999998888776 5788999999988777665554 5678999999999999988554444  78999999999999


Q ss_pred             ccCcHHHHHHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccc--cccceeEEEEEccchhhhHHHHHHH
Q 017573          152 SRGFKDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDEL--TLEGIKQFYVNVEKEEWKLETLCDL  229 (369)
Q Consensus       152 ~~~~~~~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~l~~~  229 (369)
                      +.+|...++.+++.+|+..+.-++|||......++....+.+|+.+.+.....  .+..+...|..+.+ ..+...+.++
T Consensus       171 dmgFe~~~n~ILs~LPKQRRTGLFSATq~~~v~dL~raGLRNpv~V~V~~k~~~~tPS~L~~~Y~v~~a-~eK~~~lv~~  249 (567)
T KOG0345|consen  171 DMGFEASVNTILSFLPKQRRTGLFSATQTQEVEDLARAGLRNPVRVSVKEKSKSATPSSLALEYLVCEA-DEKLSQLVHL  249 (567)
T ss_pred             cccHHHHHHHHHHhcccccccccccchhhHHHHHHHHhhccCceeeeecccccccCchhhcceeeEecH-HHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999998877665  67778888877766 4588888888


Q ss_pred             HHhccCCCeEEEeCCHhhHHHHHHHHhhC--CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEE
Q 017573          230 YETLAITQSVIFVNTRRKVDWLTDKMRSR--DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLV  307 (369)
Q Consensus       230 ~~~~~~~k~lv~~~~~~~~~~~~~~l~~~--~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~v  307 (369)
                      +.....+|+|||+++...++.+...|...  +..+..+||.+++..|.+++..|.+....+|+||+++.+|+|+|++++|
T Consensus       250 L~~~~~kK~iVFF~TCasVeYf~~~~~~~l~~~~i~~iHGK~~q~~R~k~~~~F~~~~~~vl~~TDVaARGlDip~iD~V  329 (567)
T KOG0345|consen  250 LNNNKDKKCIVFFPTCASVEYFGKLFSRLLKKREIFSIHGKMSQKARAKVLEAFRKLSNGVLFCTDVAARGLDIPGIDLV  329 (567)
T ss_pred             HhccccccEEEEecCcchHHHHHHHHHHHhCCCcEEEecchhcchhHHHHHHHHHhccCceEEeehhhhccCCCCCceEE
Confidence            88888899999999999999999998766  6689999999999999999999999778899999999999999999999


Q ss_pred             EEecCCCCccchhhhhcccccCCCceeEEEEeccccHH
Q 017573          308 INYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDER  345 (369)
Q Consensus       308 i~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~  345 (369)
                      +.+|+|.++..|.+|+||++|.|+.|.+++|..+.+..
T Consensus       330 vQ~DpP~~~~~FvHR~GRTaR~gr~G~Aivfl~p~E~a  367 (567)
T KOG0345|consen  330 VQFDPPKDPSSFVHRCGRTARAGREGNAIVFLNPREEA  367 (567)
T ss_pred             EecCCCCChhHHHhhcchhhhccCccceEEEecccHHH
Confidence            99999999999999999999999999999999995544

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

Probab=100.00  E-value=2.5e-55  Score=369.55  Aligned_cols=353  Identities=35%  Similarity=0.564  Sum_probs=327.4

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCC---ccEEEEcCCHHHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQ---CQALVLAPTRELA   77 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~---~~~liv~P~~~l~   77 (369)
                      |+|+.-+.+++..+||..|+|+|...++-.+-|++++-+|.||||||.++++++++++...+.+   .++||+||+++|+
T Consensus       186 mNLSRPlLka~~~lGy~~PTpIQ~a~IPvallgkDIca~A~TGsGKTAAF~lPiLERLlYrPk~~~~TRVLVL~PTRELa  265 (691)
T KOG0338|consen  186 MNLSRPLLKACSTLGYKKPTPIQVATIPVALLGKDICACAATGSGKTAAFALPILERLLYRPKKVAATRVLVLVPTRELA  265 (691)
T ss_pred             cccchHHHHHHHhcCCCCCCchhhhcccHHhhcchhhheecccCCchhhhHHHHHHHHhcCcccCcceeEEEEeccHHHH
Confidence            7899999999999999999999999999999999999999999999999999999998665443   3799999999999


Q ss_pred             HHHHHHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHc-CCCCCCCccEEEEechhHhhccCcH
Q 017573           78 QQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRR-QSLRPDYIKMFVLDEADEMLSRGFK  156 (369)
Q Consensus        78 ~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~-~~~~~~~~~~viiDE~H~~~~~~~~  156 (369)
                      .|.....+++...+.+.+....||.....+...+...+||+|+||..|..++.+ ..+++.++.++|+||+++++..+|.
T Consensus       266 iQv~sV~~qlaqFt~I~~~L~vGGL~lk~QE~~LRs~PDIVIATPGRlIDHlrNs~sf~ldsiEVLvlDEADRMLeegFa  345 (691)
T KOG0338|consen  266 IQVHSVTKQLAQFTDITVGLAVGGLDLKAQEAVLRSRPDIVIATPGRLIDHLRNSPSFNLDSIEVLVLDEADRMLEEGFA  345 (691)
T ss_pred             HHHHHHHHHHHhhccceeeeeecCccHHHHHHHHhhCCCEEEecchhHHHHhccCCCccccceeEEEechHHHHHHHHHH
Confidence            999999999998889999999999999888888888999999999999988875 5677888999999999999999999


Q ss_pred             HHHHHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEcc--chhhhHHHHHHHHHhcc
Q 017573          157 DQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVE--KEEWKLETLCDLYETLA  234 (369)
Q Consensus       157 ~~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~l~~~~~~~~  234 (369)
                      ..++.++..++++.|.+++|||+.....+++...+.+|+.+.+.........+.+-|+.+.  .....-..+..++.+.-
T Consensus       346 demnEii~lcpk~RQTmLFSATMteeVkdL~slSL~kPvrifvd~~~~~a~~LtQEFiRIR~~re~dRea~l~~l~~rtf  425 (691)
T KOG0338|consen  346 DEMNEIIRLCPKNRQTMLFSATMTEEVKDLASLSLNKPVRIFVDPNKDTAPKLTQEFIRIRPKREGDREAMLASLITRTF  425 (691)
T ss_pred             HHHHHHHHhccccccceeehhhhHHHHHHHHHhhcCCCeEEEeCCccccchhhhHHHheeccccccccHHHHHHHHHHhc
Confidence            9999999999999999999999999999999999999999999988888888887777665  34456667777777766


Q ss_pred             CCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCCC
Q 017573          235 ITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPT  314 (369)
Q Consensus       235 ~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~  314 (369)
                      ..+++||+.+.+.|+.+.=.|--.|.++.-+||.+++.+|.+.++.|++++++|||||+.+++|+||+++..||.+..|.
T Consensus       426 ~~~~ivFv~tKk~AHRl~IllGLlgl~agElHGsLtQ~QRlesL~kFk~~eidvLiaTDvAsRGLDI~gV~tVINy~mP~  505 (691)
T KOG0338|consen  426 QDRTIVFVRTKKQAHRLRILLGLLGLKAGELHGSLTQEQRLESLEKFKKEEIDVLIATDVASRGLDIEGVQTVINYAMPK  505 (691)
T ss_pred             ccceEEEEehHHHHHHHHHHHHHhhchhhhhcccccHHHHHHHHHHHHhccCCEEEEechhhccCCccceeEEEeccCch
Confidence            78999999999999999999988899999999999999999999999999999999999999999999999999999999


Q ss_pred             CccchhhhhcccccCCCceeEEEEeccccHHHHHHHHHH
Q 017573          315 QPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKF  353 (369)
Q Consensus       315 ~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~  353 (369)
                      +...|++|+||..|.|+.|.+++++..+|.+.++.+...
T Consensus       506 t~e~Y~HRVGRTARAGRaGrsVtlvgE~dRkllK~iik~  544 (691)
T KOG0338|consen  506 TIEHYLHRVGRTARAGRAGRSVTLVGESDRKLLKEIIKS  544 (691)
T ss_pred             hHHHHHHHhhhhhhcccCcceEEEeccccHHHHHHHHhh
Confidence            999999999999999999999999999999999887665

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

Probab=100.00  E-value=4.3e-55  Score=347.96  Aligned_cols=364  Identities=40%  Similarity=0.675  Sum_probs=341.3

Q ss_pred             CCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHH
Q 017573            2 GLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIE   81 (369)
Q Consensus         2 ~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~   81 (369)
                      .|.+++.......||+.|+|+|+++++..+.|++++..|..|+|||-++++++++.+......-++++++|+++|+-|..
T Consensus        91 ~Lkr~LLmgIfe~G~ekPSPiQeesIPiaLtGrdiLaRaKNGTGKT~a~~IP~Lekid~~~~~IQ~~ilVPtrelALQtS  170 (459)
T KOG0326|consen   91 CLKRELLMGIFEKGFEKPSPIQEESIPIALTGRDILARAKNGTGKTAAYCIPVLEKIDPKKNVIQAIILVPTRELALQTS  170 (459)
T ss_pred             hhhHHHHHHHHHhccCCCCCccccccceeecchhhhhhccCCCCCccceechhhhhcCccccceeEEEEeecchhhHHHH
Confidence            57788899999999999999999999999999999999999999999999999999988777778999999999999999


Q ss_pred             HHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHH
Q 017573           82 KVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYD  161 (369)
Q Consensus        82 ~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~  161 (369)
                      ..+.++.+.+++.+....|++...++.-.+....+++|+||.+.+.+...+-...+.+.++|+|||+.+.+..|...+..
T Consensus       171 qvc~~lskh~~i~vmvttGGT~lrDDI~Rl~~~VH~~vgTPGRIlDL~~KgVa~ls~c~~lV~DEADKlLs~~F~~~~e~  250 (459)
T KOG0326|consen  171 QVCKELSKHLGIKVMVTTGGTSLRDDIMRLNQTVHLVVGTPGRILDLAKKGVADLSDCVILVMDEADKLLSVDFQPIVEK  250 (459)
T ss_pred             HHHHHHhcccCeEEEEecCCcccccceeeecCceEEEEcCChhHHHHHhcccccchhceEEEechhhhhhchhhhhHHHH
Confidence            99999999999999999999987776655667889999999999999999988899999999999999999999999999


Q ss_pred             HHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHHHhccCCCeEEE
Q 017573          162 IFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIF  241 (369)
Q Consensus       162 ~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lv~  241 (369)
                      ++..+|+..|+++.|||.+-....++.+.+.+|..+.... +..+..+.++|..+.. ..+..-+..++.+......+||
T Consensus       251 li~~lP~~rQillySATFP~tVk~Fm~~~l~kPy~INLM~-eLtl~GvtQyYafV~e-~qKvhCLntLfskLqINQsIIF  328 (459)
T KOG0326|consen  251 LISFLPKERQILLYSATFPLTVKGFMDRHLKKPYEINLME-ELTLKGVTQYYAFVEE-RQKVHCLNTLFSKLQINQSIIF  328 (459)
T ss_pred             HHHhCCccceeeEEecccchhHHHHHHHhccCcceeehhh-hhhhcchhhheeeech-hhhhhhHHHHHHHhcccceEEE
Confidence            9999999999999999999999999999999998887644 4566778888877765 4588889999999998999999


Q ss_pred             eCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCCCCccchhh
Q 017573          242 VNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLH  321 (369)
Q Consensus       242 ~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q  321 (369)
                      |||.+.++-+++.+.+.|+.+..+|+.|.++.|.+++..|++|.++.||||+.+.+|+|++.+++||.++.|+++.+|.+
T Consensus       329 CNS~~rVELLAkKITelGyscyyiHakM~Q~hRNrVFHdFr~G~crnLVctDL~TRGIDiqavNvVINFDfpk~aEtYLH  408 (459)
T KOG0326|consen  329 CNSTNRVELLAKKITELGYSCYYIHAKMAQEHRNRVFHDFRNGKCRNLVCTDLFTRGIDIQAVNVVINFDFPKNAETYLH  408 (459)
T ss_pred             eccchHhHHHHHHHHhccchhhHHHHHHHHhhhhhhhhhhhccccceeeehhhhhcccccceeeEEEecCCCCCHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhcccccCCCceeEEEEeccccHHHHHHHHHHhccccccCCcchhh
Q 017573          322 RIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPSNVAD  367 (369)
Q Consensus       322 ~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  367 (369)
                      |+||.||.|..|.++-+++..|...+..+++.++.+++++|..+..
T Consensus       409 RIGRsGRFGhlGlAInLityedrf~L~~IE~eLGtEI~pip~~iDk  454 (459)
T KOG0326|consen  409 RIGRSGRFGHLGLAINLITYEDRFNLYRIEQELGTEIKPIPSNIDK  454 (459)
T ss_pred             HccCCccCCCcceEEEEEehhhhhhHHHHHHHhccccccCCCcCCc
Confidence            9999999999999999999999999999999999999999988754

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

Probab=100.00  E-value=8.8e-53  Score=339.23  Aligned_cols=361  Identities=37%  Similarity=0.513  Sum_probs=321.3

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQI   80 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~   80 (369)
                      +||++|+...|.++++..|+|+|...++.+++|++++=+|-||||||.++.+++++++...+.+--+++++|+++|+-|.
T Consensus        12 LGl~~Wlve~l~~l~i~~pTpiQ~~cIpkILeGrdcig~AkTGsGKT~AFaLPil~rLsedP~giFalvlTPTrELA~Qi   91 (442)
T KOG0340|consen   12 LGLSPWLVEQLKALGIKKPTPIQQACIPKILEGRDCIGCAKTGSGKTAAFALPILNRLSEDPYGIFALVLTPTRELALQI   91 (442)
T ss_pred             cCccHHHHHHHHHhcCCCCCchHhhhhHHHhcccccccccccCCCcchhhhHHHHHhhccCCCcceEEEecchHHHHHHH
Confidence            69999999999999999999999999999999999999999999999999999999999998888899999999999999


Q ss_pred             HHHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCC----CCCCCccEEEEechhHhhccCcH
Q 017573           81 EKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQS----LRPDYIKMFVLDEADEMLSRGFK  156 (369)
Q Consensus        81 ~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~----~~~~~~~~viiDE~H~~~~~~~~  156 (369)
                      .++|....+..++++.++.|+...-.+...+..++|++++||+++..++..+.    +-+.++.++++|||+.+.+..|.
T Consensus        92 aEQF~alGk~l~lK~~vivGG~d~i~qa~~L~~rPHvVvatPGRlad~l~sn~~~~~~~~~rlkflVlDEADrvL~~~f~  171 (442)
T KOG0340|consen   92 AEQFIALGKLLNLKVSVIVGGTDMIMQAAILSDRPHVVVATPGRLADHLSSNLGVCSWIFQRLKFLVLDEADRVLAGCFP  171 (442)
T ss_pred             HHHHHHhcccccceEEEEEccHHHhhhhhhcccCCCeEecCccccccccccCCccchhhhhceeeEEecchhhhhccchh
Confidence            99999999999999999999998877777788889999999999998887753    23456789999999999999999


Q ss_pred             HHHHHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCC--CEEEEecCccccccceeEEEEEccchhhhHHHHHHHHHhc-
Q 017573          157 DQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNK--PVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETL-  233 (369)
Q Consensus       157 ~~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-  233 (369)
                      ..+..+.+.+|...|.+++|||.......+...-..+  ...+...........+.+-|+.++... +..-+..++... 
T Consensus       172 d~L~~i~e~lP~~RQtLlfSATitd~i~ql~~~~i~k~~a~~~e~~~~vstvetL~q~yI~~~~~v-kdaYLv~~Lr~~~  250 (442)
T KOG0340|consen  172 DILEGIEECLPKPRQTLLFSATITDTIKQLFGCPITKSIAFELEVIDGVSTVETLYQGYILVSIDV-KDAYLVHLLRDFE  250 (442)
T ss_pred             hHHhhhhccCCCccceEEEEeehhhHHHHhhcCCcccccceEEeccCCCCchhhhhhheeecchhh-hHHHHHHHHhhhh
Confidence            9999999999999999999999987776655544444  334444556666677777777766533 333344444333 


Q ss_pred             --cCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEec
Q 017573          234 --AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYD  311 (369)
Q Consensus       234 --~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~  311 (369)
                        ..+.++||+++..+++.++..|+..++.+..+|+.|++.+|-..+..|+++..++||||+.+++|+|+|.+..|+.++
T Consensus       251 ~~~~~simIFvnttr~cQ~l~~~l~~le~r~~~lHs~m~Q~eR~~aLsrFrs~~~~iliaTDVAsRGLDIP~V~LVvN~d  330 (442)
T KOG0340|consen  251 NKENGSIMIFVNTTRECQLLSMTLKNLEVRVVSLHSQMPQKERLAALSRFRSNAARILIATDVASRGLDIPTVELVVNHD  330 (442)
T ss_pred             hccCceEEEEeehhHHHHHHHHHHhhhceeeeehhhcchHHHHHHHHHHHhhcCccEEEEechhhcCCCCCceeEEEecC
Confidence              457899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCccchhhhhcccccCCCceeEEEEeccccHHHHHHHHHHhccccccCC
Q 017573          312 LPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELP  362 (369)
Q Consensus       312 ~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  362 (369)
                      .|.++.+|++|+||..|.|+.|.++.++++.|.+.+..+++..+..+.+.+
T Consensus       331 iPr~P~~yiHRvGRtARAGR~G~aiSivt~rDv~l~~aiE~~igkKl~e~~  381 (442)
T KOG0340|consen  331 IPRDPKDYIHRVGRTARAGRKGMAISIVTQRDVELLQAIEEEIGKKLTEYN  381 (442)
T ss_pred             CCCCHHHHHHhhcchhcccCCcceEEEechhhHHHHHHHHHHHhccccccc
Confidence            999999999999999999999999999999999999999999988877655

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

Probab=100.00  E-value=1e-52  Score=358.28  Aligned_cols=365  Identities=35%  Similarity=0.515  Sum_probs=329.6

Q ss_pred             CCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCC----------CccEEEEc
Q 017573            2 GLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLV----------QCQALVLA   71 (369)
Q Consensus         2 ~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~----------~~~~liv~   71 (369)
                      .+++.+..++...++..|+|+|+.+++.+..|++.+++|+||+|||.+++++++.++.....          .+.++|++
T Consensus        80 ~l~~~l~~ni~~~~~~~ptpvQk~sip~i~~Grdl~acAqTGsGKT~aFLiPii~~~~~~~~~~~~~~~~~~~P~~lIla  159 (482)
T KOG0335|consen   80 ILGEALAGNIKRSGYTKPTPVQKYSIPIISGGRDLMACAQTGSGKTAAFLIPIISYLLDEGPEDRGESGGGVYPRALILA  159 (482)
T ss_pred             chhHHHhhccccccccCCCcceeeccceeecCCceEEEccCCCcchHHHHHHHHHHHHhcCcccCcccCCCCCCceEEEe
Confidence            36677888899999999999999999999999999999999999999999999998865422          35899999


Q ss_pred             CCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhh
Q 017573           72 PTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEML  151 (369)
Q Consensus        72 P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~  151 (369)
                      ||++|+.|.+++.+++....+++....+++.....+..-..++++|+|+||.+|..++..+.+.+..++++|+||++++.
T Consensus       160 pTReL~~Qi~nea~k~~~~s~~~~~~~ygg~~~~~q~~~~~~gcdIlvaTpGrL~d~~e~g~i~l~~~k~~vLDEADrMl  239 (482)
T KOG0335|consen  160 PTRELVDQIYNEARKFSYLSGMKSVVVYGGTDLGAQLRFIKRGCDILVATPGRLKDLIERGKISLDNCKFLVLDEADRML  239 (482)
T ss_pred             CcHHHhhHHHHHHHhhcccccceeeeeeCCcchhhhhhhhccCccEEEecCchhhhhhhcceeehhhCcEEEecchHHhh
Confidence            99999999999999999888999999999988777777788899999999999999999999999999999999999999


Q ss_pred             c-cCcHHHHHHHHhhCCc----cCcEEEEEeeCChhHHHHHHHhcCC-CEEEEecCccccccceeEEEEEccchhhhHHH
Q 017573          152 S-RGFKDQIYDIFQLLPA----KVQVGVFSATMPPEALEITRKFMNK-PVRILVKRDELTLEGIKQFYVNVEKEEWKLET  225 (369)
Q Consensus       152 ~-~~~~~~~~~~~~~~~~----~~~~i~~saT~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  225 (369)
                      + .+|...+..+......    ..|.+++|||.+.++..+...++.. .+.+.+.........+.+....+.... +...
T Consensus       240 D~mgF~p~Ir~iv~~~~~~~~~~~qt~mFSAtfp~~iq~l~~~fl~~~yi~laV~rvg~~~~ni~q~i~~V~~~~-kr~~  318 (482)
T KOG0335|consen  240 DEMGFEPQIRKIVEQLGMPPKNNRQTLLFSATFPKEIQRLAADFLKDNYIFLAVGRVGSTSENITQKILFVNEME-KRSK  318 (482)
T ss_pred             hhccccccHHHHhcccCCCCccceeEEEEeccCChhhhhhHHHHhhccceEEEEeeeccccccceeEeeeecchh-hHHH
Confidence            8 8899999999877743    6889999999999988877777776 666777777777888888888887655 4444


Q ss_pred             HHHHHH-hc---cCC-----CeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCc
Q 017573          226 LCDLYE-TL---AIT-----QSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLA  296 (369)
Q Consensus       226 l~~~~~-~~---~~~-----k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~  296 (369)
                      +.+++. ..   ..+     +++|||.+++.+..+...|...+++...+||+.++.+|.+.++.|++|...++|||.++.
T Consensus       319 Lldll~~~~~~~~~~~~~~e~tlvFvEt~~~~d~l~~~l~~~~~~~~sIhg~~tq~er~~al~~Fr~g~~pvlVaT~Vaa  398 (482)
T KOG0335|consen  319 LLDLLNKDDGPPSDGEPKWEKTLVFVETKRGADELAAFLSSNGYPAKSIHGDRTQIEREQALNDFRNGKAPVLVATNVAA  398 (482)
T ss_pred             HHHHhhcccCCcccCCcccceEEEEeeccchhhHHHHHHhcCCCCceeecchhhhhHHHHHHHHhhcCCcceEEEehhhh
Confidence            444443 32   223     899999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCCcEEEEecCCCCccchhhhhcccccCCCceeEEEEeccccHHHHHHHHHHhccccccCCcchhh
Q 017573          297 RGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPSNVAD  367 (369)
Q Consensus       297 ~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  367 (369)
                      +|+|+|++++||.++.|.+..+|++|+||+||.|+.|.+..|++..+....+.+.+.+....+++|.|+.+
T Consensus       399 RGlDi~~V~hVInyDmP~d~d~YvHRIGRTGR~Gn~G~atsf~n~~~~~i~~~L~~~l~ea~q~vP~wl~~  469 (482)
T KOG0335|consen  399 RGLDIPNVKHVINYDMPADIDDYVHRIGRTGRVGNGGRATSFFNEKNQNIAKALVEILTEANQEVPQWLSE  469 (482)
T ss_pred             cCCCCCCCceeEEeecCcchhhHHHhccccccCCCCceeEEEeccccchhHHHHHHHHHHhcccCcHHHHh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999975

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

Probab=100.00  E-value=3e-52  Score=349.93  Aligned_cols=349  Identities=32%  Similarity=0.501  Sum_probs=313.4

Q ss_pred             CCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCC----CccEEEEcCCHHHH
Q 017573            2 GLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLV----QCQALVLAPTRELA   77 (369)
Q Consensus         2 ~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~----~~~~liv~P~~~l~   77 (369)
                      .|++.+.++++.+||..+++.|+..++.++.|++++..|-||+|||+++++++++.+.+.+.    +..++|+|||++|+
T Consensus        88 ~LS~~t~kAi~~~GF~~MT~VQ~~ti~pll~gkDvl~~AKTGtGKTlAFLiPaie~l~k~~~~~r~~~~vlIi~PTRELA  167 (543)
T KOG0342|consen   88 SLSPLTLKAIKEMGFETMTPVQQKTIPPLLEGKDVLAAAKTGTGKTLAFLLPAIELLRKLKFKPRNGTGVLIICPTRELA  167 (543)
T ss_pred             ccCHHHHHHHHhcCccchhHHHHhhcCccCCCccceeeeccCCCceeeehhHHHHHHHhcccCCCCCeeEEEecccHHHH
Confidence            68999999999999999999999999999999999999999999999999999998865432    33699999999999


Q ss_pred             HHHHHHHHHhcccc-CcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCC-CCCccEEEEechhHhhccCc
Q 017573           78 QQIEKVMRALGDYL-GVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLR-PDYIKMFVLDEADEMLSRGF  155 (369)
Q Consensus        78 ~q~~~~~~~~~~~~-~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~-~~~~~~viiDE~H~~~~~~~  155 (369)
                      .|.+.+.+++.... +..+..+.|+.......+.+..+++|+|+||.+|..++.+.... ....+++|+|||+++.+.+|
T Consensus       168 ~Q~~~eak~Ll~~h~~~~v~~viGG~~~~~e~~kl~k~~niliATPGRLlDHlqNt~~f~~r~~k~lvlDEADrlLd~GF  247 (543)
T KOG0342|consen  168 MQIFAEAKELLKYHESITVGIVIGGNNFSVEADKLVKGCNILIATPGRLLDHLQNTSGFLFRNLKCLVLDEADRLLDIGF  247 (543)
T ss_pred             HHHHHHHHHHHhhCCCcceEEEeCCccchHHHHHhhccccEEEeCCchHHhHhhcCCcchhhccceeEeecchhhhhccc
Confidence            99999999998877 88999999999887777777779999999999999999886544 34467999999999999999


Q ss_pred             HHHHHHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCC-CEEEEecC--ccccccceeEEEEEccchhhhHHHHHHHHHh
Q 017573          156 KDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNK-PVRILVKR--DELTLEGIKQFYVNVEKEEWKLETLCDLYET  232 (369)
Q Consensus       156 ~~~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~-~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  232 (369)
                      .+.+..+...+|...|..++|||.++...++....+.. +..+.+..  ...+...+.+.++..+... ..-.+..++++
T Consensus       248 ~~di~~Ii~~lpk~rqt~LFSAT~~~kV~~l~~~~L~~d~~~v~~~d~~~~~The~l~Qgyvv~~~~~-~f~ll~~~LKk  326 (543)
T KOG0342|consen  248 EEDVEQIIKILPKQRQTLLFSATQPSKVKDLARGALKRDPVFVNVDDGGERETHERLEQGYVVAPSDS-RFSLLYTFLKK  326 (543)
T ss_pred             HHHHHHHHHhccccceeeEeeCCCcHHHHHHHHHhhcCCceEeecCCCCCcchhhcccceEEeccccc-hHHHHHHHHHH
Confidence            99999999999999999999999999998888877776 55555433  4455667888777666544 37777888877


Q ss_pred             ccC-CCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEec
Q 017573          233 LAI-TQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYD  311 (369)
Q Consensus       233 ~~~-~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~  311 (369)
                      +.. .|++|||++......+++.|.....++..+||+.++..|.....+|++.+..||+||++..+|+|+|++++|+.++
T Consensus       327 ~~~~~KiiVF~sT~~~vk~~~~lL~~~dlpv~eiHgk~~Q~kRT~~~~~F~kaesgIL~cTDVaARGlD~P~V~~VvQ~~  406 (543)
T KOG0342|consen  327 NIKRYKIIVFFSTCMSVKFHAELLNYIDLPVLEIHGKQKQNKRTSTFFEFCKAESGILVCTDVAARGLDIPDVDWVVQYD  406 (543)
T ss_pred             hcCCceEEEEechhhHHHHHHHHHhhcCCchhhhhcCCcccccchHHHHHhhcccceEEecchhhccCCCCCceEEEEeC
Confidence            765 8999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCccchhhhhcccccCCCceeEEEEeccccHHHHHHHH
Q 017573          312 LPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQ  351 (369)
Q Consensus       312 ~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~  351 (369)
                      +|.++.+|++|+||++|.|+.|.++++..+.+..++..+.
T Consensus       407 ~P~d~~~YIHRvGRTaR~gk~G~alL~l~p~El~Flr~LK  446 (543)
T KOG0342|consen  407 PPSDPEQYIHRVGRTAREGKEGKALLLLAPWELGFLRYLK  446 (543)
T ss_pred             CCCCHHHHHHHhccccccCCCceEEEEeChhHHHHHHHHh
Confidence            9999999999999999999999999999999999888776

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

Probab=100.00  E-value=1.2e-52  Score=342.80  Aligned_cols=366  Identities=75%  Similarity=1.122  Sum_probs=344.7

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQI   80 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~   80 (369)
                      |||++.+.+.+..+||+.|+.+|+.|+..+.+|.++.+++.+|+|||.++...+++.+........+++++|+++|+.|.
T Consensus        31 m~L~e~LLrgiy~yGFekPSaIQqraI~p~i~G~dv~~qaqsgTgKt~af~i~iLq~iD~~~ke~qalilaPtreLa~qi  110 (397)
T KOG0327|consen   31 MNLKESLLRGIYAYGFEKPSAIQQRAILPCIKGHDVIAQAQSGTGKTAAFLISILQQIDMSVKETQALILAPTRELAQQI  110 (397)
T ss_pred             cCCCHHHHhHHHhhccCCchHHHhccccccccCCceeEeeeccccchhhhHHHHHhhcCcchHHHHHHHhcchHHHHHHH
Confidence            79999999999999999999999999999999999999999999999999999999987666666899999999999999


Q ss_pred             HHHHHHhccccCcEEEEEECCcchHHH-HHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHH
Q 017573           81 EKVMRALGDYLGVKVHACVGGTSVRED-QRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQI  159 (369)
Q Consensus        81 ~~~~~~~~~~~~~~v~~~~~~~~~~~~-~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~  159 (369)
                      .+....+....+..+..+.|+.....+ ..+....++|+++||.....++....+....+.++++||++++...++.+.+
T Consensus       111 ~~v~~~lg~~~~~~v~~~igg~~~~~~~~~i~~~~~hivvGTpgrV~dml~~~~l~~~~iKmfvlDEaDEmLs~gfkdqI  190 (397)
T KOG0327|consen  111 QKVVRALGDHMDVSVHACIGGTNVRREDQALLKDKPHIVVGTPGRVFDMLNRGSLSTDGIKMFVLDEADEMLSRGFKDQI  190 (397)
T ss_pred             HHHHHhhhcccceeeeeecCcccchhhhhhhhccCceeecCCchhHHHhhccccccccceeEEeecchHhhhccchHHHH
Confidence            999999988889999988988877644 3444556899999999999999998888888999999999999999999999


Q ss_pred             HHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHHHhccCCCeE
Q 017573          160 YDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSV  239 (369)
Q Consensus       160 ~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~l  239 (369)
                      ..+++.+|++.|++++|||.+.+.......++..|+.+.+..+......+.+++....... ++..+..+..  .-...+
T Consensus       191 ~~if~~lp~~vQv~l~SAT~p~~vl~vt~~f~~~pv~i~vkk~~ltl~gikq~~i~v~k~~-k~~~l~dl~~--~~~q~~  267 (397)
T KOG0327|consen  191 YDIFQELPSDVQVVLLSATMPSDVLEVTKKFMREPVRILVKKDELTLEGIKQFYINVEKEE-KLDTLCDLYR--RVTQAV  267 (397)
T ss_pred             HHHHHHcCcchhheeecccCcHHHHHHHHHhccCceEEEecchhhhhhheeeeeeeccccc-cccHHHHHHH--hhhcce
Confidence            9999999999999999999999999999999999999999999999999999999888766 8888988888  456889


Q ss_pred             EEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCCCCccch
Q 017573          240 IFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENY  319 (369)
Q Consensus       240 v~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~  319 (369)
                      +|||+.+.+..+...|...+..+..+|+++.+.+|..++..|++|..+|||.|+.+++|+|+..++.|+.++.|.....|
T Consensus       268 if~nt~r~v~~l~~~L~~~~~~~s~~~~d~~q~~R~~~~~ef~~gssrvlIttdl~argidv~~~slvinydlP~~~~~y  347 (397)
T KOG0327|consen  268 IFCNTRRKVDNLTDKLRAHGFTVSAIHGDMEQNERDTLMREFRSGSSRVLITTDLLARGIDVQQVSLVVNYDLPARKENY  347 (397)
T ss_pred             EEecchhhHHHHHHHHhhCCceEEEeecccchhhhhHHHHHhhcCCceEEeeccccccccchhhcceeeeeccccchhhh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhcccccCCCceeEEEEeccccHHHHHHHHHHhccccccCCcchhhcC
Q 017573          320 LHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPSNVADLL  369 (369)
Q Consensus       320 ~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  369 (369)
                      .+|+||+||.|.+|.++.++...|...++.++++|..+++++|.+..+++
T Consensus       348 ihR~gr~gr~grkg~~in~v~~~d~~~lk~ie~~y~~~i~e~p~~~~~l~  397 (397)
T KOG0327|consen  348 IHRIGRAGRFGRKGVAINFVTEEDVRDLKDIEKFYNTPIEELPSNFADLL  397 (397)
T ss_pred             hhhcccccccCCCceeeeeehHhhHHHHHhHHHhcCCcceecccchhhcC
Confidence            99999999999999999999999999999999999999999999998875

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

Probab=100.00  E-value=3e-52  Score=342.42  Aligned_cols=364  Identities=32%  Similarity=0.517  Sum_probs=328.3

Q ss_pred             CCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhc------cCCCccEEEEcCCHH
Q 017573            2 GLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY------GLVQCQALVLAPTRE   75 (369)
Q Consensus         2 ~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~------~~~~~~~liv~P~~~   75 (369)
                      ...+++..++.+.||+.|+|+|.++++-+++|.+++-.|.||+|||++++++.+-++..      ...++.+|+++|+++
T Consensus       226 q~~pevmenIkK~GFqKPtPIqSQaWPI~LQG~DliGVAQTgtgKtL~~L~pg~ihi~aqp~~~~qr~~p~~lvl~ptre  305 (629)
T KOG0336|consen  226 QCYPEVMENIKKTGFQKPTPIQSQAWPILLQGIDLIGVAQTGTGKTLAFLLPGFIHIDAQPKRREQRNGPGVLVLTPTRE  305 (629)
T ss_pred             hhhHHHHHHHHhccCCCCCcchhcccceeecCcceEEEEecCCCcCHHHhccceeeeeccchhhhccCCCceEEEeccHH
Confidence            45688999999999999999999999999999999999999999999999877665532      234557999999999


Q ss_pred             HHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCc
Q 017573           76 LAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGF  155 (369)
Q Consensus        76 l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~  155 (369)
                      |+.|..-+..++. ..++....++|+.+-.++...+.++++|+++||.+|..+...+.+++..+.++|+||++++++.+|
T Consensus       306 Lalqie~e~~kys-yng~ksvc~ygggnR~eqie~lkrgveiiiatPgrlndL~~~n~i~l~siTYlVlDEADrMLDMgF  384 (629)
T KOG0336|consen  306 LALQIEGEVKKYS-YNGLKSVCVYGGGNRNEQIEDLKRGVEIIIATPGRLNDLQMDNVINLASITYLVLDEADRMLDMGF  384 (629)
T ss_pred             HHHHHHhHHhHhh-hcCcceEEEecCCCchhHHHHHhcCceEEeeCCchHhhhhhcCeeeeeeeEEEEecchhhhhcccc
Confidence            9999988887764 347788888888887788888899999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCcccccc-ceeEEEEEccchhhhHHHHHHHHHhc-
Q 017573          156 KDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLE-GIKQFYVNVEKEEWKLETLCDLYETL-  233 (369)
Q Consensus       156 ~~~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~l~~~~~~~-  233 (369)
                      ..++.+++-.+.+..|.+..|||.++....+...+++.|..+.+..-..... .+.+.+ .+.....+...+..++... 
T Consensus       385 EpqIrkilldiRPDRqtvmTSATWP~~VrrLa~sY~Kep~~v~vGsLdL~a~~sVkQ~i-~v~~d~~k~~~~~~f~~~ms  463 (629)
T KOG0336|consen  385 EPQIRKILLDIRPDRQTVMTSATWPEGVRRLAQSYLKEPMIVYVGSLDLVAVKSVKQNI-IVTTDSEKLEIVQFFVANMS  463 (629)
T ss_pred             cHHHHHHhhhcCCcceeeeecccCchHHHHHHHHhhhCceEEEecccceeeeeeeeeeE-EecccHHHHHHHHHHHHhcC
Confidence            9999999999999999999999999999999999999998887765544433 344444 5566667888888888776 


Q ss_pred             cCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCC
Q 017573          234 AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLP  313 (369)
Q Consensus       234 ~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~  313 (369)
                      +..|+||||.+...|..+...|.-.|+....+||+-++.+|+..++.|++|+.++||+|+.+++|+|+|+++||+.++.|
T Consensus       464 ~ndKvIiFv~~K~~AD~LSSd~~l~gi~~q~lHG~r~Q~DrE~al~~~ksG~vrILvaTDlaSRGlDv~DiTHV~NyDFP  543 (629)
T KOG0336|consen  464 SNDKVIIFVSRKVMADHLSSDFCLKGISSQSLHGNREQSDREMALEDFKSGEVRILVATDLASRGLDVPDITHVYNYDFP  543 (629)
T ss_pred             CCceEEEEEechhhhhhccchhhhcccchhhccCChhhhhHHHHHHhhhcCceEEEEEechhhcCCCchhcceeeccCCC
Confidence            45799999999999999999999889999999999999999999999999999999999999999999999999999999


Q ss_pred             CCccchhhhhcccccCCCceeEEEEeccccHHHHHHHHHHhccccccCCcchhh
Q 017573          314 TQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPSNVAD  367 (369)
Q Consensus       314 ~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  367 (369)
                      .+..+|.+|+||.||.|+.|.++.++...|-.+...+.+.++...+++|++|..
T Consensus       544 ~nIeeYVHRvGrtGRaGr~G~sis~lt~~D~~~a~eLI~ILe~aeQevPdeL~~  597 (629)
T KOG0336|consen  544 RNIEEYVHRVGRTGRAGRTGTSISFLTRNDWSMAEELIQILERAEQEVPDELVR  597 (629)
T ss_pred             ccHHHHHHHhcccccCCCCcceEEEEehhhHHHHHHHHHHHHHhhhhCcHHHHH
Confidence            999999999999999999999999999999999999999999999999998854

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

Probab=100.00  E-value=6.5e-51  Score=381.96  Aligned_cols=352  Identities=19%  Similarity=0.244  Sum_probs=276.1

Q ss_pred             CCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHH
Q 017573            2 GLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIE   81 (369)
Q Consensus         2 ~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~   81 (369)
                      +|++.+.+.|++.||.+|+++|.++++.+.+|+++++.+|||||||+++++++++.+...+ +.++||++|+++|+.|+.
T Consensus        20 ~l~~~l~~~L~~~g~~~p~~~Q~~ai~~il~G~nvvv~apTGSGKTla~~LPiL~~l~~~~-~~~aL~l~PtraLa~q~~   98 (742)
T TIGR03817        20 WAHPDVVAALEAAGIHRPWQHQARAAELAHAGRHVVVATGTASGKSLAYQLPVLSALADDP-RATALYLAPTKALAADQL   98 (742)
T ss_pred             cCCHHHHHHHHHcCCCcCCHHHHHHHHHHHCCCCEEEECCCCCcHHHHHHHHHHHHHhhCC-CcEEEEEcChHHHHHHHH
Confidence            5889999999999999999999999999999999999999999999999999999886543 448999999999999999


Q ss_pred             HHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHc----CCCCCCCccEEEEechhHhhccCcHH
Q 017573           82 KVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRR----QSLRPDYIKMFVLDEADEMLSRGFKD  157 (369)
Q Consensus        82 ~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~----~~~~~~~~~~viiDE~H~~~~~~~~~  157 (369)
                      +.++++. ..++++...+|+...... ..+...++|+++||+++...+..    +...+++++++|+||+|.+.+ .+..
T Consensus        99 ~~l~~l~-~~~i~v~~~~Gdt~~~~r-~~i~~~~~IivtTPd~L~~~~L~~~~~~~~~l~~l~~vViDEah~~~g-~fg~  175 (742)
T TIGR03817        99 RAVRELT-LRGVRPATYDGDTPTEER-RWAREHARYVLTNPDMLHRGILPSHARWARFLRRLRYVVIDECHSYRG-VFGS  175 (742)
T ss_pred             HHHHHhc-cCCeEEEEEeCCCCHHHH-HHHhcCCCEEEEChHHHHHhhccchhHHHHHHhcCCEEEEeChhhccC-ccHH
Confidence            9999986 447788888887764443 44555689999999998743322    112356789999999999864 2343


Q ss_pred             HH-------HHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEcc-------------
Q 017573          158 QI-------YDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVE-------------  217 (369)
Q Consensus       158 ~~-------~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------------  217 (369)
                      .+       ..+....+...|++++|||.+.. .+....++..+..... .+..........+....             
T Consensus       176 ~~~~il~rL~ri~~~~g~~~q~i~~SATi~n~-~~~~~~l~g~~~~~i~-~~~~~~~~~~~~~~~p~~~~~~~~~~~~~r  253 (742)
T TIGR03817       176 HVALVLRRLRRLCARYGASPVFVLASATTADP-AAAASRLIGAPVVAVT-EDGSPRGARTVALWEPPLTELTGENGAPVR  253 (742)
T ss_pred             HHHHHHHHHHHHHHhcCCCCEEEEEecCCCCH-HHHHHHHcCCCeEEEC-CCCCCcCceEEEEecCCccccccccccccc
Confidence            33       33334456678999999999755 4567777777755432 22222111211111111             


Q ss_pred             --chhhhHHHHHHHHHhccCCCeEEEeCCHhhHHHHHHHHhhC--------CCeeEEecCCCCHHHHHHHHHHHhcCCCc
Q 017573          218 --KEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSR--------DHTVSATHGDMDQNTRDIIMREFRSGSSR  287 (369)
Q Consensus       218 --~~~~~~~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~--------~~~~~~~~~~~~~~~r~~~~~~f~~~~~~  287 (369)
                        ....+...+..++..  +.++||||++++.++.++..+++.        +.++..+||++++++|.++++.|++|+.+
T Consensus       254 ~~~~~~~~~~l~~l~~~--~~~~IVF~~sr~~ae~l~~~l~~~l~~~~~~l~~~v~~~hgg~~~~eR~~ie~~f~~G~i~  331 (742)
T TIGR03817       254 RSASAEAADLLADLVAE--GARTLTFVRSRRGAELVAAIARRLLGEVDPDLAERVAAYRAGYLPEDRRELERALRDGELL  331 (742)
T ss_pred             cchHHHHHHHHHHHHHC--CCCEEEEcCCHHHHHHHHHHHHHHHHhhccccccchhheecCCCHHHHHHHHHHHHcCCce
Confidence              011244455555543  579999999999999999988753        56788999999999999999999999999


Q ss_pred             EEEEecCCcCCCCCCCCcEEEEecCCCCccchhhhhcccccCCCceeEEEEec--cccHHHHHHHHHHhccccccC
Q 017573          288 VLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVT--RDDERMLFDIQKFYNVVIEEL  361 (369)
Q Consensus       288 vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~  361 (369)
                      +||+|++++.|+|+|++++||+++.|.+..+|.||+||+||.|+.|.++++..  +.|...+...+++++...++.
T Consensus       332 vLVaTd~lerGIDI~~vd~VI~~~~P~s~~~y~qRiGRaGR~G~~g~ai~v~~~~~~d~~~~~~~~~~~~~~~e~~  407 (742)
T TIGR03817       332 GVATTNALELGVDISGLDAVVIAGFPGTRASLWQQAGRAGRRGQGALVVLVARDDPLDTYLVHHPEALFDRPVEAT  407 (742)
T ss_pred             EEEECchHhccCCcccccEEEEeCCCCCHHHHHHhccccCCCCCCcEEEEEeCCChHHHHHHhCHHHHhcCCCccc
Confidence            99999999999999999999999999999999999999999999999999886  446666777777877766543

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.

>KOG0343 consensus RNA Helicase [RNA processing and modification]

Probab=100.00  E-value=1.1e-50  Score=344.80  Aligned_cols=358  Identities=31%  Similarity=0.472  Sum_probs=320.0

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccC----CCccEEEEcCCHHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGL----VQCQALVLAPTREL   76 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~----~~~~~liv~P~~~l   76 (369)
                      |+|+.-+.+.|...+|..|+.+|++.++..++|++++=.|-||||||++++.++++++....    .+--+|||+||++|
T Consensus        74 lpls~~t~kgLke~~fv~~teiQ~~~Ip~aL~G~DvlGAAkTGSGKTLAFlvPvlE~L~r~kWs~~DGlGalIISPTREL  153 (758)
T KOG0343|consen   74 LPLSQKTLKGLKEAKFVKMTEIQRDTIPMALQGHDVLGAAKTGSGKTLAFLVPVLEALYRLKWSPTDGLGALIISPTREL  153 (758)
T ss_pred             CCCchHHHHhHhhcCCccHHHHHHhhcchhccCcccccccccCCCceeeehHHHHHHHHHcCCCCCCCceeEEecchHHH
Confidence            68999999999999999999999999999999999999999999999999999999885421    23359999999999


Q ss_pred             HHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcC-CCCCCCccEEEEechhHhhccCc
Q 017573           77 AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQ-SLRPDYIKMFVLDEADEMLSRGF  155 (369)
Q Consensus        77 ~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~-~~~~~~~~~viiDE~H~~~~~~~  155 (369)
                      +.|.++.+.+.+...++....+.||.....+...+. +.+|+||||.+|++++... .+..+++.++|+|||+++.+.+|
T Consensus       154 A~QtFevL~kvgk~h~fSaGLiiGG~~~k~E~eRi~-~mNILVCTPGRLLQHmde~~~f~t~~lQmLvLDEADR~LDMGF  232 (758)
T KOG0343|consen  154 ALQTFEVLNKVGKHHDFSAGLIIGGKDVKFELERIS-QMNILVCTPGRLLQHMDENPNFSTSNLQMLVLDEADRMLDMGF  232 (758)
T ss_pred             HHHHHHHHHHHhhccccccceeecCchhHHHHHhhh-cCCeEEechHHHHHHhhhcCCCCCCcceEEEeccHHHHHHHhH
Confidence            999999999999999999999999998776665554 4699999999999988764 45677799999999999999999


Q ss_pred             HHHHHHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEec--CccccccceeEEEEEccchhhhHHHHHHHHHhc
Q 017573          156 KDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVK--RDELTLEGIKQFYVNVEKEEWKLETLCDLYETL  233 (369)
Q Consensus       156 ~~~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  233 (369)
                      ...+..+++.+|+..|.+++|||...+..++++..+.+|..+.+.  .....|..+.++|+.++- ..++..|-.++..+
T Consensus       233 k~tL~~Ii~~lP~~RQTLLFSATqt~svkdLaRLsL~dP~~vsvhe~a~~atP~~L~Q~y~~v~l-~~Ki~~L~sFI~sh  311 (758)
T KOG0343|consen  233 KKTLNAIIENLPKKRQTLLFSATQTKSVKDLARLSLKDPVYVSVHENAVAATPSNLQQSYVIVPL-EDKIDMLWSFIKSH  311 (758)
T ss_pred             HHHHHHHHHhCChhheeeeeecccchhHHHHHHhhcCCCcEEEEeccccccChhhhhheEEEEeh-hhHHHHHHHHHHhc
Confidence            999999999999999999999999999999999989998777665  445678888898888766 45999999999999


Q ss_pred             cCCCeEEEeCCHhhHHHHHHHHhhC--CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEec
Q 017573          234 AITQSVIFVNTRRKVDWLTDKMRSR--DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYD  311 (369)
Q Consensus       234 ~~~k~lv~~~~~~~~~~~~~~l~~~--~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~  311 (369)
                      ...|+|||+++.+++..+++.|.+.  |..+..+||.|++..|.++..+|.....-||+||+++++|+|+|.+++||.++
T Consensus       312 lk~K~iVF~SscKqvkf~~e~F~rlrpg~~l~~L~G~~~Q~~R~ev~~~F~~~~~~vLF~TDv~aRGLDFpaVdwViQ~D  391 (758)
T KOG0343|consen  312 LKKKSIVFLSSCKQVKFLYEAFCRLRPGIPLLALHGTMSQKKRIEVYKKFVRKRAVVLFCTDVAARGLDFPAVDWVIQVD  391 (758)
T ss_pred             cccceEEEEehhhHHHHHHHHHHhcCCCCceeeeccchhHHHHHHHHHHHHHhcceEEEeehhhhccCCCcccceEEEec
Confidence            9999999999999999999999877  77899999999999999999999998888999999999999999999999999


Q ss_pred             CCCCccchhhhhcccccCCCceeEEEEecccc-HHHHHHHHHHhccccccC
Q 017573          312 LPTQPENYLHRIGRSGRFGRKGVAINFVTRDD-ERMLFDIQKFYNVVIEEL  361 (369)
Q Consensus       312 ~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~  361 (369)
                      .|-+..+|++|+||..|.+..|.++++..+.+ +.++..++... +.+.++
T Consensus       392 CPedv~tYIHRvGRtAR~~~~G~sll~L~psEeE~~l~~Lq~k~-I~i~~i  441 (758)
T KOG0343|consen  392 CPEDVDTYIHRVGRTARYKERGESLLMLTPSEEEAMLKKLQKKK-IPIKEI  441 (758)
T ss_pred             CchhHHHHHHHhhhhhcccCCCceEEEEcchhHHHHHHHHHHcC-CCHHhh
Confidence            99999999999999999999999999999998 55555555443 444433

>KOG0346 consensus RNA helicase [RNA processing and modification]

Probab=100.00  E-value=1.2e-50  Score=335.51  Aligned_cols=356  Identities=31%  Similarity=0.452  Sum_probs=311.5

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhc------cCCCccEEEEcCCH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY------GLVQCQALVLAPTR   74 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~------~~~~~~~liv~P~~   74 (369)
                      |||++.+++++.+.|++.|+-+|+.+++.+++|++++..|.||||||.+|++++++.+..      +..++.++|++||+
T Consensus        24 ~gLD~RllkAi~~lG~ekpTlIQs~aIplaLEgKDvvarArTGSGKT~AYliPllqkll~~k~t~~~e~~~sa~iLvPTk  103 (569)
T KOG0346|consen   24 FGLDSRLLKAITKLGWEKPTLIQSSAIPLALEGKDVVARARTGSGKTAAYLIPLLQKLLAEKKTNDGEQGPSAVILVPTK  103 (569)
T ss_pred             hCCCHHHHHHHHHhCcCCcchhhhcccchhhcCcceeeeeccCCCchHHHHHHHHHHHHHhhhcccccccceeEEEechH
Confidence            699999999999999999999999999999999999999999999999999999988743      33445799999999


Q ss_pred             HHHHHHHHHHHHhccccC--cEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCC-CCCCCccEEEEechhHhh
Q 017573           75 ELAQQIEKVMRALGDYLG--VKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQS-LRPDYIKMFVLDEADEML  151 (369)
Q Consensus        75 ~l~~q~~~~~~~~~~~~~--~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~-~~~~~~~~viiDE~H~~~  151 (369)
                      +|+.|.+..+.++...++  +++.-+..+.+.......+...++|+|+||..+..++..+. .....+.++|+||++.+.
T Consensus       104 EL~qQvy~viekL~~~c~k~lr~~nl~s~~sdsv~~~~L~d~pdIvV~TP~~ll~~~~~~~~~~~~~l~~LVvDEADLll  183 (569)
T KOG0346|consen  104 ELAQQVYKVIEKLVEYCSKDLRAINLASSMSDSVNSVALMDLPDIVVATPAKLLRHLAAGVLEYLDSLSFLVVDEADLLL  183 (569)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhhhhhhhcccchHHHHHHHccCCCeEEeChHHHHHHHhhccchhhhheeeEEechhhhhh
Confidence            999999998888765554  33333333344445557778889999999999999998877 556678999999999999


Q ss_pred             ccCcHHHHHHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCcccc-ccceeEEEEEccchhhhHHHHHHHH
Q 017573          152 SRGFKDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELT-LEGIKQFYVNVEKEEWKLETLCDLY  230 (369)
Q Consensus       152 ~~~~~~~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~l~~~~  230 (369)
                      .-+|.+.+..+.+.+|+..|.++||||...+...+...++.+|+.......+.. +..+.++++.+. +.++.-.+..++
T Consensus       184 sfGYeedlk~l~~~LPr~~Q~~LmSATl~dDv~~LKkL~l~nPviLkl~e~el~~~dqL~Qy~v~cs-e~DKflllyall  262 (569)
T KOG0346|consen  184 SFGYEEDLKKLRSHLPRIYQCFLMSATLSDDVQALKKLFLHNPVILKLTEGELPNPDQLTQYQVKCS-EEDKFLLLYALL  262 (569)
T ss_pred             hcccHHHHHHHHHhCCchhhheeehhhhhhHHHHHHHHhccCCeEEEeccccCCCcccceEEEEEec-cchhHHHHHHHH
Confidence            999999999999999999999999999999999999999999999877665554 567888888887 566777777666


Q ss_pred             H-hccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEec----------------
Q 017573          231 E-TLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTD----------------  293 (369)
Q Consensus       231 ~-~~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~----------------  293 (369)
                      + +.-.+|.|||+|+++.+..+.-.|++.|++.++++|.++.+.|.-++++|+.|-++++|||+                
T Consensus       263 KL~LI~gKsliFVNtIdr~YrLkLfLeqFGiksciLNseLP~NSR~Hii~QFNkG~YdivIAtD~s~~~~~~eee~kgk~  342 (569)
T KOG0346|consen  263 KLRLIRGKSLIFVNTIDRCYRLKLFLEQFGIKSCILNSELPANSRCHIIEQFNKGLYDIVIATDDSADGDKLEEEVKGKS  342 (569)
T ss_pred             HHHHhcCceEEEEechhhhHHHHHHHHHhCcHhhhhcccccccchhhHHHHhhCcceeEEEEccCccchhhhhccccccc
Confidence            5 34558999999999999999999999999999999999999999999999999999999997                


Q ss_pred             -------------------CCcCCCCCCCCcEEEEecCCCCccchhhhhcccccCCCceeEEEEeccccHHHHHHHHHHh
Q 017573          294 -------------------LLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFY  354 (369)
Q Consensus       294 -------------------~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~~  354 (369)
                                         ...+|+|+..++.|+.++.|.+...|++|+||++|.+++|.++.|+.+.+......++...
T Consensus       343 ~e~~~kndkkskkK~D~E~GVsRGIDF~~V~~VlNFD~P~t~~sYIHRvGRTaRg~n~GtalSfv~P~e~~g~~~le~~~  422 (569)
T KOG0346|consen  343 DEKNPKNDKKSKKKLDKESGVSRGIDFHHVSNVLNFDFPETVTSYIHRVGRTARGNNKGTALSFVSPKEEFGKESLESIL  422 (569)
T ss_pred             cccCCCCccccccccCchhchhccccchheeeeeecCCCCchHHHHHhccccccCCCCCceEEEecchHHhhhhHHHHHH
Confidence                               2457999999999999999999999999999999999999999999999888777777766


Q ss_pred             ccc
Q 017573          355 NVV  357 (369)
Q Consensus       355 ~~~  357 (369)
                      ...
T Consensus       423 ~d~  425 (569)
T KOG0346|consen  423 KDE  425 (569)
T ss_pred             hhH
Confidence            654

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

Probab=100.00  E-value=3.3e-49  Score=332.55  Aligned_cols=368  Identities=32%  Similarity=0.487  Sum_probs=339.8

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhcc-----CCCccEEEEcCCHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYG-----LVQCQALVLAPTRE   75 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~-----~~~~~~liv~P~~~   75 (369)
                      +|++++|..+..+..|.+|+|+|.++++-.+.+++++=.|-||||||.+++.+++-++...     ..++-.+|+||+++
T Consensus       228 ~gfDkqLm~airk~Ey~kptpiq~qalptalsgrdvigIAktgSgktaAfi~pm~~himdq~eL~~g~gPi~vilvPTre  307 (731)
T KOG0339|consen  228 FGFDKQLMTAIRKSEYEKPTPIQCQALPTALSGRDVIGIAKTGSGKTAAFIWPMIVHIMDQPELKPGEGPIGVILVPTRE  307 (731)
T ss_pred             cCchHHHHHHHhhhhcccCCcccccccccccccccchheeeccCcchhHHHHHHHHHhcchhhhcCCCCCeEEEEeccHH
Confidence            4789999999999999999999999999999999999999999999998888777665321     34557999999999


Q ss_pred             HHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCc
Q 017573           76 LAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGF  155 (369)
Q Consensus        76 l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~  155 (369)
                      |+.|...++++|++..++++..++|+....++.+-+..++.|+|+||++|..++.-+..++.++.++|+||++++.+.+|
T Consensus       308 la~Qi~~eaKkf~K~ygl~~v~~ygGgsk~eQ~k~Lk~g~EivVaTPgRlid~VkmKatn~~rvS~LV~DEadrmfdmGf  387 (731)
T KOG0339|consen  308 LASQIFSEAKKFGKAYGLRVVAVYGGGSKWEQSKELKEGAEIVVATPGRLIDMVKMKATNLSRVSYLVLDEADRMFDMGF  387 (731)
T ss_pred             HHHHHHHHHHHhhhhccceEEEeecCCcHHHHHHhhhcCCeEEEechHHHHHHHHhhcccceeeeEEEEechhhhhcccc
Confidence            99999999999999999999999999998888888889999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHH-HHHHHhcc
Q 017573          156 KDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETL-CDLYETLA  234 (369)
Q Consensus       156 ~~~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l-~~~~~~~~  234 (369)
                      ..++..|...+.+..|.+.+|||....++.+.+.++..|+.+....-......+.+.+..+.+...+..-+ .++.....
T Consensus       388 e~qVrSI~~hirpdrQtllFsaTf~~kIe~lard~L~dpVrvVqg~vgean~dITQ~V~V~~s~~~Kl~wl~~~L~~f~S  467 (731)
T KOG0339|consen  388 EPQVRSIKQHIRPDRQTLLFSATFKKKIEKLARDILSDPVRVVQGEVGEANEDITQTVSVCPSEEKKLNWLLRHLVEFSS  467 (731)
T ss_pred             HHHHHHHHhhcCCcceEEEeeccchHHHHHHHHHHhcCCeeEEEeehhccccchhheeeeccCcHHHHHHHHHHhhhhcc
Confidence            99999999999999999999999999999999999999998887766666777888877777766666544 44555567


Q ss_pred             CCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCCC
Q 017573          235 ITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPT  314 (369)
Q Consensus       235 ~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~  314 (369)
                      .+++|+|+.-...+++++..|+-.++++..+||++++.+|.+.+.+|+.+...|+++|+...+|+|+|.+..|+.++...
T Consensus       468 ~gkvlifVTKk~~~e~i~a~Lklk~~~v~llhgdkdqa~rn~~ls~fKkk~~~VlvatDvaargldI~~ikTVvnyD~ar  547 (731)
T KOG0339|consen  468 EGKVLIFVTKKADAEEIAANLKLKGFNVSLLHGDKDQAERNEVLSKFKKKRKPVLVATDVAARGLDIPSIKTVVNYDFAR  547 (731)
T ss_pred             CCcEEEEEeccCCHHHHHHHhccccceeeeecCchhhHHHHHHHHHHhhcCCceEEEeeHhhcCCCccccceeecccccc
Confidence            78999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CccchhhhhcccccCCCceeEEEEeccccHHHHHHHHHHhccccccCCcchhhc
Q 017573          315 QPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPSNVADL  368 (369)
Q Consensus       315 ~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  368 (369)
                      +...+.||+||.||.|.+|.+++++++.|.+..-.+.+.+....+.+|.++.+|
T Consensus       548 dIdththrigrtgRag~kGvayTlvTeKDa~fAG~LVnnLe~agQnVP~~l~dl  601 (731)
T KOG0339|consen  548 DIDTHTHRIGRTGRAGEKGVAYTLVTEKDAEFAGHLVNNLEGAGQNVPDELMDL  601 (731)
T ss_pred             hhHHHHHHhhhcccccccceeeEEechhhHHHhhHHHHHHhhccccCChHHHHH
Confidence            999999999999999999999999999999999999999999999999988765

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

Probab=100.00  E-value=1.2e-49  Score=323.15  Aligned_cols=359  Identities=42%  Similarity=0.693  Sum_probs=324.8

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccC--CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKG--LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQ   78 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~--~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~   78 (369)
                      |+|.|++.+.+..++|..|+.+|..+++.++..  ++.|.++..|+|||.++.++++.++......+.++-++|+++|+.
T Consensus        95 L~LkPellkgly~M~F~kPskIQe~aLPlll~~Pp~nlIaQsqsGtGKTaaFvL~MLsrvd~~~~~PQ~iCLaPtrELA~  174 (477)
T KOG0332|consen   95 LRLKPELLKGLYAMKFQKPSKIQETALPLLLAEPPQNLIAQSQSGTGKTAAFVLTMLSRVDPDVVVPQCICLAPTRELAP  174 (477)
T ss_pred             hCCCHHHHhHHHHhccCCcchHHHhhcchhhcCCchhhhhhhcCCCchhHHHHHHHHHhcCccccCCCceeeCchHHHHH
Confidence            579999999999999999999999999999875  899999999999999999999999988877778898999999999


Q ss_pred             HHHHHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHc-CCCCCCCccEEEEechhHhhc-cCcH
Q 017573           79 QIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRR-QSLRPDYIKMFVLDEADEMLS-RGFK  156 (369)
Q Consensus        79 q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~-~~~~~~~~~~viiDE~H~~~~-~~~~  156 (369)
                      |..+.+.++++..+++..+...+.....-..   -..+|+++||..+..+... .-+..+.+.++++|||+.+.+ .++.
T Consensus       175 Q~~eVv~eMGKf~~ita~yair~sk~~rG~~---i~eqIviGTPGtv~Dlm~klk~id~~kikvfVlDEAD~Mi~tqG~~  251 (477)
T KOG0332|consen  175 QTGEVVEEMGKFTELTASYAIRGSKAKRGNK---LTEQIVIGTPGTVLDLMLKLKCIDLEKIKVFVLDEADVMIDTQGFQ  251 (477)
T ss_pred             HHHHHHHHhcCceeeeEEEEecCcccccCCc---chhheeeCCCccHHHHHHHHHhhChhhceEEEecchhhhhhccccc
Confidence            9999999999888888887776663222211   1358999999999998877 667778889999999999875 4578


Q ss_pred             HHHHHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHHHhccCC
Q 017573          157 DQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAIT  236 (369)
Q Consensus       157 ~~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  236 (369)
                      ..-..+...+|+..|++++|||.......+..+...++..+....+......+.+++..+.....+.+.+.++......+
T Consensus       252 D~S~rI~~~lP~~~QllLFSATf~e~V~~Fa~kivpn~n~i~Lk~eel~L~~IkQlyv~C~~~~~K~~~l~~lyg~~tig  331 (477)
T KOG0332|consen  252 DQSIRIMRSLPRNQQLLLFSATFVEKVAAFALKIVPNANVIILKREELALDNIKQLYVLCACRDDKYQALVNLYGLLTIG  331 (477)
T ss_pred             ccchhhhhhcCCcceEEeeechhHHHHHHHHHHhcCCCceeeeehhhccccchhhheeeccchhhHHHHHHHHHhhhhhh
Confidence            88889999999999999999999999999999999999999999999999999999999999999999999998888889


Q ss_pred             CeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCCC--
Q 017573          237 QSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPT--  314 (369)
Q Consensus       237 k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~--  314 (369)
                      ..+|||.++..|.+++..+...|..+..+||++..++|..+++.|+.|..+|||+|+.+.+|+|++.++.||.+++|-  
T Consensus       332 qsiIFc~tk~ta~~l~~~m~~~Gh~V~~l~G~l~~~~R~~ii~~Fr~g~~kVLitTnV~ARGiDv~qVs~VvNydlP~~~  411 (477)
T KOG0332|consen  332 QSIIFCHTKATAMWLYEEMRAEGHQVSLLHGDLTVEQRAAIIDRFREGKEKVLITTNVCARGIDVAQVSVVVNYDLPVKY  411 (477)
T ss_pred             heEEEEeehhhHHHHHHHHHhcCceeEEeeccchhHHHHHHHHHHhcCcceEEEEechhhcccccceEEEEEecCCcccc
Confidence            999999999999999999999999999999999999999999999999999999999999999999999999999874  


Q ss_pred             ----CccchhhhhcccccCCCceeEEEEeccc-cHHHHHHHHHHhccccccCC
Q 017573          315 ----QPENYLHRIGRSGRFGRKGVAINFVTRD-DERMLFDIQKFYNVVIEELP  362 (369)
Q Consensus       315 ----~~~~~~Q~~GR~~R~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~  362 (369)
                          +..+|.+|+||+||.|++|.++-+++.. ....++.++++++..+.++.
T Consensus       412 ~~~pD~etYlHRiGRtGRFGkkG~a~n~v~~~~s~~~mn~iq~~F~~~i~~~~  464 (477)
T KOG0332|consen  412 TGEPDYETYLHRIGRTGRFGKKGLAINLVDDKDSMNIMNKIQKHFNMKIKRLD  464 (477)
T ss_pred             CCCCCHHHHHHHhcccccccccceEEEeecccCcHHHHHHHHHHHhhcceecC
Confidence                5678999999999999999999888865 66677799999977766543

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=100.00  E-value=1.2e-48  Score=353.09  Aligned_cols=325  Identities=21%  Similarity=0.276  Sum_probs=252.3

Q ss_pred             HhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhcccc
Q 017573           12 YAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYL   91 (369)
Q Consensus        12 ~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~   91 (369)
                      +.|||..|||+|+++++.+++++++++.+|||+|||++++++++..      ++.++|++|+++|+.|+.+.+..+    
T Consensus         5 ~~~g~~~~r~~Q~~ai~~~l~g~dvlv~apTGsGKTl~y~lp~l~~------~~~~lVi~P~~~L~~dq~~~l~~~----   74 (470)
T TIGR00614         5 TVFGLSSFRPVQLEVINAVLLGRDCFVVMPTGGGKSLCYQLPALCS------DGITLVISPLISLMEDQVLQLKAS----   74 (470)
T ss_pred             hhcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHhHHHHHHHHHc------CCcEEEEecHHHHHHHHHHHHHHc----
Confidence            4589999999999999999999999999999999999999887742      227999999999999999988765    


Q ss_pred             CcEEEEEECCcchHHHHH----HHccCCcEEEeccHHHHHHH-HcCCC-CCCCccEEEEechhHhhccC--cHHHHH---
Q 017573           92 GVKVHACVGGTSVREDQR----ILQAGVHVVVGTPGRVFDML-RRQSL-RPDYIKMFVLDEADEMLSRG--FKDQIY---  160 (369)
Q Consensus        92 ~~~v~~~~~~~~~~~~~~----~~~~~~~iiv~t~~~l~~~~-~~~~~-~~~~~~~viiDE~H~~~~~~--~~~~~~---  160 (369)
                      ++.+..+.++........    ...+..+|+++||+.+.... ....+ ...+++++|+||||.+.+++  +...+.   
T Consensus        75 gi~~~~l~~~~~~~~~~~i~~~~~~~~~~il~~TPe~l~~~~~~~~~l~~~~~i~~iViDEaH~i~~~g~~fr~~~~~l~  154 (470)
T TIGR00614        75 GIPATFLNSSQSKEQQKNVLTDLKDGKIKLLYVTPEKCSASNRLLQTLEERKGITLIAVDEAHCISQWGHDFRPDYKALG  154 (470)
T ss_pred             CCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHcCchhHHHHHHhcCCcCEEEEeCCcccCccccccHHHHHHHH
Confidence            677777777766543322    23456899999999874321 00111 34568999999999998765  344333   


Q ss_pred             HHHhhCCccCcEEEEEeeCChhHHHHHHHhcC--CCEEEEecCccccccceeEEEEEccchhhhHHHHHHHHH-hccCCC
Q 017573          161 DIFQLLPAKVQVGVFSATMPPEALEITRKFMN--KPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYE-TLAITQ  237 (369)
Q Consensus       161 ~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~-~~~~~k  237 (369)
                      .+...+ +..+++++|||+++.........+.  .+..+..   ....+++.....  .........+..++. ...+++
T Consensus       155 ~l~~~~-~~~~~l~lTAT~~~~~~~di~~~l~l~~~~~~~~---s~~r~nl~~~v~--~~~~~~~~~l~~~l~~~~~~~~  228 (470)
T TIGR00614       155 SLKQKF-PNVPIMALTATASPSVREDILRQLNLKNPQIFCT---SFDRPNLYYEVR--RKTPKILEDLLRFIRKEFKGKS  228 (470)
T ss_pred             HHHHHc-CCCceEEEecCCCHHHHHHHHHHcCCCCCcEEeC---CCCCCCcEEEEE--eCCccHHHHHHHHHHHhcCCCc
Confidence            334444 4677999999999876655544432  3333222   112222222211  111134455556555 445567


Q ss_pred             eEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCCCCcc
Q 017573          238 SVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPE  317 (369)
Q Consensus       238 ~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~~~~  317 (369)
                      +||||+++++++.+++.|++.+..+..+||+++.++|.++++.|.+|+++|||||+++++|+|+|++++||++++|.+..
T Consensus       229 ~IIF~~s~~~~e~la~~L~~~g~~~~~~H~~l~~~eR~~i~~~F~~g~~~vLVaT~~~~~GID~p~V~~VI~~~~P~s~~  308 (470)
T TIGR00614       229 GIIYCPSRKKSEQVTASLQNLGIAAGAYHAGLEISARDDVHHKFQRDEIQVVVATVAFGMGINKPDVRFVIHYSLPKSME  308 (470)
T ss_pred             eEEEECcHHHHHHHHHHHHhcCCCeeEeeCCCCHHHHHHHHHHHHcCCCcEEEEechhhccCCcccceEEEEeCCCCCHH
Confidence            79999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             chhhhhcccccCCCceeEEEEeccccHHHHHHHHH
Q 017573          318 NYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQK  352 (369)
Q Consensus       318 ~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~  352 (369)
                      .|.|++||+||.|++|.+++++++.|...++.+..
T Consensus       309 ~y~Qr~GRaGR~G~~~~~~~~~~~~d~~~~~~~~~  343 (470)
T TIGR00614       309 SYYQESGRAGRDGLPSECHLFYAPADINRLRRLLM  343 (470)
T ss_pred             HHHhhhcCcCCCCCCceEEEEechhHHHHHHHHHh
Confidence            99999999999999999999999988877666544

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

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

Probab=100.00  E-value=1.3e-47  Score=358.34  Aligned_cols=336  Identities=21%  Similarity=0.262  Sum_probs=258.8

Q ss_pred             CCHHHHHHHH-hCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHH
Q 017573            3 LQENLLRGIY-AYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIE   81 (369)
Q Consensus         3 l~~~i~~~l~-~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~   81 (369)
                      ....+...++ .||+..+||.|+++++.++.|+++++.+|||+|||++++++++..      .+.+|||+|+++|+.++.
T Consensus       444 w~~~L~~~lk~~FG~~sFRp~Q~eaI~aiL~GrDVLVimPTGSGKSLcYQLPAL~~------~GiTLVISPLiSLmqDQV  517 (1195)
T PLN03137        444 WTKKLEVNNKKVFGNHSFRPNQREIINATMSGYDVFVLMPTGGGKSLTYQLPALIC------PGITLVISPLVSLIQDQI  517 (1195)
T ss_pred             chHHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHHHHHHHHHHHc------CCcEEEEeCHHHHHHHHH
Confidence            3445666664 489999999999999999999999999999999999999998753      127999999999998777


Q ss_pred             HHHHHhccccCcEEEEEECCcchHHHHHHHc------cCCcEEEeccHHHHH--HHHcCC---CCCCCccEEEEechhHh
Q 017573           82 KVMRALGDYLGVKVHACVGGTSVREDQRILQ------AGVHVVVGTPGRVFD--MLRRQS---LRPDYIKMFVLDEADEM  150 (369)
Q Consensus        82 ~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~------~~~~iiv~t~~~l~~--~~~~~~---~~~~~~~~viiDE~H~~  150 (369)
                      ..+...    ++....+.++.........+.      +.++|+++||+++..  .+.+..   .....+.++||||||.+
T Consensus       518 ~~L~~~----GI~Aa~L~s~~s~~eq~~ilr~l~s~~g~~~ILyvTPERL~~~d~ll~~L~~L~~~~~LslIVIDEAHcV  593 (1195)
T PLN03137        518 MNLLQA----NIPAASLSAGMEWAEQLEILQELSSEYSKYKLLYVTPEKVAKSDSLLRHLENLNSRGLLARFVIDEAHCV  593 (1195)
T ss_pred             HHHHhC----CCeEEEEECCCCHHHHHHHHHHHHhcCCCCCEEEEChHHhhcchHHHHHHHhhhhccccceeccCcchhh
Confidence            777653    788888888877655544332      468999999999852  111111   11234789999999999


Q ss_pred             hccC--cHHHHHH---HHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhHHH
Q 017573          151 LSRG--FKDQIYD---IFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLET  225 (369)
Q Consensus       151 ~~~~--~~~~~~~---~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  225 (369)
                      ..|+  |...+..   +...+ +..+++++|||+++.....+...+........ ......+++.  +............
T Consensus       594 SqWGhDFRpdYr~L~~Lr~~f-p~vPilALTATAT~~V~eDI~~~L~l~~~~vf-r~Sf~RpNL~--y~Vv~k~kk~le~  669 (1195)
T PLN03137        594 SQWGHDFRPDYQGLGILKQKF-PNIPVLALTATATASVKEDVVQALGLVNCVVF-RQSFNRPNLW--YSVVPKTKKCLED  669 (1195)
T ss_pred             hhcccchHHHHHHHHHHHHhC-CCCCeEEEEecCCHHHHHHHHHHcCCCCcEEe-ecccCccceE--EEEeccchhHHHH
Confidence            9876  5554443   33444 46778999999998777655555443211111 1122223332  2222222223455


Q ss_pred             HHHHHHh-ccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCC
Q 017573          226 LCDLYET-LAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQV  304 (369)
Q Consensus       226 l~~~~~~-~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~  304 (369)
                      +..++.. .....+||||.+++.++.++..|...+..+..+||+|+.++|..+++.|.+|+++|||||.++++|||+|++
T Consensus       670 L~~~I~~~~~~esgIIYC~SRke~E~LAe~L~~~Gika~~YHAGLs~eeR~~vqe~F~~Gei~VLVATdAFGMGIDkPDV  749 (1195)
T PLN03137        670 IDKFIKENHFDECGIIYCLSRMDCEKVAERLQEFGHKAAFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGMGINKPDV  749 (1195)
T ss_pred             HHHHHHhcccCCCceeEeCchhHHHHHHHHHHHCCCCeeeeeCCCCHHHHHHHHHHHhcCCCcEEEEechhhcCCCccCC
Confidence            6666543 345689999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cEEEEecCCCCccchhhhhcccccCCCceeEEEEeccccHHHHHHHHH
Q 017573          305 SLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQK  352 (369)
Q Consensus       305 ~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~  352 (369)
                      ++||+++.|.+...|.|++||+||.|+.|.|++|+...|...++.+.+
T Consensus       750 R~VIHydlPkSiEsYyQriGRAGRDG~~g~cILlys~~D~~~~~~lI~  797 (1195)
T PLN03137        750 RFVIHHSLPKSIEGYHQECGRAGRDGQRSSCVLYYSYSDYIRVKHMIS  797 (1195)
T ss_pred             cEEEEcCCCCCHHHHHhhhcccCCCCCCceEEEEecHHHHHHHHHHHh
Confidence            999999999999999999999999999999999999877766655543

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=100.00  E-value=3.9e-47  Score=351.83  Aligned_cols=332  Identities=20%  Similarity=0.264  Sum_probs=257.9

Q ss_pred             CCCHHHHHHHHh-CCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHH
Q 017573            2 GLQENLLRGIYA-YGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQI   80 (369)
Q Consensus         2 ~l~~~i~~~l~~-~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~   80 (369)
                      ++++.....|++ |||..|||+|+++++.+..++++++.+|||+|||++++++++..   .   +.++|++|+++|+.|+
T Consensus         8 ~~~~~~~~~l~~~fG~~~~r~~Q~~ai~~il~g~dvlv~apTGsGKTl~y~lpal~~---~---g~tlVisPl~sL~~dq   81 (607)
T PRK11057          8 NLESLAKQVLQETFGYQQFRPGQQEIIDAVLSGRDCLVVMPTGGGKSLCYQIPALVL---D---GLTLVVSPLISLMKDQ   81 (607)
T ss_pred             CchhHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCchHHHHHHHHHHHc---C---CCEEEEecHHHHHHHH
Confidence            455666667744 89999999999999999999999999999999999999888743   1   2799999999999999


Q ss_pred             HHHHHHhccccCcEEEEEECCcchHHHHH----HHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccC--
Q 017573           81 EKVMRALGDYLGVKVHACVGGTSVREDQR----ILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRG--  154 (369)
Q Consensus        81 ~~~~~~~~~~~~~~v~~~~~~~~~~~~~~----~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~--  154 (369)
                      .+.+...    ++....+.++........    ...+..+++++||+.+........+...+++++|+||||.+..++  
T Consensus        82 v~~l~~~----gi~~~~~~s~~~~~~~~~~~~~~~~g~~~il~~tPe~l~~~~~~~~l~~~~l~~iVIDEaH~i~~~G~~  157 (607)
T PRK11057         82 VDQLLAN----GVAAACLNSTQTREQQLEVMAGCRTGQIKLLYIAPERLMMDNFLEHLAHWNPALLAVDEAHCISQWGHD  157 (607)
T ss_pred             HHHHHHc----CCcEEEEcCCCCHHHHHHHHHHHhCCCCcEEEEChHHhcChHHHHHHhhCCCCEEEEeCccccccccCc
Confidence            9998875    566777776665444332    233567899999999863222222334468999999999998765  


Q ss_pred             cHH---HHHHHHhhCCccCcEEEEEeeCChhHHHHHHHhc--CCCEEEEecCccccccceeEEEEEccchhhhHHHHHHH
Q 017573          155 FKD---QIYDIFQLLPAKVQVGVFSATMPPEALEITRKFM--NKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDL  229 (369)
Q Consensus       155 ~~~---~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  229 (369)
                      +..   .+..+...+ +..+++++|||++......+...+  ..+.....   ....+++.....   ........+..+
T Consensus       158 fr~~y~~L~~l~~~~-p~~~~v~lTAT~~~~~~~di~~~l~l~~~~~~~~---~~~r~nl~~~v~---~~~~~~~~l~~~  230 (607)
T PRK11057        158 FRPEYAALGQLRQRF-PTLPFMALTATADDTTRQDIVRLLGLNDPLIQIS---SFDRPNIRYTLV---EKFKPLDQLMRY  230 (607)
T ss_pred             ccHHHHHHHHHHHhC-CCCcEEEEecCCChhHHHHHHHHhCCCCeEEEEC---CCCCCcceeeee---eccchHHHHHHH
Confidence            333   334444444 367799999999876655444433  23332221   111222221111   122244556666


Q ss_pred             HHhccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEE
Q 017573          230 YETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVIN  309 (369)
Q Consensus       230 ~~~~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~  309 (369)
                      +....++++||||+++++++.+++.|.+.+..+..+|++++.++|.++++.|.+|+.+|||||+++++|+|+|++++||+
T Consensus       231 l~~~~~~~~IIFc~tr~~~e~la~~L~~~g~~v~~~Ha~l~~~~R~~i~~~F~~g~~~VLVaT~a~~~GIDip~V~~VI~  310 (607)
T PRK11057        231 VQEQRGKSGIIYCNSRAKVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGINKPNVRFVVH  310 (607)
T ss_pred             HHhcCCCCEEEEECcHHHHHHHHHHHHhCCCCEEEecCCCCHHHHHHHHHHHHCCCCCEEEEechhhccCCCCCcCEEEE
Confidence            66677789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCCccchhhhhcccccCCCceeEEEEeccccHHHHHHH
Q 017573          310 YDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDI  350 (369)
Q Consensus       310 ~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~  350 (369)
                      ++.|.|...|.|++||+||.|.+|.+++++++.|...++.+
T Consensus       311 ~d~P~s~~~y~Qr~GRaGR~G~~~~~ill~~~~d~~~~~~~  351 (607)
T PRK11057        311 FDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLRRC  351 (607)
T ss_pred             eCCCCCHHHHHHHhhhccCCCCCceEEEEeCHHHHHHHHHH
Confidence            99999999999999999999999999999999887665544

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

Probab=100.00  E-value=2.8e-49  Score=322.88  Aligned_cols=366  Identities=33%  Similarity=0.564  Sum_probs=314.4

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhh--------ccCCCccEEEEcC
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLD--------YGLVQCQALVLAP   72 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~--------~~~~~~~~liv~P   72 (369)
                      |-+|.-+.+.|++.|+.+|+|+|.+.++-++.|++.+=.|-||||||+++.+++.-...        ....++-.||+||
T Consensus       175 MKFP~~~L~~lk~KGI~~PTpIQvQGlPvvLsGRDmIGIAfTGSGKTlvFvLP~imf~LeqE~~lPf~~~EGP~gLiicP  254 (610)
T KOG0341|consen  175 MKFPKPLLRGLKKKGIVHPTPIQVQGLPVVLSGRDMIGIAFTGSGKTLVFVLPVIMFALEQEMMLPFARGEGPYGLIICP  254 (610)
T ss_pred             ccCCHHHHHHHHhcCCCCCCceeecCcceEeecCceeeEEeecCCceEEEeHHHHHHHHHHHhcCccccCCCCeeEEEcC
Confidence            45788999999999999999999999999999999999999999999888766553321        1234557999999


Q ss_pred             CHHHHHHHHHHHHHhcccc------CcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEec
Q 017573           73 TRELAQQIEKVMRALGDYL------GVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDE  146 (369)
Q Consensus        73 ~~~l~~q~~~~~~~~~~~~------~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE  146 (369)
                      +++|+.|..+-+..+...+      .++...+.|+....++...+.++.+|+|+||.+|..++..+...+.-++++.+||
T Consensus       255 SRELArQt~~iie~~~~~L~e~g~P~lRs~LciGG~~v~eql~~v~~GvHivVATPGRL~DmL~KK~~sLd~CRyL~lDE  334 (610)
T KOG0341|consen  255 SRELARQTHDIIEQYVAALQEAGYPELRSLLCIGGVPVREQLDVVRRGVHIVVATPGRLMDMLAKKIMSLDACRYLTLDE  334 (610)
T ss_pred             cHHHHHHHHHHHHHHHHHHHhcCChhhhhhhhhcCccHHHHHHHHhcCeeEEEcCcchHHHHHHHhhccHHHHHHhhhhh
Confidence            9999999999888775444      4567788899999888888999999999999999999999999988899999999


Q ss_pred             hhHhhccCcHHHHHHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHH
Q 017573          147 ADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETL  226 (369)
Q Consensus       147 ~H~~~~~~~~~~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  226 (369)
                      ++++.+.+|...+..++..+....|.+++|||++..+..+....+.+|+.+.+.+.....-.+.+-...+ ..+.++-.+
T Consensus       335 ADRmiDmGFEddir~iF~~FK~QRQTLLFSATMP~KIQ~FAkSALVKPvtvNVGRAGAAsldViQevEyV-kqEaKiVyl  413 (610)
T KOG0341|consen  335 ADRMIDMGFEDDIRTIFSFFKGQRQTLLFSATMPKKIQNFAKSALVKPVTVNVGRAGAASLDVIQEVEYV-KQEAKIVYL  413 (610)
T ss_pred             HHHHhhccchhhHHHHHHHHhhhhheeeeeccccHHHHHHHHhhcccceEEecccccccchhHHHHHHHH-HhhhhhhhH
Confidence            9999999999999999999999999999999999999999999999999999876654432222111111 122334444


Q ss_pred             HHHHHhccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcE
Q 017573          227 CDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSL  306 (369)
Q Consensus       227 ~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~  306 (369)
                      .+.+++.+ .++|||+....++..++++|--.|+.+..+||+-++++|...++.|+.|+.+|||+|+.++.|+|+|++.|
T Consensus       414 LeCLQKT~-PpVLIFaEkK~DVD~IhEYLLlKGVEavaIHGGKDQedR~~ai~afr~gkKDVLVATDVASKGLDFp~iqH  492 (610)
T KOG0341|consen  414 LECLQKTS-PPVLIFAEKKADVDDIHEYLLLKGVEAVAIHGGKDQEDRHYAIEAFRAGKKDVLVATDVASKGLDFPDIQH  492 (610)
T ss_pred             HHHhccCC-CceEEEeccccChHHHHHHHHHccceeEEeecCcchhHHHHHHHHHhcCCCceEEEecchhccCCCccchh
Confidence            44444433 69999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEecCCCCccchhhhhcccccCCCceeEEEEeccc-cHHHHHHHHHHhccccccCCcchhhc
Q 017573          307 VINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRD-DERMLFDIQKFYNVVIEELPSNVADL  368 (369)
Q Consensus       307 vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~  368 (369)
                      ||.++.|.....|.+|+||.||.|+.|.+.+|.... +...+-.+-..+...-+++|+.|..|
T Consensus       493 VINyDMP~eIENYVHRIGRTGRsg~~GiATTfINK~~~esvLlDLK~LL~EakQ~vP~~L~~L  555 (610)
T KOG0341|consen  493 VINYDMPEEIENYVHRIGRTGRSGKTGIATTFINKNQEESVLLDLKHLLQEAKQEVPPVLAEL  555 (610)
T ss_pred             hccCCChHHHHHHHHHhcccCCCCCcceeeeeecccchHHHHHHHHHHHHHhhccCCHHHHHh
Confidence            999999999999999999999999999999999865 66677788888888888888777654

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

Probab=100.00  E-value=1.3e-47  Score=324.88  Aligned_cols=353  Identities=29%  Similarity=0.462  Sum_probs=289.0

Q ss_pred             CCCCHHHHHHHH-hCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhc------cCCCccEEEEcCC
Q 017573            1 MGLQENLLRGIY-AYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY------GLVQCQALVLAPT   73 (369)
Q Consensus         1 ~~l~~~i~~~l~-~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~------~~~~~~~liv~P~   73 (369)
                      +||++.+.+.|+ .+++..|+.+|+++++.+++|++++|.++||||||++|++++.+.+..      ...++-+||++||
T Consensus       141 LGL~~~lv~~L~~~m~i~~pTsVQkq~IP~lL~grD~lV~aQTGSGKTLAYllPiVq~Lq~m~~ki~Rs~G~~ALVivPT  220 (708)
T KOG0348|consen  141 LGLHPHLVSHLNTKMKISAPTSVQKQAIPVLLEGRDALVRAQTGSGKTLAYLLPIVQSLQAMEPKIQRSDGPYALVIVPT  220 (708)
T ss_pred             cCCCHHHHHHHHHHhccCccchHhhcchhhhhcCcceEEEcCCCCcccHHHHHHHHHHHHhcCccccccCCceEEEEech
Confidence            699999999995 489999999999999999999999999999999999999999988743      2234569999999


Q ss_pred             HHHHHHHHHHHHHhccccCcEE-EEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHc-CCCCCCCccEEEEechhHhh
Q 017573           74 RELAQQIEKVMRALGDYLGVKV-HACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRR-QSLRPDYIKMFVLDEADEML  151 (369)
Q Consensus        74 ~~l~~q~~~~~~~~~~~~~~~v-~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~-~~~~~~~~~~viiDE~H~~~  151 (369)
                      ++|+.|.++.++++...+.+-| ..+.||+....++.-+..+++|+|+||.++..++.+ ..+..+.+..+|+||++++.
T Consensus       221 REL~~Q~y~~~qKLl~~~hWIVPg~lmGGEkkKSEKARLRKGiNILIgTPGRLvDHLknT~~i~~s~LRwlVlDEaDrll  300 (708)
T KOG0348|consen  221 RELALQIYETVQKLLKPFHWIVPGVLMGGEKKKSEKARLRKGINILIGTPGRLVDHLKNTKSIKFSRLRWLVLDEADRLL  300 (708)
T ss_pred             HHHHHHHHHHHHHHhcCceEEeeceeecccccccHHHHHhcCceEEEcCchHHHHHHhccchheeeeeeEEEecchhHHH
Confidence            9999999999999887665444 346677766666666778899999999999998876 34556778999999999999


Q ss_pred             ccCcHHHHHHHHhhCC-------------ccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCc----------------
Q 017573          152 SRGFKDQIYDIFQLLP-------------AKVQVGVFSATMPPEALEITRKFMNKPVRILVKRD----------------  202 (369)
Q Consensus       152 ~~~~~~~~~~~~~~~~-------------~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~----------------  202 (369)
                      +.+|.+.+..+++.+.             ...|-+++|||+......+...-+.+|+.+..+..                
T Consensus       301 eLGfekdit~Il~~v~~~~~~e~~~~~lp~q~q~mLlSATLtd~V~rLa~~sLkDpv~I~ld~s~~~~~p~~~a~~ev~~  380 (708)
T KOG0348|consen  301 ELGFEKDITQILKAVHSIQNAECKDPKLPHQLQNMLLSATLTDGVNRLADLSLKDPVYISLDKSHSQLNPKDKAVQEVDD  380 (708)
T ss_pred             hccchhhHHHHHHHHhhccchhcccccccHHHHhHhhhhhhHHHHHHHhhccccCceeeeccchhhhcCcchhhhhhcCC
Confidence            9999999998887762             23677899999988888888888888877762110                


Q ss_pred             ---------cccccceeEEEEEccchhhh---HHHHHHHHHhccCCCeEEEeCCHhhHHHHHHHHhhC------------
Q 017573          203 ---------ELTLEGIKQFYVNVEKEEWK---LETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSR------------  258 (369)
Q Consensus       203 ---------~~~~~~~~~~~~~~~~~~~~---~~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~------------  258 (369)
                               ...++.+.+.|..+++...-   ...+....+.....|+|||+.+.+.++.-+..|...            
T Consensus       381 ~~~~~~l~~~~iPeqL~qry~vVPpKLRLV~Laa~L~~~~k~~~~qk~iVF~S~~d~VeFHy~lf~~~l~~~~e~~s~~~  460 (708)
T KOG0348|consen  381 GPAGDKLDSFAIPEQLLQRYTVVPPKLRLVALAALLLNKVKFEEKQKMIVFFSCSDSVEFHYSLFSEALLSHLEGSSGAP  460 (708)
T ss_pred             cccccccccccCcHHhhhceEecCCchhHHHHHHHHHHHhhhhhhceeEEEEechhHHHHHHHHHHhhhhcccccccCCc
Confidence                     11223344445555543221   122333344445669999999999998888777533            


Q ss_pred             ----------CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCCCCccchhhhhccccc
Q 017573          259 ----------DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGR  328 (369)
Q Consensus       259 ----------~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R  328 (369)
                                +.++..+||.|++++|..+++.|....-.||+||+++++|+|+|.+.+||.|++|.+..+|++|+||..|
T Consensus       461 ~s~g~~~l~~~~k~~rLHGsm~QeeRts~f~~Fs~~~~~VLLcTDVAaRGLDlP~V~~vVQYd~P~s~adylHRvGRTAR  540 (708)
T KOG0348|consen  461 DSEGLPPLFMDLKFYRLHGSMEQEERTSVFQEFSHSRRAVLLCTDVAARGLDLPHVGLVVQYDPPFSTADYLHRVGRTAR  540 (708)
T ss_pred             ccCCChhhhhcceEEEecCchhHHHHHHHHHhhccccceEEEehhhhhccCCCCCcCeEEEeCCCCCHHHHHHHhhhhhh
Confidence                      3468899999999999999999999888899999999999999999999999999999999999999999


Q ss_pred             CCCceeEEEEeccccHHHHHHHHHH
Q 017573          329 FGRKGVAINFVTRDDERMLFDIQKF  353 (369)
Q Consensus       329 ~~~~~~~~~~~~~~~~~~~~~~~~~  353 (369)
                      .|.+|.+++|..+.+.++++.+...
T Consensus       541 aG~kG~alLfL~P~Eaey~~~l~~~  565 (708)
T KOG0348|consen  541 AGEKGEALLFLLPSEAEYVNYLKKH  565 (708)
T ss_pred             ccCCCceEEEecccHHHHHHHHHhh
Confidence            9999999999999999977665443

>PRK02362 ski2-like helicase; Provisional

Probab=100.00  E-value=1.1e-46  Score=357.49  Aligned_cols=328  Identities=24%  Similarity=0.317  Sum_probs=250.6

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhc-cccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVP-FCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQ   79 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~-~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q   79 (369)
                      +|||+.+.+.+.+.|+.+|+|+|.++++. +.+++++++++|||+|||+++.++++..+..+   ++++|++|+++|+.|
T Consensus         6 l~lp~~~~~~l~~~g~~~l~p~Q~~ai~~~~~~g~nvlv~APTGSGKTlia~lail~~l~~~---~kal~i~P~raLa~q   82 (737)
T PRK02362          6 LPLPEGVIEFYEAEGIEELYPPQAEAVEAGLLDGKNLLAAIPTASGKTLIAELAMLKAIARG---GKALYIVPLRALASE   82 (737)
T ss_pred             cCCCHHHHHHHHhCCCCcCCHHHHHHHHHHHhCCCcEEEECCCcchHHHHHHHHHHHHHhcC---CcEEEEeChHHHHHH
Confidence            58999999999999999999999999998 67899999999999999999999999888643   389999999999999


Q ss_pred             HHHHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHH
Q 017573           80 IEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQI  159 (369)
Q Consensus        80 ~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~  159 (369)
                      ..+.|.++.. .++++..++|+......   ....++|+|+||+++..++++.......++++|+||+|.+.+..+...+
T Consensus        83 ~~~~~~~~~~-~g~~v~~~tGd~~~~~~---~l~~~~IiV~Tpek~~~llr~~~~~l~~v~lvViDE~H~l~d~~rg~~l  158 (737)
T PRK02362         83 KFEEFERFEE-LGVRVGISTGDYDSRDE---WLGDNDIIVATSEKVDSLLRNGAPWLDDITCVVVDEVHLIDSANRGPTL  158 (737)
T ss_pred             HHHHHHHhhc-CCCEEEEEeCCcCcccc---ccCCCCEEEECHHHHHHHHhcChhhhhhcCEEEEECccccCCCcchHHH
Confidence            9999998643 47889888887653322   1245799999999998888876555677999999999998876666666


Q ss_pred             HHHHhh---CCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeE--------------EEEEccchhhh
Q 017573          160 YDIFQL---LPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQ--------------FYVNVEKEEWK  222 (369)
Q Consensus       160 ~~~~~~---~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------------~~~~~~~~~~~  222 (369)
                      ..++..   ..+..|++++|||++ +..++..++-....  .   ....+..+..              ...........
T Consensus       159 e~il~rl~~~~~~~qii~lSATl~-n~~~la~wl~~~~~--~---~~~rpv~l~~~v~~~~~~~~~~~~~~~~~~~~~~~  232 (737)
T PRK02362        159 EVTLAKLRRLNPDLQVVALSATIG-NADELADWLDAELV--D---SEWRPIDLREGVFYGGAIHFDDSQREVEVPSKDDT  232 (737)
T ss_pred             HHHHHHHHhcCCCCcEEEEcccCC-CHHHHHHHhCCCcc--c---CCCCCCCCeeeEecCCeeccccccccCCCccchHH
Confidence            555443   356789999999986 33344433322110  0   0000000000              00000111122


Q ss_pred             HHHHHHHHHhccCCCeEEEeCCHhhHHHHHHHHhhCC------------------------------------CeeEEec
Q 017573          223 LETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRD------------------------------------HTVSATH  266 (369)
Q Consensus       223 ~~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~~------------------------------------~~~~~~~  266 (369)
                      ...+.+.+.  .++++||||++++.++.+++.|....                                    ..++.+|
T Consensus       233 ~~~~~~~~~--~~~~~LVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~L~~~l~~gva~hH  310 (737)
T PRK02362        233 LNLVLDTLE--EGGQCLVFVSSRRNAEGFAKRAASALKKTLTAAERAELAELAEEIREVSDTETSKDLADCVAKGAAFHH  310 (737)
T ss_pred             HHHHHHHHH--cCCCeEEEEeCHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHhccCccccHHHHHHHHhCEEeec
Confidence            233333322  45799999999999998888776431                                    3688999


Q ss_pred             CCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEE----ec-----CCCCccchhhhhcccccCCCc--eeE
Q 017573          267 GDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVIN----YD-----LPTQPENYLHRIGRSGRFGRK--GVA  335 (369)
Q Consensus       267 ~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~----~~-----~~~~~~~~~Q~~GR~~R~~~~--~~~  335 (369)
                      ++++.++|..+++.|++|.++||+||+.+++|+|+|..++||.    ++     .|.+..+|.||+||+||.|.+  |.+
T Consensus       311 agl~~~eR~~ve~~Fr~G~i~VLvaT~tla~GvnlPa~~VVI~~~~~yd~~~g~~~~s~~~y~Qm~GRAGR~g~d~~G~~  390 (737)
T PRK02362        311 AGLSREHRELVEDAFRDRLIKVISSTPTLAAGLNLPARRVIIRDYRRYDGGAGMQPIPVLEYHQMAGRAGRPGLDPYGEA  390 (737)
T ss_pred             CCCCHHHHHHHHHHHHcCCCeEEEechhhhhhcCCCceEEEEecceeecCCCCceeCCHHHHHHHhhcCCCCCCCCCceE
Confidence            9999999999999999999999999999999999999988885    43     477889999999999999865  899


Q ss_pred             EEEecccc
Q 017573          336 INFVTRDD  343 (369)
Q Consensus       336 ~~~~~~~~  343 (369)
                      +++..+.+
T Consensus       391 ii~~~~~~  398 (737)
T PRK02362        391 VLLAKSYD  398 (737)
T ss_pred             EEEecCch
Confidence            99887653

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=100.00  E-value=1.5e-46  Score=349.22  Aligned_cols=326  Identities=22%  Similarity=0.311  Sum_probs=257.7

Q ss_pred             HHH-HhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHh
Q 017573            9 RGI-YAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRAL   87 (369)
Q Consensus         9 ~~l-~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~   87 (369)
                      ..| +.|||.++||.|.++++.++.|+++++.+|||+|||++++++++..   .   ..++|++|+++|+.|+.+.++.+
T Consensus         3 ~~l~~~fg~~~fr~~Q~~~i~~il~g~dvlv~~PTG~GKTl~y~lpal~~---~---g~~lVisPl~sL~~dq~~~l~~~   76 (591)
T TIGR01389         3 QVLKRTFGYDDFRPGQEEIISHVLDGRDVLVVMPTGGGKSLCYQVPALLL---K---GLTVVISPLISLMKDQVDQLRAA   76 (591)
T ss_pred             HHHHHhcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHhHHHHHHHHHc---C---CcEEEEcCCHHHHHHHHHHHHHc
Confidence            345 3499999999999999999999999999999999999998887742   1   27899999999999999998875


Q ss_pred             ccccCcEEEEEECCcchHHHHH----HHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccC--cHHH---
Q 017573           88 GDYLGVKVHACVGGTSVREDQR----ILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRG--FKDQ---  158 (369)
Q Consensus        88 ~~~~~~~v~~~~~~~~~~~~~~----~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~--~~~~---  158 (369)
                          +..+..++++........    ...+..+++++||+.+.............++++|+||+|.+..++  +...   
T Consensus        77 ----gi~~~~~~s~~~~~~~~~~~~~l~~~~~~il~~tpe~l~~~~~~~~l~~~~l~~iViDEaH~i~~~g~~frp~y~~  152 (591)
T TIGR01389        77 ----GVAAAYLNSTLSAKEQQDIEKALVNGELKLLYVAPERLEQDYFLNMLQRIPIALVAVDEAHCVSQWGHDFRPEYQR  152 (591)
T ss_pred             ----CCcEEEEeCCCCHHHHHHHHHHHhCCCCCEEEEChhHhcChHHHHHHhcCCCCEEEEeCCcccccccCccHHHHHH
Confidence                677888887776554433    334678999999999865333333445668999999999998765  4433   


Q ss_pred             HHHHHhhCCccCcEEEEEeeCChhHHHHHHHhcC--CCEEEEecCccccccceeEEEEEccchhhhHHHHHHHHHhccCC
Q 017573          159 IYDIFQLLPAKVQVGVFSATMPPEALEITRKFMN--KPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAIT  236 (369)
Q Consensus       159 ~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  236 (369)
                      +..+...++.. +++++|||+++.....+...+.  .+..+..   ....+++..   .......+...+..++....+.
T Consensus       153 l~~l~~~~~~~-~vi~lTAT~~~~~~~~i~~~l~~~~~~~~~~---~~~r~nl~~---~v~~~~~~~~~l~~~l~~~~~~  225 (591)
T TIGR01389       153 LGSLAERFPQV-PRIALTATADAETRQDIRELLRLADANEFIT---SFDRPNLRF---SVVKKNNKQKFLLDYLKKHRGQ  225 (591)
T ss_pred             HHHHHHhCCCC-CEEEEEeCCCHHHHHHHHHHcCCCCCCeEec---CCCCCCcEE---EEEeCCCHHHHHHHHHHhcCCC
Confidence            33444555544 4999999998877666665554  2222211   112222222   1212233556677777766678


Q ss_pred             CeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCCCCc
Q 017573          237 QSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP  316 (369)
Q Consensus       237 k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~~~  316 (369)
                      ++||||++++.++.+++.|...+..+..+|++++.++|..+++.|.+|+++|||||+++++|+|+|++++||++++|.|.
T Consensus       226 ~~IIf~~sr~~~e~la~~L~~~g~~~~~~H~~l~~~~R~~i~~~F~~g~~~vlVaT~a~~~GID~p~v~~VI~~~~p~s~  305 (591)
T TIGR01389       226 SGIIYASSRKKVEELAERLESQGISALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMGIDKPNVRFVIHYDMPGNL  305 (591)
T ss_pred             CEEEEECcHHHHHHHHHHHHhCCCCEEEEECCCCHHHHHHHHHHHHcCCCcEEEEechhhccCcCCCCCEEEEcCCCCCH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cchhhhhcccccCCCceeEEEEeccccHHHHHHHH
Q 017573          317 ENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQ  351 (369)
Q Consensus       317 ~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~  351 (369)
                      ..|.|++||+||.|+.+.+++++++.|...++.+.
T Consensus       306 ~~y~Q~~GRaGR~G~~~~~il~~~~~d~~~~~~~i  340 (591)
T TIGR01389       306 ESYYQEAGRAGRDGLPAEAILLYSPADIALLKRRI  340 (591)
T ss_pred             HHHhhhhccccCCCCCceEEEecCHHHHHHHHHHH
Confidence            99999999999999999999999988776655443

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

>KOG0347 consensus RNA helicase [RNA processing and modification]

Probab=100.00  E-value=8.8e-48  Score=326.89  Aligned_cols=356  Identities=29%  Similarity=0.441  Sum_probs=290.2

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccC-CcEEEEcCCCChhhHHHHHHHHHhhhcc-------------CCCcc
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKG-LDVIQQAQSGTGKTATFCSGILQQLDYG-------------LVQCQ   66 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~-~~~li~~~tG~GKT~~~~~~~~~~~~~~-------------~~~~~   66 (369)
                      |+||..+.++|+.+||..|+++|...++++..| .+++=.|.||||||+++-+++++.+...             ...+-
T Consensus       186 l~lp~~iL~aL~~~gFs~Pt~IQsl~lp~ai~gk~DIlGaAeTGSGKTLAFGIPiv~~l~~~s~~s~e~~~~~~k~~k~~  265 (731)
T KOG0347|consen  186 LFLPMEILRALSNLGFSRPTEIQSLVLPAAIRGKVDILGAAETGSGKTLAFGIPIVERLLESSDDSQELSNTSAKYVKPI  265 (731)
T ss_pred             CCCCHHHHHHHHhcCCCCCccchhhcccHhhccchhcccccccCCCceeeecchhhhhhhhccchHhhhhhHHhccCcce
Confidence            579999999999999999999999999999998 8999999999999999999999854221             12223


Q ss_pred             EEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCC---CCCccEEE
Q 017573           67 ALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLR---PDYIKMFV  143 (369)
Q Consensus        67 ~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~---~~~~~~vi  143 (369)
                      .||++||++|+.|....+.......++.+..+.||.....+.+++...++|+|+||.+|..++......   ...+.++|
T Consensus       266 ~LV~tPTRELa~QV~~Hl~ai~~~t~i~v~si~GGLavqKQqRlL~~~p~IVVATPGRlweli~e~n~~l~~~k~vkcLV  345 (731)
T KOG0347|consen  266 ALVVTPTRELAHQVKQHLKAIAEKTQIRVASITGGLAVQKQQRLLNQRPDIVVATPGRLWELIEEDNTHLGNFKKVKCLV  345 (731)
T ss_pred             eEEecChHHHHHHHHHHHHHhccccCeEEEEeechhHHHHHHHHHhcCCCEEEecchHHHHHHHhhhhhhhhhhhceEEE
Confidence            999999999999999999999999999999999999999999999999999999999999999876653   34578999


Q ss_pred             EechhHhhccCcHHHHHHHHhhCC-----ccCcEEEEEeeCChhHHH---------------------HHH--HhcCCCE
Q 017573          144 LDEADEMLSRGFKDQIYDIFQLLP-----AKVQVGVFSATMPPEALE---------------------ITR--KFMNKPV  195 (369)
Q Consensus       144 iDE~H~~~~~~~~~~~~~~~~~~~-----~~~~~i~~saT~~~~~~~---------------------~~~--~~~~~~~  195 (369)
                      +||++++...++...+..++..+.     ...|.+.+|||+.-....                     ++.  .+..+|.
T Consensus       346 lDEaDRmvekghF~Els~lL~~L~e~~~~~qrQTlVFSATlt~~~~~~~~~~~k~~~k~~~~~~kiq~Lmk~ig~~~kpk  425 (731)
T KOG0347|consen  346 LDEADRMVEKGHFEELSKLLKHLNEEQKNRQRQTLVFSATLTLVLQQPLSSSRKKKDKEDELNAKIQHLMKKIGFRGKPK  425 (731)
T ss_pred             EccHHHHhhhccHHHHHHHHHHhhhhhcccccceEEEEEEeehhhcChhHHhhhccchhhhhhHHHHHHHHHhCccCCCe
Confidence            999999999999999999988875     357899999998522111                     111  1223343


Q ss_pred             EEEecCccccccceeEEEEEccchhhhHHHHHHHHHhccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHH
Q 017573          196 RILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRD  275 (369)
Q Consensus       196 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~  275 (369)
                      .+...+.......+....+.++..+ +--.+..++.++ ++++|||||+++.+..+.-+|...++....+|+.|.+.+|.
T Consensus       426 iiD~t~q~~ta~~l~Es~I~C~~~e-KD~ylyYfl~ry-PGrTlVF~NsId~vKRLt~~L~~L~i~p~~LHA~M~QKqRL  503 (731)
T KOG0347|consen  426 IIDLTPQSATASTLTESLIECPPLE-KDLYLYYFLTRY-PGRTLVFCNSIDCVKRLTVLLNNLDIPPLPLHASMIQKQRL  503 (731)
T ss_pred             eEecCcchhHHHHHHHHhhcCCccc-cceeEEEEEeec-CCceEEEechHHHHHHHHHHHhhcCCCCchhhHHHHHHHHH
Confidence            3333333222222111111111100 111111112222 37999999999999999999999999999999999999999


Q ss_pred             HHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCCCCccchhhhhcccccCCCceeEEEEeccccHHHHHHHHHHhc
Q 017573          276 IIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYN  355 (369)
Q Consensus       276 ~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~  355 (369)
                      +-+++|.+....|||||+++.+|+|||++.|||+|-.|.+...|++|.||+.|.++.|..+.++.+.+...+.+++.-++
T Consensus       504 knLEkF~~~~~~VLiaTDVAARGLDIp~V~HVIHYqVPrtseiYVHRSGRTARA~~~Gvsvml~~P~e~~~~~KL~ktL~  583 (731)
T KOG0347|consen  504 KNLEKFKQSPSGVLIATDVAARGLDIPGVQHVIHYQVPRTSEIYVHRSGRTARANSEGVSVMLCGPQEVGPLKKLCKTLK  583 (731)
T ss_pred             HhHHHHhcCCCeEEEeehhhhccCCCCCcceEEEeecCCccceeEecccccccccCCCeEEEEeChHHhHHHHHHHHHHh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999998888888776


Q ss_pred             ccc
Q 017573          356 VVI  358 (369)
Q Consensus       356 ~~~  358 (369)
                      ...
T Consensus       584 k~~  586 (731)
T KOG0347|consen  584 KKE  586 (731)
T ss_pred             hcc
Confidence            543

>KOG0334 consensus RNA helicase [RNA processing and modification]

Probab=100.00  E-value=6.9e-47  Score=345.07  Aligned_cols=365  Identities=35%  Similarity=0.561  Sum_probs=335.2

Q ss_pred             CCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhcc-----CCCccEEEEcCCHHH
Q 017573            2 GLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYG-----LVQCQALVLAPTREL   76 (369)
Q Consensus         2 ~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~-----~~~~~~liv~P~~~l   76 (369)
                      |++.-|..-++++||..|+|+|.+||+++..|+++|-+|-||||||++++++++.+....     ..+|-++|++|+++|
T Consensus       371 gl~~~il~tlkkl~y~k~~~IQ~qAiP~ImsGrdvIgvakTgSGKT~af~LPmirhi~dQr~~~~gdGPi~li~aPtrel  450 (997)
T KOG0334|consen  371 GLSSKILETLKKLGYEKPTPIQAQAIPAIMSGRDVIGVAKTGSGKTLAFLLPMIRHIKDQRPLEEGDGPIALILAPTREL  450 (997)
T ss_pred             CchHHHHHHHHHhcCCCCcchhhhhcchhccCcceEEeeccCCccchhhhcchhhhhhcCCChhhCCCceEEEEcCCHHH
Confidence            788889999999999999999999999999999999999999999999988888665322     236689999999999


Q ss_pred             HHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCc---cEEEEechhHhhcc
Q 017573           77 AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYI---KMFVLDEADEMLSR  153 (369)
Q Consensus        77 ~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~---~~viiDE~H~~~~~  153 (369)
                      +.|..+++++|+..+++.+...+|+.........+.+.+.|+|+||..+...+-.+.....++   .++++||++++.+.
T Consensus       451 a~QI~r~~~kf~k~l~ir~v~vygg~~~~~qiaelkRg~eIvV~tpGRmiD~l~~n~grvtnlrR~t~lv~deaDrmfdm  530 (997)
T KOG0334|consen  451 AMQIHREVRKFLKLLGIRVVCVYGGSGISQQIAELKRGAEIVVCTPGRMIDILCANSGRVTNLRRVTYLVLDEADRMFDM  530 (997)
T ss_pred             HHHHHHHHHHHHhhcCceEEEecCCccHHHHHHHHhcCCceEEeccchhhhhHhhcCCccccccccceeeechhhhhhee
Confidence            999999999999999999999999999999988889999999999999988876655555444   49999999999999


Q ss_pred             CcHHHHHHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHHHhc
Q 017573          154 GFKDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETL  233 (369)
Q Consensus       154 ~~~~~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  233 (369)
                      +|......+++.+++..|.+.+|||.+.....+....+.+|+.+.+.........+.+.+..+.....++..+.+++...
T Consensus       531 gfePq~~~Ii~nlrpdrQtvlfSatfpr~m~~la~~vl~~Pveiiv~~~svV~k~V~q~v~V~~~e~eKf~kL~eLl~e~  610 (997)
T KOG0334|consen  531 GFEPQITRILQNLRPDRQTVLFSATFPRSMEALARKVLKKPVEIIVGGRSVVCKEVTQVVRVCAIENEKFLKLLELLGER  610 (997)
T ss_pred             ccCcccchHHhhcchhhhhhhhhhhhhHHHHHHHHHhhcCCeeEEEccceeEeccceEEEEEecCchHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999888889999999988887777888888887654


Q ss_pred             -cCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecC
Q 017573          234 -AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDL  312 (369)
Q Consensus       234 -~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~  312 (369)
                       ...++||||.+.+.|..+.+.|.+.++.+..+||+.++.+|...++.|+++..++|++|+.+..|+|++.+..||+++.
T Consensus       611 ~e~~~tiiFv~~qe~~d~l~~~L~~ag~~~~slHGgv~q~dR~sti~dfK~~~~~LLvaTsvvarGLdv~~l~Lvvnyd~  690 (997)
T KOG0334|consen  611 YEDGKTIIFVDKQEKADALLRDLQKAGYNCDSLHGGVDQHDRSSTIEDFKNGVVNLLVATSVVARGLDVKELILVVNYDF  690 (997)
T ss_pred             hhcCCEEEEEcCchHHHHHHHHHHhcCcchhhhcCCCchHHHHhHHHHHhccCceEEEehhhhhcccccccceEEEEccc
Confidence             4679999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCccchhhhhcccccCCCceeEEEEeccccHHHHHHHHHHhccccccCCcchh
Q 017573          313 PTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPSNVA  366 (369)
Q Consensus       313 ~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  366 (369)
                      |....+|.+|.||+||.|++|.+++|..+.+.+....|.+++...-..+|.+|.
T Consensus       691 pnh~edyvhR~gRTgragrkg~AvtFi~p~q~~~a~dl~~al~~~~~~~P~~l~  744 (997)
T KOG0334|consen  691 PNHYEDYVHRVGRTGRAGRKGAAVTFITPDQLKYAGDLCKALELSKQPVPKLLQ  744 (997)
T ss_pred             chhHHHHHHHhcccccCCccceeEEEeChHHhhhHHHHHHHHHhccCCCchHHH
Confidence            999999999999999999999999999999999999999999777777776554

>KOG4284 consensus DEAD box protein [Transcription]

Probab=100.00  E-value=5.5e-47  Score=327.70  Aligned_cols=341  Identities=34%  Similarity=0.574  Sum_probs=314.6

Q ss_pred             CCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHH
Q 017573            3 LQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEK   82 (369)
Q Consensus         3 l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~   82 (369)
                      |...+...|...+|..|+++|..|++.+..+-+.||++-.|+|||+++...+++.+.........+||+|+++++-|..+
T Consensus        32 l~r~vl~glrrn~f~~ptkiQaaAIP~~~~kmDliVQaKSGTGKTlVfsv~av~sl~~~~~~~q~~Iv~PTREiaVQI~~  111 (980)
T KOG4284|consen   32 LWREVLLGLRRNAFALPTKIQAAAIPAIFSKMDLIVQAKSGTGKTLVFSVLAVESLDSRSSHIQKVIVTPTREIAVQIKE  111 (980)
T ss_pred             HHHHHHHHHHhhcccCCCchhhhhhhhhhcccceEEEecCCCCceEEEEeeeehhcCcccCcceeEEEecchhhhhHHHH
Confidence            34567788899999999999999999999999999999999999999988888888877777799999999999999999


Q ss_pred             HHHHhcccc-CcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhc-cCcHHHHH
Q 017573           83 VMRALGDYL-GVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLS-RGFKDQIY  160 (369)
Q Consensus        83 ~~~~~~~~~-~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~-~~~~~~~~  160 (369)
                      .+.+.+..+ |+++.+..||+....+...+ +.++|+|+||.++.+++....++.+.++++|+|||+.+.+ ..+...++
T Consensus       112 tv~~v~~sf~g~~csvfIGGT~~~~d~~rl-k~~rIvIGtPGRi~qL~el~~~n~s~vrlfVLDEADkL~~t~sfq~~In  190 (980)
T KOG4284|consen  112 TVRKVAPSFTGARCSVFIGGTAHKLDLIRL-KQTRIVIGTPGRIAQLVELGAMNMSHVRLFVLDEADKLMDTESFQDDIN  190 (980)
T ss_pred             HHHHhcccccCcceEEEecCchhhhhhhhh-hhceEEecCchHHHHHHHhcCCCccceeEEEeccHHhhhchhhHHHHHH
Confidence            999988744 89999999999866654443 3578999999999999999999999999999999999986 67889999


Q ss_pred             HHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccch-------hhhHHHHHHHHHhc
Q 017573          161 DIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKE-------EWKLETLCDLYETL  233 (369)
Q Consensus       161 ~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~l~~~~~~~  233 (369)
                      .+++.+|...|++.+|||.+.++.+.+..++.+|..+....+....-+++++++.....       ..+.+.|.++++..
T Consensus       191 ~ii~slP~~rQv~a~SATYp~nLdn~Lsk~mrdp~lVr~n~~d~~L~GikQyv~~~~s~nnsveemrlklq~L~~vf~~i  270 (980)
T KOG4284|consen  191 IIINSLPQIRQVAAFSATYPRNLDNLLSKFMRDPALVRFNADDVQLFGIKQYVVAKCSPNNSVEEMRLKLQKLTHVFKSI  270 (980)
T ss_pred             HHHHhcchhheeeEEeccCchhHHHHHHHHhcccceeecccCCceeechhheeeeccCCcchHHHHHHHHHHHHHHHhhC
Confidence            99999999999999999999999999999999999999999999999999998877653       34778888899998


Q ss_pred             cCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCC
Q 017573          234 AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLP  313 (369)
Q Consensus       234 ~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~  313 (369)
                      +-...||||+....|+-++.+|...|+.+.+++|.|++.+|..+++++++-..+|||+|+...+|+|-+.++.||..++|
T Consensus       271 py~QAlVF~~~~sra~~~a~~L~ssG~d~~~ISgaM~Q~~Rl~a~~~lr~f~~rILVsTDLtaRGIDa~~vNLVVNiD~p  350 (980)
T KOG4284|consen  271 PYVQALVFCDQISRAEPIATHLKSSGLDVTFISGAMSQKDRLLAVDQLRAFRVRILVSTDLTARGIDADNVNLVVNIDAP  350 (980)
T ss_pred             chHHHHhhhhhhhhhhHHHHHhhccCCCeEEeccccchhHHHHHHHHhhhceEEEEEecchhhccCCccccceEEecCCC
Confidence            88899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCccchhhhhcccccCCCceeEEEEeccccH
Q 017573          314 TQPENYLHRIGRSGRFGRKGVAINFVTRDDE  344 (369)
Q Consensus       314 ~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~  344 (369)
                      .+..+|.+||||+||.|..|.+++|+....+
T Consensus       351 ~d~eTY~HRIGRAgRFG~~G~aVT~~~~~~e  381 (980)
T KOG4284|consen  351 ADEETYFHRIGRAGRFGAHGAAVTLLEDERE  381 (980)
T ss_pred             cchHHHHHHhhhcccccccceeEEEeccchh
Confidence            9999999999999999999999999987655

>PRK00254 ski2-like helicase; Provisional

Probab=100.00  E-value=5.3e-45  Score=345.12  Aligned_cols=332  Identities=20%  Similarity=0.273  Sum_probs=252.7

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhc-cccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVP-FCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQ   79 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~-~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q   79 (369)
                      +++++.+.+.+++.|+..|+|+|.++++. +..++++++++|||+|||+++.+++++.+...  +.+++|++|+++|+.|
T Consensus         6 l~l~~~~~~~l~~~g~~~l~~~Q~~ai~~~~~~g~nvlv~apTGsGKT~~~~l~il~~l~~~--~~~~l~l~P~~aLa~q   83 (720)
T PRK00254          6 LRVDERIKRVLKERGIEELYPPQAEALKSGVLEGKNLVLAIPTASGKTLVAEIVMVNKLLRE--GGKAVYLVPLKALAEE   83 (720)
T ss_pred             cCCCHHHHHHHHhCCCCCCCHHHHHHHHHHHhCCCcEEEECCCCcHHHHHHHHHHHHHHHhc--CCeEEEEeChHHHHHH
Confidence            57999999999999999999999999986 78899999999999999999999998876542  2389999999999999


Q ss_pred             HHHHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHH
Q 017573           80 IEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQI  159 (369)
Q Consensus        80 ~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~  159 (369)
                      +.+.+.++. ..+.++..++|+......  . ...++|+|+||+++..++.+.....++++++|+||+|.+.+......+
T Consensus        84 ~~~~~~~~~-~~g~~v~~~~Gd~~~~~~--~-~~~~~IiV~Tpe~~~~ll~~~~~~l~~l~lvViDE~H~l~~~~rg~~l  159 (720)
T PRK00254         84 KYREFKDWE-KLGLRVAMTTGDYDSTDE--W-LGKYDIIIATAEKFDSLLRHGSSWIKDVKLVVADEIHLIGSYDRGATL  159 (720)
T ss_pred             HHHHHHHHh-hcCCEEEEEeCCCCCchh--h-hccCCEEEEcHHHHHHHHhCCchhhhcCCEEEEcCcCccCCccchHHH
Confidence            999998864 458899999888764322  2 246799999999998888766556778999999999999877778888


Q ss_pred             HHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccc-cc-eeEEEEEccc------hhhhHHHHHHHHH
Q 017573          160 YDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTL-EG-IKQFYVNVEK------EEWKLETLCDLYE  231 (369)
Q Consensus       160 ~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~-~~~~~~~~~~------~~~~~~~l~~~~~  231 (369)
                      ..++..++...|++++|||++ +..++.. |+....... ....... .. ..+.+.....      .......+.+.+.
T Consensus       160 e~il~~l~~~~qiI~lSATl~-n~~~la~-wl~~~~~~~-~~rpv~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~  236 (720)
T PRK00254        160 EMILTHMLGRAQILGLSATVG-NAEELAE-WLNAELVVS-DWRPVKLRKGVFYQGFLFWEDGKIERFPNSWESLVYDAVK  236 (720)
T ss_pred             HHHHHhcCcCCcEEEEEccCC-CHHHHHH-HhCCccccC-CCCCCcceeeEecCCeeeccCcchhcchHHHHHHHHHHHH
Confidence            888988888999999999996 3444444 443322111 1111000 00 0000111111      0112223333333


Q ss_pred             hccCCCeEEEeCCHhhHHHHHHHHhhC---------------------------------CCeeEEecCCCCHHHHHHHH
Q 017573          232 TLAITQSVIFVNTRRKVDWLTDKMRSR---------------------------------DHTVSATHGDMDQNTRDIIM  278 (369)
Q Consensus       232 ~~~~~k~lv~~~~~~~~~~~~~~l~~~---------------------------------~~~~~~~~~~~~~~~r~~~~  278 (369)
                        .++++||||++++.++.++..|...                                 ...+..+|+++++++|..++
T Consensus       237 --~~~~vLVF~~sr~~~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~gv~~hHagl~~~eR~~ve  314 (720)
T PRK00254        237 --KGKGALVFVNTRRSAEKEALELAKKIKRFLTKPELRALKELADSLEENPTNEKLKKALRGGVAFHHAGLGRTERVLIE  314 (720)
T ss_pred             --hCCCEEEEEcChHHHHHHHHHHHHHHHHhcCchhHHHHHHHHHHHhcCCCcHHHHHHHhhCEEEeCCCCCHHHHHHHH
Confidence              3579999999999988776655321                                 23589999999999999999


Q ss_pred             HHHhcCCCcEEEEecCCcCCCCCCCCcEEEE-------ecC-CCCccchhhhhcccccCC--CceeEEEEecccc
Q 017573          279 REFRSGSSRVLITTDLLARGIDVQQVSLVIN-------YDL-PTQPENYLHRIGRSGRFG--RKGVAINFVTRDD  343 (369)
Q Consensus       279 ~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~-------~~~-~~~~~~~~Q~~GR~~R~~--~~~~~~~~~~~~~  343 (369)
                      +.|++|.++|||||+.++.|+|+|..++||.       ++. +.+..+|.||+||+||.|  ..|.++++....+
T Consensus       315 ~~F~~G~i~VLvaT~tLa~Gvnipa~~vVI~~~~~~~~~~~~~~~~~~~~Qm~GRAGR~~~d~~G~~ii~~~~~~  389 (720)
T PRK00254        315 DAFREGLIKVITATPTLSAGINLPAFRVIIRDTKRYSNFGWEDIPVLEIQQMMGRAGRPKYDEVGEAIIVATTEE  389 (720)
T ss_pred             HHHHCCCCeEEEeCcHHhhhcCCCceEEEECCceEcCCCCceeCCHHHHHHhhhccCCCCcCCCceEEEEecCcc
Confidence            9999999999999999999999999988884       222 224568999999999975  5699999988755

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

Probab=100.00  E-value=9.1e-46  Score=305.08  Aligned_cols=358  Identities=32%  Similarity=0.532  Sum_probs=327.9

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccC-CCccEEEEcCCHHHHHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGL-VQCQALVLAPTRELAQQ   79 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~-~~~~~liv~P~~~l~~q   79 (369)
                      |||+.-+.+++.+.||.+|+|+|++.++.+++++++.-.+-||+|||.++++++++++.... .+.+++++.|+++|+.|
T Consensus        26 mgL~~~v~raI~kkg~~~ptpiqRKTipliLe~~dvv~martgsgktaaf~ipm~e~Lk~~s~~g~RalilsptreLa~q  105 (529)
T KOG0337|consen   26 MGLDYKVLRAIHKKGFNTPTPIQRKTIPLILEGRDVVGMARTGSGKTAAFLIPMIEKLKSHSQTGLRALILSPTRELALQ  105 (529)
T ss_pred             cCCCHHHHHHHHHhhcCCCCchhcccccceeeccccceeeecCCcchhhHHHHHHHHHhhccccccceeeccCcHHHHHH
Confidence            79999999999999999999999999999999999999999999999999999999987544 44589999999999999


Q ss_pred             HHHHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHH
Q 017573           80 IEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQI  159 (369)
Q Consensus        80 ~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~  159 (369)
                      ..+...++...++++...+.|+....++...+..+.|||++||..+.++.-...+.++.+.+||+||++.+...+|.+++
T Consensus       106 tlkvvkdlgrgt~lr~s~~~ggD~~eeqf~~l~~npDii~ATpgr~~h~~vem~l~l~sveyVVfdEadrlfemgfqeql  185 (529)
T KOG0337|consen  106 TLKVVKDLGRGTKLRQSLLVGGDSIEEQFILLNENPDIIIATPGRLLHLGVEMTLTLSSVEYVVFDEADRLFEMGFQEQL  185 (529)
T ss_pred             HHHHHHHhccccchhhhhhcccchHHHHHHHhccCCCEEEecCceeeeeehheeccccceeeeeehhhhHHHhhhhHHHH
Confidence            99999999999999999999999988888888878899999999999888877788899999999999999999999999


Q ss_pred             HHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHHHh-ccCCCe
Q 017573          160 YDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYET-LAITQS  238 (369)
Q Consensus       160 ~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~~~~k~  238 (369)
                      ..++..++...|.++||||.+..+.+..+..+..|..+..+.+....+.....+..+...+ +...|..++.. ..++.+
T Consensus       186 ~e~l~rl~~~~QTllfSatlp~~lv~fakaGl~~p~lVRldvetkise~lk~~f~~~~~a~-K~aaLl~il~~~~~~~~t  264 (529)
T KOG0337|consen  186 HEILSRLPESRQTLLFSATLPRDLVDFAKAGLVPPVLVRLDVETKISELLKVRFFRVRKAE-KEAALLSILGGRIKDKQT  264 (529)
T ss_pred             HHHHHhCCCcceEEEEeccCchhhHHHHHccCCCCceEEeehhhhcchhhhhheeeeccHH-HHHHHHHHHhccccccce
Confidence            9999999999999999999999999999999999999887777777777777777666644 55555555544 345689


Q ss_pred             EEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCCCCccc
Q 017573          239 VIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPEN  318 (369)
Q Consensus       239 lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~  318 (369)
                      ++|+.+.++++.+...|...+..+..+++.+++..|..-+..|..+...+++.|+.+.+|+|+|..+.||.++.|.....
T Consensus       265 ~vf~~tk~hve~~~~ll~~~g~~~s~iysslD~~aRk~~~~~F~~~k~~~lvvTdvaaRG~diplldnvinyd~p~~~kl  344 (529)
T KOG0337|consen  265 IVFVATKHHVEYVRGLLRDFGGEGSDIYSSLDQEARKINGRDFRGRKTSILVVTDVAARGLDIPLLDNVINYDFPPDDKL  344 (529)
T ss_pred             eEEecccchHHHHHHHHHhcCCCccccccccChHhhhhccccccCCccceEEEehhhhccCCCccccccccccCCCCCce
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhhcccccCCCceeEEEEeccccHHHHHHHHHHhccccc
Q 017573          319 YLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIE  359 (369)
Q Consensus       319 ~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  359 (369)
                      |.+|+||+.|.|+.|.+|.++.+.+..++-++.-++...+.
T Consensus       345 FvhRVgr~aragrtg~aYs~V~~~~~~yl~DL~lflgr~~~  385 (529)
T KOG0337|consen  345 FVHRVGRVARAGRTGRAYSLVASTDDPYLLDLQLFLGRPLI  385 (529)
T ss_pred             EEEEecchhhccccceEEEEEecccchhhhhhhhhcCCcee
Confidence            99999999999999999999999999999999998887653

>PRK13767 ATP-dependent helicase; Provisional

Probab=100.00  E-value=1.5e-44  Score=345.66  Aligned_cols=333  Identities=22%  Similarity=0.316  Sum_probs=245.1

Q ss_pred             CCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhcc------CCCccEEEEcCCHHH
Q 017573            3 LQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYG------LVQCQALVLAPTREL   76 (369)
Q Consensus         3 l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~------~~~~~~liv~P~~~l   76 (369)
                      |++.+.+.+.+ +|..|+|+|.++++.+.+|++++++||||||||+++++++++.+...      ..+.+++|++|+++|
T Consensus        18 l~~~v~~~~~~-~~~~~tpiQ~~Ai~~il~g~nvli~APTGSGKTlaa~Lpil~~l~~~~~~~~~~~~~~~LyIsPtraL   96 (876)
T PRK13767         18 LRPYVREWFKE-KFGTFTPPQRYAIPLIHEGKNVLISSPTGSGKTLAAFLAIIDELFRLGREGELEDKVYCLYVSPLRAL   96 (876)
T ss_pred             cCHHHHHHHHH-ccCCCCHHHHHHHHHHHcCCCEEEECCCCCcHHHHHHHHHHHHHHhhccccCCCCCeEEEEEcCHHHH
Confidence            67777777766 68899999999999999999999999999999999999999877532      223479999999999


Q ss_pred             HHHHHHHHHH-------hc----ccc-CcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCC--CCCCccEE
Q 017573           77 AQQIEKVMRA-------LG----DYL-GVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSL--RPDYIKMF  142 (369)
Q Consensus        77 ~~q~~~~~~~-------~~----~~~-~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~--~~~~~~~v  142 (369)
                      +.|+.+.+.+       +.    ... ++++...+|+.........+.+.++|+|+||++|..++....+  .+.++++|
T Consensus        97 a~di~~~L~~~l~~i~~~~~~~g~~~~~i~v~v~~Gdt~~~~r~~~l~~~p~IlVtTPE~L~~ll~~~~~~~~l~~l~~V  176 (876)
T PRK13767         97 NNDIHRNLEEPLTEIREIAKERGEELPEIRVAIRTGDTSSYEKQKMLKKPPHILITTPESLAILLNSPKFREKLRTVKWV  176 (876)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCcCCeeEEEEcCCCCHHHHHHHHhCCCCEEEecHHHHHHHhcChhHHHHHhcCCEE
Confidence            9999886653       21    222 6788889999887777777777889999999999877755433  35678999


Q ss_pred             EEechhHhhccCcHHH----HHHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCC-------CEEEEecCccccccceeE
Q 017573          143 VLDEADEMLSRGFKDQ----IYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNK-------PVRILVKRDELTLEGIKQ  211 (369)
Q Consensus       143 iiDE~H~~~~~~~~~~----~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~  211 (369)
                      |+||+|.+.+......    +.++....+...|++++|||+++ .......+...       +..+. .........+..
T Consensus       177 VIDE~H~l~~~~RG~~l~~~L~rL~~l~~~~~q~IglSATl~~-~~~va~~L~~~~~~~~~r~~~iv-~~~~~k~~~i~v  254 (876)
T PRK13767        177 IVDEIHSLAENKRGVHLSLSLERLEELAGGEFVRIGLSATIEP-LEEVAKFLVGYEDDGEPRDCEIV-DARFVKPFDIKV  254 (876)
T ss_pred             EEechhhhccCccHHHHHHHHHHHHHhcCCCCeEEEEecccCC-HHHHHHHhcCccccCCCCceEEE-ccCCCccceEEE
Confidence            9999999986544333    33444444467899999999864 23333333221       11111 111111100100


Q ss_pred             EE-----EEccch---hhhHHHHHHHHHhccCCCeEEEeCCHhhHHHHHHHHhhC------CCeeEEecCCCCHHHHHHH
Q 017573          212 FY-----VNVEKE---EWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSR------DHTVSATHGDMDQNTRDII  277 (369)
Q Consensus       212 ~~-----~~~~~~---~~~~~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~------~~~~~~~~~~~~~~~r~~~  277 (369)
                      ..     ......   ......+.+++.  ..+++||||++++.++.++..|.+.      +..+..+||+++.++|..+
T Consensus       255 ~~p~~~l~~~~~~~~~~~l~~~L~~~i~--~~~~~LVF~nTr~~ae~la~~L~~~~~~~~~~~~i~~hHg~ls~~~R~~v  332 (876)
T PRK13767        255 ISPVDDLIHTPAEEISEALYETLHELIK--EHRTTLIFTNTRSGAERVLYNLRKRFPEEYDEDNIGAHHSSLSREVRLEV  332 (876)
T ss_pred             eccCccccccccchhHHHHHHHHHHHHh--cCCCEEEEeCCHHHHHHHHHHHHHhchhhccccceeeeeCCCCHHHHHHH
Confidence            00     000111   111223333332  3468999999999999999999873      4579999999999999999


Q ss_pred             HHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCCCCccchhhhhcccccC-CCceeEEEEec
Q 017573          278 MREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRF-GRKGVAINFVT  340 (369)
Q Consensus       278 ~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~-~~~~~~~~~~~  340 (369)
                      ++.|++|..++||||+.++.|+|+|++++||.++.|.+...|.||+||+||. |..+..+++..
T Consensus       333 e~~fk~G~i~vLVaTs~Le~GIDip~Vd~VI~~~~P~sv~~ylQRiGRaGR~~g~~~~g~ii~~  396 (876)
T PRK13767        333 EEKLKRGELKVVVSSTSLELGIDIGYIDLVVLLGSPKSVSRLLQRIGRAGHRLGEVSKGRIIVV  396 (876)
T ss_pred             HHHHHcCCCeEEEECChHHhcCCCCCCcEEEEeCCCCCHHHHHHhcccCCCCCCCCCcEEEEEc
Confidence            9999999999999999999999999999999999999999999999999987 44444444444

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

Probab=100.00  E-value=5.1e-44  Score=302.78  Aligned_cols=326  Identities=22%  Similarity=0.249  Sum_probs=253.7

Q ss_pred             CCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcE
Q 017573           15 GFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVK   94 (369)
Q Consensus        15 ~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~   94 (369)
                      +..++|.||.......+.+ |++|+.|||-|||+++++.+...+...+.  ++|+++||+.|+.|+++.+.+........
T Consensus        12 ~~ie~R~YQ~~i~a~al~~-NtLvvlPTGLGKT~IA~~V~~~~l~~~~~--kvlfLAPTKPLV~Qh~~~~~~v~~ip~~~   88 (542)
T COG1111          12 NTIEPRLYQLNIAAKALFK-NTLVVLPTGLGKTFIAAMVIANRLRWFGG--KVLFLAPTKPLVLQHAEFCRKVTGIPEDE   88 (542)
T ss_pred             ccccHHHHHHHHHHHHhhc-CeEEEecCCccHHHHHHHHHHHHHHhcCC--eEEEecCCchHHHHHHHHHHHHhCCChhh
Confidence            3458999999998777766 99999999999999999999988876543  89999999999999999999998776778


Q ss_pred             EEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEE
Q 017573           95 VHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGV  174 (369)
Q Consensus        95 v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~  174 (369)
                      +..++|...+++..... ....|+|+||+...+.+..+.++...+.++|+||||+..+...+..+.+.+....+++.+++
T Consensus        89 i~~ltGev~p~~R~~~w-~~~kVfvaTPQvveNDl~~Grid~~dv~~lifDEAHRAvGnyAYv~Va~~y~~~~k~~~ilg  167 (542)
T COG1111          89 IAALTGEVRPEEREELW-AKKKVFVATPQVVENDLKAGRIDLDDVSLLIFDEAHRAVGNYAYVFVAKEYLRSAKNPLILG  167 (542)
T ss_pred             eeeecCCCChHHHHHHH-hhCCEEEeccHHHHhHHhcCccChHHceEEEechhhhccCcchHHHHHHHHHHhccCceEEE
Confidence            88999988876555443 44689999999999999999999999999999999998766655666665666667888999


Q ss_pred             EEeeCChhHHHH---HHHhcCCCEEEEecCcccccc---ceeEEEEEccchh----------------------------
Q 017573          175 FSATMPPEALEI---TRKFMNKPVRILVKRDELTLE---GIKQFYVNVEKEE----------------------------  220 (369)
Q Consensus       175 ~saT~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~----------------------------  220 (369)
                      +||||..+.+..   +..+.-..+.+....+....+   .++.-+..+.-..                            
T Consensus       168 LTASPGs~~ekI~eV~~nLgIe~vevrTE~d~DV~~Yv~~~kve~ikV~lp~e~~~ir~~l~~~l~~~Lk~L~~~g~~~~  247 (542)
T COG1111         168 LTASPGSDLEKIQEVVENLGIEKVEVRTEEDPDVRPYVKKIKVEWIKVDLPEEIKEIRDLLRDALKPRLKPLKELGVIES  247 (542)
T ss_pred             EecCCCCCHHHHHHHHHhCCcceEEEecCCCccHHHhhccceeEEEeccCcHHHHHHHHHHHHHHHHHHHHHHHcCceec
Confidence            999998655433   222222222222211111100   0001111110000                            


Q ss_pred             --------------------------------------------------------------------------------
Q 017573          221 --------------------------------------------------------------------------------  220 (369)
Q Consensus       221 --------------------------------------------------------------------------------  220 (369)
                                                                                                      
T Consensus       248 ~~~~~~kdl~~~~~~~~~~a~~~~~~~~~~l~~~a~~~kl~~a~elletqGi~~~~~Yl~~l~e~~~~~~sk~a~~l~~d  327 (542)
T COG1111         248 SSPVSKKDLLELRQIRLIMAKNEDSDKFRLLSVLAEAIKLAHALELLETQGIRPFYQYLEKLEEEATKGGSKAAKSLLAD  327 (542)
T ss_pred             cCcccHhHHHHHHHHHHHhccCccHHHHHHHHHHHHHHHHHHHHHHHHhhChHHHHHHHHHHHHHhcccchHHHHHHhcC
Confidence                                                                                            


Q ss_pred             --------------------hhHHHHHHHH----HhccCCCeEEEeCCHhhHHHHHHHHhhCCCeeE--Eec-------C
Q 017573          221 --------------------WKLETLCDLY----ETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVS--ATH-------G  267 (369)
Q Consensus       221 --------------------~~~~~l~~~~----~~~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~--~~~-------~  267 (369)
                                          .+++.+.+++    ++.++.++|||++.++.|+.+.+.|.+.+.++.  ++.       .
T Consensus       328 ~~~~~al~~~~~~~~~~v~HPKl~~l~eilke~~~k~~~~RvIVFT~yRdTae~i~~~L~~~~~~~~~rFiGQa~r~~~~  407 (542)
T COG1111         328 PYFKRALRLLIRADESGVEHPKLEKLREILKEQLEKNGDSRVIVFTEYRDTAEEIVNFLKKIGIKARVRFIGQASREGDK  407 (542)
T ss_pred             hhhHHHHHHHHHhccccCCCccHHHHHHHHHHHHhcCCCceEEEEehhHhHHHHHHHHHHhcCCcceeEEeecccccccc
Confidence                                0444444444    344567999999999999999999999988764  222       4


Q ss_pred             CCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCCCCccchhhhhcccccCCCceeEEEEeccccHH
Q 017573          268 DMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDER  345 (369)
Q Consensus       268 ~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~  345 (369)
                      +|++.++.+++++|++|+++|||||++.++|+|+|.++.||++++..|+..++||.||+||. ++|.+++++..++.+
T Consensus       408 GMsQkeQ~eiI~~Fr~Ge~nVLVaTSVgEEGLDIp~vDlVifYEpvpSeIR~IQR~GRTGR~-r~Grv~vLvt~gtrd  484 (542)
T COG1111         408 GMSQKEQKEIIDQFRKGEYNVLVATSVGEEGLDIPEVDLVIFYEPVPSEIRSIQRKGRTGRK-RKGRVVVLVTEGTRD  484 (542)
T ss_pred             ccCHHHHHHHHHHHhcCCceEEEEcccccccCCCCcccEEEEecCCcHHHHHHHhhCccccC-CCCeEEEEEecCchH
Confidence            58999999999999999999999999999999999999999999999999999999999997 889999999988433

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

Probab=100.00  E-value=3.1e-44  Score=329.06  Aligned_cols=333  Identities=21%  Similarity=0.274  Sum_probs=267.9

Q ss_pred             CCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccC-----CCccEEEEcCCHHHH
Q 017573            3 LQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGL-----VQCQALVLAPTRELA   77 (369)
Q Consensus         3 l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~-----~~~~~liv~P~~~l~   77 (369)
                      |++.+++.+... |.+||+.|.+|++.+.+|+|+++.||||||||.+++++++..+....     .+-.+|||+|.++|.
T Consensus         8 l~~~v~~~~~~~-~~~~t~~Q~~a~~~i~~G~nvLiiAPTGsGKTeAAfLpil~~l~~~~~~~~~~~i~~lYIsPLkALn   86 (814)
T COG1201           8 LDPRVREWFKRK-FTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLSLGKGKLEDGIYALYISPLKALN   86 (814)
T ss_pred             cCHHHHHHHHHh-cCCCCHHHHHHHHHHhCCCceEEEcCCCCChHHHHHHHHHHHHHhccCCCCCCceEEEEeCcHHHHH
Confidence            789999999888 99999999999999999999999999999999999999999987652     234799999999999


Q ss_pred             HHHHHHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCC--CCCccEEEEechhHhhccCc
Q 017573           78 QQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLR--PDYIKMFVLDEADEMLSRGF  155 (369)
Q Consensus        78 ~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~--~~~~~~viiDE~H~~~~~~~  155 (369)
                      .++.+++..+...+|+++.+-+|+++..+..+...+++||++|||++|.-++....+.  +.++..||+||+|.+.+...
T Consensus        87 ~Di~~rL~~~~~~~G~~v~vRhGDT~~~er~r~~~~PPdILiTTPEsL~lll~~~~~r~~l~~vr~VIVDEiHel~~sKR  166 (814)
T COG1201          87 NDIRRRLEEPLRELGIEVAVRHGDTPQSEKQKMLKNPPHILITTPESLAILLNSPKFRELLRDVRYVIVDEIHALAESKR  166 (814)
T ss_pred             HHHHHHHHHHHHHcCCccceecCCCChHHhhhccCCCCcEEEeChhHHHHHhcCHHHHHHhcCCcEEEeehhhhhhcccc
Confidence            9999999999999999999999999999998888999999999999998777654332  56689999999999985543


Q ss_pred             H----HHHHHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCC--EEEEecCccccccceeEEEEEcc------chhhhH
Q 017573          156 K----DQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKP--VRILVKRDELTLEGIKQFYVNVE------KEEWKL  223 (369)
Q Consensus       156 ~----~~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~  223 (369)
                      .    -.+.++....+ ..|.|++|||-. +.....+.+....  ..+..... .....+.-..-...      ......
T Consensus       167 G~~Lsl~LeRL~~l~~-~~qRIGLSATV~-~~~~varfL~g~~~~~~Iv~~~~-~k~~~i~v~~p~~~~~~~~~~~~~~~  243 (814)
T COG1201         167 GVQLALSLERLRELAG-DFQRIGLSATVG-PPEEVAKFLVGFGDPCEIVDVSA-AKKLEIKVISPVEDLIYDEELWAALY  243 (814)
T ss_pred             chhhhhhHHHHHhhCc-ccEEEeehhccC-CHHHHHHHhcCCCCceEEEEccc-CCcceEEEEecCCccccccchhHHHH
Confidence            3    23344444445 889999999997 4445555555543  22222211 11111111111111      112234


Q ss_pred             HHHHHHHHhccCCCeEEEeCCHhhHHHHHHHHhhCC-CeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCC
Q 017573          224 ETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRD-HTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQ  302 (369)
Q Consensus       224 ~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~~-~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~  302 (369)
                      ..+.++++++.  .+|||+|++..++.++..|++.+ ..+...||.++.+.|.++.+.|++|+.+.+|||+.++-|+|+.
T Consensus       244 ~~i~~~v~~~~--ttLIF~NTR~~aE~l~~~L~~~~~~~i~~HHgSlSre~R~~vE~~lk~G~lravV~TSSLELGIDiG  321 (814)
T COG1201         244 ERIAELVKKHR--TTLIFTNTRSGAERLAFRLKKLGPDIIEVHHGSLSRELRLEVEERLKEGELKAVVATSSLELGIDIG  321 (814)
T ss_pred             HHHHHHHhhcC--cEEEEEeChHHHHHHHHHHHHhcCCceeeecccccHHHHHHHHHHHhcCCceEEEEccchhhccccC
Confidence            55556666554  89999999999999999999987 7899999999999999999999999999999999999999999


Q ss_pred             CCcEEEEecCCCCccchhhhhcccccC-CCceeEEEEecc
Q 017573          303 QVSLVINYDLPTQPENYLHRIGRSGRF-GRKGVAINFVTR  341 (369)
Q Consensus       303 ~~~~vi~~~~~~~~~~~~Q~~GR~~R~-~~~~~~~~~~~~  341 (369)
                      +++.||+++.|.+...+.||+||+|+. +.....+++...
T Consensus       322 ~vdlVIq~~SP~sV~r~lQRiGRsgHr~~~~Skg~ii~~~  361 (814)
T COG1201         322 DIDLVIQLGSPKSVNRFLQRIGRAGHRLGEVSKGIIIAED  361 (814)
T ss_pred             CceEEEEeCCcHHHHHHhHhccccccccCCcccEEEEecC
Confidence            999999999999999999999999986 555666666655

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=100.00  E-value=1.5e-43  Score=335.30  Aligned_cols=321  Identities=20%  Similarity=0.253  Sum_probs=248.6

Q ss_pred             CCHHHHHHH-HhCCCCCCcHhhhhhhhccccC------CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHH
Q 017573            3 LQENLLRGI-YAYGFEKPSAIQQRGIVPFCKG------LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRE   75 (369)
Q Consensus         3 l~~~i~~~l-~~~~~~~~~~~Q~~~~~~~~~~------~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~   75 (369)
                      .+..+...+ ..++| +|++.|.++++.+.++      .+.++++|||+|||.+++.+++..+..+.   +++|++||++
T Consensus       436 ~~~~~~~~~~~~~~f-~~T~~Q~~aI~~I~~d~~~~~~~d~Ll~adTGsGKT~val~a~l~al~~g~---qvlvLvPT~~  511 (926)
T TIGR00580       436 PDLEWQQEFEDSFPF-EETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVLDGK---QVAVLVPTTL  511 (926)
T ss_pred             CCHHHHHHHHHhCCC-CCCHHHHHHHHHHHhhhcccCcCCEEEECCCCccHHHHHHHHHHHHHHhCC---eEEEEeCcHH
Confidence            345556666 55898 6999999999999874      68999999999999999999988876653   8999999999


Q ss_pred             HHHHHHHHHHHhccccCcEEEEEECCcchHHHHHH----HccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhh
Q 017573           76 LAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRI----LQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEML  151 (369)
Q Consensus        76 l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~----~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~  151 (369)
                      |+.|+++.++++....++++..+++.....+....    ..+.++|+|+||..+     .......+++++|+||+|++.
T Consensus       512 LA~Q~~~~f~~~~~~~~i~v~~Lsg~~~~~e~~~~~~~l~~g~~dIVIGTp~ll-----~~~v~f~~L~llVIDEahrfg  586 (926)
T TIGR00580       512 LAQQHFETFKERFANFPVTIELLSRFRSAKEQNEILKELASGKIDILIGTHKLL-----QKDVKFKDLGLLIIDEEQRFG  586 (926)
T ss_pred             HHHHHHHHHHHHhccCCcEEEEEeccccHHHHHHHHHHHHcCCceEEEchHHHh-----hCCCCcccCCEEEeecccccc
Confidence            99999999999888788888888887665444332    234689999998533     234566779999999999863


Q ss_pred             ccCcHHHHHHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHHH
Q 017573          152 SRGFKDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYE  231 (369)
Q Consensus       152 ~~~~~~~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  231 (369)
                      .     .....+..+++..++++|||||.+...........++..+......  ...+..++..... ......+...+ 
T Consensus       587 v-----~~~~~L~~~~~~~~vL~~SATpiprtl~~~l~g~~d~s~I~~~p~~--R~~V~t~v~~~~~-~~i~~~i~~el-  657 (926)
T TIGR00580       587 V-----KQKEKLKELRTSVDVLTLSATPIPRTLHMSMSGIRDLSIIATPPED--RLPVRTFVMEYDP-ELVREAIRREL-  657 (926)
T ss_pred             h-----hHHHHHHhcCCCCCEEEEecCCCHHHHHHHHhcCCCcEEEecCCCC--ccceEEEEEecCH-HHHHHHHHHHH-
Confidence            2     2234455567788999999999877665555444455444332221  2234444333322 11112222222 


Q ss_pred             hccCCCeEEEeCCHhhHHHHHHHHhhC--CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEE
Q 017573          232 TLAITQSVIFVNTRRKVDWLTDKMRSR--DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVIN  309 (369)
Q Consensus       232 ~~~~~k~lv~~~~~~~~~~~~~~l~~~--~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~  309 (369)
                       ..++++++||++++.++.+++.|++.  +.++..+||+|+.++|.+++++|.+|+.+|||||+++++|+|+|++++||+
T Consensus       658 -~~g~qv~if~n~i~~~e~l~~~L~~~~p~~~v~~lHG~m~~~eRe~im~~F~~Gk~~ILVaT~iie~GIDIp~v~~VIi  736 (926)
T TIGR00580       658 -LRGGQVFYVHNRIESIEKLATQLRELVPEARIAIAHGQMTENELEEVMLEFYKGEFQVLVCTTIIETGIDIPNANTIII  736 (926)
T ss_pred             -HcCCeEEEEECCcHHHHHHHHHHHHhCCCCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEECChhhcccccccCCEEEE
Confidence             24578999999999999999999985  678999999999999999999999999999999999999999999999999


Q ss_pred             ecCCC-CccchhhhhcccccCCCceeEEEEeccc
Q 017573          310 YDLPT-QPENYLHRIGRSGRFGRKGVAINFVTRD  342 (369)
Q Consensus       310 ~~~~~-~~~~~~Q~~GR~~R~~~~~~~~~~~~~~  342 (369)
                      .+.+. +..++.|++||+||.|+.|.|++++++.
T Consensus       737 ~~a~~~gls~l~Qr~GRvGR~g~~g~aill~~~~  770 (926)
T TIGR00580       737 ERADKFGLAQLYQLRGRVGRSKKKAYAYLLYPHQ  770 (926)
T ss_pred             ecCCCCCHHHHHHHhcCCCCCCCCeEEEEEECCc
Confidence            88754 5678999999999999999999998754

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.

>PRK01172 ski2-like helicase; Provisional

Probab=100.00  E-value=5.1e-44  Score=337.19  Aligned_cols=328  Identities=21%  Similarity=0.282  Sum_probs=243.7

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQI   80 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~   80 (369)
                      ++||+.+.+.+++.++. |+++|.++++.+.+++++++++|||+|||+++.+++++.+..+.   +++|++|+++|+.|.
T Consensus         6 ~~l~~~~~~~~~~~~~~-l~~~Q~~ai~~l~~~~nvlv~apTGSGKTl~a~lail~~l~~~~---k~v~i~P~raLa~q~   81 (674)
T PRK01172          6 LGYDDEFLNLFTGNDFE-LYDHQRMAIEQLRKGENVIVSVPTAAGKTLIAYSAIYETFLAGL---KSIYIVPLRSLAMEK   81 (674)
T ss_pred             cCCCHHHHHHHhhCCCC-CCHHHHHHHHHHhcCCcEEEECCCCchHHHHHHHHHHHHHHhCC---cEEEEechHHHHHHH
Confidence            58999999999999985 99999999999999999999999999999999999988776543   899999999999999


Q ss_pred             HHHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHH
Q 017573           81 EKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIY  160 (369)
Q Consensus        81 ~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~  160 (369)
                      ++++.++. ..+..+....|+......   ....++|+|+||+++..++.++.....+++++|+||+|.+.+..+...+.
T Consensus        82 ~~~~~~l~-~~g~~v~~~~G~~~~~~~---~~~~~dIiv~Tpek~~~l~~~~~~~l~~v~lvViDEaH~l~d~~rg~~le  157 (674)
T PRK01172         82 YEELSRLR-SLGMRVKISIGDYDDPPD---FIKRYDVVILTSEKADSLIHHDPYIINDVGLIVADEIHIIGDEDRGPTLE  157 (674)
T ss_pred             HHHHHHHh-hcCCeEEEEeCCCCCChh---hhccCCEEEECHHHHHHHHhCChhHHhhcCEEEEecchhccCCCccHHHH
Confidence            99998864 457888888877653322   12457999999999998888877667789999999999987666555555


Q ss_pred             HHH---hhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEE-----EccchhhhHHHHHHHHHh
Q 017573          161 DIF---QLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYV-----NVEKEEWKLETLCDLYET  232 (369)
Q Consensus       161 ~~~---~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~l~~~~~~  232 (369)
                      .++   ...++..|++++|||++ +..++.. |+...... .   ...+..+.....     ...........+..++..
T Consensus       158 ~ll~~~~~~~~~~riI~lSATl~-n~~~la~-wl~~~~~~-~---~~r~vpl~~~i~~~~~~~~~~~~~~~~~~~~~i~~  231 (674)
T PRK01172        158 TVLSSARYVNPDARILALSATVS-NANELAQ-WLNASLIK-S---NFRPVPLKLGILYRKRLILDGYERSQVDINSLIKE  231 (674)
T ss_pred             HHHHHHHhcCcCCcEEEEeCccC-CHHHHHH-HhCCCccC-C---CCCCCCeEEEEEecCeeeecccccccccHHHHHHH
Confidence            554   34456789999999986 3444444 43322111 0   111111111000     000000001112222222


Q ss_pred             --ccCCCeEEEeCCHhhHHHHHHHHhhCC-------------------------CeeEEecCCCCHHHHHHHHHHHhcCC
Q 017573          233 --LAITQSVIFVNTRRKVDWLTDKMRSRD-------------------------HTVSATHGDMDQNTRDIIMREFRSGS  285 (369)
Q Consensus       233 --~~~~k~lv~~~~~~~~~~~~~~l~~~~-------------------------~~~~~~~~~~~~~~r~~~~~~f~~~~  285 (369)
                        ..++++||||++++.++.+++.|....                         ..+..+|++++.++|..+++.|++|.
T Consensus       232 ~~~~~~~vLVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~gv~~~hagl~~~eR~~ve~~f~~g~  311 (674)
T PRK01172        232 TVNDGGQVLVFVSSRKNAEDYAEMLIQHFPEFNDFKVSSENNNVYDDSLNEMLPHGVAFHHAGLSNEQRRFIEEMFRNRY  311 (674)
T ss_pred             HHhCCCcEEEEeccHHHHHHHHHHHHHhhhhcccccccccccccccHHHHHHHhcCEEEecCCCCHHHHHHHHHHHHcCC
Confidence              245799999999999999998886531                         24788999999999999999999999


Q ss_pred             CcEEEEecCCcCCCCCCCCcEEEEecC---------CCCccchhhhhcccccCCC--ceeEEEEecccc
Q 017573          286 SRVLITTDLLARGIDVQQVSLVINYDL---------PTQPENYLHRIGRSGRFGR--KGVAINFVTRDD  343 (369)
Q Consensus       286 ~~vli~t~~~~~G~d~~~~~~vi~~~~---------~~~~~~~~Q~~GR~~R~~~--~~~~~~~~~~~~  343 (369)
                      ++|||||++++.|+|+|... ||+.+.         +.+..++.||+||+||.|.  .|.++++....+
T Consensus       312 i~VLvaT~~la~Gvnipa~~-VII~~~~~~~~~~~~~~s~~~~~Qm~GRAGR~g~d~~g~~~i~~~~~~  379 (674)
T PRK01172        312 IKVIVATPTLAAGVNLPARL-VIVRDITRYGNGGIRYLSNMEIKQMIGRAGRPGYDQYGIGYIYAASPA  379 (674)
T ss_pred             CeEEEecchhhccCCCcceE-EEEcCceEeCCCCceeCCHHHHHHHhhcCCCCCCCCcceEEEEecCcc
Confidence            99999999999999999754 444442         3467789999999999985  477887766543

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

Probab=100.00  E-value=2.1e-44  Score=303.14  Aligned_cols=350  Identities=27%  Similarity=0.436  Sum_probs=281.6

Q ss_pred             HHHHHHHhCCCCCCcHhhhhhhhcccc---------CCcEEEEcCCCChhhHHHHHHHHHhhhccCCC-ccEEEEcCCHH
Q 017573            6 NLLRGIYAYGFEKPSAIQQRGIVPFCK---------GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQ-CQALVLAPTRE   75 (369)
Q Consensus         6 ~i~~~l~~~~~~~~~~~Q~~~~~~~~~---------~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~-~~~liv~P~~~   75 (369)
                      .+..++.++++.+.-|.|...++.+++         .+++.|.||||||||++|.++|.+.+...+.. -+++||+|++.
T Consensus       147 ~~~q~l~k~~is~~FPVQ~aVlp~ll~~~~~p~~~r~rDIcV~ApTGSGKTLaY~iPIVQ~L~~R~v~~LRavVivPtr~  226 (620)
T KOG0350|consen  147 TIDQLLVKMAISRLFPVQYAVLPSLLEEIRSPPPSRPRDICVNAPTGSGKTLAYVIPIVQLLSSRPVKRLRAVVIVPTRE  226 (620)
T ss_pred             HHHHHHHHhhcccccchHHHHHHHHHHhhcCCCCCCCCceEEecCCCCCceeeehhHHHHHHccCCccceEEEEEeeHHH
Confidence            344568899999999999999888743         58999999999999999999999998766433 37999999999


Q ss_pred             HHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHcc-C----CcEEEeccHHHHHHHH-cCCCCCCCccEEEEechhH
Q 017573           76 LAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQA-G----VHVVVGTPGRVFDMLR-RQSLRPDYIKMFVLDEADE  149 (369)
Q Consensus        76 l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~-~----~~iiv~t~~~l~~~~~-~~~~~~~~~~~viiDE~H~  149 (369)
                      |+.|.++.|.++....++.|..+.|......+.+.+.+ .    .||+|+||.+|..++. ...+.+++++++|+||+++
T Consensus       227 L~~QV~~~f~~~~~~tgL~V~~~sgq~sl~~E~~qL~~~~~~~~~DIlVaTPGRLVDHl~~~k~f~Lk~LrfLVIDEADR  306 (620)
T KOG0350|consen  227 LALQVYDTFKRLNSGTGLAVCSLSGQNSLEDEARQLASDPPECRIDILVATPGRLVDHLNNTKSFDLKHLRFLVIDEADR  306 (620)
T ss_pred             HHHHHHHHHHHhccCCceEEEecccccchHHHHHHHhcCCCccccceEEcCchHHHHhccCCCCcchhhceEEEechHHH
Confidence            99999999999999999999999998887666555543 3    4899999999999998 6778899999999999999


Q ss_pred             hhccCcHHHHHHHHhhC----------------------------------CccCcEEEEEeeCChhHHHHHHHhcCCCE
Q 017573          150 MLSRGFKDQIYDIFQLL----------------------------------PAKVQVGVFSATMPPEALEITRKFMNKPV  195 (369)
Q Consensus       150 ~~~~~~~~~~~~~~~~~----------------------------------~~~~~~i~~saT~~~~~~~~~~~~~~~~~  195 (369)
                      +.+..|...+..++..+                                  .+....+.+|||+..+...+...-+..|.
T Consensus       307 ll~qsfQ~Wl~~v~~~~~~~k~~~~~~nii~~~~~~~pt~~~e~~t~~~~~~~~l~kL~~satLsqdP~Kl~~l~l~~Pr  386 (620)
T KOG0350|consen  307 LLDQSFQEWLDTVMSLCKTMKRVACLDNIIRQRQAPQPTVLSELLTKLGKLYPPLWKLVFSATLSQDPSKLKDLTLHIPR  386 (620)
T ss_pred             HHHHHHHHHHHHHHHHhCCchhhcChhhhhhhcccCCchhhHHHHhhcCCcCchhHhhhcchhhhcChHHHhhhhcCCCc
Confidence            98765444333222221                                  12234566788887766666666666664


Q ss_pred             EEEec----CccccccceeEEEEEccchhhhHHHHHHHHHhccCCCeEEEeCCHhhHHHHHHHHh----hCCCeeEEecC
Q 017573          196 RILVK----RDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMR----SRDHTVSATHG  267 (369)
Q Consensus       196 ~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~----~~~~~~~~~~~  267 (369)
                      ...+.    .....+..+.+..+.... ..+--.+..++......++|+|+++.+.+..++..|+    +-+.++..++|
T Consensus       387 l~~v~~~~~~ryslp~~l~~~~vv~~~-~~kpl~~~~lI~~~k~~r~lcf~~S~~sa~Rl~~~L~v~~~~~~~~~s~~t~  465 (620)
T KOG0350|consen  387 LFHVSKPLIGRYSLPSSLSHRLVVTEP-KFKPLAVYALITSNKLNRTLCFVNSVSSANRLAHVLKVEFCSDNFKVSEFTG  465 (620)
T ss_pred             eEEeecccceeeecChhhhhceeeccc-ccchHhHHHHHHHhhcceEEEEecchHHHHHHHHHHHHHhccccchhhhhhh
Confidence            44333    233344455555554433 2244556667777777899999999999999999887    22455666889


Q ss_pred             CCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCCCCccchhhhhcccccCCCceeEEEEeccccHHHH
Q 017573          268 DMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERML  347 (369)
Q Consensus       268 ~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~  347 (369)
                      .++...|.+.++.|..|++++|||++++.+|+|+.+++.||.|++|.+..+|++|+||.+|.|+.|.++.+.+..+...+
T Consensus       466 ~l~~k~r~k~l~~f~~g~i~vLIcSD~laRGiDv~~v~~VINYd~P~~~ktyVHR~GRTARAgq~G~a~tll~~~~~r~F  545 (620)
T KOG0350|consen  466 QLNGKRRYKMLEKFAKGDINVLICSDALARGIDVNDVDNVINYDPPASDKTYVHRAGRTARAGQDGYAITLLDKHEKRLF  545 (620)
T ss_pred             hhhHHHHHHHHHHHhcCCceEEEehhhhhcCCcccccceEeecCCCchhhHHHHhhcccccccCCceEEEeeccccchHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999888


Q ss_pred             HHHHHHhcc
Q 017573          348 FDIQKFYNV  356 (369)
Q Consensus       348 ~~~~~~~~~  356 (369)
                      .++-+....
T Consensus       546 ~klL~~~~~  554 (620)
T KOG0350|consen  546 SKLLKKTNL  554 (620)
T ss_pred             HHHHHHhcc
Confidence            877666554

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

Probab=100.00  E-value=3.1e-44  Score=308.65  Aligned_cols=366  Identities=32%  Similarity=0.455  Sum_probs=318.2

Q ss_pred             CCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhcc-----CCCccEEEEcCCHHH
Q 017573            2 GLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYG-----LVQCQALVLAPTREL   76 (369)
Q Consensus         2 ~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~-----~~~~~~liv~P~~~l   76 (369)
                      ..++.++.++...+|..|+|.|.++++-+.++++++.++|||+|||+++.++++..+...     ..+-+++|+.|+++|
T Consensus       142 ~~~~~ll~nl~~~~F~~Pt~iq~~aipvfl~~r~~lAcapTGsgKtlaf~~Pil~~L~~~~~~~~~~gl~a~Il~ptreL  221 (593)
T KOG0344|consen  142 SMNKRLLENLQELGFDEPTPIQKQAIPVFLEKRDVLACAPTGSGKTLAFNLPILQHLKDLSQEKHKVGLRALILSPTREL  221 (593)
T ss_pred             hhcHHHHHhHhhCCCCCCCcccchhhhhhhcccceEEeccCCCcchhhhhhHHHHHHHHhhcccCccceEEEEecchHHH
Confidence            346788999999999999999999999999999999999999999999999999888543     334479999999999


Q ss_pred             HHHHHHHHHHhc--cccCcEEEEEECCcchHHH-HHHHccCCcEEEeccHHHHHHHHcCC--CCCCCccEEEEechhHhh
Q 017573           77 AQQIEKVMRALG--DYLGVKVHACVGGTSVRED-QRILQAGVHVVVGTPGRVFDMLRRQS--LRPDYIKMFVLDEADEML  151 (369)
Q Consensus        77 ~~q~~~~~~~~~--~~~~~~v~~~~~~~~~~~~-~~~~~~~~~iiv~t~~~l~~~~~~~~--~~~~~~~~viiDE~H~~~  151 (369)
                      +.|.++++.++.  ...++.+............ .......++++++||..+...+....  .+++.+..+|+||++.+.
T Consensus       222 a~Qi~re~~k~~~~~~t~~~a~~~~~~~~~~qk~a~~~~~k~dili~TP~ri~~~~~~~~~~idl~~V~~lV~dEaD~lf  301 (593)
T KOG0344|consen  222 AAQIYREMRKYSIDEGTSLRAAQFSKPAYPSQKPAFLSDEKYDILISTPMRIVGLLGLGKLNIDLSKVEWLVVDEADLLF  301 (593)
T ss_pred             HHHHHHHHHhcCCCCCCchhhhhcccccchhhccchhHHHHHHHHhcCHHHHHHHhcCCCccchhheeeeEeechHHhhh
Confidence            999999999998  4445554443333221111 11122357999999999988888766  667888999999999999


Q ss_pred             cc-CcHHHHHHHHhhCCc-cCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHH
Q 017573          152 SR-GFKDQIYDIFQLLPA-KVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDL  229 (369)
Q Consensus       152 ~~-~~~~~~~~~~~~~~~-~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  229 (369)
                      .. .+..++..+++.+.+ ...+-++|||.+...++...........+.+...+.....+.+-...+.....+.-.+.++
T Consensus       302 e~~~f~~Qla~I~sac~s~~i~~a~FSat~~~~VEE~~~~i~~~~~~vivg~~~sa~~~V~QelvF~gse~~K~lA~rq~  381 (593)
T KOG0344|consen  302 EPEFFVEQLADIYSACQSPDIRVALFSATISVYVEEWAELIKSDLKRVIVGLRNSANETVDQELVFCGSEKGKLLALRQL  381 (593)
T ss_pred             ChhhHHHHHHHHHHHhcCcchhhhhhhccccHHHHHHHHHhhccceeEEEecchhHhhhhhhhheeeecchhHHHHHHHH
Confidence            88 888888888888765 4455569999999999999998889988888887777788888888888888899999999


Q ss_pred             HHhccCCCeEEEeCCHhhHHHHHHHH-hhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEE
Q 017573          230 YETLAITQSVIFVNTRRKVDWLTDKM-RSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVI  308 (369)
Q Consensus       230 ~~~~~~~k~lv~~~~~~~~~~~~~~l-~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi  308 (369)
                      +...-..+++||+.+.+.|..+...| .-.+.++.++||+.+..+|++.++.|+.|++.||+||+.+++|+|+.+++.||
T Consensus       382 v~~g~~PP~lIfVQs~eRak~L~~~L~~~~~i~v~vIh~e~~~~qrde~~~~FR~g~IwvLicTdll~RGiDf~gvn~VI  461 (593)
T KOG0344|consen  382 VASGFKPPVLIFVQSKERAKQLFEELEIYDNINVDVIHGERSQKQRDETMERFRIGKIWVLICTDLLARGIDFKGVNLVI  461 (593)
T ss_pred             HhccCCCCeEEEEecHHHHHHHHHHhhhccCcceeeEecccchhHHHHHHHHHhccCeeEEEehhhhhccccccCcceEE
Confidence            98877789999999999999999999 56688999999999999999999999999999999999999999999999999


Q ss_pred             EecCCCCccchhhhhcccccCCCceeEEEEeccccHHHHHHHHHHhccccccCCcchhh
Q 017573          309 NYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPSNVAD  367 (369)
Q Consensus       309 ~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  367 (369)
                      .+|.|.+...|++|+||+||.|+.|.+++|++..|...+..+.+.+...--++++++..
T Consensus       462 nyD~p~s~~syihrIGRtgRag~~g~Aitfytd~d~~~ir~iae~~~~sG~evpe~~m~  520 (593)
T KOG0344|consen  462 NYDFPQSDLSYIHRIGRTGRAGRSGKAITFYTDQDMPRIRSIAEVMEQSGCEVPEKIMG  520 (593)
T ss_pred             ecCCCchhHHHHHHhhccCCCCCCcceEEEeccccchhhhhHHHHHHHcCCcchHHHHh
Confidence            99999999999999999999999999999999999999999999999988888887643

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

Probab=100.00  E-value=1.4e-43  Score=313.56  Aligned_cols=333  Identities=22%  Similarity=0.269  Sum_probs=261.6

Q ss_pred             HHHHH-HhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHH
Q 017573            7 LLRGI-YAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMR   85 (369)
Q Consensus         7 i~~~l-~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~   85 (369)
                      +...| +-||+..+|+-|.++++.+..++++++..|||+|||+|+.++++-.     .+ .+|+|+|..+|.+++.+.++
T Consensus         5 ~~~~L~~~fGy~~FR~gQ~evI~~~l~g~d~lvvmPTGgGKSlCyQiPAll~-----~G-~TLVVSPLiSLM~DQV~~l~   78 (590)
T COG0514           5 AQQVLKQVFGYASFRPGQQEIIDALLSGKDTLVVMPTGGGKSLCYQIPALLL-----EG-LTLVVSPLISLMKDQVDQLE   78 (590)
T ss_pred             HHHHHHHHhCccccCCCHHHHHHHHHcCCcEEEEccCCCCcchHhhhHHHhc-----CC-CEEEECchHHHHHHHHHHHH
Confidence            34556 4489999999999999999999999999999999999999887753     22 79999999999999999998


Q ss_pred             HhccccCcEEEEEECCcchHHHHHH----HccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccC--cHHHH
Q 017573           86 ALGDYLGVKVHACVGGTSVREDQRI----LQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRG--FKDQI  159 (369)
Q Consensus        86 ~~~~~~~~~v~~~~~~~~~~~~~~~----~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~--~~~~~  159 (369)
                      ..    |+.+..+++....++....    ..+..++++.+||.+........+....+.+++|||||.++.|+  |...+
T Consensus        79 ~~----Gi~A~~lnS~l~~~e~~~v~~~l~~g~~klLyisPErl~~~~f~~~L~~~~i~l~vIDEAHCiSqWGhdFRP~Y  154 (590)
T COG0514          79 AA----GIRAAYLNSTLSREERQQVLNQLKSGQLKLLYISPERLMSPRFLELLKRLPISLVAIDEAHCISQWGHDFRPDY  154 (590)
T ss_pred             Hc----CceeehhhcccCHHHHHHHHHHHhcCceeEEEECchhhcChHHHHHHHhCCCceEEechHHHHhhcCCccCHhH
Confidence            86    7788888887666655443    34468999999999854333323334457999999999999886  55555


Q ss_pred             H---HHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCC--EEEEecCccccccceeEEEEEccchhhhHHHHHHHHHhcc
Q 017573          160 Y---DIFQLLPAKVQVGVFSATMPPEALEITRKFMNKP--VRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLA  234 (369)
Q Consensus       160 ~---~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  234 (369)
                      .   .+...++ +..++++|||.++.....+...+.-.  ..+..   ....+++............+...+.+ .....
T Consensus       155 ~~lg~l~~~~~-~~p~~AlTATA~~~v~~DI~~~L~l~~~~~~~~---sfdRpNi~~~v~~~~~~~~q~~fi~~-~~~~~  229 (590)
T COG0514         155 RRLGRLRAGLP-NPPVLALTATATPRVRDDIREQLGLQDANIFRG---SFDRPNLALKVVEKGEPSDQLAFLAT-VLPQL  229 (590)
T ss_pred             HHHHHHHhhCC-CCCEEEEeCCCChHHHHHHHHHhcCCCcceEEe---cCCCchhhhhhhhcccHHHHHHHHHh-hcccc
Confidence            4   4455565 67799999999987777665555432  12221   22222332222222222222332222 12445


Q ss_pred             CCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCCC
Q 017573          235 ITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPT  314 (369)
Q Consensus       235 ~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~  314 (369)
                      .+..||||.+++.++.+++.|...|.++..||++++.++|..+.+.|.+++.+|+|||.++++|+|-|++++||+++.|.
T Consensus       230 ~~~GIIYc~sRk~~E~ia~~L~~~g~~a~~YHaGl~~~eR~~~q~~f~~~~~~iiVAT~AFGMGIdKpdVRfViH~~lP~  309 (590)
T COG0514         230 SKSGIIYCLTRKKVEELAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKVMVATNAFGMGIDKPDVRFVIHYDLPG  309 (590)
T ss_pred             CCCeEEEEeeHHhHHHHHHHHHHCCCceEEecCCCCHHHHHHHHHHHhcCCCcEEEEeccccCccCCCCceEEEEecCCC
Confidence            56789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CccchhhhhcccccCCCceeEEEEeccccHHHHHHHHHHh
Q 017573          315 QPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFY  354 (369)
Q Consensus       315 ~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~~  354 (369)
                      |...|.|.+|||||.|.+..+++++++.|....+.+.+..
T Consensus       310 s~EsYyQE~GRAGRDG~~a~aill~~~~D~~~~~~~i~~~  349 (590)
T COG0514         310 SIESYYQETGRAGRDGLPAEAILLYSPEDIRWQRYLIEQS  349 (590)
T ss_pred             CHHHHHHHHhhccCCCCcceEEEeeccccHHHHHHHHHhh
Confidence            9999999999999999999999999999977666555543

>PRK10689 transcription-repair coupling factor; Provisional

Probab=100.00  E-value=2e-42  Score=334.57  Aligned_cols=318  Identities=18%  Similarity=0.210  Sum_probs=249.0

Q ss_pred             HHHHHHHhCCCCCCcHhhhhhhhccccC------CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHH
Q 017573            6 NLLRGIYAYGFEKPSAIQQRGIVPFCKG------LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQ   79 (369)
Q Consensus         6 ~i~~~l~~~~~~~~~~~Q~~~~~~~~~~------~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q   79 (369)
                      +..+....|+| .|++.|.++++.+..+      .+++++++||+|||.+++.+++..+..+   ++++|++|+++|+.|
T Consensus       589 ~~~~~~~~~~~-~~T~~Q~~aI~~il~d~~~~~~~d~Ll~a~TGsGKT~val~aa~~~~~~g---~qvlvLvPT~eLA~Q  664 (1147)
T PRK10689        589 QYQLFCDSFPF-ETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVENH---KQVAVLVPTTLLAQQ  664 (1147)
T ss_pred             HHHHHHHhCCC-CCCHHHHHHHHHHHHHhhcCCCCCEEEEcCCCcCHHHHHHHHHHHHHHcC---CeEEEEeCcHHHHHH
Confidence            34455588999 8999999999999886      7899999999999999887777665543   389999999999999


Q ss_pred             HHHHHHHhccccCcEEEEEECCcchHHHHHHH----ccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCc
Q 017573           80 IEKVMRALGDYLGVKVHACVGGTSVREDQRIL----QAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGF  155 (369)
Q Consensus        80 ~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~----~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~  155 (369)
                      +++.+.+.....++++..+.+..+..++...+    .+.++|+|+||+.+.     ......+++++|+||+|++..   
T Consensus       665 ~~~~f~~~~~~~~v~i~~l~g~~s~~e~~~il~~l~~g~~dIVVgTp~lL~-----~~v~~~~L~lLVIDEahrfG~---  736 (1147)
T PRK10689        665 HYDNFRDRFANWPVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLLQ-----SDVKWKDLGLLIVDEEHRFGV---  736 (1147)
T ss_pred             HHHHHHHhhccCCceEEEEECCCCHHHHHHHHHHHHhCCCCEEEECHHHHh-----CCCCHhhCCEEEEechhhcch---
Confidence            99999987776678888888877766655443    246899999996442     234556789999999999731   


Q ss_pred             HHHHHHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHHHhccC
Q 017573          156 KDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAI  235 (369)
Q Consensus       156 ~~~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  235 (369)
                      .  ....+..++.+.+++++||||.+....+....+.++..+......  ...+..+.........+...+.++.   .+
T Consensus       737 ~--~~e~lk~l~~~~qvLl~SATpiprtl~l~~~gl~d~~~I~~~p~~--r~~v~~~~~~~~~~~~k~~il~el~---r~  809 (1147)
T PRK10689        737 R--HKERIKAMRADVDILTLTATPIPRTLNMAMSGMRDLSIIATPPAR--RLAVKTFVREYDSLVVREAILREIL---RG  809 (1147)
T ss_pred             h--HHHHHHhcCCCCcEEEEcCCCCHHHHHHHHhhCCCcEEEecCCCC--CCCceEEEEecCcHHHHHHHHHHHh---cC
Confidence            1  234456677889999999999888777777777676655443222  2234444433322222222222222   35


Q ss_pred             CCeEEEeCCHhhHHHHHHHHhhC--CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecC-
Q 017573          236 TQSVIFVNTRRKVDWLTDKMRSR--DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDL-  312 (369)
Q Consensus       236 ~k~lv~~~~~~~~~~~~~~l~~~--~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~-  312 (369)
                      +++++||++++.++.+++.|++.  +.++..+||+|+.++|.+++.+|.+|+++|||||+++++|+|+|++++||+.+. 
T Consensus       810 gqv~vf~n~i~~ie~la~~L~~~~p~~~v~~lHG~m~q~eRe~im~~Fr~Gk~~VLVaTdIierGIDIP~v~~VIi~~ad  889 (1147)
T PRK10689        810 GQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERAD  889 (1147)
T ss_pred             CeEEEEECCHHHHHHHHHHHHHhCCCCcEEEEeCCCCHHHHHHHHHHHHhcCCCEEEECchhhcccccccCCEEEEecCC
Confidence            78999999999999999999887  678999999999999999999999999999999999999999999999997654 


Q ss_pred             CCCccchhhhhcccccCCCceeEEEEeccc
Q 017573          313 PTQPENYLHRIGRSGRFGRKGVAINFVTRD  342 (369)
Q Consensus       313 ~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~  342 (369)
                      .++...|.|++||+||.|+.|.|++++...
T Consensus       890 ~fglaq~~Qr~GRvGR~g~~g~a~ll~~~~  919 (1147)
T PRK10689        890 HFGLAQLHQLRGRVGRSHHQAYAWLLTPHP  919 (1147)
T ss_pred             CCCHHHHHHHhhccCCCCCceEEEEEeCCC
Confidence            346678999999999999999999988653

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=100.00  E-value=3.2e-42  Score=322.38  Aligned_cols=317  Identities=19%  Similarity=0.256  Sum_probs=237.3

Q ss_pred             HHHHHHhCCCCCCcHhhhhhhhccccC------CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHH
Q 017573            7 LLRGIYAYGFEKPSAIQQRGIVPFCKG------LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQI   80 (369)
Q Consensus         7 i~~~l~~~~~~~~~~~Q~~~~~~~~~~------~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~   80 (369)
                      +.+-...++| +|++.|+++++.+..+      .+.++++|||||||.+++++++..+..+.   +++|++|+++|+.|+
T Consensus       251 ~~~~~~~l~f-~lt~~Q~~ai~~I~~d~~~~~~~~~Ll~~~TGSGKT~va~~~il~~~~~g~---q~lilaPT~~LA~Q~  326 (681)
T PRK10917        251 LKKFLASLPF-ELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIEAGY---QAALMAPTEILAEQH  326 (681)
T ss_pred             HHHHHHhCCC-CCCHHHHHHHHHHHHhhhccCCceEEEECCCCCcHHHHHHHHHHHHHHcCC---eEEEEeccHHHHHHH
Confidence            3444467888 7999999999999876      47999999999999999999988876544   899999999999999


Q ss_pred             HHHHHHhccccCcEEEEEECCcchHHHHHH----HccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcH
Q 017573           81 EKVMRALGDYLGVKVHACVGGTSVREDQRI----LQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFK  156 (369)
Q Consensus        81 ~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~----~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~  156 (369)
                      ++.++++....++++..++|+.+.......    ..+.++|+|+|+..+..     .....+++++|+||+|++....  
T Consensus       327 ~~~l~~l~~~~~i~v~ll~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~-----~v~~~~l~lvVIDE~Hrfg~~q--  399 (681)
T PRK10917        327 YENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQD-----DVEFHNLGLVIIDEQHRFGVEQ--  399 (681)
T ss_pred             HHHHHHHHhhcCcEEEEEcCCCCHHHHHHHHHHHhCCCCCEEEchHHHhcc-----cchhcccceEEEechhhhhHHH--
Confidence            999999998889999999999886554332    33469999999876643     2345678999999999974322  


Q ss_pred             HHHHHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHHHhccCC
Q 017573          157 DQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAIT  236 (369)
Q Consensus       157 ~~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  236 (369)
                         ...+.......++++|||||.+....+..  ..................+...+..........+.+...+  ..+.
T Consensus       400 ---r~~l~~~~~~~~iL~~SATp~prtl~~~~--~g~~~~s~i~~~p~~r~~i~~~~~~~~~~~~~~~~i~~~~--~~g~  472 (681)
T PRK10917        400 ---RLALREKGENPHVLVMTATPIPRTLAMTA--YGDLDVSVIDELPPGRKPITTVVIPDSRRDEVYERIREEI--AKGR  472 (681)
T ss_pred             ---HHHHHhcCCCCCEEEEeCCCCHHHHHHHH--cCCCceEEEecCCCCCCCcEEEEeCcccHHHHHHHHHHHH--HcCC
Confidence               12222334467899999999776544332  2221111111111112223333333222222223333332  2456


Q ss_pred             CeEEEeCCHh--------hHHHHHHHHhhC--CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcE
Q 017573          237 QSVIFVNTRR--------KVDWLTDKMRSR--DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSL  306 (369)
Q Consensus       237 k~lv~~~~~~--------~~~~~~~~l~~~--~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~  306 (369)
                      +++|||+.++        .+..+++.|.+.  +.++..+||+++.++|.+++++|++|+.+|||||+++++|+|+|++++
T Consensus       473 q~~v~~~~ie~s~~l~~~~~~~~~~~L~~~~~~~~v~~lHG~m~~~eR~~i~~~F~~g~~~ILVaT~vie~GiDip~v~~  552 (681)
T PRK10917        473 QAYVVCPLIEESEKLDLQSAEETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGVDVPNATV  552 (681)
T ss_pred             cEEEEEcccccccchhHHHHHHHHHHHHHHCCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEECcceeeCcccCCCcE
Confidence            8999999643        456677777765  468999999999999999999999999999999999999999999999


Q ss_pred             EEEecCCC-CccchhhhhcccccCCCceeEEEEecc
Q 017573          307 VINYDLPT-QPENYLHRIGRSGRFGRKGVAINFVTR  341 (369)
Q Consensus       307 vi~~~~~~-~~~~~~Q~~GR~~R~~~~~~~~~~~~~  341 (369)
                      ||+++.+. ....+.|+.||+||.|..|.|++++..
T Consensus       553 VIi~~~~r~gls~lhQ~~GRvGR~g~~g~~ill~~~  588 (681)
T PRK10917        553 MVIENAERFGLAQLHQLRGRVGRGAAQSYCVLLYKD  588 (681)
T ss_pred             EEEeCCCCCCHHHHHHHhhcccCCCCceEEEEEECC
Confidence            99999876 567899999999999999999999953

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=100.00  E-value=2.3e-41  Score=314.71  Aligned_cols=317  Identities=21%  Similarity=0.269  Sum_probs=234.6

Q ss_pred             HHHHHHHhCCCCCCcHhhhhhhhccccC------CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHH
Q 017573            6 NLLRGIYAYGFEKPSAIQQRGIVPFCKG------LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQ   79 (369)
Q Consensus         6 ~i~~~l~~~~~~~~~~~Q~~~~~~~~~~------~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q   79 (369)
                      .+.+.++.++| +|++.|+++++.+..+      .+.++++|||||||.+++++++..+..+.   +++|++|+++|+.|
T Consensus       224 ~~~~~~~~lpf-~lt~~Q~~ai~~I~~~~~~~~~~~~Ll~g~TGSGKT~va~l~il~~~~~g~---qvlilaPT~~LA~Q  299 (630)
T TIGR00643       224 LLTKFLASLPF-KLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEAGY---QVALMAPTEILAEQ  299 (630)
T ss_pred             HHHHHHHhCCC-CCCHHHHHHHHHHHHHhccCCCccEEEECCCCCcHHHHHHHHHHHHHHcCC---cEEEECCHHHHHHH
Confidence            34566688999 8999999999999865      35899999999999999999988876544   89999999999999


Q ss_pred             HHHHHHHhccccCcEEEEEECCcchHHHHH----HHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCc
Q 017573           80 IEKVMRALGDYLGVKVHACVGGTSVREDQR----ILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGF  155 (369)
Q Consensus        80 ~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~----~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~  155 (369)
                      +++.+++++...++++..++|+........    ...+.++|+|+|+..+..     .....+++++|+||+|++.... 
T Consensus       300 ~~~~~~~l~~~~gi~v~lltg~~~~~~r~~~~~~i~~g~~~IiVgT~~ll~~-----~~~~~~l~lvVIDEaH~fg~~q-  373 (630)
T TIGR00643       300 HYNSLRNLLAPLGIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQE-----KVEFKRLALVIIDEQHRFGVEQ-  373 (630)
T ss_pred             HHHHHHHHhcccCcEEEEEecCCCHHHHHHHHHHHhCCCCCEEEecHHHHhc-----cccccccceEEEechhhccHHH-
Confidence            999999998888999999999887655333    234568999999987653     3445678999999999864322 


Q ss_pred             HHHHHHHHhhCC--ccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHHHh-
Q 017573          156 KDQIYDIFQLLP--AKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYET-  232 (369)
Q Consensus       156 ~~~~~~~~~~~~--~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-  232 (369)
                         ...+.....  ..+++++|||||.+....+..  ..................+...+.....   ....+..+... 
T Consensus       374 ---r~~l~~~~~~~~~~~~l~~SATp~prtl~l~~--~~~l~~~~i~~~p~~r~~i~~~~~~~~~---~~~~~~~i~~~l  445 (630)
T TIGR00643       374 ---RKKLREKGQGGFTPHVLVMSATPIPRTLALTV--YGDLDTSIIDELPPGRKPITTVLIKHDE---KDIVYEFIEEEI  445 (630)
T ss_pred             ---HHHHHHhcccCCCCCEEEEeCCCCcHHHHHHh--cCCcceeeeccCCCCCCceEEEEeCcch---HHHHHHHHHHHH
Confidence               222333332  257899999999765443322  1111111111111111223333322211   22222222222 


Q ss_pred             ccCCCeEEEeCCH--------hhHHHHHHHHhhC--CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCC
Q 017573          233 LAITQSVIFVNTR--------RKVDWLTDKMRSR--DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQ  302 (369)
Q Consensus       233 ~~~~k~lv~~~~~--------~~~~~~~~~l~~~--~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~  302 (369)
                      ..+.+++|||+..        ..++.+++.|.+.  +..+..+||+++.++|.++++.|++|+.+|||||+++++|+|+|
T Consensus       446 ~~g~q~~v~~~~i~~s~~~~~~~a~~~~~~L~~~~~~~~v~~lHG~m~~~eR~~i~~~F~~g~~~ILVaT~vie~GvDiP  525 (630)
T TIGR00643       446 AKGRQAYVVYPLIEESEKLDLKAAEALYERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVP  525 (630)
T ss_pred             HhCCcEEEEEccccccccchHHHHHHHHHHHHhhCCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEECceeecCcccC
Confidence            2356899999876        3456667777653  66899999999999999999999999999999999999999999


Q ss_pred             CCcEEEEecCCC-CccchhhhhcccccCCCceeEEEEec
Q 017573          303 QVSLVINYDLPT-QPENYLHRIGRSGRFGRKGVAINFVT  340 (369)
Q Consensus       303 ~~~~vi~~~~~~-~~~~~~Q~~GR~~R~~~~~~~~~~~~  340 (369)
                      ++++||+++.+. +...+.|+.||+||.|+.|.|++++.
T Consensus       526 ~v~~VIi~~~~r~gls~lhQ~~GRvGR~g~~g~~il~~~  564 (630)
T TIGR00643       526 NATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLLVYK  564 (630)
T ss_pred             CCcEEEEeCCCcCCHHHHHHHhhhcccCCCCcEEEEEEC
Confidence            999999999875 57789999999999999999999993

>PHA02558 uvsW UvsW helicase; Provisional

Probab=100.00  E-value=4.4e-41  Score=305.37  Aligned_cols=300  Identities=15%  Similarity=0.142  Sum_probs=215.6

Q ss_pred             CCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEE
Q 017573           17 EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVH   96 (369)
Q Consensus        17 ~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~   96 (369)
                      ..||++|++++..+..+++.++++|||+|||.++...+...+.. . ..++||++|+++|+.||.+.+.++.......+.
T Consensus       113 ~~~r~~Q~~av~~~l~~~~~il~apTGsGKT~i~~~l~~~~~~~-~-~~~vLilvpt~eL~~Q~~~~l~~~~~~~~~~~~  190 (501)
T PHA02558        113 IEPHWYQYDAVYEGLKNNRRLLNLPTSAGKSLIQYLLSRYYLEN-Y-EGKVLIIVPTTSLVTQMIDDFVDYRLFPREAMH  190 (501)
T ss_pred             CCCCHHHHHHHHHHHhcCceEEEeCCCCCHHHHHHHHHHHHHhc-C-CCeEEEEECcHHHHHHHHHHHHHhcccccccee
Confidence            58999999999999999999999999999998765433322222 2 238999999999999999999998654333444


Q ss_pred             EEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEE
Q 017573           97 ACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFS  176 (369)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~s  176 (369)
                      .+.++....       .+.+|+|+|++++......   ....++++|+||||++.+..    +..++..+++..+++++|
T Consensus       191 ~i~~g~~~~-------~~~~I~VaT~qsl~~~~~~---~~~~~~~iIvDEaH~~~~~~----~~~il~~~~~~~~~lGLT  256 (501)
T PHA02558        191 KIYSGTAKD-------TDAPIVVSTWQSAVKQPKE---WFDQFGMVIVDECHLFTGKS----LTSIITKLDNCKFKFGLT  256 (501)
T ss_pred             EEecCcccC-------CCCCEEEeeHHHHhhchhh---hccccCEEEEEchhcccchh----HHHHHHhhhccceEEEEe
Confidence            444444321       3468999999998754322   34568999999999986543    456666676677899999


Q ss_pred             eeCChhHHHH--HHHhcCCCEEEEecCccc------cccceeEEEEEc--------------------cchhhhHHHHHH
Q 017573          177 ATMPPEALEI--TRKFMNKPVRILVKRDEL------TLEGIKQFYVNV--------------------EKEEWKLETLCD  228 (369)
Q Consensus       177 aT~~~~~~~~--~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~--------------------~~~~~~~~~l~~  228 (369)
                      |||.......  ....+++ +.........      ....+.......                    .........+..
T Consensus       257 ATp~~~~~~~~~~~~~fG~-i~~~v~~~~li~~g~l~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~l~~~~~Rn~~I~~  335 (501)
T PHA02558        257 GSLRDGKANILQYVGLFGD-IFKPVTTSQLMEEGQVTDLKINSIFLRYPDEDRVKLKGEDYQEEIKYITSHTKRNKWIAN  335 (501)
T ss_pred             ccCCCccccHHHHHHhhCC-ceEEecHHHHHhCCCcCCceEEEEeccCCHHHhhhhcccchHHHHHHHhccHHHHHHHHH
Confidence            9996432211  1122222 2211111000      000000000000                    001112233333


Q ss_pred             HHHhc--cCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEe-cCCcCCCCCCCCc
Q 017573          229 LYETL--AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITT-DLLARGIDVQQVS  305 (369)
Q Consensus       229 ~~~~~--~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t-~~~~~G~d~~~~~  305 (369)
                      +....  .+.+++|||.+.++++.+++.|++.+.++..+||+++.++|.++++.|++|+..+||+| +.+++|+|+|+++
T Consensus       336 ~~~~~~~~~~~~lV~~~~~~h~~~L~~~L~~~g~~v~~i~G~~~~~eR~~i~~~~~~~~~~vLvaT~~~l~eG~Dip~ld  415 (501)
T PHA02558        336 LALKLAKKGENTFVMFKYVEHGKPLYEMLKKVYDKVYYVSGEVDTEDRNEMKKIAEGGKGIIIVASYGVFSTGISIKNLH  415 (501)
T ss_pred             HHHHHHhcCCCEEEEEEEHHHHHHHHHHHHHcCCCEEEEeCCCCHHHHHHHHHHHhCCCCeEEEEEcceecccccccccc
Confidence            33222  35689999999999999999999999999999999999999999999999998999998 7999999999999


Q ss_pred             EEEEecCCCCccchhhhhcccccCCCce
Q 017573          306 LVINYDLPTQPENYLHRIGRSGRFGRKG  333 (369)
Q Consensus       306 ~vi~~~~~~~~~~~~Q~~GR~~R~~~~~  333 (369)
                      +||+..++.|...|.|++||++|.+..+
T Consensus       416 ~vIl~~p~~s~~~~~QriGR~~R~~~~K  443 (501)
T PHA02558        416 HVIFAHPSKSKIIVLQSIGRVLRKHGSK  443 (501)
T ss_pred             EEEEecCCcchhhhhhhhhccccCCCCC
Confidence            9999999999999999999999986554

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

Probab=100.00  E-value=2.8e-40  Score=304.78  Aligned_cols=314  Identities=21%  Similarity=0.250  Sum_probs=232.4

Q ss_pred             CCCCCCcHhhhhhhhccccCC-cEEEEcCCCChhhHHHHHHHHHhhhccCCCc-cEEEEcCCHHHHHHHHHHHHHhcccc
Q 017573           14 YGFEKPSAIQQRGIVPFCKGL-DVIQQAQSGTGKTATFCSGILQQLDYGLVQC-QALVLAPTRELAQQIEKVMRALGDYL   91 (369)
Q Consensus        14 ~~~~~~~~~Q~~~~~~~~~~~-~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~-~~liv~P~~~l~~q~~~~~~~~~~~~   91 (369)
                      .||+ |+|+|.++++.++.|+ .+++++|||||||.++.++.+.. ..+...+ ..++++|+++|+.|..+.+.++...+
T Consensus        12 ~G~~-PtpiQ~~~i~~il~G~~~v~~~apTGSGKTaa~aafll~~-~~~~~~~~rLv~~vPtReLa~Qi~~~~~~~~k~l   89 (844)
T TIGR02621        12 HGYS-PFPWQLSLAERFVAGQPPESCSTPTGLGKTSIIAAWLLAV-EIGAKVPRRLVYVVNRRTVVDQVTEEAEKIGERL   89 (844)
T ss_pred             hCCC-CCHHHHHHHHHHHcCCCcceEecCCCCcccHHHHHhhccc-cccccccceEEEeCchHHHHHHHHHHHHHHHHHh
Confidence            4776 9999999999999997 57888999999998655444432 2222222 45557799999999999998887644


Q ss_pred             -----------------------CcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHc---------CCC---CC
Q 017573           92 -----------------------GVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRR---------QSL---RP  136 (369)
Q Consensus        92 -----------------------~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~---------~~~---~~  136 (369)
                                             ++++..+.|+.....+...+..+++|+|+|++.+.+....         +.+   .+
T Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~GG~~~~~q~~~l~~~p~IIVgT~D~i~sr~L~~gYg~~~~~~pi~ag~L  169 (844)
T TIGR02621        90 PDVPEVEAALWALCSTRPEKKDRPLAISTLRGQFADNDEWMLDPHRPAVIVGTVDMIGSRLLFSGYGCGFKSRPLHAGFL  169 (844)
T ss_pred             cccchhhhhhhhhhccccccccCCeEEEEEECCCChHHHHHhcCCCCcEEEECHHHHcCCccccccccccccccchhhhh
Confidence                                   4788899999988777777778899999997655332110         001   14


Q ss_pred             CCccEEEEechhHhhccCcHHHHHHHHhhC--Ccc---CcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeE
Q 017573          137 DYIKMFVLDEADEMLSRGFKDQIYDIFQLL--PAK---VQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQ  211 (369)
Q Consensus       137 ~~~~~viiDE~H~~~~~~~~~~~~~~~~~~--~~~---~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  211 (369)
                      .+..++|+||||  .+.+|...+..+++.+  ++.   .|+++||||++.+.......+...+..+...........+.+
T Consensus       170 ~~v~~LVLDEAD--Ld~gF~~~l~~Il~~l~rp~~~rprQtLLFSAT~p~ei~~l~~~~~~~p~~i~V~~~~l~a~ki~q  247 (844)
T TIGR02621       170 GQDALIVHDEAH--LEPAFQELLKQIMNEQQRPPDFLPLRVVELTATSRTDGPDRTTLLSAEDYKHPVLKKRLAAKKIVK  247 (844)
T ss_pred             ccceEEEEehhh--hccccHHHHHHHHHhcccCcccccceEEEEecCCCccHHHHHHHHccCCceeecccccccccceEE
Confidence            567899999999  4678899999999864  332   689999999987777777677766665555444444444444


Q ss_pred             EEEEccchhhhHHH----HHHHHHhccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHH-----HHHHHHh
Q 017573          212 FYVNVEKEEWKLET----LCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRD-----IIMREFR  282 (369)
Q Consensus       212 ~~~~~~~~~~~~~~----l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~-----~~~~~f~  282 (369)
                      + +.... ..+...    +..++ ....+++|||||+++.++.+++.|++.+.  ..+||++++.+|.     .+++.|+
T Consensus       248 ~-v~v~~-e~Kl~~lv~~L~~ll-~e~g~~vLVF~NTv~~Aq~L~~~L~~~g~--~lLHG~m~q~dR~~~~~~~il~~Fk  322 (844)
T TIGR02621       248 L-VPPSD-EKFLSTMVKELNLLM-KDSGGAILVFCRTVKHVRKVFAKLPKEKF--ELLTGTLRGAERDDLVKKEIFNRFL  322 (844)
T ss_pred             E-EecCh-HHHHHHHHHHHHHHH-hhCCCcEEEEECCHHHHHHHHHHHHhcCC--eEeeCCCCHHHHhhHHHHHHHHHHh
Confidence            3 22222 222222    22222 23457899999999999999999998766  8999999999999     7889998


Q ss_pred             c----CC-------CcEEEEecCCcCCCCCCCCcEEEEecCCCCccchhhhhcccccCCCce-eEEEEe
Q 017573          283 S----GS-------SRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKG-VAINFV  339 (369)
Q Consensus       283 ~----~~-------~~vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~-~~~~~~  339 (369)
                      +    |.       ..|||+|+++++|+|++. ++||....|  ...|+||+||++|.|+.+ ..+.++
T Consensus       323 ~~~~~g~~~~~~~g~~ILVATdVaerGLDId~-d~VI~d~aP--~esyIQRiGRtgR~G~~~~~~i~vv  388 (844)
T TIGR02621       323 PQMLSGSRARPQQGTVYLVCTSAGEVGVNISA-DHLVCDLAP--FESMQQRFGRVNRFGELQACQIAVV  388 (844)
T ss_pred             ccccccccccccccceEEeccchhhhcccCCc-ceEEECCCC--HHHHHHHhcccCCCCCCCCceEEEE
Confidence            6    43       679999999999999986 777775544  589999999999998753 334444

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.

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

Probab=100.00  E-value=8.6e-41  Score=286.16  Aligned_cols=333  Identities=20%  Similarity=0.244  Sum_probs=264.9

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhc-cccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVP-FCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQ   79 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~-~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q   79 (369)
                      +++|+.+.+.|+..|++.+.|.|..++++ +++|+|.+|..+|+||||++.-++-+..+..+..  |.|+++|..+|++|
T Consensus       199 Ldipe~fk~~lk~~G~~eLlPVQ~laVe~GLLeG~nllVVSaTasGKTLIgElAGi~~~l~~g~--KmlfLvPLVALANQ  276 (830)
T COG1202         199 LDIPEKFKRMLKREGIEELLPVQVLAVEAGLLEGENLLVVSATASGKTLIGELAGIPRLLSGGK--KMLFLVPLVALANQ  276 (830)
T ss_pred             cCCcHHHHHHHHhcCcceecchhhhhhhhccccCCceEEEeccCCCcchHHHhhCcHHHHhCCC--eEEEEehhHHhhcc
Confidence            57999999999999999999999999988 5689999999999999999998887777665332  89999999999999


Q ss_pred             HHHHHHHhccccCcEEEEEECCcchHHHHH----HHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCc
Q 017573           80 IEKVMRALGDYLGVKVHACVGGTSVREDQR----ILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGF  155 (369)
Q Consensus        80 ~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~----~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~  155 (369)
                      -+++|++-+..+++.+..-.|.........    ....++||||+||+.+-.+++.+ -.+.+++.||+||+|.+.+...
T Consensus       277 Ky~dF~~rYs~LglkvairVG~srIk~~~~pv~~~t~~dADIIVGTYEGiD~lLRtg-~~lgdiGtVVIDEiHtL~deER  355 (830)
T COG1202         277 KYEDFKERYSKLGLKVAIRVGMSRIKTREEPVVVDTSPDADIIVGTYEGIDYLLRTG-KDLGDIGTVVIDEIHTLEDEER  355 (830)
T ss_pred             hHHHHHHHhhcccceEEEEechhhhcccCCccccCCCCCCcEEEeechhHHHHHHcC-CcccccceEEeeeeeeccchhc
Confidence            999999988888998877777655443321    12347899999999998777776 5677799999999999876443


Q ss_pred             HHHHH---HHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHHHh
Q 017573          156 KDQIY---DIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYET  232 (369)
Q Consensus       156 ~~~~~---~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  232 (369)
                      ...+.   .-++.+-+..|++++|||.. +..++...+-.+.+.+...     |-.++...........+.+.+.++.+.
T Consensus       356 G~RLdGLI~RLr~l~~~AQ~i~LSATVg-Np~elA~~l~a~lV~y~~R-----PVplErHlvf~~~e~eK~~ii~~L~k~  429 (830)
T COG1202         356 GPRLDGLIGRLRYLFPGAQFIYLSATVG-NPEELAKKLGAKLVLYDER-----PVPLERHLVFARNESEKWDIIARLVKR  429 (830)
T ss_pred             ccchhhHHHHHHHhCCCCeEEEEEeecC-ChHHHHHHhCCeeEeecCC-----CCChhHeeeeecCchHHHHHHHHHHHH
Confidence            33333   22344445899999999986 6667887777776655432     223344444455555566666666543


Q ss_pred             c--------cCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCC
Q 017573          233 L--------AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQV  304 (369)
Q Consensus       233 ~--------~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~  304 (369)
                      -        -.+++|||++|+..++.+++.|...|.+...||++++..+|..+...|.++++.++|+|.+++.|+|+|.-
T Consensus       430 E~~~~sskg~rGQtIVFT~SRrr~h~lA~~L~~kG~~a~pYHaGL~y~eRk~vE~~F~~q~l~~VVTTAAL~AGVDFPAS  509 (830)
T COG1202         430 EFSTESSKGYRGQTIVFTYSRRRCHELADALTGKGLKAAPYHAGLPYKERKSVERAFAAQELAAVVTTAALAAGVDFPAS  509 (830)
T ss_pred             HHhhhhccCcCCceEEEecchhhHHHHHHHhhcCCcccccccCCCcHHHHHHHHHHHhcCCcceEeehhhhhcCCCCchH
Confidence            2        22589999999999999999999999999999999999999999999999999999999999999999854


Q ss_pred             cEEE---EecCCC-CccchhhhhcccccCC--CceeEEEEeccc
Q 017573          305 SLVI---NYDLPT-QPENYLHRIGRSGRFG--RKGVAINFVTRD  342 (369)
Q Consensus       305 ~~vi---~~~~~~-~~~~~~Q~~GR~~R~~--~~~~~~~~~~~~  342 (369)
                      .+++   -.+..| |+.+|.||.||+||.+  ..|.++++..+.
T Consensus       510 QVIFEsLaMG~~WLs~~EF~QM~GRAGRp~yHdrGkVyllvepg  553 (830)
T COG1202         510 QVIFESLAMGIEWLSVREFQQMLGRAGRPDYHDRGKVYLLVEPG  553 (830)
T ss_pred             HHHHHHHHcccccCCHHHHHHHhcccCCCCcccCceEEEEecCC
Confidence            4442   123333 7899999999999986  458899888765

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=100.00  E-value=2.6e-39  Score=314.80  Aligned_cols=321  Identities=20%  Similarity=0.296  Sum_probs=231.0

Q ss_pred             EEcCCCChhhHHHHHHHHHhhhcc----------CCCccEEEEcCCHHHHHHHHHHHHHhc------------cccCcEE
Q 017573           38 QQAQSGTGKTATFCSGILQQLDYG----------LVQCQALVLAPTRELAQQIEKVMRALG------------DYLGVKV   95 (369)
Q Consensus        38 i~~~tG~GKT~~~~~~~~~~~~~~----------~~~~~~liv~P~~~l~~q~~~~~~~~~------------~~~~~~v   95 (369)
                      |++|||||||++++++++..+...          ..+.++|||+|+++|+.|..++++...            ...++++
T Consensus         1 V~APTGSGKTLAA~LpaL~~Ll~~~~~~~~~~~~~~~~raLYISPLKALa~Dv~~~L~~pl~~i~~~~~~~g~~~~~i~V   80 (1490)
T PRK09751          1 VIAPTGSGKTLAAFLYALDRLFREGGEDTREAHKRKTSRILYISPIKALGTDVQRNLQIPLKGIADERRRRGETEVNLRV   80 (1490)
T ss_pred             CcCCCCcHHHHHHHHHHHHHHHhcccccccccccCCCCEEEEEeChHHHHHHHHHHHHHHHHhhhhhhhhcccccCceEE
Confidence            579999999999999998887532          124589999999999999999886421            1246889


Q ss_pred             EEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCC-CCCCCccEEEEechhHhhccC----cHHHHHHHHhhCCccC
Q 017573           96 HACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQS-LRPDYIKMFVLDEADEMLSRG----FKDQIYDIFQLLPAKV  170 (369)
Q Consensus        96 ~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~-~~~~~~~~viiDE~H~~~~~~----~~~~~~~~~~~~~~~~  170 (369)
                      ...+|+....+..+...+.++|+|+||++|..++.+.. ..++++++||+||+|.+.+..    +...+.++...++.+.
T Consensus        81 ~vrtGDt~~~eR~rll~~ppdILVTTPEsL~~LLtsk~r~~L~~Vr~VIVDE~H~L~g~kRG~~Lel~LeRL~~l~~~~~  160 (1490)
T PRK09751         81 GIRTGDTPAQERSKLTRNPPDILITTPESLYLMLTSRARETLRGVETVIIDEVHAVAGSKRGAHLALSLERLDALLHTSA  160 (1490)
T ss_pred             EEEECCCCHHHHHHHhcCCCCEEEecHHHHHHHHhhhhhhhhccCCEEEEecHHHhcccccccHHHHHHHHHHHhCCCCC
Confidence            99999999888777777789999999999988776532 346779999999999998543    2345556666667788


Q ss_pred             cEEEEEeeCChhHHHHHHHhcCC-CEEEEecCccccccceeEEEEEccchh-------------------hhHHHH-HHH
Q 017573          171 QVGVFSATMPPEALEITRKFMNK-PVRILVKRDELTLEGIKQFYVNVEKEE-------------------WKLETL-CDL  229 (369)
Q Consensus       171 ~~i~~saT~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~-------------------~~~~~l-~~~  229 (369)
                      |+|++|||..+ ..+....+... +..+.. ........+. ++.......                   .....+ ..+
T Consensus       161 QrIgLSATI~n-~eevA~~L~g~~pv~Iv~-~~~~r~~~l~-v~vp~~d~~~~~~~~~~~~~~~~~~r~~~i~~~v~~~i  237 (1490)
T PRK09751        161 QRIGLSATVRS-ASDVAAFLGGDRPVTVVN-PPAMRHPQIR-IVVPVANMDDVSSVASGTGEDSHAGREGSIWPYIETGI  237 (1490)
T ss_pred             eEEEEEeeCCC-HHHHHHHhcCCCCEEEEC-CCCCcccceE-EEEecCchhhccccccccccccchhhhhhhhHHHHHHH
Confidence            99999999975 44555444332 444432 2222222222 112111100                   000111 122


Q ss_pred             HHh-ccCCCeEEEeCCHhhHHHHHHHHhhCC---------------------------------CeeEEecCCCCHHHHH
Q 017573          230 YET-LAITQSVIFVNTRRKVDWLTDKMRSRD---------------------------------HTVSATHGDMDQNTRD  275 (369)
Q Consensus       230 ~~~-~~~~k~lv~~~~~~~~~~~~~~l~~~~---------------------------------~~~~~~~~~~~~~~r~  275 (369)
                      +.. ....++|||||+++.++.++..|++..                                 ..+..+||+++.++|.
T Consensus       238 l~~i~~~~stLVFvNSR~~AE~La~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ia~~HHGsLSkeeR~  317 (1490)
T PRK09751        238 LDEVLRHRSTIVFTNSRGLAEKLTARLNELYAARLQRSPSIAVDAAHFESTSGATSNRVQSSDVFIARSHHGSVSKEQRA  317 (1490)
T ss_pred             HHHHhcCCCEEEECCCHHHHHHHHHHHHHhhhhhccccccccchhhhhhhccccchhccccccceeeeeccccCCHHHHH
Confidence            222 235789999999999999999887542                                 1256789999999999


Q ss_pred             HHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCCCCccchhhhhcccccC-CCceeEEEEeccccHHHHH---HHH
Q 017573          276 IIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRF-GRKGVAINFVTRDDERMLF---DIQ  351 (369)
Q Consensus       276 ~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~-~~~~~~~~~~~~~~~~~~~---~~~  351 (369)
                      .+++.|++|+.++||||+.++.|||++.+++||.++.|.+..+|.||+||+||. +..+.++++.... .+.++   -++
T Consensus       318 ~IE~~fK~G~LrvLVATssLELGIDIg~VDlVIq~gsP~sVas~LQRiGRAGR~~gg~s~gli~p~~r-~dlle~~~~ve  396 (1490)
T PRK09751        318 ITEQALKSGELRCVVATSSLELGIDMGAVDLVIQVATPLSVASGLQRIGRAGHQVGGVSKGLFFPRTR-RDLVDSAVIVE  396 (1490)
T ss_pred             HHHHHHHhCCceEEEeCcHHHccCCcccCCEEEEeCCCCCHHHHHHHhCCCCCCCCCccEEEEEeCcH-HHHHhhHHHHH
Confidence            999999999999999999999999999999999999999999999999999997 3334555333322 22222   256


Q ss_pred             HHhccccccCC
Q 017573          352 KFYNVVIEELP  362 (369)
Q Consensus       352 ~~~~~~~~~~~  362 (369)
                      .+++..++++.
T Consensus       397 ~~l~g~iE~~~  407 (1490)
T PRK09751        397 CMFAGRLENLT  407 (1490)
T ss_pred             HHhcCCCCccC
Confidence            66666666544

>PRK09401 reverse gyrase; Reviewed

Probab=100.00  E-value=5.5e-38  Score=304.46  Aligned_cols=283  Identities=23%  Similarity=0.299  Sum_probs=216.9

Q ss_pred             CCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCc
Q 017573           14 YGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGV   93 (369)
Q Consensus        14 ~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~   93 (369)
                      +|+ .|+++|+.+++.++.|++++++||||+|||..++..+. .+..  .+.+++|++|+++|+.|+.+.++++....+.
T Consensus        77 ~G~-~pt~iQ~~~i~~il~g~dv~i~ApTGsGKT~f~l~~~~-~l~~--~g~~alIL~PTreLa~Qi~~~l~~l~~~~~~  152 (1176)
T PRK09401         77 TGS-KPWSLQRTWAKRLLLGESFAIIAPTGVGKTTFGLVMSL-YLAK--KGKKSYIIFPTRLLVEQVVEKLEKFGEKVGC  152 (1176)
T ss_pred             cCC-CCcHHHHHHHHHHHCCCcEEEEcCCCCCHHHHHHHHHH-HHHh--cCCeEEEEeccHHHHHHHHHHHHHHhhhcCc
Confidence            466 89999999999999999999999999999975544333 3322  2448999999999999999999999888888


Q ss_pred             EEEEEECCcch-----HHHH-HHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhc-----------cCcH
Q 017573           94 KVHACVGGTSV-----REDQ-RILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLS-----------RGFK  156 (369)
Q Consensus        94 ~v~~~~~~~~~-----~~~~-~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~-----------~~~~  156 (369)
                      .+..+.++...     .... ....++++|+|+||+.+.+.+.  .+....++++|+||||++..           .+|.
T Consensus       153 ~~~~~~g~~~~~~~ek~~~~~~l~~~~~~IlV~Tp~rL~~~~~--~l~~~~~~~lVvDEaD~~L~~~k~id~~l~~lGF~  230 (1176)
T PRK09401        153 GVKILYYHSSLKKKEKEEFLERLKEGDFDILVTTSQFLSKNFD--ELPKKKFDFVFVDDVDAVLKSSKNIDKLLYLLGFS  230 (1176)
T ss_pred             eEEEEEccCCcchhHHHHHHHHHhcCCCCEEEECHHHHHHHHH--hccccccCEEEEEChHHhhhcccchhhHHHhCCCC
Confidence            87777665431     1111 2233568999999999988776  35556699999999999885           3453


Q ss_pred             -HHHHHHHhhCCc------------------------cCcEEEEEeeCChh-HHHHHHHhcCCCEEEEecCcccccccee
Q 017573          157 -DQIYDIFQLLPA------------------------KVQVGVFSATMPPE-ALEITRKFMNKPVRILVKRDELTLEGIK  210 (369)
Q Consensus       157 -~~~~~~~~~~~~------------------------~~~~i~~saT~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~  210 (369)
                       ..+..++..++.                        ..|++++|||.++. ...   .++..+..+.+........++.
T Consensus       231 ~~~i~~i~~~i~~~~~~~~~~~~i~~l~~~i~~~~~~~~q~ilfSAT~~~~~~~~---~l~~~ll~~~v~~~~~~~rnI~  307 (1176)
T PRK09401        231 EEDIEKAMELIRLKRKYEEIYEKIRELEEKIAELKDKKGVLVVSSATGRPRGNRV---KLFRELLGFEVGSPVFYLRNIV  307 (1176)
T ss_pred             HHHHHHHHHhcccccccchhhhHHHHHHHhhhhcccCCceEEEEeCCCCccchHH---HHhhccceEEecCcccccCCce
Confidence             456666665543                        67899999999763 322   2233444444444444556677


Q ss_pred             EEEEEccchhhhHHHHHHHHHhccCCCeEEEeCCHhh---HHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCc
Q 017573          211 QFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRK---VDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSR  287 (369)
Q Consensus       211 ~~~~~~~~~~~~~~~l~~~~~~~~~~k~lv~~~~~~~---~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~  287 (369)
                      +.+....   .+...+..++.... .++||||++.+.   ++.+++.|+..|+++..+||++     .+.++.|++|+++
T Consensus       308 ~~yi~~~---~k~~~L~~ll~~l~-~~~LIFv~t~~~~~~ae~l~~~L~~~gi~v~~~hg~l-----~~~l~~F~~G~~~  378 (1176)
T PRK09401        308 DSYIVDE---DSVEKLVELVKRLG-DGGLIFVPSDKGKEYAEELAEYLEDLGINAELAISGF-----ERKFEKFEEGEVD  378 (1176)
T ss_pred             EEEEEcc---cHHHHHHHHHHhcC-CCEEEEEecccChHHHHHHHHHHHHCCCcEEEEeCcH-----HHHHHHHHCCCCC
Confidence            7776554   35566777776654 589999999777   9999999999999999999998     2345999999999


Q ss_pred             EEEE----ecCCcCCCCCCC-CcEEEEecCCC
Q 017573          288 VLIT----TDLLARGIDVQQ-VSLVINYDLPT  314 (369)
Q Consensus       288 vli~----t~~~~~G~d~~~-~~~vi~~~~~~  314 (369)
                      |||+    |+.+++|+|+|+ ++.||+++.|.
T Consensus       379 VLVatas~tdv~aRGIDiP~~IryVI~y~vP~  410 (1176)
T PRK09401        379 VLVGVASYYGVLVRGIDLPERIRYAIFYGVPK  410 (1176)
T ss_pred             EEEEecCCCCceeecCCCCcceeEEEEeCCCC
Confidence            9999    588999999999 89999988775

>COG1204 Superfamily II helicase [General function prediction only]

Probab=100.00  E-value=3.6e-39  Score=299.67  Aligned_cols=334  Identities=23%  Similarity=0.302  Sum_probs=249.0

Q ss_pred             CCHHHHHHHHhCCCCCCcHhhhhhhhccccC-CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHH
Q 017573            3 LQENLLRGIYAYGFEKPSAIQQRGIVPFCKG-LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIE   81 (369)
Q Consensus         3 l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~-~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~   81 (369)
                      +++.+..-++..++.++.+.|+.++.....+ +|+++++|||+|||++++++++..+.++  +.+++|+||+++|+.+..
T Consensus        16 ~~~~v~~i~~~~~~~el~~~qq~av~~~~~~~~N~li~aPTgsGKTlIA~lai~~~l~~~--~~k~vYivPlkALa~Ek~   93 (766)
T COG1204          16 LDDRVLEILKGDGIDELFNPQQEAVEKGLLSDENVLISAPTGSGKTLIALLAILSTLLEG--GGKVVYIVPLKALAEEKY   93 (766)
T ss_pred             ccHHHHHHhccCChHHhhHHHHHHhhccccCCCcEEEEcCCCCchHHHHHHHHHHHHHhc--CCcEEEEeChHHHHHHHH
Confidence            6778888888899999999999999887765 9999999999999999999999999876  238999999999999999


Q ss_pred             HHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHH
Q 017573           82 KVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYD  161 (369)
Q Consensus        82 ~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~  161 (369)
                      ++|++ ...+|++|...+|+......   ...+++|+|+|||+|....++.......+++||+||+|.+.+......+..
T Consensus        94 ~~~~~-~~~~GirV~~~TgD~~~~~~---~l~~~~ViVtT~EK~Dsl~R~~~~~~~~V~lvViDEiH~l~d~~RG~~lE~  169 (766)
T COG1204          94 EEFSR-LEELGIRVGISTGDYDLDDE---RLARYDVIVTTPEKLDSLTRKRPSWIEEVDLVVIDEIHLLGDRTRGPVLES  169 (766)
T ss_pred             HHhhh-HHhcCCEEEEecCCcccchh---hhccCCEEEEchHHhhHhhhcCcchhhcccEEEEeeeeecCCcccCceehh
Confidence            99993 34569999999998874442   134689999999999988888777677799999999999887644444444


Q ss_pred             HHhh---CCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCcc-ccccceeEEEEEcc-ch-----hhhHHHHHHHHH
Q 017573          162 IFQL---LPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDE-LTLEGIKQFYVNVE-KE-----EWKLETLCDLYE  231 (369)
Q Consensus       162 ~~~~---~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~-~~-----~~~~~~l~~~~~  231 (369)
                      +...   .....+++++|||.+ +..+...++-.++......... .........+.... ..     ......+.....
T Consensus       170 iv~r~~~~~~~~rivgLSATlp-N~~evA~wL~a~~~~~~~rp~~l~~~v~~~~~~~~~~~~~k~~~~~~~~~~~~~v~~  248 (766)
T COG1204         170 IVARMRRLNELIRIVGLSATLP-NAEEVADWLNAKLVESDWRPVPLRRGVPYVGAFLGADGKKKTWPLLIDNLALELVLE  248 (766)
T ss_pred             HHHHHHhhCcceEEEEEeeecC-CHHHHHHHhCCcccccCCCCcccccCCccceEEEEecCccccccccchHHHHHHHHH
Confidence            4333   334479999999996 6667776666665421111111 11111111111111 11     111222333333


Q ss_pred             hc-cCCCeEEEeCCHhhHHHHHHHHhhC-------------------------------------CCeeEEecCCCCHHH
Q 017573          232 TL-AITQSVIFVNTRRKVDWLTDKMRSR-------------------------------------DHTVSATHGDMDQNT  273 (369)
Q Consensus       232 ~~-~~~k~lv~~~~~~~~~~~~~~l~~~-------------------------------------~~~~~~~~~~~~~~~  273 (369)
                      .. .++.++|||++++.+...++.+...                                     -..+++.|++++.++
T Consensus       249 ~~~~~~qvLvFv~sR~~a~~~A~~l~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~l~e~v~~GvafHhAGL~~~~  328 (766)
T COG1204         249 SLAEGGQVLVFVHSRKEAEKTAKKLRIKMSATLSDDEKIVLDEGASPILIPETPTSEDEELAELVLRGVAFHHAGLPRED  328 (766)
T ss_pred             HHhcCCeEEEEEecCchHHHHHHHHHHHHhhcCChhhhhhccccccccccccccccchHHHHHHHHhCccccccCCCHHH
Confidence            33 4569999999999999888888731                                     123788999999999


Q ss_pred             HHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEE----ec-----CCCCccchhhhhcccccCCC--ceeEEEEeccc
Q 017573          274 RDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVIN----YD-----LPTQPENYLHRIGRSGRFGR--KGVAINFVTRD  342 (369)
Q Consensus       274 r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~----~~-----~~~~~~~~~Q~~GR~~R~~~--~~~~~~~~~~~  342 (369)
                      |..+.+.|+.|.++||++|+.+..|+|.|.-++||-    ++     .+.+..++.|++||+||.|-  .|.++++....
T Consensus       329 R~~vE~~Fr~g~ikVlv~TpTLA~GVNLPA~~VIIk~~~~y~~~~g~~~i~~~dv~QM~GRAGRPg~d~~G~~~i~~~~~  408 (766)
T COG1204         329 RQLVEDAFRKGKIKVLVSTPTLAAGVNLPARTVIIKDTRRYDPKGGIVDIPVLDVLQMAGRAGRPGYDDYGEAIILATSH  408 (766)
T ss_pred             HHHHHHHHhcCCceEEEechHHhhhcCCcceEEEEeeeEEEcCCCCeEECchhhHhhccCcCCCCCcCCCCcEEEEecCc
Confidence            999999999999999999999999999996666652    33     23456789999999999874  47777777444


Q ss_pred             c
Q 017573          343 D  343 (369)
Q Consensus       343 ~  343 (369)
                      +
T Consensus       409 ~  409 (766)
T COG1204         409 D  409 (766)
T ss_pred             c
Confidence            3

>TIGR00603 rad25 DNA repair helicase rad25

Probab=100.00  E-value=6.5e-39  Score=292.82  Aligned_cols=310  Identities=15%  Similarity=0.132  Sum_probs=218.2

Q ss_pred             CCCcHhhhhhhhccccC---CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCc
Q 017573           17 EKPSAIQQRGIVPFCKG---LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGV   93 (369)
Q Consensus        17 ~~~~~~Q~~~~~~~~~~---~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~   93 (369)
                      ..|||||++++..+..+   ++.++++|||+|||++++.++... .     .++|||||+..|+.||.+++.++......
T Consensus       254 ~~LRpYQ~eAl~~~~~~gr~r~GIIvLPtGaGKTlvai~aa~~l-~-----k~tLILvps~~Lv~QW~~ef~~~~~l~~~  327 (732)
T TIGR00603       254 TQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGVTAACTV-K-----KSCLVLCTSAVSVEQWKQQFKMWSTIDDS  327 (732)
T ss_pred             CCcCHHHHHHHHHHHhcCCCCCcEEEeCCCCChHHHHHHHHHHh-C-----CCEEEEeCcHHHHHHHHHHHHHhcCCCCc
Confidence            57999999999998743   478999999999999987665532 1     27999999999999999999998654455


Q ss_pred             EEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHc--------CCCCCCCccEEEEechhHhhccCcHHHHHHHHhh
Q 017573           94 KVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRR--------QSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQL  165 (369)
Q Consensus        94 ~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~--------~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~  165 (369)
                      .+....++....     ......|+|+|++++.....+        ..+....|+++|+||||++.+..    ...+...
T Consensus       328 ~I~~~tg~~k~~-----~~~~~~VvVtTYq~l~~~~~r~~~~~~~l~~l~~~~~gLII~DEvH~lpA~~----fr~il~~  398 (732)
T TIGR00603       328 QICRFTSDAKER-----FHGEAGVVVSTYSMVAHTGKRSYESEKVMEWLTNREWGLILLDEVHVVPAAM----FRRVLTI  398 (732)
T ss_pred             eEEEEecCcccc-----cccCCcEEEEEHHHhhcccccchhhhHHHHHhccccCCEEEEEccccccHHH----HHHHHHh
Confidence            666666654321     123468999999988532211        11233458999999999985443    3345555


Q ss_pred             CCccCcEEEEEeeCChhHHH--HHHHhcCCCEEEEecCccc------cccceeEEEEEcc--------------------
Q 017573          166 LPAKVQVGVFSATMPPEALE--ITRKFMNKPVRILVKRDEL------TLEGIKQFYVNVE--------------------  217 (369)
Q Consensus       166 ~~~~~~~i~~saT~~~~~~~--~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~--------------------  217 (369)
                      +.. ...+++||||..+...  .+..+++. ..+.....+.      .+......++...                    
T Consensus       399 l~a-~~RLGLTATP~ReD~~~~~L~~LiGP-~vye~~~~eLi~~G~LA~~~~~ev~v~~t~~~~~~yl~~~~~~k~~l~~  476 (732)
T TIGR00603       399 VQA-HCKLGLTATLVREDDKITDLNFLIGP-KLYEANWMELQKKGFIANVQCAEVWCPMTPEFYREYLRENSRKRMLLYV  476 (732)
T ss_pred             cCc-CcEEEEeecCcccCCchhhhhhhcCC-eeeecCHHHHHhCCccccceEEEEEecCCHHHHHHHHHhcchhhhHHhh
Confidence            543 3479999999643221  22223332 2222211111      1111111111111                    


Q ss_pred             chhhhHHHHHHHHHhc--cCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcC-CCcEEEEecC
Q 017573          218 KEEWKLETLCDLYETL--AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSG-SSRVLITTDL  294 (369)
Q Consensus       218 ~~~~~~~~l~~~~~~~--~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~-~~~vli~t~~  294 (369)
                      ....+...+..++..+  .+.++||||.+...+..+++.|.     +..++|+++..+|.++++.|++| .+++||+|++
T Consensus       477 ~np~K~~~~~~Li~~he~~g~kiLVF~~~~~~l~~~a~~L~-----~~~I~G~ts~~ER~~il~~Fr~~~~i~vLv~SkV  551 (732)
T TIGR00603       477 MNPNKFRACQFLIRFHEQRGDKIIVFSDNVFALKEYAIKLG-----KPFIYGPTSQQERMQILQNFQHNPKVNTIFLSKV  551 (732)
T ss_pred             hChHHHHHHHHHHHHHhhcCCeEEEEeCCHHHHHHHHHHcC-----CceEECCCCHHHHHHHHHHHHhCCCccEEEEecc
Confidence            1122445555566544  66799999999999999998872     46789999999999999999875 7899999999


Q ss_pred             CcCCCCCCCCcEEEEecCC-CCccchhhhhcccccCCCceeE-------EEEeccccHHHHH
Q 017573          295 LARGIDVQQVSLVINYDLP-TQPENYLHRIGRSGRFGRKGVA-------INFVTRDDERMLF  348 (369)
Q Consensus       295 ~~~G~d~~~~~~vi~~~~~-~~~~~~~Q~~GR~~R~~~~~~~-------~~~~~~~~~~~~~  348 (369)
                      +.+|+|+|++++||+++.+ .|...|.||+||++|.+..|.+       |.+++.++.++..
T Consensus       552 gdeGIDlP~a~vvI~~s~~~gS~~q~iQRlGRilR~~~~~~~~~~~A~fY~lVs~dT~E~~~  613 (732)
T TIGR00603       552 GDTSIDLPEANVLIQISSHYGSRRQEAQRLGRILRAKKGSDAEEYNAFFYSLVSKDTQEMYY  613 (732)
T ss_pred             cccccCCCCCCEEEEeCCCCCCHHHHHHHhcccccCCCCCccccccceEEEEecCCchHHHH
Confidence            9999999999999999987 5999999999999999766554       8888887666553

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).

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

Probab=100.00  E-value=7e-39  Score=287.09  Aligned_cols=327  Identities=22%  Similarity=0.273  Sum_probs=230.6

Q ss_pred             CCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEE
Q 017573           16 FEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKV   95 (369)
Q Consensus        16 ~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v   95 (369)
                      ...+|+||.+++...+ ++|++|++|||+|||++|...+.+++...+. .|+++++|++-|+.|+...+..++..  ..+
T Consensus        60 ~~~lR~YQ~eivq~AL-gkNtii~lPTG~GKTfIAa~Vm~nh~rw~p~-~KiVF~aP~~pLv~QQ~a~~~~~~~~--~~~  135 (746)
T KOG0354|consen   60 NLELRNYQEELVQPAL-GKNTIIALPTGSGKTFIAAVIMKNHFEWRPK-GKVVFLAPTRPLVNQQIACFSIYLIP--YSV  135 (746)
T ss_pred             cccccHHHHHHhHHhh-cCCeEEEeecCCCccchHHHHHHHHHhcCCc-ceEEEeeCCchHHHHHHHHHhhccCc--ccc
Confidence            3579999999999999 9999999999999999999999988877655 49999999999999999888887654  455


Q ss_pred             EEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCC-CCccEEEEechhHhhccCcHHHHH-HHHhhCCccCcEE
Q 017573           96 HACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRP-DYIKMFVLDEADEMLSRGFKDQIY-DIFQLLPAKVQVG  173 (369)
Q Consensus        96 ~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~-~~~~~viiDE~H~~~~~~~~~~~~-~~~~~~~~~~~~i  173 (369)
                      ....++.........+....+|+|+||+.+...+.+..... +.|.++|+||||+......+..+. ..+..-....|++
T Consensus       136 T~~l~~~~~~~~r~~i~~s~~vff~TpQil~ndL~~~~~~~ls~fs~iv~DE~Hra~kn~~Y~~Vmr~~l~~k~~~~qIL  215 (746)
T KOG0354|consen  136 TGQLGDTVPRSNRGEIVASKRVFFRTPQILENDLKSGLHDELSDFSLIVFDECHRTSKNHPYNNIMREYLDLKNQGNQIL  215 (746)
T ss_pred             eeeccCccCCCchhhhhcccceEEeChHhhhhhcccccccccceEEEEEEcccccccccccHHHHHHHHHHhhhccccEE
Confidence            55555544333333344557999999999999888876665 889999999999987554444444 4444444455999


Q ss_pred             EEEeeCChhHHHHHH---HhcCC----------------------CEEE------------------------------E
Q 017573          174 VFSATMPPEALEITR---KFMNK----------------------PVRI------------------------------L  198 (369)
Q Consensus       174 ~~saT~~~~~~~~~~---~~~~~----------------------~~~~------------------------------~  198 (369)
                      ++||||+.+......   .++-.                      +..+                              .
T Consensus       216 gLTASpG~~~~~v~~~I~~L~asldvr~~ssi~~~y~~lr~~~~i~v~~~~~~~~~~~~f~~~i~p~l~~l~~~~l~~~~  295 (746)
T KOG0354|consen  216 GLTASPGSKLEQVQNVIDNLCASLDVRTESSIKSNYEELREHVQIPVDLSLCERDIEDPFGMIIEPLLQQLQEEGLIEIS  295 (746)
T ss_pred             EEecCCCccHHHHHHHHHhhheecccchhhhhhhhHHHHhccCcccCcHHHhhhhhhhhHHHHHHHHHHHHHhcCccccc
Confidence            999999854433211   11100                      0000                              0


Q ss_pred             ecC----------cccccc--------------------------cee--------------------------------
Q 017573          199 VKR----------DELTLE--------------------------GIK--------------------------------  210 (369)
Q Consensus       199 ~~~----------~~~~~~--------------------------~~~--------------------------------  210 (369)
                      ...          ......                          .++                                
T Consensus       296 ~~~~~~~~~~~~~~~~~~~~~~~~q~~~f~~~~~~~~~~~ll~~~gir~~~~l~~~~~f~~e~~~~k~~~~~~e~~~~~~  375 (746)
T KOG0354|consen  296 DKSTSYEQWVVQAEKAAAPNGPENQRNCFYALHLRKYNLALLISDGIRFVDALDYLEDFYEEVALKKYLKLELEARLIRN  375 (746)
T ss_pred             cccccccchhhhhhhhhccCCCccchhhHHHHHHHHHHHHHHhhcchhhHHHHhhhhhhccccchhHHHHHHhcchhhHH
Confidence            000          000000                          000                                


Q ss_pred             ---------EEEEEccchhhhHHHHHHHHH----hccCCCeEEEeCCHhhHHHHHHHHhhC---CCeeEEec--------
Q 017573          211 ---------QFYVNVEKEEWKLETLCDLYE----TLAITQSVIFVNTRRKVDWLTDKMRSR---DHTVSATH--------  266 (369)
Q Consensus       211 ---------~~~~~~~~~~~~~~~l~~~~~----~~~~~k~lv~~~~~~~~~~~~~~l~~~---~~~~~~~~--------  266 (369)
                               +.....+....+++.+.+++.    ..+..++|||+..++.|..+.+.|.+.   +++...+-        
T Consensus       376 ~~~~m~~~~~l~~~~~~~npkle~l~~~l~e~f~~~~dsR~IIFve~R~sa~~l~~~l~~~~~~~ir~~~fiGq~~s~~~  455 (746)
T KOG0354|consen  376 FTENMNELEHLSLDPPKENPKLEKLVEILVEQFEQNPDSRTIIFVETRESALALKKWLLQLHELGIKAEIFIGQGKSTQS  455 (746)
T ss_pred             HHHHHHhhhhhhcCCCccChhHHHHHHHHHHHhhcCCCccEEEEEehHHHHHHHHHHHHhhhhcccccceeeeccccccc
Confidence                     000000000013333433332    234568999999999999999999832   22222222        


Q ss_pred             CCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCCCCccchhhhhcccccCCCceeEEEEeccccHHH
Q 017573          267 GDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERM  346 (369)
Q Consensus       267 ~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~  346 (369)
                      .+|++.++.+++++|++|+++|||||+++++|+|++.|+.||.|+...|+...+||.|| ||. +.|.++++.+......
T Consensus       456 ~gmtqk~Q~evl~~Fr~G~~NvLVATSV~EEGLDI~ec~lVIcYd~~snpIrmIQrrGR-gRa-~ns~~vll~t~~~~~~  533 (746)
T KOG0354|consen  456 TGMTQKEQKEVLDKFRDGEINVLVATSVAEEGLDIGECNLVICYDYSSNPIRMVQRRGR-GRA-RNSKCVLLTTGSEVIE  533 (746)
T ss_pred             cccCHHHHHHHHHHHhCCCccEEEEecchhccCCcccccEEEEecCCccHHHHHHHhcc-ccc-cCCeEEEEEcchhHHH
Confidence            36889999999999999999999999999999999999999999999999999999999 997 5688888888554444


Q ss_pred             HH
Q 017573          347 LF  348 (369)
Q Consensus       347 ~~  348 (369)
                      .+
T Consensus       534 ~E  535 (746)
T KOG0354|consen  534 FE  535 (746)
T ss_pred             HH
Confidence            43

>PRK13766 Hef nuclease; Provisional

Probab=100.00  E-value=7.6e-38  Score=300.84  Aligned_cols=330  Identities=20%  Similarity=0.251  Sum_probs=241.2

Q ss_pred             HHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccc
Q 017573           11 IYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDY   90 (369)
Q Consensus        11 l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~   90 (369)
                      +-.-+..++|+||++++..+.++ ++++++|||+|||.++++.+...+.  ..+.++||++|+++|+.||.+.++++...
T Consensus         8 ~~~~~~~~~r~yQ~~~~~~~l~~-n~lv~~ptG~GKT~~a~~~i~~~l~--~~~~~vLvl~Pt~~L~~Q~~~~~~~~~~~   84 (773)
T PRK13766          8 LIKPNTIEARLYQQLLAATALKK-NTLVVLPTGLGKTAIALLVIAERLH--KKGGKVLILAPTKPLVEQHAEFFRKFLNI   84 (773)
T ss_pred             ccCcCcCCccHHHHHHHHHHhcC-CeEEEcCCCccHHHHHHHHHHHHHH--hCCCeEEEEeCcHHHHHHHHHHHHHHhCC
Confidence            33335568999999999888776 9999999999999998888887763  23348999999999999999999988654


Q ss_pred             cCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCccC
Q 017573           91 LGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKV  170 (369)
Q Consensus        91 ~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~  170 (369)
                      .+..+..++|+........ ...+++|+|+||+.+...+.........++++|+||||++.+......+...+.......
T Consensus        85 ~~~~v~~~~g~~~~~~r~~-~~~~~~iiv~T~~~l~~~l~~~~~~~~~~~liVvDEaH~~~~~~~~~~i~~~~~~~~~~~  163 (773)
T PRK13766         85 PEEKIVVFTGEVSPEKRAE-LWEKAKVIVATPQVIENDLIAGRISLEDVSLLIFDEAHRAVGNYAYVYIAERYHEDAKNP  163 (773)
T ss_pred             CCceEEEEeCCCCHHHHHH-HHhCCCEEEECHHHHHHHHHcCCCChhhCcEEEEECCccccccccHHHHHHHHHhcCCCC
Confidence            4557777888776554333 344579999999999888877777788899999999999875543444444444444567


Q ss_pred             cEEEEEeeCChhHHH---HHHHhcCCCEEEEecCcc--------------------------------------------
Q 017573          171 QVGVFSATMPPEALE---ITRKFMNKPVRILVKRDE--------------------------------------------  203 (369)
Q Consensus       171 ~~i~~saT~~~~~~~---~~~~~~~~~~~~~~~~~~--------------------------------------------  203 (369)
                      +++++||||..+...   ....+....+.+......                                            
T Consensus       164 ~il~lTaTP~~~~~~i~~~~~~L~i~~v~~~~~~~~~v~~~~~~~~v~~~~v~l~~~~~~i~~~l~~~~~~~l~~l~~~~  243 (773)
T PRK13766        164 LVLGLTASPGSDEEKIKEVCENLGIEHVEVRTEDDPDVKPYVHKVKIEWVRVELPEELKEIRDLLNEALKDRLKKLKELG  243 (773)
T ss_pred             EEEEEEcCCCCCHHHHHHHHHhCCceEEEEcCCCChhHHhhhccceeEEEEeCCcHHHHHHHHHHHHHHHHHHHHHHHCC
Confidence            799999999543221   122211111100000000                                            


Q ss_pred             cc--cc-----------------ceeEEE---------------------------------------------------
Q 017573          204 LT--LE-----------------GIKQFY---------------------------------------------------  213 (369)
Q Consensus       204 ~~--~~-----------------~~~~~~---------------------------------------------------  213 (369)
                      ..  ..                 .+....                                                   
T Consensus       244 ~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~y~~~l~~~~~~~~~~~~~  323 (773)
T PRK13766        244 VIVSISPDVSKKELLGLQKKLQQEIANDDSEGYEAISILAEAMKLRHAVELLETQGVEALRRYLERLREEARSSGGSKAS  323 (773)
T ss_pred             CcccCCCCcCHHHHHHHHHHHHHHhhcCchHHHHHHHHHHHHHHHHHHHHHHHHhCHHHHHHHHHHHHhhccccCCcHHH
Confidence            00  00                 000000                                                   


Q ss_pred             ----------------EEccchhhhHHHHHHHHHh----ccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCC-----
Q 017573          214 ----------------VNVEKEEWKLETLCDLYET----LAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGD-----  268 (369)
Q Consensus       214 ----------------~~~~~~~~~~~~l~~~~~~----~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~-----  268 (369)
                                      ........+.+.+.+++..    ..+.++||||++.+.+..+.+.|...+..+..++|.     
T Consensus       324 ~~l~~~~~~~~~~~~~~~~~~~~pK~~~L~~il~~~~~~~~~~kvlIF~~~~~t~~~L~~~L~~~~~~~~~~~g~~~~~~  403 (773)
T PRK13766        324 KRLVEDPRFRKAVRKAKELDIEHPKLEKLREIVKEQLGKNPDSRIIVFTQYRDTAEKIVDLLEKEGIKAVRFVGQASKDG  403 (773)
T ss_pred             HHHHhCHHHHHHHHHHHhcccCChHHHHHHHHHHHHHhcCCCCeEEEEeCcHHHHHHHHHHHHhCCCceEEEEccccccc
Confidence                            0000112234444455533    456799999999999999999999989988888886     


Q ss_pred             ---CCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCCCCccchhhhhcccccCCCceeEEEEeccccHH
Q 017573          269 ---MDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDER  345 (369)
Q Consensus       269 ---~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~  345 (369)
                         ++..+|.++++.|++|+.++||+|+++++|+|+|.+++||++++++++..++||+||+||.+. |.+++++..++.+
T Consensus       404 ~~~~~~~~r~~~~~~F~~g~~~vLvaT~~~~eGldi~~~~~VI~yd~~~s~~r~iQR~GR~gR~~~-~~v~~l~~~~t~e  482 (773)
T PRK13766        404 DKGMSQKEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEPVPSEIRSIQRKGRTGRQEE-GRVVVLIAKGTRD  482 (773)
T ss_pred             cCCCCHHHHHHHHHHHHcCCCCEEEECChhhcCCCcccCCEEEEeCCCCCHHHHHHHhcccCcCCC-CEEEEEEeCCChH
Confidence               888999999999999999999999999999999999999999999999999999999999865 8888888766443

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

Probab=100.00  E-value=3.6e-38  Score=297.00  Aligned_cols=349  Identities=23%  Similarity=0.337  Sum_probs=275.0

Q ss_pred             CHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHH
Q 017573            4 QENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKV   83 (369)
Q Consensus         4 ~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~   83 (369)
                      +..+..+|.+.|+..||+||.+|+..+.+|++++|..|||||||.++++++++.+...... ++|+|.|+++|++++.+.
T Consensus        56 ~~~l~~~l~~~g~~~lY~HQ~~A~~~~~~G~~vvVtTgTgSGKTe~FllPIld~~l~~~~a-~AL~lYPtnALa~DQ~~r  134 (851)
T COG1205          56 DESLKSALVKAGIERLYSHQVDALRLIREGRNVVVTTGTGSGKTESFLLPILDHLLRDPSA-RALLLYPTNALANDQAER  134 (851)
T ss_pred             hhHHHHHHHHhccccccHHHHHHHHHHHCCCCEEEECCCCCchhHHHHHHHHHHHhhCcCc-cEEEEechhhhHhhHHHH
Confidence            3456778889999999999999999999999999999999999999999999999887765 899999999999999999


Q ss_pred             HHHhccccC--cEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCC----CCCCCccEEEEechhHhhccC---
Q 017573           84 MRALGDYLG--VKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQS----LRPDYIKMFVLDEADEMLSRG---  154 (369)
Q Consensus        84 ~~~~~~~~~--~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~----~~~~~~~~viiDE~H~~~~~~---  154 (369)
                      ++++....+  ++....+|+.+......+..++++|++|||+++...+.++.    ...+++++||+||+|.+....   
T Consensus       135 l~~~~~~~~~~v~~~~y~Gdt~~~~r~~~~~~pp~IllTNpdMLh~~llr~~~~~~~~~~~Lk~lVvDElHtYrGv~GS~  214 (851)
T COG1205         135 LRELISDLPGKVTFGRYTGDTPPEERRAIIRNPPDILLTNPDMLHYLLLRNHDAWLWLLRNLKYLVVDELHTYRGVQGSE  214 (851)
T ss_pred             HHHHHHhCCCcceeeeecCCCChHHHHHHHhCCCCEEEeCHHHHHHHhccCcchHHHHHhcCcEEEEecceeccccchhH
Confidence            999988877  78888889888777778888999999999999987554432    334568999999999875432   


Q ss_pred             ---cHHHHHHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccc--------hhhhH
Q 017573          155 ---FKDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEK--------EEWKL  223 (369)
Q Consensus       155 ---~~~~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------~~~~~  223 (369)
                         ..+.+..++...++..|+++.|||.. +..+....+.+......+..+.. +.....+....+.        .....
T Consensus       215 vA~llRRL~~~~~~~~~~~q~i~~SAT~~-np~e~~~~l~~~~f~~~v~~~g~-~~~~~~~~~~~p~~~~~~~~~r~s~~  292 (851)
T COG1205         215 VALLLRRLLRRLRRYGSPLQIICTSATLA-NPGEFAEELFGRDFEVPVDEDGS-PRGLRYFVRREPPIRELAESIRRSAL  292 (851)
T ss_pred             HHHHHHHHHHHHhccCCCceEEEEecccc-ChHHHHHHhcCCcceeeccCCCC-CCCceEEEEeCCcchhhhhhcccchH
Confidence               22555566666677899999999996 55567777777766664333322 3333333333330        11233


Q ss_pred             HHHHHHHHhc--cCCCeEEEeCCHhhHHHHH----HHHhhCC----CeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEec
Q 017573          224 ETLCDLYETL--AITQSVIFVNTRRKVDWLT----DKMRSRD----HTVSATHGDMDQNTRDIIMREFRSGSSRVLITTD  293 (369)
Q Consensus       224 ~~l~~~~~~~--~~~k~lv~~~~~~~~~~~~----~~l~~~~----~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~  293 (369)
                      ..+..+....  .+-++|+|+.+++.++.+.    +.+...+    ..+..+++.+..++|.++...|+.|+..++++|+
T Consensus       293 ~~~~~~~~~~~~~~~~tL~F~~sr~~~e~~~~~~~~~~~~~~~~l~~~v~~~~~~~~~~er~~ie~~~~~g~~~~~~st~  372 (851)
T COG1205         293 AELATLAALLVRNGIQTLVFFRSRKQVELLYLSPRRRLVREGGKLLDAVSTYRAGLHREERRRIEAEFKEGELLGVIATN  372 (851)
T ss_pred             HHHHHHHHHHHHcCceEEEEEehhhhhhhhhhchhHHHhhcchhhhhheeeccccCCHHHHHHHHHHHhcCCccEEecch
Confidence            4444444332  3459999999999999886    4444445    5789999999999999999999999999999999


Q ss_pred             CCcCCCCCCCCcEEEEecCCC-CccchhhhhcccccCCCceeEEEEeccc--cHHHHHHHHHHhc
Q 017573          294 LLARGIDVQQVSLVINYDLPT-QPENYLHRIGRSGRFGRKGVAINFVTRD--DERMLFDIQKFYN  355 (369)
Q Consensus       294 ~~~~G~d~~~~~~vi~~~~~~-~~~~~~Q~~GR~~R~~~~~~~~~~~~~~--~~~~~~~~~~~~~  355 (369)
                      +++-|+|+.+++.||..+.|. +..++.|+.||+||.++.+..+.+....  |..+...-+.++.
T Consensus       373 AlelgidiG~ldavi~~g~P~~s~~~~~Q~~GRaGR~~~~~l~~~v~~~~~~d~yy~~~p~~~~~  437 (851)
T COG1205         373 ALELGIDIGSLDAVIAYGYPGVSVLSFRQRAGRAGRRGQESLVLVVLRSDPLDSYYLRHPEELLE  437 (851)
T ss_pred             hhhhceeehhhhhHhhcCCCCchHHHHHHhhhhccCCCCCceEEEEeCCCccchhhhhCcHhhhh
Confidence            999999999999999999999 8999999999999998777666665532  4444444455554

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

Probab=100.00  E-value=8.1e-40  Score=253.07  Aligned_cols=327  Identities=42%  Similarity=0.721  Sum_probs=288.6

Q ss_pred             CCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHH
Q 017573            3 LQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEK   82 (369)
Q Consensus         3 l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~   82 (369)
                      |.|++.+++.+.||++|+..|.+.++...-|-+++++|..|.|||.++.++.++++..-.....++++|.+++|+-|..+
T Consensus        49 lkpellraivdcgfehpsevqhecipqailgmdvlcqaksgmgktavfvl~tlqqiepv~g~vsvlvmchtrelafqi~~  128 (387)
T KOG0329|consen   49 LKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQIEPVDGQVSVLVMCHTRELAFQISK  128 (387)
T ss_pred             cCHHHHHHHHhccCCCchHhhhhhhhHHhhcchhheecccCCCceeeeehhhhhhcCCCCCeEEEEEEeccHHHHHHHHH
Confidence            78999999999999999999999999999999999999999999999999999999877777789999999999999999


Q ss_pred             HHHHhcccc-CcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhc-cCcHHHHH
Q 017573           83 VMRALGDYL-GVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLS-RGFKDQIY  160 (369)
Q Consensus        83 ~~~~~~~~~-~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~-~~~~~~~~  160 (369)
                      +..+|.+.. +.++.+..|+.....+...+++-++|+|+||.++..+.++..+++.++...|+|||+.+.. ....+...
T Consensus       129 ey~rfskymP~vkvaVFfGG~~Ikkdee~lk~~PhivVgTPGrilALvr~k~l~lk~vkhFvlDEcdkmle~lDMrRDvQ  208 (387)
T KOG0329|consen  129 EYERFSKYMPSVKVSVFFGGLFIKKDEELLKNCPHIVVGTPGRILALVRNRSLNLKNVKHFVLDECDKMLEQLDMRRDVQ  208 (387)
T ss_pred             HHHHHHhhCCCceEEEEEcceeccccHHHHhCCCeEEEcCcHHHHHHHHhccCchhhcceeehhhHHHHHHHHHHHHHHH
Confidence            988887766 6789999999998888888888889999999999999999999999999999999998763 45678899


Q ss_pred             HHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCcc-ccccceeEEEEEccchhhhHHHHHHHHHhccCCCeE
Q 017573          161 DIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDE-LTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSV  239 (369)
Q Consensus       161 ~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~l  239 (369)
                      .+.+..|...|+..+|||.+.++.-...+++.+|..+.++.+. ....++.++|..+... .+...+.+++....-..++
T Consensus       209 Eifr~tp~~KQvmmfsatlskeiRpvC~kFmQdPmEi~vDdE~KLtLHGLqQ~YvkLke~-eKNrkl~dLLd~LeFNQVv  287 (387)
T KOG0329|consen  209 EIFRMTPHEKQVMMFSATLSKEIRPVCHKFMQDPMEIFVDDEAKLTLHGLQQYYVKLKEN-EKNRKLNDLLDVLEFNQVV  287 (387)
T ss_pred             HHhhcCcccceeeeeeeecchhhHHHHHhhhcCchhhhccchhhhhhhhHHHHHHhhhhh-hhhhhhhhhhhhhhhccee
Confidence            9999999999999999999999999999999999887766543 4566777777776653 4677778888877778999


Q ss_pred             EEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCCCCccch
Q 017573          240 IFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENY  319 (369)
Q Consensus       240 v~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~  319 (369)
                      ||+.+.....                               |   ..+ +++|+..++|+|+.+++.++.++.|.++.+|
T Consensus       288 IFvKsv~Rl~-------------------------------f---~kr-~vat~lfgrgmdiervNi~~NYdmp~~~DtY  332 (387)
T KOG0329|consen  288 IFVKSVQRLS-------------------------------F---QKR-LVATDLFGRGMDIERVNIVFNYDMPEDSDTY  332 (387)
T ss_pred             Eeeehhhhhh-------------------------------h---hhh-hHHhhhhccccCcccceeeeccCCCCCchHH
Confidence            9998875500                               2   223 8899999999999999999999999999999


Q ss_pred             hhhhcccccCCCceeEEEEecc-ccHHHHHHHHHHhccccccCCcch
Q 017573          320 LHRIGRSGRFGRKGVAINFVTR-DDERMLFDIQKFYNVVIEELPSNV  365 (369)
Q Consensus       320 ~Q~~GR~~R~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~  365 (369)
                      .++.||+||.|.+|.++.+++. .|.+.+...++.+...+.++|+++
T Consensus       333 lHrv~rAgrfGtkglaitfvs~e~da~iLn~vqdRf~v~i~eLpdei  379 (387)
T KOG0329|consen  333 LHRVARAGRFGTKGLAITFVSDENDAKILNPVQDRFEVNIKELPDEI  379 (387)
T ss_pred             HHHhhhhhccccccceeehhcchhhHHHhchhhHhhhccHhhcCccc
Confidence            9999999999999999999885 577888889999999999988874

>PHA02653 RNA helicase NPH-II; Provisional

Probab=100.00  E-value=1.1e-37  Score=286.09  Aligned_cols=314  Identities=18%  Similarity=0.204  Sum_probs=224.3

Q ss_pred             HhhhhhhhccccCCcEEEEcCCCChhhHHH---------HHHHHHhhh---ccCCCccEEEEcCCHHHHHHHHHHHHHhc
Q 017573           21 AIQQRGIVPFCKGLDVIQQAQSGTGKTATF---------CSGILQQLD---YGLVQCQALVLAPTRELAQQIEKVMRALG   88 (369)
Q Consensus        21 ~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~---------~~~~~~~~~---~~~~~~~~liv~P~~~l~~q~~~~~~~~~   88 (369)
                      ..|+++++.+.++++++++|+||+|||.+.         +++.+..+.   ......++++++|+++|+.|+...+.+..
T Consensus       167 ~iQ~qil~~i~~gkdvIv~A~TGSGKTtqvPq~l~~~~flf~~l~~l~~~~~~~~~~~ilvt~PrreLa~qi~~~i~~~v  246 (675)
T PHA02653        167 DVQLKIFEAWISRKPVVLTGGTGVGKTSQVPKLLLWFNYLFGGFDNLDKIDPNFIERPIVLSLPRVALVRLHSITLLKSL  246 (675)
T ss_pred             HHHHHHHHHHHhCCCEEEECCCCCCchhHHHHHHHHhhhccchhhhhhhcccccCCcEEEEECcHHHHHHHHHHHHHHHh
Confidence            458999999999999999999999999863         122333322   12233489999999999999999988755


Q ss_pred             cc---cCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhh
Q 017573           89 DY---LGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQL  165 (369)
Q Consensus        89 ~~---~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~  165 (369)
                      ..   .+..+....|+... .......+..+++++|+....       ..+++++++|+||+|+....+  ..+..++..
T Consensus       247 g~~~~~g~~v~v~~Gg~~~-~~~~t~~k~~~Ilv~T~~L~l-------~~L~~v~~VVIDEaHEr~~~~--DllL~llk~  316 (675)
T PHA02653        247 GFDEIDGSPISLKYGSIPD-ELINTNPKPYGLVFSTHKLTL-------NKLFDYGTVIIDEVHEHDQIG--DIIIAVARK  316 (675)
T ss_pred             CccccCCceEEEEECCcch-HHhhcccCCCCEEEEeCcccc-------cccccCCEEEccccccCccch--hHHHHHHHH
Confidence            43   35667777887763 211222235689999964211       245668999999999975443  444444444


Q ss_pred             CC-ccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccc---------hhhhHHHHHHHHHh--c
Q 017573          166 LP-AKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEK---------EEWKLETLCDLYET--L  233 (369)
Q Consensus       166 ~~-~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------~~~~~~~l~~~~~~--~  233 (369)
                      .. ...|+++||||++.+...+ ..++.++..+....  .....+.+.+.....         ...+...+..+...  .
T Consensus       317 ~~~~~rq~ILmSATl~~dv~~l-~~~~~~p~~I~I~g--rt~~pV~~~yi~~~~~~~~~~~y~~~~k~~~l~~L~~~~~~  393 (675)
T PHA02653        317 HIDKIRSLFLMTATLEDDRDRI-KEFFPNPAFVHIPG--GTLFPISEVYVKNKYNPKNKRAYIEEEKKNIVTALKKYTPP  393 (675)
T ss_pred             hhhhcCEEEEEccCCcHhHHHH-HHHhcCCcEEEeCC--CcCCCeEEEEeecCcccccchhhhHHHHHHHHHHHHHhhcc
Confidence            33 3358999999998776555 57777776666542  223445555543221         11111222222222  2


Q ss_pred             cCCCeEEEeCCHhhHHHHHHHHhhC--CCeeEEecCCCCHHHHHHHHHHH-hcCCCcEEEEecCCcCCCCCCCCcEEEEe
Q 017573          234 AITQSVIFVNTRRKVDWLTDKMRSR--DHTVSATHGDMDQNTRDIIMREF-RSGSSRVLITTDLLARGIDVQQVSLVINY  310 (369)
Q Consensus       234 ~~~k~lv~~~~~~~~~~~~~~l~~~--~~~~~~~~~~~~~~~r~~~~~~f-~~~~~~vli~t~~~~~G~d~~~~~~vi~~  310 (369)
                      ..+++|||+++.++++.+++.|++.  +..+..+||++++.  ++.++.| ++|+.+|||||+++++|+|+|++++||..
T Consensus       394 ~~g~iLVFlpg~~ei~~l~~~L~~~~~~~~v~~LHG~Lsq~--eq~l~~ff~~gk~kILVATdIAERGIDIp~V~~VID~  471 (675)
T PHA02653        394 KGSSGIVFVASVSQCEEYKKYLEKRLPIYDFYIIHGKVPNI--DEILEKVYSSKNPSIIISTPYLESSVTIRNATHVYDT  471 (675)
T ss_pred             cCCcEEEEECcHHHHHHHHHHHHhhcCCceEEeccCCcCHH--HHHHHHHhccCceeEEeccChhhccccccCeeEEEEC
Confidence            3468999999999999999999887  68999999999875  4566676 68999999999999999999999999999


Q ss_pred             c---CCC---------CccchhhhhcccccCCCceeEEEEeccccHHHHHHH
Q 017573          311 D---LPT---------QPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDI  350 (369)
Q Consensus       311 ~---~~~---------~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~  350 (369)
                      +   .|.         |..++.||.||+||. ++|.|+.++++.+...+..+
T Consensus       472 G~~k~p~~~~g~~~~iSkasa~QRaGRAGR~-~~G~c~rLyt~~~~~pI~ri  522 (675)
T PHA02653        472 GRVYVPEPFGGKEMFISKSMRTQRKGRVGRV-SPGTYVYFYDLDLLKPIKRI  522 (675)
T ss_pred             CCccCCCcccCcccccCHHHHHHhccCcCCC-CCCeEEEEECHHHhHHHHHH
Confidence            8   443         677899999999999 88999999998765444333

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=100.00  E-value=2.3e-37  Score=272.60  Aligned_cols=301  Identities=16%  Similarity=0.177  Sum_probs=203.6

Q ss_pred             cEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHH--------
Q 017573           35 DVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVRE--------  106 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~--------  106 (369)
                      ++++.+|||+|||.+++++++..+.... ..+++|++|+++|+.|+.+.+.+++..   .+...+++.....        
T Consensus         1 ~vvi~apTGsGKT~~~~~~~l~~~~~~~-~~~ii~v~P~~~L~~q~~~~l~~~f~~---~~~~~~~~~~~~~~~~~~~~~   76 (358)
T TIGR01587         1 LLVIEAPTGYGKTEAALLWALHSIKSQK-ADRVIIALPTRATINAMYRRAKELFGS---NLGLLHSSSSFKRIKEMGDSE   76 (358)
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHHHhhCC-CCeEEEEeehHHHHHHHHHHHHHHhCc---ccEEeeccHHHHHHhccCCch
Confidence            4789999999999999999998765433 348999999999999999999987532   2333333222100        


Q ss_pred             ----HHHHH-c-----cCCcEEEeccHHHHHHHHcCCCC------CCCccEEEEechhHhhccCcHHHHHHHHhhCC-cc
Q 017573          107 ----DQRIL-Q-----AGVHVVVGTPGRVFDMLRRQSLR------PDYIKMFVLDEADEMLSRGFKDQIYDIFQLLP-AK  169 (369)
Q Consensus       107 ----~~~~~-~-----~~~~iiv~t~~~l~~~~~~~~~~------~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~-~~  169 (369)
                          ..... .     ...+|+++|++++...+......      .-..+++|+||+|.+....+.. +..++..+. .+
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~I~v~T~~~l~~~~~~~~~~~~~~~~~~~~~~iViDE~h~~~~~~~~~-l~~~l~~l~~~~  155 (358)
T TIGR01587        77 EFEHLFPLYIHSNDKLFLDPITVCTIDQVLKSVFGEFGHYEFTLASIANSLLIFDEVHFYDEYTLAL-ILAVLEVLKDND  155 (358)
T ss_pred             hHHHHHHHHhhchhhhhhCCeeeCCHHHHHHHHhcccchHHHHHHHhcCCEEEEeCCCCCCHHHHHH-HHHHHHHHHHcC
Confidence                00000 0     13579999999998766552110      0113789999999987654322 444444443 46


Q ss_pred             CcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEE-EEccchhhhHHHHHHHHHhc-cCCCeEEEeCCHhh
Q 017573          170 VQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFY-VNVEKEEWKLETLCDLYETL-AITQSVIFVNTRRK  247 (369)
Q Consensus       170 ~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~l~~~~~~~-~~~k~lv~~~~~~~  247 (369)
                      .|++++|||++....+........+........... ....+.+ ........+...+..++... .++++||||++++.
T Consensus       156 ~~~i~~SATlp~~l~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~lVf~~t~~~  234 (358)
T TIGR01587       156 VPILLMSATLPKFLKEYAEKIGYVEFNEPLDLKEER-RFERHRFIKIESDKVGEISSLERLLEFIKKGGKIAIIVNTVDR  234 (358)
T ss_pred             CCEEEEecCchHHHHHHHhcCCCcccccCCCCcccc-ccccccceeeccccccCHHHHHHHHHHhhCCCeEEEEECCHHH
Confidence            789999999986655555444322111111100000 0011111 11112223444555555443 45799999999999


Q ss_pred             HHHHHHHHhhCCC--eeEEecCCCCHHHHHH----HHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCCCCccchhh
Q 017573          248 VDWLTDKMRSRDH--TVSATHGDMDQNTRDI----IMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLH  321 (369)
Q Consensus       248 ~~~~~~~l~~~~~--~~~~~~~~~~~~~r~~----~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q  321 (369)
                      ++.+++.|++.+.  .+..+||++++.+|.+    +++.|++|+.++||||+++++|+|++ ++.+|....|  ...|.|
T Consensus       235 ~~~~~~~L~~~~~~~~~~~~h~~~~~~~r~~~~~~~~~~f~~~~~~ilvaT~~~~~GiDi~-~~~vi~~~~~--~~~~iq  311 (358)
T TIGR01587       235 AQEFYQQLKENAPEEEIMLLHSRFTEKDRAKKEAELLEEMKKNEKFVIVATQVIEASLDIS-ADVMITELAP--IDSLIQ  311 (358)
T ss_pred             HHHHHHHHHhhcCCCeEEEEECCCCHHHHHHHHHHHHHHhcCCCCeEEEECcchhceeccC-CCEEEEcCCC--HHHHHH
Confidence            9999999988765  5999999999999876    48899999999999999999999996 7777766544  679999


Q ss_pred             hhcccccCCCc----eeEEEEeccccH
Q 017573          322 RIGRSGRFGRK----GVAINFVTRDDE  344 (369)
Q Consensus       322 ~~GR~~R~~~~----~~~~~~~~~~~~  344 (369)
                      |+||+||.|+.    |.++++....+.
T Consensus       312 r~GR~gR~g~~~~~~~~~~v~~~~~~~  338 (358)
T TIGR01587       312 RLGRLHRYGRKNGENFEVYIITIAPEG  338 (358)
T ss_pred             HhccccCCCCCCCCCCeEEEEeecCCC
Confidence            99999998754    378888775543

This model represents the highly conserved core region of an alignment of Cas3, a protein found in association with CRISPR repeat elements in a broad range of bacteria and archaea. Cas3 appears to be a helicase, with regions found by pfam00270 (DEAD/DEAH box helicase) and pfam00271 (Helicase conserved C-terminal domain). Some but not all members have an N-terminal HD domain region (pfam01966) that is not included within this model.

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=100.00  E-value=1.6e-36  Score=284.94  Aligned_cols=306  Identities=16%  Similarity=0.265  Sum_probs=230.6

Q ss_pred             hhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHH-hccccCcEEEEEEC
Q 017573           22 IQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRA-LGDYLGVKVHACVG  100 (369)
Q Consensus        22 ~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~-~~~~~~~~v~~~~~  100 (369)
                      +-.+++..+..+++++++|+||||||.++.+++++....   +++++++.|++.++.|.++.+.+ +....+..+.+..+
T Consensus         6 ~~~~i~~~l~~~~~vIi~a~TGSGKTT~vpl~lL~~~~~---~~~ilvlqPrR~aA~qiA~rva~~~~~~~g~~VGy~vr   82 (819)
T TIGR01970         6 VLPALRDALAAHPQVVLEAPPGAGKSTAVPLALLDAPGI---GGKIIMLEPRRLAARSAAQRLASQLGEAVGQTVGYRVR   82 (819)
T ss_pred             HHHHHHHHHHcCCcEEEECCCCCCHHHHHHHHHHHhhcc---CCeEEEEeCcHHHHHHHHHHHHHHhCCCcCcEEEEEEc
Confidence            445667777788999999999999999999998877532   33899999999999999998864 44444566665554


Q ss_pred             CcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhH-hhccCcH-HHHHHHHhhCCccCcEEEEEee
Q 017573          101 GTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADE-MLSRGFK-DQIYDIFQLLPAKVQVGVFSAT  178 (369)
Q Consensus       101 ~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~-~~~~~~~-~~~~~~~~~~~~~~~~i~~saT  178 (369)
                      ...      ....+.+|+|+|+..|.+.+... ..++++++||+||+|+ ..+..+. ..+..+...+++..++++||||
T Consensus        83 ~~~------~~s~~t~I~v~T~G~Llr~l~~d-~~L~~v~~VIiDEaHER~L~~Dl~L~ll~~i~~~lr~dlqlIlmSAT  155 (819)
T TIGR01970        83 GEN------KVSRRTRLEVVTEGILTRMIQDD-PELDGVGALIFDEFHERSLDADLGLALALDVQSSLREDLKILAMSAT  155 (819)
T ss_pred             ccc------ccCCCCcEEEECCcHHHHHHhhC-cccccCCEEEEeccchhhhccchHHHHHHHHHHhcCCCceEEEEeCC
Confidence            432      12345789999999999888764 5678899999999995 4444432 2334455667778999999999


Q ss_pred             CChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhH----HHHHHHHHhccCCCeEEEeCCHhhHHHHHHH
Q 017573          179 MPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKL----ETLCDLYETLAITQSVIFVNTRRKVDWLTDK  254 (369)
Q Consensus       179 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~  254 (369)
                      ++...   ...++.+...+......   ..+..+|..........    ..+..++.. ..+++|||+++..+++.+++.
T Consensus       156 l~~~~---l~~~l~~~~vI~~~gr~---~pVe~~y~~~~~~~~~~~~v~~~l~~~l~~-~~g~iLVFlpg~~eI~~l~~~  228 (819)
T TIGR01970       156 LDGER---LSSLLPDAPVVESEGRS---FPVEIRYLPLRGDQRLEDAVSRAVEHALAS-ETGSILVFLPGQAEIRRVQEQ  228 (819)
T ss_pred             CCHHH---HHHHcCCCcEEEecCcc---eeeeeEEeecchhhhHHHHHHHHHHHHHHh-cCCcEEEEECCHHHHHHHHHH
Confidence            97543   34556544334333221   12445554443322221    233333333 357899999999999999999


Q ss_pred             Hhh---CCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCCCC----------------
Q 017573          255 MRS---RDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQ----------------  315 (369)
Q Consensus       255 l~~---~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~~----------------  315 (369)
                      |++   .+..+..+||+++.++|.++++.|.+|..+|+|+|+++++|+|+|++++||..+.+..                
T Consensus       229 L~~~~~~~~~v~pLHg~L~~~eq~~~~~~~~~G~rkVlVATnIAErgItIp~V~~VID~Gl~r~~~yd~~~g~~~L~~~~  308 (819)
T TIGR01970       229 LAERLDSDVLICPLYGELSLAAQDRAIKPDPQGRRKVVLATNIAETSLTIEGIRVVIDSGLARVARFDPKTGITRLETVR  308 (819)
T ss_pred             HHhhcCCCcEEEEecCCCCHHHHHHHHhhcccCCeEEEEecchHhhcccccCceEEEEcCcccccccccccCCceeeEEE
Confidence            987   3688999999999999999999999999999999999999999999999999987642                


Q ss_pred             --ccchhhhhcccccCCCceeEEEEeccccHH
Q 017573          316 --PENYLHRIGRSGRFGRKGVAINFVTRDDER  345 (369)
Q Consensus       316 --~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~  345 (369)
                        ..++.||.||+||. ++|.||.+++..+..
T Consensus       309 iSkasa~QR~GRAGR~-~~G~cyrL~t~~~~~  339 (819)
T TIGR01970       309 ISQASATQRAGRAGRL-EPGVCYRLWSEEQHQ  339 (819)
T ss_pred             ECHHHHHhhhhhcCCC-CCCEEEEeCCHHHHH
Confidence              23479999999999 899999999876544

This model represents HrpB, one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria, but also in a few species of other lineages. The member from Rhizobium meliloti has been designated HelO. HrpB is typically about 800 residues in length, while its paralog HrpA (TIGR01967), also uncharacterized, is about 1300 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing.

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=100.00  E-value=1.2e-36  Score=286.46  Aligned_cols=307  Identities=17%  Similarity=0.283  Sum_probs=230.7

Q ss_pred             HhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHH-hccccCcEEEEEE
Q 017573           21 AIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRA-LGDYLGVKVHACV   99 (369)
Q Consensus        21 ~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~-~~~~~~~~v~~~~   99 (369)
                      .+-.+++..+.++++++++||||||||+++.+++++....   ..+++++.|++.++.|.++.+.+ +....+..+.+..
T Consensus         8 ~~~~~i~~~l~~~~~vvv~A~TGSGKTt~~pl~lL~~~~~---~~~ilvlqPrR~aA~qia~rva~~l~~~~g~~VGy~v   84 (812)
T PRK11664          8 AVLPELLTALKTAPQVLLKAPTGAGKSTWLPLQLLQHGGI---NGKIIMLEPRRLAARNVAQRLAEQLGEKPGETVGYRM   84 (812)
T ss_pred             HHHHHHHHHHHhCCCEEEEcCCCCCHHHHHHHHHHHcCCc---CCeEEEECChHHHHHHHHHHHHHHhCcccCceEEEEe
Confidence            3445677777888999999999999999998888875432   23899999999999999998864 4444566777666


Q ss_pred             CCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHh-hccC-cHHHHHHHHhhCCccCcEEEEEe
Q 017573          100 GGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEM-LSRG-FKDQIYDIFQLLPAKVQVGVFSA  177 (369)
Q Consensus       100 ~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~-~~~~-~~~~~~~~~~~~~~~~~~i~~sa  177 (369)
                      ++...      ......|+|+|+..+.+++... ..++++++||+||+|+. .+.. ....+..+.+.+++..|+++|||
T Consensus        85 r~~~~------~~~~t~I~v~T~G~Llr~l~~d-~~L~~v~~IIlDEaHER~l~~Dl~L~ll~~i~~~lr~~lqlilmSA  157 (812)
T PRK11664         85 RAESK------VGPNTRLEVVTEGILTRMIQRD-PELSGVGLVILDEFHERSLQADLALALLLDVQQGLRDDLKLLIMSA  157 (812)
T ss_pred             cCccc------cCCCCcEEEEChhHHHHHHhhC-CCcCcCcEEEEcCCCccccccchHHHHHHHHHHhCCccceEEEEec
Confidence            65431      1234689999999999888764 56788999999999973 2222 12333455566778889999999


Q ss_pred             eCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhHH----HHHHHHHhccCCCeEEEeCCHhhHHHHHH
Q 017573          178 TMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLE----TLCDLYETLAITQSVIFVNTRRKVDWLTD  253 (369)
Q Consensus       178 T~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~l~~~~~~~~~~k~lv~~~~~~~~~~~~~  253 (369)
                      |++.+.   ...++.....+......   ..+...|..........+    .+..++.. ..+.+|||+++..+++.+++
T Consensus       158 Tl~~~~---l~~~~~~~~~I~~~gr~---~pV~~~y~~~~~~~~~~~~v~~~l~~~l~~-~~g~iLVFlpg~~ei~~l~~  230 (812)
T PRK11664        158 TLDNDR---LQQLLPDAPVIVSEGRS---FPVERRYQPLPAHQRFDEAVARATAELLRQ-ESGSLLLFLPGVGEIQRVQE  230 (812)
T ss_pred             CCCHHH---HHHhcCCCCEEEecCcc---ccceEEeccCchhhhHHHHHHHHHHHHHHh-CCCCEEEEcCCHHHHHHHHH
Confidence            997542   34555544334332221   234555554433222222    23333332 35799999999999999999


Q ss_pred             HHhh---CCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCCCC---------------
Q 017573          254 KMRS---RDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQ---------------  315 (369)
Q Consensus       254 ~l~~---~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~~---------------  315 (369)
                      .|+.   .+..+..+||+++.++|.++++.|.+|..+|+|+|+++++|+|+|++++||..+.+..               
T Consensus       231 ~L~~~~~~~~~v~~Lhg~l~~~eq~~~~~~~~~G~rkVlvATnIAErsLtIp~V~~VID~Gl~r~~~yd~~~g~~~L~~~  310 (812)
T PRK11664        231 QLASRVASDVLLCPLYGALSLAEQQKAILPAPAGRRKVVLATNIAETSLTIEGIRLVVDSGLERVARFDPKTGLTRLVTQ  310 (812)
T ss_pred             HHHHhccCCceEEEeeCCCCHHHHHHHhccccCCCeEEEEecchHHhcccccCceEEEECCCcccccccccCCcceeEEE
Confidence            9987   5678999999999999999999999999999999999999999999999999886542               


Q ss_pred             ---ccchhhhhcccccCCCceeEEEEeccccHH
Q 017573          316 ---PENYLHRIGRSGRFGRKGVAINFVTRDDER  345 (369)
Q Consensus       316 ---~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~  345 (369)
                         ..++.||.||+||. ++|.||.+++..+..
T Consensus       311 ~iSkasa~QR~GRaGR~-~~G~cyrL~t~~~~~  342 (812)
T PRK11664        311 RISQASMTQRAGRAGRL-EPGICLHLYSKEQAE  342 (812)
T ss_pred             eechhhhhhhccccCCC-CCcEEEEecCHHHHh
Confidence               34799999999999 799999999977554

>PRK14701 reverse gyrase; Provisional

Probab=100.00  E-value=1.8e-36  Score=299.92  Aligned_cols=324  Identities=19%  Similarity=0.190  Sum_probs=241.8

Q ss_pred             HHHHHHHh-CCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHH
Q 017573            6 NLLRGIYA-YGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVM   84 (369)
Q Consensus         6 ~i~~~l~~-~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~   84 (369)
                      ++...+++ +|| +|++.|+++++.+++|+++++.||||+|||++++.+++.....   +.+++|++|+++|+.|+.+.+
T Consensus        67 ~~~~~f~~~~G~-~pt~iQ~~~i~~il~G~d~li~APTGsGKTl~~~~~al~~~~~---g~~aLVl~PTreLa~Qi~~~l  142 (1638)
T PRK14701         67 EFEEFFEKITGF-EFWSIQKTWAKRILRGKSFSIVAPTGMGKSTFGAFIALFLALK---GKKCYIILPTTLLVKQTVEKI  142 (1638)
T ss_pred             HHHHHHHHhhCC-CCCHHHHHHHHHHHcCCCEEEEEcCCCCHHHHHHHHHHHHHhc---CCeEEEEECHHHHHHHHHHHH
Confidence            34555655 799 7999999999999999999999999999999665555443322   338999999999999999999


Q ss_pred             HHhcccc--CcEEEEEECCcchHHHHH----HHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhcc-----
Q 017573           85 RALGDYL--GVKVHACVGGTSVREDQR----ILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSR-----  153 (369)
Q Consensus        85 ~~~~~~~--~~~v~~~~~~~~~~~~~~----~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~-----  153 (369)
                      +.+....  +..+..++|+........    ...++++|+|+||+.+...+...  ...+++++|+||||.+..+     
T Consensus       143 ~~l~~~~~~~v~v~~~~g~~s~~e~~~~~~~l~~g~~dILV~TPgrL~~~~~~l--~~~~i~~iVVDEAD~ml~~~knid  220 (1638)
T PRK14701        143 ESFCEKANLDVRLVYYHSNLRKKEKEEFLERIENGDFDILVTTAQFLARNFPEM--KHLKFDFIFVDDVDAFLKASKNID  220 (1638)
T ss_pred             HHHHhhcCCceeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECCchhHHhHHHH--hhCCCCEEEEECceeccccccccc
Confidence            9987765  456677888877555432    23346899999999888766542  2256899999999998752     


Q ss_pred             ------CcHHHHHH----HHh----------------------hCCccCc-EEEEEeeCChhHHHHHHHhcCCCEEEEec
Q 017573          154 ------GFKDQIYD----IFQ----------------------LLPAKVQ-VGVFSATMPPEALEITRKFMNKPVRILVK  200 (369)
Q Consensus       154 ------~~~~~~~~----~~~----------------------~~~~~~~-~i~~saT~~~~~~~~~~~~~~~~~~~~~~  200 (369)
                            +|...+..    ++.                      .+++..+ .+.+|||.++..  ....++..+..+.+.
T Consensus       221 ~~L~llGF~~e~~~~~~~il~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~ll~~SAT~~~r~--~~~~l~~~~l~f~v~  298 (1638)
T PRK14701        221 RSLQLLGFYEEIIEKAWKIIYLKKQGNIEDAMEKREILNKEIEKIGNKIGCLIVASATGKAKG--DRVKLYRELLGFEVG  298 (1638)
T ss_pred             hhhhcCCChHHHHHHHHHhhhcccccccchhhhhhhhhhhhhhhcCCCccEEEEEecCCCchh--HHHHHhhcCeEEEec
Confidence                  55555542    221                      2344455 566899997531  122344566666666


Q ss_pred             CccccccceeEEEEEccchhhhHHHHHHHHHhccCCCeEEEeCCHhh---HHHHHHHHhhCCCeeEEecCCCCHHHHHHH
Q 017573          201 RDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRK---VDWLTDKMRSRDHTVSATHGDMDQNTRDII  277 (369)
Q Consensus       201 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lv~~~~~~~---~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~  277 (369)
                      ........+.+.+....... + ..+..++... +..+||||++.+.   ++.+++.|...|+++..+|++     |...
T Consensus       299 ~~~~~lr~i~~~yi~~~~~~-k-~~L~~ll~~~-g~~gIVF~~t~~~~e~ae~la~~L~~~Gi~a~~~h~~-----R~~~  370 (1638)
T PRK14701        299 SGRSALRNIVDVYLNPEKII-K-EHVRELLKKL-GKGGLIFVPIDEGAEKAEEIEKYLLEDGFKIELVSAK-----NKKG  370 (1638)
T ss_pred             CCCCCCCCcEEEEEECCHHH-H-HHHHHHHHhC-CCCeEEEEeccccchHHHHHHHHHHHCCCeEEEecch-----HHHH
Confidence            55555667777776554332 2 4566777665 4689999998775   589999999999999999995     8899


Q ss_pred             HHHHhcCCCcEEEEec----CCcCCCCCCC-CcEEEEecCCC---Cccchhhhh-------------cccccCCCceeEE
Q 017573          278 MREFRSGSSRVLITTD----LLARGIDVQQ-VSLVINYDLPT---QPENYLHRI-------------GRSGRFGRKGVAI  336 (369)
Q Consensus       278 ~~~f~~~~~~vli~t~----~~~~G~d~~~-~~~vi~~~~~~---~~~~~~Q~~-------------GR~~R~~~~~~~~  336 (369)
                      ++.|.+|+.+|||+|.    .+.+|+|+|+ ++.||+++.|.   +...+.|..             ||++|.|..+.++
T Consensus       371 l~~F~~G~~~VLVaT~s~~gvaaRGIDiP~~Vryvi~~~~Pk~~~~~e~~~~~~~~~~~~~~~~~~~~~a~~~g~~~~~~  450 (1638)
T PRK14701        371 FDLFEEGEIDYLIGVATYYGTLVRGLDLPERIRFAVFYGVPKFRFRVDLEDPTIYRILGLLSEILKIEEELKEGIPIEGV  450 (1638)
T ss_pred             HHHHHcCCCCEEEEecCCCCeeEecCccCCccCEEEEeCCCCCCcchhhcccchhhhhcchHHHHHhhhhcccCCcchhH
Confidence            9999999999999994    7889999998 99999999998   766666655             9999999887776


Q ss_pred             EEeccccHH
Q 017573          337 NFVTRDDER  345 (369)
Q Consensus       337 ~~~~~~~~~  345 (369)
                      ..+...+..
T Consensus       451 ~~~~~~~~~  459 (1638)
T PRK14701        451 LDVFPEDVE  459 (1638)
T ss_pred             HHhHHHHHH
Confidence            444433333

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

Probab=100.00  E-value=3.2e-35  Score=259.95  Aligned_cols=320  Identities=20%  Similarity=0.260  Sum_probs=250.4

Q ss_pred             HHHHHHhCCCCCCcHhhhhhhhccccC------CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHH
Q 017573            7 LLRGIYAYGFEKPSAIQQRGIVPFCKG------LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQI   80 (369)
Q Consensus         7 i~~~l~~~~~~~~~~~Q~~~~~~~~~~------~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~   80 (369)
                      +.+.+...+| +||..|++++..+...      -+-++++..|||||.+++++++..+..+.   ++...+||.-|++|.
T Consensus       252 ~~~~~~~LPF-~LT~aQ~~vi~EI~~Dl~~~~~M~RLlQGDVGSGKTvVA~laml~ai~~G~---Q~ALMAPTEILA~QH  327 (677)
T COG1200         252 LAKFLAALPF-KLTNAQKRVIKEILADLASPVPMNRLLQGDVGSGKTVVALLAMLAAIEAGY---QAALMAPTEILAEQH  327 (677)
T ss_pred             HHHHHHhCCC-CccHHHHHHHHHHHhhhcCchhhHHHhccCcCCCHHHHHHHHHHHHHHcCC---eeEEeccHHHHHHHH
Confidence            3444577898 9999999999998864      45799999999999999999999988877   899999999999999


Q ss_pred             HHHHHHhccccCcEEEEEECCcchHHHHHH----HccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcH
Q 017573           81 EKVMRALGDYLGVKVHACVGGTSVREDQRI----LQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFK  156 (369)
Q Consensus        81 ~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~----~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~  156 (369)
                      ++.+.++....+++|..++|+.+.......    ..+..+++|+|+     .+.+......++.++|+||=|++.-.   
T Consensus       328 ~~~~~~~l~~~~i~V~lLtG~~kgk~r~~~l~~l~~G~~~ivVGTH-----ALiQd~V~F~~LgLVIiDEQHRFGV~---  399 (677)
T COG1200         328 YESLRKWLEPLGIRVALLTGSLKGKARKEILEQLASGEIDIVVGTH-----ALIQDKVEFHNLGLVIIDEQHRFGVH---  399 (677)
T ss_pred             HHHHHHHhhhcCCeEEEeecccchhHHHHHHHHHhCCCCCEEEEcc-----hhhhcceeecceeEEEEeccccccHH---
Confidence            999999999999999999999887666543    346799999994     45555667777899999999997422   


Q ss_pred             HHHHHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHHHhccCC
Q 017573          157 DQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAIT  236 (369)
Q Consensus       157 ~~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  236 (369)
                       +-..+.++-...+.++.|||||.|....+  ..+.+-..-..+.-+.....+...+..........+.+..-+.  .+.
T Consensus       400 -QR~~L~~KG~~~Ph~LvMTATPIPRTLAl--t~fgDldvS~IdElP~GRkpI~T~~i~~~~~~~v~e~i~~ei~--~Gr  474 (677)
T COG1200         400 -QRLALREKGEQNPHVLVMTATPIPRTLAL--TAFGDLDVSIIDELPPGRKPITTVVIPHERRPEVYERIREEIA--KGR  474 (677)
T ss_pred             -HHHHHHHhCCCCCcEEEEeCCCchHHHHH--HHhccccchhhccCCCCCCceEEEEeccccHHHHHHHHHHHHH--cCC
Confidence             22233333222678999999998765433  3444433333333444445666666666555545555544444  456


Q ss_pred             CeEEEeCCHhhH--------HHHHHHHhhC--CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcE
Q 017573          237 QSVIFVNTRRKV--------DWLTDKMRSR--DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSL  306 (369)
Q Consensus       237 k~lv~~~~~~~~--------~~~~~~l~~~--~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~  306 (369)
                      ++.+.|+-+++.        ...++.|+..  +.++..+||+|+.++++++++.|++|+.+|||||..++.|+|+|+++.
T Consensus       475 QaY~VcPLIeESE~l~l~~a~~~~~~L~~~~~~~~vgL~HGrm~~~eKd~vM~~Fk~~e~~ILVaTTVIEVGVdVPnATv  554 (677)
T COG1200         475 QAYVVCPLIEESEKLELQAAEELYEELKSFLPELKVGLVHGRMKPAEKDAVMEAFKEGEIDILVATTVIEVGVDVPNATV  554 (677)
T ss_pred             EEEEEeccccccccchhhhHHHHHHHHHHHcccceeEEEecCCChHHHHHHHHHHHcCCCcEEEEeeEEEecccCCCCeE
Confidence            888999877654        4556666644  456999999999999999999999999999999999999999999999


Q ss_pred             EEEecCC-CCccchhhhhcccccCCCceeEEEEecccc
Q 017573          307 VINYDLP-TQPENYLHRIGRSGRFGRKGVAINFVTRDD  343 (369)
Q Consensus       307 vi~~~~~-~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~  343 (369)
                      +++.+.- ...+++=|.-||+||.+..+.|++++.+..
T Consensus       555 MVIe~AERFGLaQLHQLRGRVGRG~~qSyC~Ll~~~~~  592 (677)
T COG1200         555 MVIENAERFGLAQLHQLRGRVGRGDLQSYCVLLYKPPL  592 (677)
T ss_pred             EEEechhhhhHHHHHHhccccCCCCcceEEEEEeCCCC
Confidence            9987753 456788999999999999999999999876

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=100.00  E-value=1.8e-35  Score=270.32  Aligned_cols=319  Identities=15%  Similarity=0.145  Sum_probs=227.3

Q ss_pred             CCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEE
Q 017573           18 KPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHA   97 (369)
Q Consensus        18 ~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~   97 (369)
                      .++|+|.+++..+.-+++.+++++||+|||++++++++.....+.   .++|++|++.|+.|+.+++..+...+|+.+..
T Consensus        68 glrpydVQlig~l~l~~G~Iaem~TGeGKTLta~Lpa~l~aL~g~---~V~VVTpn~yLA~Rdae~m~~l~~~LGLsv~~  144 (762)
T TIGR03714        68 GMFPYDVQVLGAIVLHQGNIAEMKTGEGKTLTATMPLYLNALTGK---GAMLVTTNDYLAKRDAEEMGPVYEWLGLTVSL  144 (762)
T ss_pred             CCCccHHHHHHHHHhcCCceeEecCCcchHHHHHHHHHHHhhcCC---ceEEeCCCHHHHHHHHHHHHHHHhhcCCcEEE
Confidence            456677777766666666899999999999999998765554443   79999999999999999999999999999988


Q ss_pred             EECCcc---hHHHHHHHccCCcEEEeccHHH-HHHHHc------CCCCCCCccEEEEechhHhhccC-------------
Q 017573           98 CVGGTS---VREDQRILQAGVHVVVGTPGRV-FDMLRR------QSLRPDYIKMFVLDEADEMLSRG-------------  154 (369)
Q Consensus        98 ~~~~~~---~~~~~~~~~~~~~iiv~t~~~l-~~~~~~------~~~~~~~~~~viiDE~H~~~~~~-------------  154 (369)
                      ..++..   .....+.....++|+++||..| +..+..      +......+.++|+||+|.+.-..             
T Consensus       145 ~~~~s~~~~~~~~~rr~~y~~dIvygTp~~LgfDyLrD~l~~~~~~~~~r~l~~~IVDEaDsILiDeartpliisg~~~~  224 (762)
T TIGR03714       145 GVVDDPDEEYDANEKRKIYNSDIVYTTNSALGFDYLIDNLASNKEGKFLRPFNYVIVDEVDSVLLDSAQTPLVISGAPRV  224 (762)
T ss_pred             EECCCCccccCHHHHHHhCCCCEEEECchhhhhhHHHHHhhcchhhcccccCcEEEEecHhhHhhccCcCCeeeeCCCcc
Confidence            776521   1111222335689999999999 454433      22335668999999999874210             


Q ss_pred             ---cHHHHHHHHhhCCc---------------------------------------------------------------
Q 017573          155 ---FKDQIYDIFQLLPA---------------------------------------------------------------  168 (369)
Q Consensus       155 ---~~~~~~~~~~~~~~---------------------------------------------------------------  168 (369)
                         .......+...+..                                                               
T Consensus       225 ~~~~y~~~~~~v~~l~~~~dy~~d~~~~~v~lt~~G~~~~e~~~~~~~l~~~~~~~~~~~i~~al~A~~~~~~d~dYiV~  304 (762)
T TIGR03714       225 QSNLYHIADTFVRTLKEDVDYIFKKDKKEVWLTDKGIEKAEQYFKIDNLYSEEYFELVRHINLALRAHYLFKRNKDYVVT  304 (762)
T ss_pred             chHHHHHHHHHHHhcCCCCCeEEEcCCCeeeecHhHHHHHHHHcCCCccCChhhHHHHHHHHHHHHHHHHHhcCCceEEE
Confidence               00111111111000                                                               


Q ss_pred             ------------------------------------------------------cCcEEEEEeeCChhHHHHHHHhcCCC
Q 017573          169 ------------------------------------------------------KVQVGVFSATMPPEALEITRKFMNKP  194 (369)
Q Consensus       169 ------------------------------------------------------~~~~i~~saT~~~~~~~~~~~~~~~~  194 (369)
                                                                            -.++.+||+|......++. ..++-.
T Consensus       305 ~~~v~ivD~~TGr~~~gr~~~~GLhQaieaKE~v~i~~e~~t~a~It~qn~Fr~Y~kl~GmTGTa~~~~~Ef~-~iY~l~  383 (762)
T TIGR03714       305 NGEVVLLDRITGRLLEGTKLQSGIHQAIEAKEHVELSKETRAMASITYQNLFKMFNKLSGMTGTGKVAEKEFI-ETYSLS  383 (762)
T ss_pred             CCEEEEEECCCCcCCCCCCcchHHHHHHHhhcCCCCCCCceeeeeeeHHHHHhhCchhcccCCCChhHHHHHH-HHhCCC
Confidence                                                                  0467788999765554443 444444


Q ss_pred             EEEEecCccccccceeEEEEEccchhhhHHHHHHHHHh--ccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHH
Q 017573          195 VRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYET--LAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQN  272 (369)
Q Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~--~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~  272 (369)
                      +.......+.........++  .....+...+.+.+..  ..+.++||||++++.++.+.+.|.+.++++..+|++++..
T Consensus       384 v~~IPt~kp~~r~d~~d~i~--~~~~~K~~ai~~~i~~~~~~~~pvLIft~s~~~se~ls~~L~~~gi~~~~L~a~~~~~  461 (762)
T TIGR03714       384 VVKIPTNKPIIRIDYPDKIY--ATLPEKLMATLEDVKEYHETGQPVLLITGSVEMSEIYSELLLREGIPHNLLNAQNAAK  461 (762)
T ss_pred             EEEcCCCCCeeeeeCCCeEE--ECHHHHHHHHHHHHHHHhhCCCCEEEEECcHHHHHHHHHHHHHCCCCEEEecCCChHH
Confidence            43333222222111111111  2234466666666644  3567999999999999999999999999999999999988


Q ss_pred             HHHHHHHHHhcCCCcEEEEecCCcCCCCCC---------CCcEEEEecCCCCccchhhhhcccccCCCceeEEEEecccc
Q 017573          273 TRDIIMREFRSGSSRVLITTDLLARGIDVQ---------QVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDD  343 (369)
Q Consensus       273 ~r~~~~~~f~~~~~~vli~t~~~~~G~d~~---------~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~  343 (369)
                      ++..+.+.+..|  .|+|||+++++|+|+|         ++++|+.+++|....+ .|+.||+||.|++|.++.|++..|
T Consensus       462 E~~ii~~ag~~g--~VlIATdmAgRGtDI~l~~~v~~~GGL~vIit~~~ps~rid-~qr~GRtGRqG~~G~s~~~is~eD  538 (762)
T TIGR03714       462 EAQIIAEAGQKG--AVTVATSMAGRGTDIKLGKGVAELGGLAVIGTERMENSRVD-LQLRGRSGRQGDPGSSQFFVSLED  538 (762)
T ss_pred             HHHHHHHcCCCC--eEEEEccccccccCCCCCccccccCCeEEEEecCCCCcHHH-HHhhhcccCCCCceeEEEEEccch
Confidence            887777766665  6999999999999999         8999999998877656 999999999999999999998754


Q ss_pred             HH
Q 017573          344 ER  345 (369)
Q Consensus       344 ~~  345 (369)
                      .-
T Consensus       539 ~l  540 (762)
T TIGR03714       539 DL  540 (762)
T ss_pred             hh
Confidence            43

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.

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

Probab=100.00  E-value=3.1e-36  Score=268.24  Aligned_cols=293  Identities=19%  Similarity=0.245  Sum_probs=205.7

Q ss_pred             CCCcHhhhhhhhcccc----CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccC
Q 017573           17 EKPSAIQQRGIVPFCK----GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLG   92 (369)
Q Consensus        17 ~~~~~~Q~~~~~~~~~----~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~   92 (369)
                      ..||++|+++++++..    +++.++++|||+|||.+++..+.....      ++|||||+..|+.||.+.+.++.... 
T Consensus        35 ~~lr~yQ~~al~a~~~~~~~~~~gvivlpTGaGKT~va~~~~~~~~~------~~Lvlv~~~~L~~Qw~~~~~~~~~~~-  107 (442)
T COG1061          35 FELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAEAIAELKR------STLVLVPTKELLDQWAEALKKFLLLN-  107 (442)
T ss_pred             CCCcHHHHHHHHHHHhhcccCCceEEEeCCCCCHHHHHHHHHHHhcC------CEEEEECcHHHHHHHHHHHHHhcCCc-
Confidence            4699999999999998    899999999999999988666554321      59999999999999998777765331 


Q ss_pred             cEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCccCcE
Q 017573           93 VKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQV  172 (369)
Q Consensus        93 ~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~  172 (369)
                      ..+....++.. ...     . ..|.|+|++++........+....+++||+||||++.+..+.....    .+.....+
T Consensus       108 ~~~g~~~~~~~-~~~-----~-~~i~vat~qtl~~~~~l~~~~~~~~~liI~DE~Hh~~a~~~~~~~~----~~~~~~~~  176 (442)
T COG1061         108 DEIGIYGGGEK-ELE-----P-AKVTVATVQTLARRQLLDEFLGNEFGLIIFDEVHHLPAPSYRRILE----LLSAAYPR  176 (442)
T ss_pred             cccceecCcee-ccC-----C-CcEEEEEhHHHhhhhhhhhhcccccCEEEEEccccCCcHHHHHHHH----hhhcccce
Confidence            12333333332 111     1 3699999999987532222334468999999999987655443333    33222228


Q ss_pred             EEEEeeCChhHHH---HHHHhcCCCEEEEecCcc------ccccceeEEEEEcc--------------------------
Q 017573          173 GVFSATMPPEALE---ITRKFMNKPVRILVKRDE------LTLEGIKQFYVNVE--------------------------  217 (369)
Q Consensus       173 i~~saT~~~~~~~---~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~--------------------------  217 (369)
                      +++||||......   .....++ +..+.....+      ..+...........                          
T Consensus       177 LGLTATp~R~D~~~~~~l~~~~g-~~vy~~~~~~li~~g~Lap~~~~~i~~~~t~~~~~~~~~~~~~~~~~~~~~~~~~~  255 (442)
T COG1061         177 LGLTATPEREDGGRIGDLFDLIG-PIVYEVSLKELIDEGYLAPYKYVEIKVTLTEDEEREYAKESARFRELLRARGTLRA  255 (442)
T ss_pred             eeeccCceeecCCchhHHHHhcC-CeEeecCHHHHHhCCCccceEEEEEEeccchHHHHHhhhhhhhhhhhhhhhhhhhH
Confidence            9999998643311   1111111 2222221110      00111111111000                          


Q ss_pred             ---------chhhhHHHHHHHHHhc-cCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCc
Q 017573          218 ---------KEEWKLETLCDLYETL-AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSR  287 (369)
Q Consensus       218 ---------~~~~~~~~l~~~~~~~-~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~  287 (369)
                               ....+...+..++..+ ...++++|+.+..+++.++..+...+. +..++++.+..+|..+++.|+.|+++
T Consensus       256 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lif~~~~~~a~~i~~~~~~~~~-~~~it~~t~~~eR~~il~~fr~g~~~  334 (442)
T COG1061         256 ENEARRIAIASERKIAAVRGLLLKHARGDKTLIFASDVEHAYEIAKLFLAPGI-VEAITGETPKEEREAILERFRTGGIK  334 (442)
T ss_pred             HHHHHHHhhccHHHHHHHHHHHHHhcCCCcEEEEeccHHHHHHHHHHhcCCCc-eEEEECCCCHHHHHHHHHHHHcCCCC
Confidence                     0111333344444444 367999999999999999999988777 88999999999999999999999999


Q ss_pred             EEEEecCCcCCCCCCCCcEEEEecCCCCccchhhhhcccccC
Q 017573          288 VLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRF  329 (369)
Q Consensus       288 vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~  329 (369)
                      +|+++.++.+|+|+|+++++|+..+..|...|.|++||+.|.
T Consensus       335 ~lv~~~vl~EGvDiP~~~~~i~~~~t~S~~~~~Q~lGR~LR~  376 (442)
T COG1061         335 VLVTVKVLDEGVDIPDADVLIILRPTGSRRLFIQRLGRGLRP  376 (442)
T ss_pred             EEEEeeeccceecCCCCcEEEEeCCCCcHHHHHHHhhhhccC
Confidence            999999999999999999999999999999999999999993

>TIGR01054 rgy reverse gyrase

Probab=100.00  E-value=1.2e-34  Score=281.67  Aligned_cols=290  Identities=21%  Similarity=0.262  Sum_probs=211.1

Q ss_pred             HHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHH
Q 017573            7 LLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRA   86 (369)
Q Consensus         7 i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~   86 (369)
                      +.+.+.+.....|+++|+.+++.++.|++++++||||+|||..++ ++...+..  .+++++|++|+++|+.|+.+.+.+
T Consensus        67 f~~~f~~~~g~~p~~iQ~~~i~~il~G~d~vi~ApTGsGKT~f~l-~~~~~l~~--~g~~vLIL~PTreLa~Qi~~~l~~  143 (1171)
T TIGR01054        67 FEEFFKKAVGSEPWSIQKMWAKRVLRGDSFAIIAPTGVGKTTFGL-AMSLFLAK--KGKRCYIILPTTLLVIQVAEKISS  143 (1171)
T ss_pred             HHHHHHHhcCCCCcHHHHHHHHHHhCCCeEEEECCCCCCHHHHHH-HHHHHHHh--cCCeEEEEeCHHHHHHHHHHHHHH
Confidence            344444444458999999999999999999999999999997544 33333332  234899999999999999999999


Q ss_pred             hccccCcEEE---EEECCcchHHHHH----HHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhc-------
Q 017573           87 LGDYLGVKVH---ACVGGTSVREDQR----ILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLS-------  152 (369)
Q Consensus        87 ~~~~~~~~v~---~~~~~~~~~~~~~----~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~-------  152 (369)
                      +....++.+.   ..+|+.+......    ...++++|+|+||+.+...+....  . .++++|+||||++.+       
T Consensus       144 l~~~~~i~~~~i~~~~Gg~~~~e~~~~~~~l~~~~~dIlV~Tp~rL~~~~~~l~--~-~~~~iVvDEaD~~L~~~k~vd~  220 (1171)
T TIGR01054       144 LAEKAGVGTVNIGAYHSRLPTKEKKEFMERIENGDFDILITTTMFLSKNYDELG--P-KFDFIFVDDVDALLKASKNVDK  220 (1171)
T ss_pred             HHHhcCCceeeeeeecCCCCHHHHHHHHHHHhcCCCCEEEECHHHHHHHHHHhc--C-CCCEEEEeChHhhhhccccHHH
Confidence            9876665543   4567766544322    233468999999999988776522  2 689999999999986       


Q ss_pred             ----cCcHHH-HHHH----------------------HhhCCccCc--EEEEEeeC-ChhHHHHHHHhcCCCEEEEecCc
Q 017573          153 ----RGFKDQ-IYDI----------------------FQLLPAKVQ--VGVFSATM-PPEALEITRKFMNKPVRILVKRD  202 (369)
Q Consensus       153 ----~~~~~~-~~~~----------------------~~~~~~~~~--~i~~saT~-~~~~~~~~~~~~~~~~~~~~~~~  202 (369)
                          .+|... +..+                      ++.++...|  ++++|||+ +....   ..++.....+.+...
T Consensus       221 il~llGF~~e~i~~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~li~~SAT~~p~~~~---~~l~r~ll~~~v~~~  297 (1171)
T TIGR01054       221 LLKLLGFSEELIEKAWKLIRLRLKLYRALHAKKRLELLEAIPGKKRGCLIVSSATGRPRGKR---AKLFRELLGFEVGGG  297 (1171)
T ss_pred             HHHHcCCCHHHHHHHHHHhhhccccchHHHHHHHHHHHHhhhhccCcEEEEEeCCCCccccH---HHHcccccceEecCc
Confidence                344432 3332                      223344444  56689994 33322   133444444555444


Q ss_pred             cccccceeEEEEEccchhhhHHHHHHHHHhccCCCeEEEeCCH---hhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHH
Q 017573          203 ELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTR---RKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMR  279 (369)
Q Consensus       203 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lv~~~~~---~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~  279 (369)
                      .....++.+.+.....   ....+.+++... +.++||||++.   +.++.+++.|.+.|+++..+||+++    .+.++
T Consensus       298 ~~~~r~I~~~~~~~~~---~~~~L~~ll~~l-~~~~IVFv~t~~~~~~a~~l~~~L~~~g~~a~~lhg~~~----~~~l~  369 (1171)
T TIGR01054       298 SDTLRNVVDVYVEDED---LKETLLEIVKKL-GTGGIVYVSIDYGKEKAEEIAEFLENHGVKAVAYHATKP----KEDYE  369 (1171)
T ss_pred             cccccceEEEEEeccc---HHHHHHHHHHHc-CCCEEEEEeccccHHHHHHHHHHHHhCCceEEEEeCCCC----HHHHH
Confidence            4455667766664433   234566666654 36899999998   9999999999999999999999986    36899


Q ss_pred             HHhcCCCcEEEEe----cCCcCCCCCCC-CcEEEEecCC
Q 017573          280 EFRSGSSRVLITT----DLLARGIDVQQ-VSLVINYDLP  313 (369)
Q Consensus       280 ~f~~~~~~vli~t----~~~~~G~d~~~-~~~vi~~~~~  313 (369)
                      .|++|+++|||+|    +.+++|+|+|+ +++||+++.|
T Consensus       370 ~Fr~G~~~vLVata~~tdv~aRGIDip~~V~~vI~~~~P  408 (1171)
T TIGR01054       370 KFAEGEIDVLIGVASYYGTLVRGLDLPERVRYAVFLGVP  408 (1171)
T ss_pred             HHHcCCCCEEEEeccccCcccccCCCCccccEEEEECCC
Confidence            9999999999995    89999999999 8999986654

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

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=100.00  E-value=6e-35  Score=254.05  Aligned_cols=289  Identities=15%  Similarity=0.225  Sum_probs=198.1

Q ss_pred             hhhhhhhccccCCc--EEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccc----cCcEE
Q 017573           22 IQQRGIVPFCKGLD--VIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDY----LGVKV   95 (369)
Q Consensus        22 ~Q~~~~~~~~~~~~--~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~----~~~~v   95 (369)
                      +|.++++++.++++  +++.+|||+|||.+++++++..      ..++++++|+++|++|+.+.+.++...    .+..+
T Consensus         1 hQ~~~~~~~~~~~~~~~~i~apTGsGKT~~~~~~~l~~------~~~~~~~~P~~aL~~~~~~~~~~~~~~~~~~~~~~v   74 (357)
T TIGR03158         1 HQVATFEALQSKDADIIFNTAPTGAGKTLAWLTPLLHG------ENDTIALYPTNALIEDQTEAIKEFVDVFKPERDVNL   74 (357)
T ss_pred             CHHHHHHHHHcCCCCEEEEECCCCCCHHHHHHHHHHHc------CCCEEEEeChHHHHHHHHHHHHHHHHhcCCCCCceE
Confidence            69999999998864  7899999999999998887742      127899999999999999999887643    24556


Q ss_pred             EEEECCcchHH--H------------------HHHHccCCcEEEeccHHHHHHHHcCCCC--------CCCccEEEEech
Q 017573           96 HACVGGTSVRE--D------------------QRILQAGVHVVVGTPGRVFDMLRRQSLR--------PDYIKMFVLDEA  147 (369)
Q Consensus        96 ~~~~~~~~~~~--~------------------~~~~~~~~~iiv~t~~~l~~~~~~~~~~--------~~~~~~viiDE~  147 (369)
                      ..+.|....+.  .                  .......+.|++|||+.|..++..+...        ...++++|+||+
T Consensus        75 ~~~~g~~~~d~~~~~~~~~~~~~g~~~~~~~r~~~~~~~p~illT~p~~l~~llr~~~~~~~~~~~~~~~~~~~iV~DE~  154 (357)
T TIGR03158        75 LHVSKATLKDIKEYANDKVGSSKGEKLYNLLRNPIGTSTPIILLTNPDIFVYLTRFAYIDRGDIAAGFYTKFSTVIFDEF  154 (357)
T ss_pred             EEecCCchHHHHHhhhhhcccCccchhhhhHHHHHhcCCCCEEEecHHHHHHHHhhhccCcccchhhhhcCCCEEEEecc
Confidence            66666532220  0                  0111235789999999998766543211        356899999999


Q ss_pred             hHhhccCcH-----HHHHHHHhhCCccCcEEEEEeeCChhHHHHHHHh--cCCCEEEEecC-----c------cc-----
Q 017573          148 DEMLSRGFK-----DQIYDIFQLLPAKVQVGVFSATMPPEALEITRKF--MNKPVRILVKR-----D------EL-----  204 (369)
Q Consensus       148 H~~~~~~~~-----~~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~--~~~~~~~~~~~-----~------~~-----  204 (369)
                      |.+..+...     -....+........+++++|||+++.....+...  +..+.......     +      ..     
T Consensus       155 H~~~~~~~~~~~~~l~~~~~~~~~~~~~~~i~lSAT~~~~~~~~l~~~~~~~~~~~~v~g~~~~~~~~~~~~~~~~~~~~  234 (357)
T TIGR03158       155 HLYDAKQLVGMLFLLAYMQLIRFFECRRKFVFLSATPDPALILRLQNAKQAGVKIAPIDGEKYQFPDNPELEADNKTQSF  234 (357)
T ss_pred             cccCcccchhhhhhhHHHHHHHhhhcCCcEEEEecCCCHHHHHHHHhccccCceeeeecCcccccCCChhhhcccccccc
Confidence            998643321     1222333333445789999999998777666654  33333221111     0      00     


Q ss_pred             --cccceeEEEEEccchhhhHHHHHH-------HHHhccCCCeEEEeCCHhhHHHHHHHHhhCC--CeeEEecCCCCHHH
Q 017573          205 --TLEGIKQFYVNVEKEEWKLETLCD-------LYETLAITQSVIFVNTRRKVDWLTDKMRSRD--HTVSATHGDMDQNT  273 (369)
Q Consensus       205 --~~~~~~~~~~~~~~~~~~~~~l~~-------~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~~--~~~~~~~~~~~~~~  273 (369)
                        ..+.+...+.. . ...+...+..       .++..+++++||||++.+.++.+++.|++.+  ..+..+||.+++.+
T Consensus       235 ~~~~~~i~~~~~~-~-~~~~~~~l~~l~~~i~~~~~~~~~~k~LIf~nt~~~~~~l~~~L~~~~~~~~~~~l~g~~~~~~  312 (357)
T TIGR03158       235 RPVLPPVELELIP-A-PDFKEEELSELAEEVIERFRQLPGERGAIILDSLDEVNRLSDLLQQQGLGDDIGRITGFAPKKD  312 (357)
T ss_pred             ceeccceEEEEEe-C-CchhHHHHHHHHHHHHHHHhccCCCeEEEEECCHHHHHHHHHHHhhhCCCceEEeeecCCCHHH
Confidence              00233333333 1 1122222222       2222356799999999999999999999864  47888999999998


Q ss_pred             HHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCCCCccchhhhhcccc
Q 017573          274 RDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSG  327 (369)
Q Consensus       274 r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~  327 (369)
                      |.+.      ++.++||||+++++|+|+|.. .|| ++ |.+...|+||+||+|
T Consensus       313 R~~~------~~~~iLVaTdv~~rGiDi~~~-~vi-~~-p~~~~~yiqR~GR~g  357 (357)
T TIGR03158       313 RERA------MQFDILLGTSTVDVGVDFKRD-WLI-FS-ARDAAAFWQRLGRLG  357 (357)
T ss_pred             HHHh------ccCCEEEEecHHhcccCCCCc-eEE-EC-CCCHHHHhhhcccCC
Confidence            8654      367899999999999999976 555 44 788999999999986

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.

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=100.00  E-value=4e-35  Score=265.05  Aligned_cols=319  Identities=20%  Similarity=0.199  Sum_probs=238.2

Q ss_pred             CCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCc
Q 017573           14 YGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGV   93 (369)
Q Consensus        14 ~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~   93 (369)
                      .|. .|++.|..++..+.+|+  +.++.||+|||+++.++++.....+.   .++|++|++.|+.|.++++.+++..+++
T Consensus       100 lg~-~p~~VQ~~~~~~ll~G~--Iae~~TGeGKTla~~lp~~~~al~G~---~v~VvTptreLA~qdae~~~~l~~~lGl  173 (656)
T PRK12898        100 LGQ-RHFDVQLMGGLALLSGR--LAEMQTGEGKTLTATLPAGTAALAGL---PVHVITVNDYLAERDAELMRPLYEALGL  173 (656)
T ss_pred             hCC-CCChHHHHHHHHHhCCC--eeeeeCCCCcHHHHHHHHHHHhhcCC---eEEEEcCcHHHHHHHHHHHHHHHhhcCC
Confidence            354 89999999999999998  99999999999999999997765543   8999999999999999999999999999


Q ss_pred             EEEEEECCcchHHHHHHHccCCcEEEeccHHH-HHHHHcCCCC-------------------------CCCccEEEEech
Q 017573           94 KVHACVGGTSVREDQRILQAGVHVVVGTPGRV-FDMLRRQSLR-------------------------PDYIKMFVLDEA  147 (369)
Q Consensus        94 ~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l-~~~~~~~~~~-------------------------~~~~~~viiDE~  147 (369)
                      ++..+.++......  .....++|+++|...| +.+++.+-..                         ...++++|+||+
T Consensus       174 sv~~i~gg~~~~~r--~~~y~~dIvygT~~e~~FDyLrd~~~~~~~~~~~~~~~~~l~~~~~~~~~~v~r~~~~aIvDEv  251 (656)
T PRK12898        174 TVGCVVEDQSPDER--RAAYGADITYCTNKELVFDYLRDRLALGQRASDARLALESLHGRSSRSTQLLLRGLHFAIVDEA  251 (656)
T ss_pred             EEEEEeCCCCHHHH--HHHcCCCEEEECCCchhhhhccccccccccccchhhhhhhhccccCchhhhcccccceeEeecc
Confidence            99999998764432  2345689999999888 4444433211                         234789999999


Q ss_pred             hHhh-cc-----------------CcHHHHHHHHhhCCc-----------------------------------------
Q 017573          148 DEML-SR-----------------GFKDQIYDIFQLLPA-----------------------------------------  168 (369)
Q Consensus       148 H~~~-~~-----------------~~~~~~~~~~~~~~~-----------------------------------------  168 (369)
                      +.+. +.                 ........+...+..                                         
T Consensus       252 DSiLiDeartpliis~~~~~~~~~~~y~~~~~~~~~l~~~~~y~~d~~~~~v~lt~~g~~~~e~~~~~l~~~~~~~~~~~  331 (656)
T PRK12898        252 DSVLIDEARTPLIISAPAKEADEAEVYRQALELAAQLKEGEDYTIDAAEKRIELTEAGRARIAELAESLPPAWRGAVRRE  331 (656)
T ss_pred             cceeeccCCCceEEECCCCCCchhHHHHHHHHHHHhcCCCCceEEECCCCeEEEcHHHHHHHHHHhCcchhhcccchHHH
Confidence            9744 10                 000000000000000                                         


Q ss_pred             ----------------------------------------------------------------------------cCcE
Q 017573          169 ----------------------------------------------------------------------------KVQV  172 (369)
Q Consensus       169 ----------------------------------------------------------------------------~~~~  172 (369)
                                                                                                  -.++
T Consensus       332 ~~i~~Al~A~~l~~~d~dYiV~d~~V~ivD~~TGR~~~gr~w~~GLhQaieaKE~v~i~~e~~t~a~It~q~~Fr~Y~kl  411 (656)
T PRK12898        332 ELVRQALSALHLFRRDEHYIVRDGKVVIVDEFTGRVMPDRSWEDGLHQMIEAKEGCELTDPRETLARITYQRFFRRYLRL  411 (656)
T ss_pred             HHHHHHHHHHHHHhcCCceEEECCeEEEEECCCCeECCCCCcChHHHHHHHHhcCCCCCcCceeeeeehHHHHHHhhHHH
Confidence                                                                                        0467


Q ss_pred             EEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHHHhc--cCCCeEEEeCCHhhHHH
Q 017573          173 GVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETL--AITQSVIFVNTRRKVDW  250 (369)
Q Consensus       173 i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~--~~~k~lv~~~~~~~~~~  250 (369)
                      .+||||......++...+...++.+....+....  ..+.++... ...+...+.+.+...  .+.++||||++.+.++.
T Consensus       412 ~GmTGTa~~~~~El~~~y~l~vv~IPt~kp~~r~--~~~~~v~~t-~~~K~~aL~~~i~~~~~~~~pvLIft~t~~~se~  488 (656)
T PRK12898        412 AGMTGTAREVAGELWSVYGLPVVRIPTNRPSQRR--HLPDEVFLT-AAAKWAAVAARVRELHAQGRPVLVGTRSVAASER  488 (656)
T ss_pred             hcccCcChHHHHHHHHHHCCCeEEeCCCCCccce--ecCCEEEeC-HHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHH
Confidence            7899999877666666666666555544433221  223233333 345666777777553  25689999999999999


Q ss_pred             HHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCC---CCc-----EEEEecCCCCccchhhh
Q 017573          251 LTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQ---QVS-----LVINYDLPTQPENYLHR  322 (369)
Q Consensus       251 ~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~---~~~-----~vi~~~~~~~~~~~~Q~  322 (369)
                      +++.|.+.++++..+||+++..+  ..+..+..+...|+|||+++++|+|++   ++.     +||.++.|.+...|.|+
T Consensus       489 L~~~L~~~gi~~~~Lhg~~~~rE--~~ii~~ag~~g~VlVATdmAgRGtDI~l~~~V~~~GGLhVI~~d~P~s~r~y~hr  566 (656)
T PRK12898        489 LSALLREAGLPHQVLNAKQDAEE--AAIVARAGQRGRITVATNMAGRGTDIKLEPGVAARGGLHVILTERHDSARIDRQL  566 (656)
T ss_pred             HHHHHHHCCCCEEEeeCCcHHHH--HHHHHHcCCCCcEEEEccchhcccCcCCccchhhcCCCEEEEcCCCCCHHHHHHh
Confidence            99999999999999999865444  444555555567999999999999999   565     89999999999999999


Q ss_pred             hcccccCCCceeEEEEeccccHH
Q 017573          323 IGRSGRFGRKGVAINFVTRDDER  345 (369)
Q Consensus       323 ~GR~~R~~~~~~~~~~~~~~~~~  345 (369)
                      +||+||.|++|.++.+++..|.-
T Consensus       567 ~GRTGRqG~~G~s~~~is~eD~l  589 (656)
T PRK12898        567 AGRCGRQGDPGSYEAILSLEDDL  589 (656)
T ss_pred             cccccCCCCCeEEEEEechhHHH
Confidence            99999999999999999985543

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

Probab=100.00  E-value=1.7e-35  Score=269.24  Aligned_cols=333  Identities=20%  Similarity=0.270  Sum_probs=247.5

Q ss_pred             HHhCCCCCCcHhhhhhhhccccC-CcEEEEcCCCChhhHHHHHHHHHhhhc-------cCCCccEEEEcCCHHHHHHHHH
Q 017573           11 IYAYGFEKPSAIQQRGIVPFCKG-LDVIQQAQSGTGKTATFCSGILQQLDY-------GLVQCQALVLAPTRELAQQIEK   82 (369)
Q Consensus        11 l~~~~~~~~~~~Q~~~~~~~~~~-~~~li~~~tG~GKT~~~~~~~~~~~~~-------~~~~~~~liv~P~~~l~~q~~~   82 (369)
                      ..-|+|..++..|.++++..++. .|.+|+||||+|||.+++++|++.+..       ...+.|++||+|.++|+.++.+
T Consensus       103 k~~f~f~~fN~iQS~vFp~aY~SneNMLIcAPTGsGKT~la~L~ILr~ik~~~~~~~i~k~~fKiVYIaPmKALa~Em~~  182 (1230)
T KOG0952|consen  103 KGFFSFEEFNRIQSEVFPVAYKSNENMLICAPTGSGKTVLAELCILRTIKEHEEQGDIAKDDFKIVYIAPMKALAAEMVD  182 (1230)
T ss_pred             hhcccHHHHHHHHHHhhhhhhcCCCCEEEECCCCCCchHHHHHHHHHHHHhhccccccccCCceEEEEechHHHHHHHHH
Confidence            34578899999999999998864 899999999999999999999998874       2234589999999999999999


Q ss_pred             HHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCC---CCCCCccEEEEechhHhhccCcHHHH
Q 017573           83 VMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQS---LRPDYIKMFVLDEADEMLSRGFKDQI  159 (369)
Q Consensus        83 ~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~---~~~~~~~~viiDE~H~~~~~~~~~~~  159 (369)
                      .|.+-+...|+.|..++|+.......   -.+++|+|+|||+|--.-+++.   ...+.+.+||+||+|.+-+.- ...+
T Consensus       183 ~~~kkl~~~gi~v~ELTGD~ql~~te---i~~tqiiVTTPEKwDvvTRk~~~d~~l~~~V~LviIDEVHlLhd~R-Gpvl  258 (1230)
T KOG0952|consen  183 KFSKKLAPLGISVRELTGDTQLTKTE---IADTQIIVTTPEKWDVVTRKSVGDSALFSLVRLVIIDEVHLLHDDR-GPVL  258 (1230)
T ss_pred             HHhhhcccccceEEEecCcchhhHHH---HHhcCEEEecccceeeeeeeeccchhhhhheeeEEeeeehhhcCcc-cchH
Confidence            99998888899999999998754433   2358999999999943333322   123447899999999876432 3333


Q ss_pred             HHHH-------hhCCccCcEEEEEeeCChhHHHHHHHhcCC-CEEEEecCccccccceeEEEEEccch--hh--------
Q 017573          160 YDIF-------QLLPAKVQVGVFSATMPPEALEITRKFMNK-PVRILVKRDELTLEGIKQFYVNVEKE--EW--------  221 (369)
Q Consensus       160 ~~~~-------~~~~~~~~~i~~saT~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~--~~--------  221 (369)
                      +.+.       ....+..+++++|||.| +..+....+-.+ +..+......+.+-.+...+...+..  ..        
T Consensus       259 EtiVaRtlr~vessqs~IRivgLSATlP-N~eDvA~fL~vn~~~glfsFd~~yRPvpL~~~~iG~k~~~~~~~~~~~d~~  337 (1230)
T KOG0952|consen  259 ETIVARTLRLVESSQSMIRIVGLSATLP-NYEDVARFLRVNPYAGLFSFDQRYRPVPLTQGFIGIKGKKNRQQKKNIDEV  337 (1230)
T ss_pred             HHHHHHHHHHHHhhhhheEEEEeeccCC-CHHHHHHHhcCCCccceeeecccccccceeeeEEeeecccchhhhhhHHHH
Confidence            3332       23345778999999995 777776666554 34455555566666666666555443  11        


Q ss_pred             hHHHHHHHHHhccCCCeEEEeCCHhhHHHHHHHHhhC----C-------------------CeeEEecCCCCHHHHHHHH
Q 017573          222 KLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSR----D-------------------HTVSATHGDMDQNTRDIIM  278 (369)
Q Consensus       222 ~~~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~----~-------------------~~~~~~~~~~~~~~r~~~~  278 (369)
                      ..+.+.+.++  .+..++|||.++..+.+.++.|.+.    |                   ....+.|+++..++|.-..
T Consensus       338 ~~~kv~e~~~--~g~qVlvFvhsR~~Ti~tA~~l~~~a~~~g~~~~f~~~~~~k~l~elf~~g~~iHhAGm~r~DR~l~E  415 (1230)
T KOG0952|consen  338 CYDKVVEFLQ--EGHQVLVFVHSRNETIRTAKKLRERAETNGEKDLFLPSPRNKQLKELFQQGMGIHHAGMLRSDRQLVE  415 (1230)
T ss_pred             HHHHHHHHHH--cCCeEEEEEecChHHHHHHHHHHHHHHhcCcccccCCChhhHHHHHHHHhhhhhcccccchhhHHHHH
Confidence            1222233332  3458999999999988888888644    1                   2467889999999999999


Q ss_pred             HHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCCC----------CccchhhhhcccccCC--CceeEEEEeccccHHH
Q 017573          279 REFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPT----------QPENYLHRIGRSGRFG--RKGVAINFVTRDDERM  346 (369)
Q Consensus       279 ~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~----------~~~~~~Q~~GR~~R~~--~~~~~~~~~~~~~~~~  346 (369)
                      +.|..|.++||+||..+..|+|+|.-.++|.-...+          +..+..|.+|||||.+  ..|.++++.+.+....
T Consensus       416 ~~F~~G~i~vL~cTaTLAwGVNLPA~aViIKGT~~ydsskg~f~dlgilDVlQifGRAGRPqFd~~G~giIiTt~dkl~~  495 (1230)
T KOG0952|consen  416 KEFKEGHIKVLCCTATLAWGVNLPAYAVIIKGTQVYDSSKGSFVDLGILDVLQIFGRAGRPQFDSSGEGIIITTRDKLDH  495 (1230)
T ss_pred             HHHhcCCceEEEecceeeeccCCcceEEEecCCcccccccCceeeehHHHHHHHHhccCCCCCCCCceEEEEecccHHHH
Confidence            999999999999999999999998555554322222          2346799999999974  6699998888877666


Q ss_pred             HHHH
Q 017573          347 LFDI  350 (369)
Q Consensus       347 ~~~~  350 (369)
                      +.++
T Consensus       496 Y~sL  499 (1230)
T KOG0952|consen  496 YESL  499 (1230)
T ss_pred             HHHH
Confidence            6555

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=100.00  E-value=1e-34  Score=274.45  Aligned_cols=335  Identities=17%  Similarity=0.137  Sum_probs=226.1

Q ss_pred             CCCcHhhhhhhhccccC--CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcE
Q 017573           17 EKPSAIQQRGIVPFCKG--LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVK   94 (369)
Q Consensus        17 ~~~~~~Q~~~~~~~~~~--~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~   94 (369)
                      ..|.|||..++..+...  .++++..++|.|||..+.+.+...+..+... ++|||||. +|..||..++.+.+   ++.
T Consensus       151 ~~l~pHQl~~~~~vl~~~~~R~LLADEvGLGKTIeAglil~~l~~~g~~~-rvLIVvP~-sL~~QW~~El~~kF---~l~  225 (956)
T PRK04914        151 ASLIPHQLYIAHEVGRRHAPRVLLADEVGLGKTIEAGMIIHQQLLTGRAE-RVLILVPE-TLQHQWLVEMLRRF---NLR  225 (956)
T ss_pred             CCCCHHHHHHHHHHhhccCCCEEEEeCCcCcHHHHHHHHHHHHHHcCCCC-cEEEEcCH-HHHHHHHHHHHHHh---CCC
Confidence            36999999999877643  6899999999999998876666555554433 89999997 89999999986543   344


Q ss_pred             EEEEECCcchHHHHH--HHccCCcEEEeccHHHHHHH-HcCCCCCCCccEEEEechhHhhccC--cHHHHHHHHhhCCcc
Q 017573           95 VHACVGGTSVREDQR--ILQAGVHVVVGTPGRVFDML-RRQSLRPDYIKMFVLDEADEMLSRG--FKDQIYDIFQLLPAK  169 (369)
Q Consensus        95 v~~~~~~~~~~~~~~--~~~~~~~iiv~t~~~l~~~~-~~~~~~~~~~~~viiDE~H~~~~~~--~~~~~~~~~~~~~~~  169 (369)
                      ...+.++........  ......+++|+|++.+...- ....+....|+++|+||||++....  ....+..+.......
T Consensus       226 ~~i~~~~~~~~~~~~~~~pf~~~~~vI~S~~~l~~~~~~~~~l~~~~wdlvIvDEAH~lk~~~~~~s~~y~~v~~La~~~  305 (956)
T PRK04914        226 FSLFDEERYAEAQHDADNPFETEQLVICSLDFLRRNKQRLEQALAAEWDLLVVDEAHHLVWSEEAPSREYQVVEQLAEVI  305 (956)
T ss_pred             eEEEcCcchhhhcccccCccccCcEEEEEHHHhhhCHHHHHHHhhcCCCEEEEechhhhccCCCCcCHHHHHHHHHhhcc
Confidence            444433321110000  01124689999999886421 1112333458999999999986321  122233333333334


Q ss_pred             CcEEEEEeeCChh-HHH------------------HH-------------HHhc-CCC----------------------
Q 017573          170 VQVGVFSATMPPE-ALE------------------IT-------------RKFM-NKP----------------------  194 (369)
Q Consensus       170 ~~~i~~saT~~~~-~~~------------------~~-------------~~~~-~~~----------------------  194 (369)
                      ..++++||||..+ ..+                  +.             ..+. .++                      
T Consensus       306 ~~~LLLTATP~q~~~~e~falL~lLdP~~f~~~~~F~~e~~~~~~~a~~v~~l~~~~~~~~~~~~~l~~ll~~~~~~~l~  385 (956)
T PRK04914        306 PGVLLLTATPEQLGQESHFARLRLLDPDRFHDYEAFVEEQQQYRPVADAVQALLAGEKLSDDALNALGELLGEQDIEPLL  385 (956)
T ss_pred             CCEEEEEcCcccCCcHHHHHhhhhhCCCcCCCHHHHHHHHHhhHHHHHHHHHHhcCCcCCHHHHHHHHHHhcccchhHHH
Confidence            5689999999621 110                  00             0000 000                      


Q ss_pred             -----------------------------EEEEecCc---cccccceeEEEEEcc-------------------------
Q 017573          195 -----------------------------VRILVKRD---ELTLEGIKQFYVNVE-------------------------  217 (369)
Q Consensus       195 -----------------------------~~~~~~~~---~~~~~~~~~~~~~~~-------------------------  217 (369)
                                                   +.+...+.   ..+......+....+                         
T Consensus       386 ~~~~~~~~~~~~~~~~~i~~L~d~hg~~rvm~RntR~~v~~fp~R~~~~~~l~~~~~y~~~~~~~~~~~~~~~l~pe~~~  465 (956)
T PRK04914        386 QAANSDSEEAQAARQELISELLDRHGTGRVLFRNTRAAVKGFPKRELHPIPLPLPEQYQTAIKVSLEARARDMLYPEQIY  465 (956)
T ss_pred             hhhcccccccHHHHHHHHHHHHhhcCcceEEEeccHHhhcCCCcCceeEeecCCCHHHHHHHHHhHHHHHHhhcCHHHHH
Confidence                                         00000000   000000011101000                         


Q ss_pred             ----------chhhhHHHHHHHHHhccCCCeEEEeCCHhhHHHHHHHH-hhCCCeeEEecCCCCHHHHHHHHHHHhcC--
Q 017573          218 ----------KEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKM-RSRDHTVSATHGDMDQNTRDIIMREFRSG--  284 (369)
Q Consensus       218 ----------~~~~~~~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l-~~~~~~~~~~~~~~~~~~r~~~~~~f~~~--  284 (369)
                                ....+.+.+.++++.....|+||||++...+..+.+.| ...|+++..+||+++..+|.++++.|+++  
T Consensus       466 ~~~~~~~~~~~~d~Ki~~L~~~L~~~~~~KvLVF~~~~~t~~~L~~~L~~~~Gi~~~~ihG~~s~~eR~~~~~~F~~~~~  545 (956)
T PRK04914        466 QEFEDNATWWNFDPRVEWLIDFLKSHRSEKVLVICAKAATALQLEQALREREGIRAAVFHEGMSIIERDRAAAYFADEED  545 (956)
T ss_pred             HHHhhhhhccccCHHHHHHHHHHHhcCCCeEEEEeCcHHHHHHHHHHHhhccCeeEEEEECCCCHHHHHHHHHHHhcCCC
Confidence                      01124556677777777789999999999999999999 56799999999999999999999999974  


Q ss_pred             CCcEEEEecCCcCCCCCCCCcEEEEecCCCCccchhhhhcccccCCCceeEEEEeccccHHHHHHHHHHhcc
Q 017573          285 SSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNV  356 (369)
Q Consensus       285 ~~~vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~  356 (369)
                      ...|||||.++++|+|++.+++||++++|||+..|+||+||++|.|+.+.+.++.........+.+.+.+..
T Consensus       546 ~~~VLIsTdvgseGlNlq~a~~VInfDlP~nP~~~eQRIGR~~RiGQ~~~V~i~~~~~~~t~~e~i~~~~~~  617 (956)
T PRK04914        546 GAQVLLCSEIGSEGRNFQFASHLVLFDLPFNPDLLEQRIGRLDRIGQKHDIQIHVPYLEGTAQERLFRWYHE  617 (956)
T ss_pred             CccEEEechhhccCCCcccccEEEEecCCCCHHHHHHHhcccccCCCCceEEEEEccCCCCHHHHHHHHHhh
Confidence            589999999999999999999999999999999999999999999999998888876655555666666555

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=100.00  E-value=1e-34  Score=267.91  Aligned_cols=319  Identities=18%  Similarity=0.208  Sum_probs=235.2

Q ss_pred             CCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCc
Q 017573           14 YGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGV   93 (369)
Q Consensus        14 ~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~   93 (369)
                      .|. .|++.|..+...+.+|+  +..+.||+|||++++++++.....+.   .++|++|++.|+.|.++++..+...+|+
T Consensus        75 ~g~-~p~~vQl~~~~~l~~G~--Iaem~TGeGKTL~a~lp~~l~al~G~---~v~VvTpt~~LA~qd~e~~~~l~~~lGl  148 (790)
T PRK09200         75 LGM-RPYDVQLIGALVLHEGN--IAEMQTGEGKTLTATMPLYLNALEGK---GVHLITVNDYLAKRDAEEMGQVYEFLGL  148 (790)
T ss_pred             hCC-CCchHHHHhHHHHcCCc--eeeecCCCcchHHHHHHHHHHHHcCC---CeEEEeCCHHHHHHHHHHHHHHHhhcCC
Confidence            355 78888888888777665  99999999999999999886555544   8999999999999999999999999999


Q ss_pred             EEEEEECCcc-hHHHHHHHccCCcEEEeccHHH-HHHHHcCC------CCCCCccEEEEechhHhhccC-----------
Q 017573           94 KVHACVGGTS-VREDQRILQAGVHVVVGTPGRV-FDMLRRQS------LRPDYIKMFVLDEADEMLSRG-----------  154 (369)
Q Consensus        94 ~v~~~~~~~~-~~~~~~~~~~~~~iiv~t~~~l-~~~~~~~~------~~~~~~~~viiDE~H~~~~~~-----------  154 (369)
                      ++....++.+ ......  ...++|+++|+..| +.++...-      .....+.++|+||+|.+.=..           
T Consensus       149 ~v~~i~g~~~~~~~r~~--~y~~dIvygT~~~l~fDyLrd~~~~~~~~~~~r~~~~~IvDEaDsiLiDea~tpliisg~~  226 (790)
T PRK09200        149 TVGLNFSDIDDASEKKA--IYEADIIYTTNSELGFDYLRDNLADSKEDKVQRPLNYAIIDEIDSILLDEAQTPLIISGKP  226 (790)
T ss_pred             eEEEEeCCCCcHHHHHH--hcCCCEEEECCccccchhHHhccccchhhhcccccceEEEeccccceeccCCCceeeeCCC
Confidence            9999999887 444332  24589999999888 44444322      234568899999999754100           


Q ss_pred             -----cHHHHHHHHhhCCc-------------------------------------------------------------
Q 017573          155 -----FKDQIYDIFQLLPA-------------------------------------------------------------  168 (369)
Q Consensus       155 -----~~~~~~~~~~~~~~-------------------------------------------------------------  168 (369)
                           .......+...+..                                                             
T Consensus       227 ~~~~~~y~~~~~~~~~l~~~~dy~~d~~~~~~~lt~~g~~~~e~~~~i~~l~~~~~~~~~~~i~~Al~A~~~~~~d~dYi  306 (790)
T PRK09200        227 RVQSNLYHIAAKFVKTLEEDVDYEFDEEKKEVWLTDQGIEKAESYFGIDNLYSLEHQVLYRHIILALRAHVLFKRDVDYI  306 (790)
T ss_pred             ccccHHHHHHHHHHHhcccCCCeEEecCCCeEEecHhHHHHHHHhcCCccccChhhhHHHHHHHHHHHHHHHhhcCCcEE
Confidence                 01111111111100                                                             


Q ss_pred             --------------------------------------------------------cCcEEEEEeeCChhHHHHHHHhcC
Q 017573          169 --------------------------------------------------------KVQVGVFSATMPPEALEITRKFMN  192 (369)
Q Consensus       169 --------------------------------------------------------~~~~i~~saT~~~~~~~~~~~~~~  192 (369)
                                                                              -.++.+||+|......++ ...++
T Consensus       307 V~~~~v~ivD~~TGr~~~gr~~s~GlhQaieaKe~v~i~~e~~t~a~It~q~~fr~Y~kl~GmTGTa~t~~~e~-~~~Y~  385 (790)
T PRK09200        307 VYDGEIVLVDRFTGRVLPGRKLQDGLHQAIEAKEGVEITEENRTMASITIQNLFRMFPKLSGMTGTAKTEEKEF-FEVYN  385 (790)
T ss_pred             EECCEEEEEECCCCcCCCCCccChHHHHHHHHhcCCCcCCCceehhhhhHHHHHHHhHHHhccCCCChHHHHHH-HHHhC
Confidence                                                                    045778888886544433 44444


Q ss_pred             CCEEEEecCccccccceeEEEEEccchhhhHHHHHHHHHh--ccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCC
Q 017573          193 KPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYET--LAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMD  270 (369)
Q Consensus       193 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~--~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~  270 (369)
                      -.+.......+.........++  .....+...+...+..  ....++||||++.+.++.++..|.+.+.++..+||+++
T Consensus       386 l~v~~IPt~kp~~r~d~~~~i~--~~~~~K~~al~~~i~~~~~~~~pvLIf~~t~~~se~l~~~L~~~gi~~~~L~~~~~  463 (790)
T PRK09200        386 MEVVQIPTNRPIIRIDYPDKVF--VTLDEKYKAVIEEVKERHETGRPVLIGTGSIEQSETFSKLLDEAGIPHNLLNAKNA  463 (790)
T ss_pred             CcEEECCCCCCcccccCCCeEE--cCHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHCCCCEEEecCCcc
Confidence            4443332222222222221222  2334466777666654  35679999999999999999999999999999999998


Q ss_pred             HHHHHHHHHHHhcCCCcEEEEecCCcCCCCC---CCCc-----EEEEecCCCCccchhhhhcccccCCCceeEEEEeccc
Q 017573          271 QNTRDIIMREFRSGSSRVLITTDLLARGIDV---QQVS-----LVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRD  342 (369)
Q Consensus       271 ~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~---~~~~-----~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~  342 (369)
                      ..++..+...+..|  .|+|||+++++|+|+   |++.     +||.++.|.+...|.|++||+||.|++|.++.|++..
T Consensus       464 ~~e~~~i~~ag~~g--~VlIATdmAgRG~DI~l~~~V~~~GGL~VI~~d~p~s~r~y~qr~GRtGR~G~~G~s~~~is~e  541 (790)
T PRK09200        464 AKEAQIIAEAGQKG--AVTVATNMAGRGTDIKLGEGVHELGGLAVIGTERMESRRVDLQLRGRSGRQGDPGSSQFFISLE  541 (790)
T ss_pred             HHHHHHHHHcCCCC--eEEEEccchhcCcCCCcccccccccCcEEEeccCCCCHHHHHHhhccccCCCCCeeEEEEEcch
Confidence            88887777776655  699999999999999   6888     9999999999999999999999999999999999875


Q ss_pred             cHH
Q 017573          343 DER  345 (369)
Q Consensus       343 ~~~  345 (369)
                      |.-
T Consensus       542 D~l  544 (790)
T PRK09200        542 DDL  544 (790)
T ss_pred             HHH
Confidence            443

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=100.00  E-value=2.8e-34  Score=260.92  Aligned_cols=319  Identities=21%  Similarity=0.251  Sum_probs=235.6

Q ss_pred             CCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcE
Q 017573           15 GFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVK   94 (369)
Q Consensus        15 ~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~   94 (369)
                      |. .|++.|.-+...+.+|+  +.+++||+|||+++.++++-....+.   .+.+++|+..|+.|.++++..+...+|++
T Consensus        54 g~-~p~~vQlig~~~l~~G~--Iaem~TGeGKTLva~lpa~l~aL~G~---~V~VvTpt~~LA~qdae~~~~l~~~LGLs  127 (745)
T TIGR00963        54 GM-RPFDVQLIGGIALHKGK--IAEMKTGEGKTLTATLPAYLNALTGK---GVHVVTVNDYLAQRDAEWMGQVYRFLGLS  127 (745)
T ss_pred             CC-CccchHHhhhhhhcCCc--eeeecCCCccHHHHHHHHHHHHHhCC---CEEEEcCCHHHHHHHHHHHHHHhccCCCe
Confidence            44 67778877777766655  99999999999999988853333333   79999999999999999999999999999


Q ss_pred             EEEEECCcchHHHHHHHccCCcEEEeccHHH-HHHHHcC------CCCCCCccEEEEechhHhhc-cC------------
Q 017573           95 VHACVGGTSVREDQRILQAGVHVVVGTPGRV-FDMLRRQ------SLRPDYIKMFVLDEADEMLS-RG------------  154 (369)
Q Consensus        95 v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l-~~~~~~~------~~~~~~~~~viiDE~H~~~~-~~------------  154 (369)
                      +..+.++..........  .++|+++|+..| +.+++.+      ......++++|+||+|++.- ..            
T Consensus       128 v~~i~g~~~~~~r~~~y--~~dIvyGT~~rlgfDyLrd~~~~~~~~~~~r~l~~aIIDEaDs~LIDeaRtpLiisg~~~~  205 (745)
T TIGR00963       128 VGLILSGMSPEERREAY--ACDITYGTNNELGFDYLRDNMAHSKEEKVQRPFHFAIIDEVDSILIDEARTPLIISGPAEK  205 (745)
T ss_pred             EEEEeCCCCHHHHHHhc--CCCEEEECCCchhhHHHhcccccchhhhhccccceeEeecHHHHhHHhhhhHHhhcCCCCC
Confidence            99999988765544333  479999999999 7777765      23456789999999998652 10            


Q ss_pred             ---cHHHHHHHHhhCC----------------------------------------------------------------
Q 017573          155 ---FKDQIYDIFQLLP----------------------------------------------------------------  167 (369)
Q Consensus       155 ---~~~~~~~~~~~~~----------------------------------------------------------------  167 (369)
                         .......+...+.                                                                
T Consensus       206 ~~~ly~~a~~i~r~L~~~~dy~~de~~k~v~Lt~~G~~~~e~~~~~~~ly~~~~~~~~~~i~~Al~A~~l~~~d~dYiV~  285 (745)
T TIGR00963       206 STELYLQANRFAKALEKEVHYEVDEKNRAVLLTEKGIKKAEDLLGVDNLYDLENSPLIHYINNALKAKELFEKDVDYIVR  285 (745)
T ss_pred             chHHHHHHHHHHHhhccCCCeEEecCCCceeECHHHHHHHHHHcCCccccChhhhHHHHHHHHHHHHHHHHhcCCcEEEE
Confidence               0000000000000                                                                


Q ss_pred             -----------------------------------------------------ccCcEEEEEeeCChhHHHHHHHhcCCC
Q 017573          168 -----------------------------------------------------AKVQVGVFSATMPPEALEITRKFMNKP  194 (369)
Q Consensus       168 -----------------------------------------------------~~~~~i~~saT~~~~~~~~~~~~~~~~  194 (369)
                                                                           --.++.+||+|...... .....++-+
T Consensus       286 d~~V~ivD~~TGR~~~gr~ws~GLhQaiEaKE~v~i~~e~~t~a~It~qn~Fr~Y~kl~GmTGTa~te~~-E~~~iY~l~  364 (745)
T TIGR00963       286 DGEVVIVDEFTGRIMEGRRWSDGLHQAIEAKEGVEIQNENQTLATITYQNFFRLYEKLSGMTGTAKTEEE-EFEKIYNLE  364 (745)
T ss_pred             CCEEEEEECCCCcCCCCCccchHHHHHHHHhcCCCcCCCceeeeeeeHHHHHhhCchhhccCCCcHHHHH-HHHHHhCCC
Confidence                                                                 00457789999865443 344444444


Q ss_pred             EEEEecCccccccceeEEEEEccchhhhHHHHHHHH-Hh-ccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHH
Q 017573          195 VRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLY-ET-LAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQN  272 (369)
Q Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~-~~-~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~  272 (369)
                      +.......+.........++  .+...+...+.+.+ .. ..+.++||||++++.++.+++.|.+.+++...+|++  ..
T Consensus       365 vv~IPtnkp~~R~d~~d~i~--~t~~~k~~ai~~~i~~~~~~grpvLV~t~si~~se~ls~~L~~~gi~~~~Lna~--q~  440 (745)
T TIGR00963       365 VVVVPTNRPVIRKDLSDLVY--KTEEEKWKAVVDEIKERHAKGQPVLVGTTSVEKSELLSNLLKERGIPHNVLNAK--NH  440 (745)
T ss_pred             EEEeCCCCCeeeeeCCCeEE--cCHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHcCCCeEEeeCC--hH
Confidence            44433222222222121222  22233444554433 22 256799999999999999999999999999999998  77


Q ss_pred             HHHHHHHHHhcCCCcEEEEecCCcCCCCCCC-------CcEEEEecCCCCccchhhhhcccccCCCceeEEEEeccccHH
Q 017573          273 TRDIIMREFRSGSSRVLITTDLLARGIDVQQ-------VSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDER  345 (369)
Q Consensus       273 ~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~-------~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~  345 (369)
                      +|+..+..|..+...|+|||+++++|+|++.       ..+||.++.|.|...+.|+.||+||.|.+|.+..|++..|.-
T Consensus       441 ~rEa~ii~~ag~~g~VtIATnmAgRGtDI~l~~V~~~GGl~VI~t~~p~s~ri~~q~~GRtGRqG~~G~s~~~ls~eD~l  520 (745)
T TIGR00963       441 EREAEIIAQAGRKGAVTIATNMAGRGTDIKLEEVKELGGLYVIGTERHESRRIDNQLRGRSGRQGDPGSSRFFLSLEDNL  520 (745)
T ss_pred             HHHHHHHHhcCCCceEEEEeccccCCcCCCccchhhcCCcEEEecCCCCcHHHHHHHhccccCCCCCcceEEEEeccHHH
Confidence            8888899999999999999999999999987       559999999999999999999999999999999999987654


Q ss_pred             H
Q 017573          346 M  346 (369)
Q Consensus       346 ~  346 (369)
                      +
T Consensus       521 ~  521 (745)
T TIGR00963       521 M  521 (745)
T ss_pred             H
Confidence            4

The proteins SecA-F and SecY, not all of which are necessary, comprise the standard prokaryotic protein translocation apparatus. Other, specialized translocation systems also exist but are not as broadly distributed. This model describes SecA, an essential member of the apparatus.

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

Probab=100.00  E-value=6.5e-35  Score=273.24  Aligned_cols=332  Identities=19%  Similarity=0.223  Sum_probs=255.1

Q ss_pred             HHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhc
Q 017573            9 RGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALG   88 (369)
Q Consensus         9 ~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~   88 (369)
                      .....||...+|+-|.+++...+.|+++++.+|||.||++||.++++-.      ++-+++|.|..+|.+.+...+.+. 
T Consensus       255 ~l~~~Fg~~~FR~~Q~eaI~~~l~Gkd~fvlmpTG~GKSLCYQlPA~l~------~gitvVISPL~SLm~DQv~~L~~~-  327 (941)
T KOG0351|consen  255 LLKEVFGHKGFRPNQLEAINATLSGKDCFVLMPTGGGKSLCYQLPALLL------GGVTVVISPLISLMQDQVTHLSKK-  327 (941)
T ss_pred             HHHHHhccccCChhHHHHHHHHHcCCceEEEeecCCceeeEeecccccc------CCceEEeccHHHHHHHHHHhhhhc-
Confidence            3447799999999999999999999999999999999999997765521      227999999999999888877443 


Q ss_pred             cccCcEEEEEECCcchHHH----HHHHcc--CCcEEEeccHHHHHH--HHcCCCCCCC---ccEEEEechhHhhccC--c
Q 017573           89 DYLGVKVHACVGGTSVRED----QRILQA--GVHVVVGTPGRVFDM--LRRQSLRPDY---IKMFVLDEADEMLSRG--F  155 (369)
Q Consensus        89 ~~~~~~v~~~~~~~~~~~~----~~~~~~--~~~iiv~t~~~l~~~--~~~~~~~~~~---~~~viiDE~H~~~~~~--~  155 (369)
                         ++....+.++......    ..+..+  ..+|++.|||++...  +......+..   +.++|+||||..+.|+  |
T Consensus       328 ---~I~a~~L~s~q~~~~~~~i~q~l~~~~~~ikilYvtPE~v~~~~~l~~~~~~L~~~~~lal~vIDEAHCVSqWgHdF  404 (941)
T KOG0351|consen  328 ---GIPACFLSSIQTAAERLAILQKLANGNPIIKILYVTPEKVVASEGLLESLADLYARGLLALFVIDEAHCVSQWGHDF  404 (941)
T ss_pred             ---CcceeeccccccHHHHHHHHHHHhCCCCeEEEEEeCHHHhhcccchhhHHHhccCCCeeEEEEecHHHHhhhhcccc
Confidence               6777777777765433    233334  688999999998432  2222222222   7899999999998776  3


Q ss_pred             H---HHHHHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHHHh
Q 017573          156 K---DQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYET  232 (369)
Q Consensus       156 ~---~~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  232 (369)
                      +   ..+..+....+. ..++++|||........+-..++-.... .......+.++...+..-.........+...-..
T Consensus       405 Rp~Yk~l~~l~~~~~~-vP~iALTATAT~~v~~DIi~~L~l~~~~-~~~~sfnR~NL~yeV~~k~~~~~~~~~~~~~~~~  482 (941)
T KOG0351|consen  405 RPSYKRLGLLRIRFPG-VPFIALTATATERVREDVIRSLGLRNPE-LFKSSFNRPNLKYEVSPKTDKDALLDILEESKLR  482 (941)
T ss_pred             cHHHHHHHHHHhhCCC-CCeEEeehhccHHHHHHHHHHhCCCCcc-eecccCCCCCceEEEEeccCccchHHHHHHhhhc
Confidence            3   344444555554 6799999999877666555544422111 2223333444433333332223233444444455


Q ss_pred             ccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecC
Q 017573          233 LAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDL  312 (369)
Q Consensus       233 ~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~  312 (369)
                      .+.+.+||||.++.+++.+...|++.+++...||++|++.+|..+...|..++++|++||=++++|+|-|+++.||++..
T Consensus       483 ~~~~s~IIYC~sr~~ce~vs~~L~~~~~~a~~YHAGl~~~~R~~Vq~~w~~~~~~VivATVAFGMGIdK~DVR~ViH~~l  562 (941)
T KOG0351|consen  483 HPDQSGIIYCLSRKECEQVSAVLRSLGKSAAFYHAGLPPKERETVQKAWMSDKIRVIVATVAFGMGIDKPDVRFVIHYSL  562 (941)
T ss_pred             CCCCCeEEEeCCcchHHHHHHHHHHhchhhHhhhcCCCHHHHHHHHHHHhcCCCeEEEEEeeccCCCCCCceeEEEECCC
Confidence            67789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCccchhhhhcccccCCCceeEEEEeccccHHHHHHHHH
Q 017573          313 PTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQK  352 (369)
Q Consensus       313 ~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~  352 (369)
                      |++...|.|.+|||||.|....|++|++..|...+..+..
T Consensus       563 Pks~E~YYQE~GRAGRDG~~s~C~l~y~~~D~~~l~~ll~  602 (941)
T KOG0351|consen  563 PKSFEGYYQEAGRAGRDGLPSSCVLLYGYADISELRRLLT  602 (941)
T ss_pred             chhHHHHHHhccccCcCCCcceeEEecchhHHHHHHHHHH
Confidence            9999999999999999999999999999998777765543

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

Probab=100.00  E-value=6.6e-35  Score=241.74  Aligned_cols=329  Identities=19%  Similarity=0.272  Sum_probs=245.6

Q ss_pred             HHHHHHHh-CCCCC-CcHhhhhhhhccccC-CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHH
Q 017573            6 NLLRGIYA-YGFEK-PSAIQQRGIVPFCKG-LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEK   82 (369)
Q Consensus         6 ~i~~~l~~-~~~~~-~~~~Q~~~~~~~~~~-~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~   82 (369)
                      .+..+|++ ||+.. -++.|++++..+.++ +++.|++|||+||++++.++++-.   +.   -++++.|..+|++++.+
T Consensus         6 ~VreaLKK~FGh~kFKs~LQE~A~~c~VK~k~DVyVsMPTGaGKSLCyQLPaL~~---~g---ITIV~SPLiALIkDQiD   79 (641)
T KOG0352|consen    6 KVREALKKLFGHKKFKSRLQEQAINCIVKRKCDVYVSMPTGAGKSLCYQLPALVH---GG---ITIVISPLIALIKDQID   79 (641)
T ss_pred             HHHHHHHHHhCchhhcChHHHHHHHHHHhccCcEEEeccCCCchhhhhhchHHHh---CC---eEEEehHHHHHHHHHHH
Confidence            45566755 77754 579999999998875 899999999999999999887643   22   78999999999999999


Q ss_pred             HHHHhccccCcEEEEEECCcchHHHHHHH------ccCCcEEEeccHHHHHH----HHcCCCCCCCccEEEEechhHhhc
Q 017573           83 VMRALGDYLGVKVHACVGGTSVREDQRIL------QAGVHVVVGTPGRVFDM----LRRQSLRPDYIKMFVLDEADEMLS  152 (369)
Q Consensus        83 ~~~~~~~~~~~~v~~~~~~~~~~~~~~~~------~~~~~iiv~t~~~l~~~----~~~~~~~~~~~~~viiDE~H~~~~  152 (369)
                      .+.++    .+++..+.+.....+..+++      .....+++.||++....    +.+...+...+.++++||+|..+.
T Consensus        80 HL~~L----KVp~~SLNSKlSt~ER~ri~~DL~~ekp~~K~LYITPE~AAt~~FQ~lLn~L~~r~~L~Y~vVDEAHCVSQ  155 (641)
T KOG0352|consen   80 HLKRL----KVPCESLNSKLSTVERSRIMGDLAKEKPTIKMLYITPEGAATDGFQKLLNGLANRDVLRYIVVDEAHCVSQ  155 (641)
T ss_pred             HHHhc----CCchhHhcchhhHHHHHHHHHHHHhcCCceeEEEEchhhhhhhhHHHHHHHHhhhceeeeEEechhhhHhh
Confidence            88876    55565566555555554433      23567999999876332    222223334478999999999987


Q ss_pred             cC--cHHH---HHHHHhhCCccCcEEEEEeeCChhHHHHHHHh--cCCCEEEEecCccccccceeEEEEEccch---hhh
Q 017573          153 RG--FKDQ---IYDIFQLLPAKVQVGVFSATMPPEALEITRKF--MNKPVRILVKRDELTLEGIKQFYVNVEKE---EWK  222 (369)
Q Consensus       153 ~~--~~~~---~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~  222 (369)
                      |+  |...   +..+.+.++ ....+.+|||..+...+.+...  +.+|+.+......     -...++.....   .+.
T Consensus       156 WGHDFRPDYL~LG~LRS~~~-~vpwvALTATA~~~VqEDi~~qL~L~~PVAiFkTP~F-----R~NLFYD~~~K~~I~D~  229 (641)
T KOG0352|consen  156 WGHDFRPDYLTLGSLRSVCP-GVPWVALTATANAKVQEDIAFQLKLRNPVAIFKTPTF-----RDNLFYDNHMKSFITDC  229 (641)
T ss_pred             hccccCcchhhhhhHHhhCC-CCceEEeecccChhHHHHHHHHHhhcCcHHhccCcch-----hhhhhHHHHHHHHhhhH
Confidence            76  3333   334444443 6669999999998776655433  3445433321111     11112211111   112


Q ss_pred             HHHHHHHHHhcc-------------CCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEE
Q 017573          223 LETLCDLYETLA-------------ITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVL  289 (369)
Q Consensus       223 ~~~l~~~~~~~~-------------~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vl  289 (369)
                      ...|.++....-             .+-.||||.+++.++.++-.|...|++...||+++...+|.++.+.|.++++.|+
T Consensus       230 ~~~LaDF~~~~LG~~~~~~~~~K~~~GCGIVYCRTR~~cEq~AI~l~~~Gi~A~AYHAGLK~~ERTeVQe~WM~~~~PvI  309 (641)
T KOG0352|consen  230 LTVLADFSSSNLGKHEKASQNKKTFTGCGIVYCRTRNECEQVAIMLEIAGIPAMAYHAGLKKKERTEVQEKWMNNEIPVI  309 (641)
T ss_pred             hHhHHHHHHHhcCChhhhhcCCCCcCcceEEEeccHHHHHHHHHHhhhcCcchHHHhcccccchhHHHHHHHhcCCCCEE
Confidence            333444333221             1356999999999999999999999999999999999999999999999999999


Q ss_pred             EEecCCcCCCCCCCCcEEEEecCCCCccchhhhhcccccCCCceeEEEEeccccHHHHHHH
Q 017573          290 ITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDI  350 (369)
Q Consensus       290 i~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~  350 (369)
                      ++|..+++|+|-|++++||+++++.|..-|.|..||+||.|+.+.|-+|++..|.+.+.-+
T Consensus       310 ~AT~SFGMGVDKp~VRFViHW~~~qn~AgYYQESGRAGRDGk~SyCRLYYsR~D~~~i~FL  370 (641)
T KOG0352|consen  310 AATVSFGMGVDKPDVRFVIHWSPSQNLAGYYQESGRAGRDGKRSYCRLYYSRQDKNALNFL  370 (641)
T ss_pred             EEEeccccccCCcceeEEEecCchhhhHHHHHhccccccCCCccceeeeecccchHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999988876544

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

Probab=100.00  E-value=2.7e-33  Score=229.35  Aligned_cols=336  Identities=18%  Similarity=0.255  Sum_probs=254.7

Q ss_pred             CCCHHHHHHH-HhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHH
Q 017573            2 GLQENLLRGI-YAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQI   80 (369)
Q Consensus         2 ~l~~~i~~~l-~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~   80 (369)
                      |-+....+.| +.|..+.+||.|..+++....+++.++..|||.||++++.++++-.      .+-+|++||..+|++++
T Consensus        77 pws~e~~~ilk~~f~lekfrplq~~ain~~ma~ed~~lil~tgggkslcyqlpal~a------dg~alvi~plislmedq  150 (695)
T KOG0353|consen   77 PWSDEAKDILKEQFHLEKFRPLQLAAINATMAGEDAFLILPTGGGKSLCYQLPALCA------DGFALVICPLISLMEDQ  150 (695)
T ss_pred             CCchHHHHHHHHHhhHHhcChhHHHHhhhhhccCceEEEEeCCCccchhhhhhHHhc------CCceEeechhHHHHHHH
Confidence            3445555666 4578899999999999999999999999999999999998887742      22799999999999999


Q ss_pred             HHHHHHhccccCcEEEEEECCcchHHHHHH----H--ccCCcEEEeccHHHHHHH-----HcCCCCCCCccEEEEechhH
Q 017573           81 EKVMRALGDYLGVKVHACVGGTSVREDQRI----L--QAGVHVVVGTPGRVFDML-----RRQSLRPDYIKMFVLDEADE  149 (369)
Q Consensus        81 ~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~----~--~~~~~iiv~t~~~l~~~~-----~~~~~~~~~~~~viiDE~H~  149 (369)
                      .-.++.+    |+....+......++..+.    .  ......++.||+.+...-     ....+....+.++.+||+|.
T Consensus       151 il~lkql----gi~as~lnansske~~k~v~~~i~nkdse~kliyvtpekiaksk~~mnkleka~~~~~~~~iaidevhc  226 (695)
T KOG0353|consen  151 ILQLKQL----GIDASMLNANSSKEEAKRVEAAITNKDSEFKLIYVTPEKIAKSKKFMNKLEKALEAGFFKLIAIDEVHC  226 (695)
T ss_pred             HHHHHHh----CcchhhccCcccHHHHHHHHHHHcCCCceeEEEEecHHHHHHHHHHHHHHHHHhhcceeEEEeecceee
Confidence            8888887    5555555544443333221    1  234678999999884321     12234455689999999999


Q ss_pred             hhccC--cH---HHHHHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEc-cchhhhH
Q 017573          150 MLSRG--FK---DQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNV-EKEEWKL  223 (369)
Q Consensus       150 ~~~~~--~~---~~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~  223 (369)
                      .+.|+  |.   ..+.-+.+.+ ++..++++|||......+.....+.-...+.. ......+++....... ...+...
T Consensus       227 csqwghdfr~dy~~l~ilkrqf-~~~~iigltatatn~vl~d~k~il~ie~~~tf-~a~fnr~nl~yev~qkp~n~dd~~  304 (695)
T KOG0353|consen  227 CSQWGHDFRPDYKALGILKRQF-KGAPIIGLTATATNHVLDDAKDILCIEAAFTF-RAGFNRPNLKYEVRQKPGNEDDCI  304 (695)
T ss_pred             hhhhCcccCcchHHHHHHHHhC-CCCceeeeehhhhcchhhHHHHHHhHHhhhee-ecccCCCCceeEeeeCCCChHHHH
Confidence            98776  22   2333333444 46779999999987776666655543322222 2233333443333333 3445566


Q ss_pred             HHHHHHHH-hccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCC
Q 017573          224 ETLCDLYE-TLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQ  302 (369)
Q Consensus       224 ~~l~~~~~-~~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~  302 (369)
                      +.+..+++ +..+...||||-+.++++.++..|+.+|+....+|+.+.++++.-+-+.|..|++.|+|+|-+.++|+|-|
T Consensus       305 edi~k~i~~~f~gqsgiiyc~sq~d~ekva~alkn~gi~a~~yha~lep~dks~~hq~w~a~eiqvivatvafgmgidkp  384 (695)
T KOG0353|consen  305 EDIAKLIKGDFAGQSGIIYCFSQKDCEKVAKALKNHGIHAGAYHANLEPEDKSGAHQGWIAGEIQVIVATVAFGMGIDKP  384 (695)
T ss_pred             HHHHHHhccccCCCcceEEEeccccHHHHHHHHHhcCccccccccccCccccccccccccccceEEEEEEeeecccCCCC
Confidence            66666665 45677899999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCcEEEEecCCCCccchhh-------------------------------------------hhcccccCCCceeEEEEe
Q 017573          303 QVSLVINYDLPTQPENYLH-------------------------------------------RIGRSGRFGRKGVAINFV  339 (369)
Q Consensus       303 ~~~~vi~~~~~~~~~~~~Q-------------------------------------------~~GR~~R~~~~~~~~~~~  339 (369)
                      ++++||+...|.|...|.|                                           ..||+||.+.+..|++|+
T Consensus       385 dvrfvihhsl~ksienyyqasarillrmtkqknksdtggstqinilevctnfkiffavfsekesgragrd~~~a~cilyy  464 (695)
T KOG0353|consen  385 DVRFVIHHSLPKSIENYYQASARILLRMTKQKNKSDTGGSTQINILEVCTNFKIFFAVFSEKESGRAGRDDMKADCILYY  464 (695)
T ss_pred             CeeEEEecccchhHHHHHHHHHHHHHHHhhhcccccCCCcceeehhhhhccceeeeeeecchhccccccCCCcccEEEEe
Confidence            9999999999999999999                                           789999999999999999


Q ss_pred             ccccHHHHHH
Q 017573          340 TRDDERMLFD  349 (369)
Q Consensus       340 ~~~~~~~~~~  349 (369)
                      .-.|.-...+
T Consensus       465 ~~~difk~ss  474 (695)
T KOG0353|consen  465 GFADIFKISS  474 (695)
T ss_pred             chHHHHhHHH
Confidence            8665544433

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

Probab=100.00  E-value=2.6e-32  Score=254.68  Aligned_cols=322  Identities=20%  Similarity=0.262  Sum_probs=253.9

Q ss_pred             CCCHHHHHHH-HhCCCCCCcHhhhhhhhccccC------CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCH
Q 017573            2 GLQENLLRGI-YAYGFEKPSAIQQRGIVPFCKG------LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTR   74 (369)
Q Consensus         2 ~l~~~i~~~l-~~~~~~~~~~~Q~~~~~~~~~~------~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~   74 (369)
                      +.+...+..+ ..|+| .-|+-|..|++.+.+.      -+-+|||..|.|||.+|+-++..+...++   ++.++|||.
T Consensus       578 ~~d~~~q~~F~~~FPy-eET~DQl~AI~eVk~DM~~~kpMDRLiCGDVGFGKTEVAmRAAFkAV~~GK---QVAvLVPTT  653 (1139)
T COG1197         578 PPDTEWQEEFEASFPY-EETPDQLKAIEEVKRDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVMDGK---QVAVLVPTT  653 (1139)
T ss_pred             CCChHHHHHHHhcCCC-cCCHHHHHHHHHHHHHhccCCcchheeecCcCCcHHHHHHHHHHHHhcCCC---eEEEEcccH
Confidence            4455666677 45888 7899999999998753      46799999999999999999888887764   999999999


Q ss_pred             HHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHH----ccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHh
Q 017573           75 ELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL----QAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEM  150 (369)
Q Consensus        75 ~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~----~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~  150 (369)
                      -|++|.++.|++-....++++..+..-.+.++...++    .+..||+|+|+     .+.+..+...+++++|+||=|++
T Consensus       654 lLA~QHy~tFkeRF~~fPV~I~~LSRF~s~kE~~~il~~la~G~vDIvIGTH-----rLL~kdv~FkdLGLlIIDEEqRF  728 (1139)
T COG1197         654 LLAQQHYETFKERFAGFPVRIEVLSRFRSAKEQKEILKGLAEGKVDIVIGTH-----RLLSKDVKFKDLGLLIIDEEQRF  728 (1139)
T ss_pred             HhHHHHHHHHHHHhcCCCeeEEEecccCCHHHHHHHHHHHhcCCccEEEech-----HhhCCCcEEecCCeEEEechhhc
Confidence            9999999999998888899999999888777766554    46899999994     44455667777899999999997


Q ss_pred             hccCcHHHHHHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHH
Q 017573          151 LSRGFKDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLY  230 (369)
Q Consensus       151 ~~~~~~~~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~  230 (369)
                      .-. ..+.+    +.+..+.-++-|||||.|....+....+...-.+....  .....+..++...++..-+...+.++ 
T Consensus       729 GVk-~KEkL----K~Lr~~VDvLTLSATPIPRTL~Msm~GiRdlSvI~TPP--~~R~pV~T~V~~~d~~~ireAI~REl-  800 (1139)
T COG1197         729 GVK-HKEKL----KELRANVDVLTLSATPIPRTLNMSLSGIRDLSVIATPP--EDRLPVKTFVSEYDDLLIREAILREL-  800 (1139)
T ss_pred             Ccc-HHHHH----HHHhccCcEEEeeCCCCcchHHHHHhcchhhhhccCCC--CCCcceEEEEecCChHHHHHHHHHHH-
Confidence            422 23333    44445666999999999988777766666543333322  22233444444444432222222222 


Q ss_pred             HhccCCCeEEEeCCHhhHHHHHHHHhhC--CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEE
Q 017573          231 ETLAITQSVIFVNTRRKVDWLTDKMRSR--DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVI  308 (369)
Q Consensus       231 ~~~~~~k~lv~~~~~~~~~~~~~~l~~~--~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi  308 (369)
                        ..++++.-.+|.++..+.+++.|+..  .-++++.||.|++.+-++++..|.+|+++|||||.+++.|+|+|+++.+|
T Consensus       801 --~RgGQvfYv~NrV~~Ie~~~~~L~~LVPEarI~vaHGQM~e~eLE~vM~~F~~g~~dVLv~TTIIEtGIDIPnANTiI  878 (1139)
T COG1197         801 --LRGGQVFYVHNRVESIEKKAERLRELVPEARIAVAHGQMRERELEEVMLDFYNGEYDVLVCTTIIETGIDIPNANTII  878 (1139)
T ss_pred             --hcCCEEEEEecchhhHHHHHHHHHHhCCceEEEEeecCCCHHHHHHHHHHHHcCCCCEEEEeeeeecCcCCCCCceEE
Confidence              34678888999999999999999987  44799999999999999999999999999999999999999999999998


Q ss_pred             EecCC-CCccchhhhhcccccCCCceeEEEEeccc
Q 017573          309 NYDLP-TQPENYLHRIGRSGRFGRKGVAINFVTRD  342 (369)
Q Consensus       309 ~~~~~-~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~  342 (369)
                      +-+.. ...+++-|.-||+||.++.+.||.++.+.
T Consensus       879 Ie~AD~fGLsQLyQLRGRVGRS~~~AYAYfl~p~~  913 (1139)
T COG1197         879 IERADKFGLAQLYQLRGRVGRSNKQAYAYFLYPPQ  913 (1139)
T ss_pred             EeccccccHHHHHHhccccCCccceEEEEEeecCc
Confidence            87653 46789999999999999999999999854

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

Probab=100.00  E-value=5.9e-33  Score=230.76  Aligned_cols=289  Identities=29%  Similarity=0.469  Sum_probs=233.9

Q ss_pred             CCCccEEEEcCCHHHHHHHHHHHHHhcccc---CcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCC
Q 017573           62 LVQCQALVLAPTRELAQQIEKVMRALGDYL---GVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDY  138 (369)
Q Consensus        62 ~~~~~~liv~P~~~l~~q~~~~~~~~~~~~---~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~  138 (369)
                      ++.++++|+-|+++|++|..+++.+|...+   .++...+.++.....+...+..+.+|+|+||.++.+.+......+..
T Consensus       284 pNap~avivepsrelaEqt~N~i~~Fk~h~~np~~r~lLmiggv~~r~Q~~ql~~g~~ivvGtpgRl~~~is~g~~~lt~  363 (725)
T KOG0349|consen  284 PNAPEAVIVEPSRELAEQTHNQIEEFKMHTSNPEVRSLLMIGGVLKRTQCKQLKDGTHIVVGTPGRLLQPISKGLVTLTH  363 (725)
T ss_pred             CCCcceeEecCcHHHHHHHHhhHHHHHhhcCChhhhhhhhhhhHHhHHHHHHhhcCceeeecCchhhhhhhhccceeeee
Confidence            344579999999999999999776664333   34444677777777777888889999999999999999999999999


Q ss_pred             ccEEEEechhHhhccCcHHHHHHHHhhCCc------cCcEEEEEeeCCh-hHHHHHHHhcCCCEEEEecCccccccceeE
Q 017573          139 IKMFVLDEADEMLSRGFKDQIYDIFQLLPA------KVQVGVFSATMPP-EALEITRKFMNKPVRILVKRDELTLEGIKQ  211 (369)
Q Consensus       139 ~~~viiDE~H~~~~~~~~~~~~~~~~~~~~------~~~~i~~saT~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  211 (369)
                      +.++++||++.+...++...+.++...+|.      ..|.+..|||.+. +.....++.+.-|..+....+...+....+
T Consensus       364 crFlvlDead~lL~qgy~d~I~r~h~qip~~tsdg~rlq~~vCsatlh~feVkk~~ervmhfptwVdLkgeD~vpetvHh  443 (725)
T KOG0349|consen  364 CRFLVLDEADLLLGQGYDDKIYRFHGQIPHMTSDGFRLQSPVCSATLHIFEVKKVGERVMHFPTWVDLKGEDLVPETVHH  443 (725)
T ss_pred             eEEEEecchhhhhhcccHHHHHHHhccchhhhcCCcccccceeeeEEeEEEeeehhhhhccCceeEecccccccchhhcc
Confidence            999999999999998999999988877763      5688899999864 444566677778888877777776666665


Q ss_pred             EEEEccchhh---------------------------------hH-----HHHHHHHHhccCCCeEEEeCCHhhHHHHHH
Q 017573          212 FYVNVEKEEW---------------------------------KL-----ETLCDLYETLAITQSVIFVNTRRKVDWLTD  253 (369)
Q Consensus       212 ~~~~~~~~~~---------------------------------~~-----~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~  253 (369)
                      +.....+...                                 ..     +.-...+++++-.++|+||.+..++..+.+
T Consensus       444 vv~lv~p~~d~sw~~lr~~i~td~vh~kdn~~pg~~Spe~~s~a~kilkgEy~v~ai~~h~mdkaiifcrtk~dcDnLer  523 (725)
T KOG0349|consen  444 VVKLVCPSVDGSWCDLRQFIETDKVHTKDNLLPGQVSPENPSSATKILKGEYGVVAIRRHAMDKAIIFCRTKQDCDNLER  523 (725)
T ss_pred             ceeecCCccCccHHHHhhhhccCCcccccccccccCCCCChhhhhHHhcCchhhhhhhhhccCceEEEEeccccchHHHH
Confidence            5554433211                                 00     111122344566789999999999999999


Q ss_pred             HHhhCC---CeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCCCCccchhhhhcccccCC
Q 017573          254 KMRSRD---HTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFG  330 (369)
Q Consensus       254 ~l~~~~---~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~  330 (369)
                      ++.+.+   +.+..+||+..+.+|..-++.|+.++.++||||+.+.+|+|+.++..+|.+.+|.....|.+|+||+||..
T Consensus       524 ~~~qkgg~~~scvclhgDrkP~Erk~nle~Fkk~dvkflictdvaargldi~g~p~~invtlpd~k~nyvhrigrvgrae  603 (725)
T KOG0349|consen  524 MMNQKGGKHYSCVCLHGDRKPDERKANLESFKKFDVKFLICTDVAARGLDITGLPFMINVTLPDDKTNYVHRIGRVGRAE  603 (725)
T ss_pred             HHHHcCCccceeEEEecCCChhHHHHHHHhhhhcCeEEEEEehhhhccccccCCceEEEEecCcccchhhhhhhccchhh
Confidence            998774   47899999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CceeEEEEeccccHHHHHHH
Q 017573          331 RKGVAINFVTRDDERMLFDI  350 (369)
Q Consensus       331 ~~~~~~~~~~~~~~~~~~~~  350 (369)
                      +.|.++.++....++.++..
T Consensus       604 rmglaislvat~~ekvwyh~  623 (725)
T KOG0349|consen  604 RMGLAISLVATVPEKVWYHW  623 (725)
T ss_pred             hcceeEEEeeccchheeehh
Confidence            88999888876655555444

>PRK05580 primosome assembly protein PriA; Validated

Probab=100.00  E-value=1.3e-31  Score=250.16  Aligned_cols=315  Identities=20%  Similarity=0.267  Sum_probs=218.1

Q ss_pred             CCcHhhhhhhhccccC---CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcE
Q 017573           18 KPSAIQQRGIVPFCKG---LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVK   94 (369)
Q Consensus        18 ~~~~~Q~~~~~~~~~~---~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~   94 (369)
                      .|++.|+++++.+.++   +++++.++||+|||.+++.++...+..+.   ++|+++|+++|+.|+.+.+++..   +..
T Consensus       144 ~Lt~~Q~~ai~~i~~~~~~~~~Ll~~~TGSGKT~v~l~~i~~~l~~g~---~vLvLvPt~~L~~Q~~~~l~~~f---g~~  217 (679)
T PRK05580        144 TLNPEQAAAVEAIRAAAGFSPFLLDGVTGSGKTEVYLQAIAEVLAQGK---QALVLVPEIALTPQMLARFRARF---GAP  217 (679)
T ss_pred             CCCHHHHHHHHHHHhccCCCcEEEECCCCChHHHHHHHHHHHHHHcCC---eEEEEeCcHHHHHHHHHHHHHHh---CCC
Confidence            5899999999999874   78999999999999999888777776543   89999999999999999998754   567


Q ss_pred             EEEEECCcchHHHH----HHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCc------HHHHHHHHh
Q 017573           95 VHACVGGTSVREDQ----RILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGF------KDQIYDIFQ  164 (369)
Q Consensus        95 v~~~~~~~~~~~~~----~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~------~~~~~~~~~  164 (369)
                      +..++++.+..+..    ....+..+|+|+|+..++       ....+++++|+||+|.....+.      .+.+. ...
T Consensus       218 v~~~~s~~s~~~r~~~~~~~~~g~~~IVVgTrsal~-------~p~~~l~liVvDEeh~~s~~~~~~p~y~~r~va-~~r  289 (679)
T PRK05580        218 VAVLHSGLSDGERLDEWRKAKRGEAKVVIGARSALF-------LPFKNLGLIIVDEEHDSSYKQQEGPRYHARDLA-VVR  289 (679)
T ss_pred             EEEEECCCCHHHHHHHHHHHHcCCCCEEEeccHHhc-------ccccCCCEEEEECCCccccccCcCCCCcHHHHH-HHH
Confidence            88888887654432    234457899999998764       2345689999999998653321      12222 223


Q ss_pred             hCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCcc--ccccceeEEEEEccch------hhhHHHHHHHH-Hhc-c
Q 017573          165 LLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDE--LTLEGIKQFYVNVEKE------EWKLETLCDLY-ETL-A  234 (369)
Q Consensus       165 ~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~------~~~~~~l~~~~-~~~-~  234 (369)
                      ....+.+++++||||+..........  ...........  ...+.+.  .......      ......+.+.+ +.. .
T Consensus       290 a~~~~~~~il~SATps~~s~~~~~~g--~~~~~~l~~r~~~~~~p~v~--~id~~~~~~~~~~~~ls~~l~~~i~~~l~~  365 (679)
T PRK05580        290 AKLENIPVVLGSATPSLESLANAQQG--RYRLLRLTKRAGGARLPEVE--IIDMRELLRGENGSFLSPPLLEAIKQRLER  365 (679)
T ss_pred             hhccCCCEEEEcCCCCHHHHHHHhcc--ceeEEEeccccccCCCCeEE--EEechhhhhhcccCCCCHHHHHHHHHHHHc
Confidence            33457889999999986655444321  11111111111  1111111  1111000      00112222222 222 2


Q ss_pred             CCCeEEEeCCHh------------------------------------------------------------hHHHHHHH
Q 017573          235 ITQSVIFVNTRR------------------------------------------------------------KVDWLTDK  254 (369)
Q Consensus       235 ~~k~lv~~~~~~------------------------------------------------------------~~~~~~~~  254 (369)
                      ++++|+|+|.+.                                                            -++.+++.
T Consensus       366 g~qvll~~nrrGy~~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~l~~~g~G~e~~~e~  445 (679)
T PRK05580        366 GEQVLLFLNRRGYAPFLLCRDCGWVAECPHCDASLTLHRFQRRLRCHHCGYQEPIPKACPECGSTDLVPVGPGTERLEEE  445 (679)
T ss_pred             CCeEEEEEcCCCCCCceEhhhCcCccCCCCCCCceeEECCCCeEECCCCcCCCCCCCCCCCCcCCeeEEeeccHHHHHHH
Confidence            347788776421                                                            34567777


Q ss_pred             HhhC--CCeeEEecCCCC--HHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCCC--C----------ccc
Q 017573          255 MRSR--DHTVSATHGDMD--QNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPT--Q----------PEN  318 (369)
Q Consensus       255 l~~~--~~~~~~~~~~~~--~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~--~----------~~~  318 (369)
                      |++.  +.++..+|+++.  .++++++++.|.+|+.+|||+|+++..|+|+|+++.|++++...  +          ...
T Consensus       446 l~~~fp~~~v~~~~~d~~~~~~~~~~~l~~f~~g~~~ILVgT~~iakG~d~p~v~lV~il~aD~~l~~pdfra~Er~~~~  525 (679)
T PRK05580        446 LAELFPEARILRIDRDTTRRKGALEQLLAQFARGEADILIGTQMLAKGHDFPNVTLVGVLDADLGLFSPDFRASERTFQL  525 (679)
T ss_pred             HHHhCCCCcEEEEeccccccchhHHHHHHHHhcCCCCEEEEChhhccCCCCCCcCEEEEEcCchhccCCccchHHHHHHH
Confidence            7775  568889999885  46789999999999999999999999999999999997776432  2          246


Q ss_pred             hhhhhcccccCCCceeEEEEeccccHHHHHHH
Q 017573          319 YLHRIGRSGRFGRKGVAINFVTRDDERMLFDI  350 (369)
Q Consensus       319 ~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~  350 (369)
                      +.|++||+||.++.|.+++.....+...++.+
T Consensus       526 l~q~~GRagR~~~~g~viiqT~~p~~~~~~~~  557 (679)
T PRK05580        526 LTQVAGRAGRAEKPGEVLIQTYHPEHPVIQAL  557 (679)
T ss_pred             HHHHHhhccCCCCCCEEEEEeCCCCCHHHHHH
Confidence            89999999999999999988877765555444

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

Probab=100.00  E-value=4.6e-32  Score=262.01  Aligned_cols=304  Identities=18%  Similarity=0.212  Sum_probs=196.8

Q ss_pred             CCCcHhhhhhhhcccc-----CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhcccc
Q 017573           17 EKPSAIQQRGIVPFCK-----GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYL   91 (369)
Q Consensus        17 ~~~~~~Q~~~~~~~~~-----~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~   91 (369)
                      ..+|+||.+|+.++.+     .++.++++|||||||.+++..+...+.... ..++|+++|+++|+.|+.+.|..+....
T Consensus       412 ~~lR~YQ~~AI~ai~~a~~~g~r~~Ll~maTGSGKT~tai~li~~L~~~~~-~~rVLfLvDR~~L~~Qa~~~F~~~~~~~  490 (1123)
T PRK11448        412 LGLRYYQEDAIQAVEKAIVEGQREILLAMATGTGKTRTAIALMYRLLKAKR-FRRILFLVDRSALGEQAEDAFKDTKIEG  490 (1123)
T ss_pred             CCCCHHHHHHHHHHHHHHHhccCCeEEEeCCCCCHHHHHHHHHHHHHhcCc-cCeEEEEecHHHHHHHHHHHHHhccccc
Confidence            4699999999988763     367999999999999987665554444433 3489999999999999999998874321


Q ss_pred             CcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcC-----CCCCCCccEEEEechhHhhcc-------------
Q 017573           92 GVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQ-----SLRPDYIKMFVLDEADEMLSR-------------  153 (369)
Q Consensus        92 ~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~-----~~~~~~~~~viiDE~H~~~~~-------------  153 (369)
                      +.......+...  ...........|+|+|++++...+...     ......+++||+||||+....             
T Consensus       491 ~~~~~~i~~i~~--L~~~~~~~~~~I~iaTiQtl~~~~~~~~~~~~~~~~~~fdlIIiDEaHRs~~~d~~~~~~~~~~~~  568 (1123)
T PRK11448        491 DQTFASIYDIKG--LEDKFPEDETKVHVATVQGMVKRILYSDDPMDKPPVDQYDCIIVDEAHRGYTLDKEMSEGELQFRD  568 (1123)
T ss_pred             ccchhhhhchhh--hhhhcccCCCCEEEEEHHHHHHhhhccccccccCCCCcccEEEEECCCCCCccccccccchhccch
Confidence            211111111000  011112345789999999997765321     133566899999999985310             


Q ss_pred             --CcHHHHHHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCcccccc---------cee------------
Q 017573          154 --GFKDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLE---------GIK------------  210 (369)
Q Consensus       154 --~~~~~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------~~~------------  210 (369)
                        .+...+..++..+.  ...++|||||......    +++.++......+.....         .+.            
T Consensus       569 ~~~~~~~yr~iL~yFd--A~~IGLTATP~r~t~~----~FG~pv~~Ysl~eAI~DG~Lv~~~~p~~i~t~~~~~gi~~~~  642 (1123)
T PRK11448        569 QLDYVSKYRRVLDYFD--AVKIGLTATPALHTTE----IFGEPVYTYSYREAVIDGYLIDHEPPIRIETRLSQEGIHFEK  642 (1123)
T ss_pred             hhhHHHHHHHHHhhcC--ccEEEEecCCccchhH----HhCCeeEEeeHHHHHhcCCcccCcCCEEEEEEeccccccccc
Confidence              11345566666553  4689999999754332    222322211100000000         000            


Q ss_pred             ------------EE-EEEccch------h--------hhH----HHHHHHHHhccCCCeEEEeCCHhhHHHHHHHHhhC-
Q 017573          211 ------------QF-YVNVEKE------E--------WKL----ETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSR-  258 (369)
Q Consensus       211 ------------~~-~~~~~~~------~--------~~~----~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~-  258 (369)
                                  .. ....+..      .        ...    +.+.+.+.....+|+||||.+.++|+.+.+.|.+. 
T Consensus       643 ~e~~~~~~~~~~~i~~~~l~d~~~~~~~~~~~~vi~~~~~~~i~~~l~~~l~~~~~~KtiIF~~s~~HA~~i~~~L~~~f  722 (1123)
T PRK11448        643 GEEVEVINTQTGEIDLATLEDEVDFEVEDFNRRVITESFNRVVCEELAKYLDPTGEGKTLIFAATDAHADMVVRLLKEAF  722 (1123)
T ss_pred             cchhhhcchhhhhhhhccCcHHHhhhHHHHHHHHhhHHHHHHHHHHHHHHHhccCCCcEEEEEcCHHHHHHHHHHHHHHH
Confidence                        00 0000000      0        000    11112222223479999999999999998887653 


Q ss_pred             -----C---CeeEEecCCCCHHHHHHHHHHHhcCCC-cEEEEecCCcCCCCCCCCcEEEEecCCCCccchhhhhcccccC
Q 017573          259 -----D---HTVSATHGDMDQNTRDIIMREFRSGSS-RVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRF  329 (369)
Q Consensus       259 -----~---~~~~~~~~~~~~~~r~~~~~~f~~~~~-~vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~  329 (369)
                           +   ..+..++|+.+  ++..+++.|+++.. .|+|+++++.+|+|+|.+++|+++.++.|...|.|++||+.|.
T Consensus       723 ~~~~~~~~~~~v~~itg~~~--~~~~li~~Fk~~~~p~IlVsvdmL~TG~DvP~v~~vVf~rpvkS~~lf~QmIGRgtR~  800 (1123)
T PRK11448        723 KKKYGQVEDDAVIKITGSID--KPDQLIRRFKNERLPNIVVTVDLLTTGIDVPSICNLVFLRRVRSRILYEQMLGRATRL  800 (1123)
T ss_pred             HhhcCCcCccceEEEeCCcc--chHHHHHHHhCCCCCeEEEEecccccCCCcccccEEEEecCCCCHHHHHHHHhhhccC
Confidence                 1   24556888764  46789999999876 6899999999999999999999999999999999999999997


Q ss_pred             CC
Q 017573          330 GR  331 (369)
Q Consensus       330 ~~  331 (369)
                      ..
T Consensus       801 ~~  802 (1123)
T PRK11448        801 CP  802 (1123)
T ss_pred             Cc
Confidence            54

>cd00268 DEADc DEAD-box helicases

Probab=100.00  E-value=7.5e-32  Score=218.62  Aligned_cols=197  Identities=54%  Similarity=0.804  Sum_probs=176.8

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhcc--CCCccEEEEcCCHHHHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYG--LVQCQALVLAPTRELAQ   78 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~--~~~~~~liv~P~~~l~~   78 (369)
                      +++++.+.+.+.++|+..|+++|+++++.+.+++++++.+|||+|||++++++++..+...  ..+++++|++|+++|+.
T Consensus         4 ~~~~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~TG~GKT~~~~~~~l~~~~~~~~~~~~~viii~p~~~L~~   83 (203)
T cd00268           4 LGLSPELLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEKLDPSPKKDGPQALILAPTRELAL   83 (203)
T ss_pred             CCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHHHHHHHHHHhhcccCCceEEEEcCCHHHHH
Confidence            5899999999999999999999999999999999999999999999999999999888776  45568999999999999


Q ss_pred             HHHHHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHH
Q 017573           79 QIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQ  158 (369)
Q Consensus        79 q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~  158 (369)
                      |+.+.+..+....+..+....++...........++++|+|+|++.+...+.+.......++++|+||+|.+.+..+...
T Consensus        84 q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~l~~~~~~~~~l~~lIvDE~h~~~~~~~~~~  163 (203)
T cd00268          84 QIAEVARKLGKHTNLKVVVIYGGTSIDKQIRKLKRGPHIVVATPGRLLDLLERGKLDLSKVKYLVLDEADRMLDMGFEDQ  163 (203)
T ss_pred             HHHHHHHHHhccCCceEEEEECCCCHHHHHHHhcCCCCEEEEChHHHHHHHHcCCCChhhCCEEEEeChHHhhccChHHH
Confidence            99999999887778888888888887666666666789999999999999988877778899999999999988888889


Q ss_pred             HHHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEE
Q 017573          159 IYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRI  197 (369)
Q Consensus       159 ~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~  197 (369)
                      +..+.+.++...+++++|||+++........++..++.+
T Consensus       164 ~~~~~~~l~~~~~~~~~SAT~~~~~~~~~~~~~~~~~~~  202 (203)
T cd00268         164 IREILKLLPKDRQTLLFSATMPKEVRDLARKFLRNPVRI  202 (203)
T ss_pred             HHHHHHhCCcccEEEEEeccCCHHHHHHHHHHCCCCEEe
Confidence            999999998899999999999988888888888877654

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.

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

Probab=100.00  E-value=2.3e-31  Score=214.92  Aligned_cols=309  Identities=17%  Similarity=0.178  Sum_probs=222.9

Q ss_pred             CCCcHhhhhhhhccc----cCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccC
Q 017573           17 EKPSAIQQRGIVPFC----KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLG   92 (369)
Q Consensus        17 ~~~~~~Q~~~~~~~~----~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~   92 (369)
                      .++++.|+.+-+.+.    +.++.+++|-||+|||.+....+...+..+.   .+.+.+|+...+.+++.+++..+.  +
T Consensus        96 G~Ls~~Q~~as~~l~q~i~~k~~~lv~AV~GaGKTEMif~~i~~al~~G~---~vciASPRvDVclEl~~Rlk~aF~--~  170 (441)
T COG4098          96 GTLSPGQKKASNQLVQYIKQKEDTLVWAVTGAGKTEMIFQGIEQALNQGG---RVCIASPRVDVCLELYPRLKQAFS--N  170 (441)
T ss_pred             cccChhHHHHHHHHHHHHHhcCcEEEEEecCCCchhhhHHHHHHHHhcCC---eEEEecCcccchHHHHHHHHHhhc--c
Confidence            369999999877765    4689999999999999998878887777776   899999999999999999887654  4


Q ss_pred             cEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCccCcE
Q 017573           93 VKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQV  172 (369)
Q Consensus        93 ~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~  172 (369)
                      ..+..++|+.....       ...++|+|.+++++....       ||++|+||+|.+.-..-......+.+........
T Consensus       171 ~~I~~Lyg~S~~~f-------r~plvVaTtHQLlrFk~a-------FD~liIDEVDAFP~~~d~~L~~Av~~ark~~g~~  236 (441)
T COG4098         171 CDIDLLYGDSDSYF-------RAPLVVATTHQLLRFKQA-------FDLLIIDEVDAFPFSDDQSLQYAVKKARKKEGAT  236 (441)
T ss_pred             CCeeeEecCCchhc-------cccEEEEehHHHHHHHhh-------ccEEEEeccccccccCCHHHHHHHHHhhcccCce
Confidence            56777887765222       268999999999887666       8999999999876444333344444555556678


Q ss_pred             EEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhH------HHHHHHHHhc--cCCCeEEEeCC
Q 017573          173 GVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKL------ETLCDLYETL--AITQSVIFVNT  244 (369)
Q Consensus       173 i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~l~~~~~~~--~~~k~lv~~~~  244 (369)
                      +++||||+..++.-+...-...  .......-..+-..+.+.....-..++      ..+..++++.  .+.+++||+++
T Consensus       237 IylTATp~k~l~r~~~~g~~~~--~klp~RfH~~pLpvPkf~w~~~~~k~l~r~kl~~kl~~~lekq~~~~~P~liF~p~  314 (441)
T COG4098         237 IYLTATPTKKLERKILKGNLRI--LKLPARFHGKPLPVPKFVWIGNWNKKLQRNKLPLKLKRWLEKQRKTGRPVLIFFPE  314 (441)
T ss_pred             EEEecCChHHHHHHhhhCCeeE--eecchhhcCCCCCCCceEEeccHHHHhhhccCCHHHHHHHHHHHhcCCcEEEEecc
Confidence            9999999876655443322211  222211111111111222222111111      2566666554  34699999999


Q ss_pred             HhhHHHHHHHHhhC--CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCC--CCccchh
Q 017573          245 RRKVDWLTDKMRSR--DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLP--TQPENYL  320 (369)
Q Consensus       245 ~~~~~~~~~~l~~~--~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~--~~~~~~~  320 (369)
                      ++.++.++..|++.  ...++.+|+.  ...|.+..+.|++|++++||+|.++++|+.+|++++.++-.-.  .+...++
T Consensus       315 I~~~eq~a~~lk~~~~~~~i~~Vhs~--d~~R~EkV~~fR~G~~~lLiTTTILERGVTfp~vdV~Vlgaeh~vfTesaLV  392 (441)
T COG4098         315 IETMEQVAAALKKKLPKETIASVHSE--DQHRKEKVEAFRDGKITLLITTTILERGVTFPNVDVFVLGAEHRVFTESALV  392 (441)
T ss_pred             hHHHHHHHHHHHhhCCccceeeeecc--CccHHHHHHHHHcCceEEEEEeehhhcccccccceEEEecCCcccccHHHHH
Confidence            99999999999554  3355677774  5678999999999999999999999999999999998866543  6788999


Q ss_pred             hhhcccccCC--CceeEEEEeccccHHHHH
Q 017573          321 HRIGRSGRFG--RKGVAINFVTRDDERMLF  348 (369)
Q Consensus       321 Q~~GR~~R~~--~~~~~~~~~~~~~~~~~~  348 (369)
                      |..||+||.-  ..|.+..|.......+.+
T Consensus       393 QIaGRvGRs~~~PtGdv~FFH~G~skaM~~  422 (441)
T COG4098         393 QIAGRVGRSLERPTGDVLFFHYGKSKAMKQ  422 (441)
T ss_pred             HHhhhccCCCcCCCCcEEEEeccchHHHHH
Confidence            9999999974  348888777766555443

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=100.00  E-value=4.9e-31  Score=250.38  Aligned_cols=317  Identities=20%  Similarity=0.211  Sum_probs=216.5

Q ss_pred             CCcHhhhhhhhccc----cCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCc
Q 017573           18 KPSAIQQRGIVPFC----KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGV   93 (369)
Q Consensus        18 ~~~~~Q~~~~~~~~----~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~   93 (369)
                      +|++||.+++..+.    .+.++|+..++|.|||+.++..+...........++|||||. ++..+|.+++.+++.  .+
T Consensus       169 ~Lr~YQleGlnWLi~l~~~g~gGILADEMGLGKTlQaIalL~~L~~~~~~~gp~LIVvP~-SlL~nW~~Ei~kw~p--~l  245 (1033)
T PLN03142        169 KMRDYQLAGLNWLIRLYENGINGILADEMGLGKTLQTISLLGYLHEYRGITGPHMVVAPK-STLGNWMNEIRRFCP--VL  245 (1033)
T ss_pred             chHHHHHHHHHHHHHHHhcCCCEEEEeCCCccHHHHHHHHHHHHHHhcCCCCCEEEEeCh-HHHHHHHHHHHHHCC--CC
Confidence            68999999998875    468899999999999998765554433333333379999997 677889999999875  35


Q ss_pred             EEEEEECCcchHHHH---HHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCccC
Q 017573           94 KVHACVGGTSVREDQ---RILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKV  170 (369)
Q Consensus        94 ~v~~~~~~~~~~~~~---~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~  170 (369)
                      .+...+|........   .......+|+|+|++.+......  +....|++||+||+|++.+..  ......+..+.. .
T Consensus       246 ~v~~~~G~~~eR~~~~~~~~~~~~~dVvITSYe~l~~e~~~--L~k~~W~~VIvDEAHrIKN~~--Sklskalr~L~a-~  320 (1033)
T PLN03142        246 RAVKFHGNPEERAHQREELLVAGKFDVCVTSFEMAIKEKTA--LKRFSWRYIIIDEAHRIKNEN--SLLSKTMRLFST-N  320 (1033)
T ss_pred             ceEEEeCCHHHHHHHHHHHhcccCCCcceecHHHHHHHHHH--hccCCCCEEEEcCccccCCHH--HHHHHHHHHhhc-C
Confidence            666667655432221   12235689999999998654322  333458999999999986543  445555556653 3


Q ss_pred             cEEEEEeeCChhHHHHHHHhcC--CCEEE----------------------------------Ee-cC---cccccccee
Q 017573          171 QVGVFSATMPPEALEITRKFMN--KPVRI----------------------------------LV-KR---DELTLEGIK  210 (369)
Q Consensus       171 ~~i~~saT~~~~~~~~~~~~~~--~~~~~----------------------------------~~-~~---~~~~~~~~~  210 (369)
                      ..+++||||-.+....+..++.  .|..+                                  .. ..   ...++....
T Consensus       321 ~RLLLTGTPlqNnl~ELwsLL~FL~P~~f~s~~~F~~~f~~~~~~~~~e~i~~L~~~L~pf~LRR~KsdV~~~LPpK~e~  400 (1033)
T PLN03142        321 YRLLITGTPLQNNLHELWALLNFLLPEIFSSAETFDEWFQISGENDQQEVVQQLHKVLRPFLLRRLKSDVEKGLPPKKET  400 (1033)
T ss_pred             cEEEEecCCCCCCHHHHHHHHhcCCCCcCCCHHHHHHHHccccccchHHHHHHHHHHhhHHHhhhhHHHHhhhCCCceeE
Confidence            4688999996432221111100  00000                                  00 00   000000000


Q ss_pred             EEEEEccc------------------------------------------------------------hhhhHHHHHHHH
Q 017573          211 QFYVNVEK------------------------------------------------------------EEWKLETLCDLY  230 (369)
Q Consensus       211 ~~~~~~~~------------------------------------------------------------~~~~~~~l~~~~  230 (369)
                      ..++....                                                            ...++..+..++
T Consensus       401 iv~v~LS~~Qk~lY~~ll~k~~~~l~~g~~~~~LlnilmqLRk~cnHP~L~~~~ep~~~~~~~e~lie~SgKl~lLdkLL  480 (1033)
T PLN03142        401 ILKVGMSQMQKQYYKALLQKDLDVVNAGGERKRLLNIAMQLRKCCNHPYLFQGAEPGPPYTTGEHLVENSGKMVLLDKLL  480 (1033)
T ss_pred             EEeeCCCHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHhCCHHhhhcccccCcccchhHHhhhhhHHHHHHHHH
Confidence            01111100                                                            112333444444


Q ss_pred             Hhc--cCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCC---CcEEEEecCCcCCCCCCCCc
Q 017573          231 ETL--AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGS---SRVLITTDLLARGIDVQQVS  305 (369)
Q Consensus       231 ~~~--~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~---~~vli~t~~~~~G~d~~~~~  305 (369)
                      ...  .+.|+|||+.....+..+.++|...++.+..++|.++..+|..+++.|++..   ..+|++|.+.+.|+|+..++
T Consensus       481 ~~Lk~~g~KVLIFSQft~~LdiLed~L~~~g~~y~rIdGsts~~eRq~~Id~Fn~~~s~~~VfLLSTrAGGlGINLt~Ad  560 (1033)
T PLN03142        481 PKLKERDSRVLIFSQMTRLLDILEDYLMYRGYQYCRIDGNTGGEDRDASIDAFNKPGSEKFVFLLSTRAGGLGINLATAD  560 (1033)
T ss_pred             HHHHhcCCeEEeehhHHHHHHHHHHHHHHcCCcEEEECCCCCHHHHHHHHHHhccccCCceEEEEeccccccCCchhhCC
Confidence            332  3469999999999999999999999999999999999999999999997643   34678999999999999999


Q ss_pred             EEEEecCCCCccchhhhhcccccCCCceeEE--EEeccc
Q 017573          306 LVINYDLPTQPENYLHRIGRSGRFGRKGVAI--NFVTRD  342 (369)
Q Consensus       306 ~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~--~~~~~~  342 (369)
                      +||+++++||+....|++||+.|.|+...|.  .++..+
T Consensus       561 ~VIiyD~dWNP~~d~QAidRaHRIGQkk~V~VyRLIt~g  599 (1033)
T PLN03142        561 IVILYDSDWNPQVDLQAQDRAHRIGQKKEVQVFRFCTEY  599 (1033)
T ss_pred             EEEEeCCCCChHHHHHHHHHhhhcCCCceEEEEEEEeCC
Confidence            9999999999999999999999999886554  444444

>PRK09694 helicase Cas3; Provisional

Probab=100.00  E-value=2.1e-30  Score=243.75  Aligned_cols=313  Identities=17%  Similarity=0.156  Sum_probs=201.0

Q ss_pred             CCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhcccc--
Q 017573           14 YGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYL--   91 (369)
Q Consensus        14 ~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~--   91 (369)
                      ++..+|||+|+.+......++.+++.||||+|||.+++.++...+..+.. .+++|..|++++++++++++.++....  
T Consensus       282 ~~~~~p~p~Q~~~~~~~~~pgl~ileApTGsGKTEAAL~~A~~l~~~~~~-~gi~~aLPT~Atan~m~~Rl~~~~~~~f~  360 (878)
T PRK09694        282 DNGYQPRQLQTLVDALPLQPGLTIIEAPTGSGKTEAALAYAWRLIDQGLA-DSIIFALPTQATANAMLSRLEALASKLFP  360 (878)
T ss_pred             cCCCCChHHHHHHHhhccCCCeEEEEeCCCCCHHHHHHHHHHHHHHhCCC-CeEEEECcHHHHHHHHHHHHHHHHHHhcC
Confidence            33568999999886544456789999999999999998877755544433 389999999999999999987643221  


Q ss_pred             CcEEEEEECCcchHHH---------------------HHHHc---c---CCcEEEeccHHHHHHHHcCC-CCCCCc----
Q 017573           92 GVKVHACVGGTSVRED---------------------QRILQ---A---GVHVVVGTPGRVFDMLRRQS-LRPDYI----  139 (369)
Q Consensus        92 ~~~v~~~~~~~~~~~~---------------------~~~~~---~---~~~iiv~t~~~l~~~~~~~~-~~~~~~----  139 (369)
                      ...+...+|.......                     ...+.   +   -..++|+|.++++....... .....+    
T Consensus       361 ~~~v~L~Hg~a~l~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~kr~llapi~V~TiDQlL~a~l~~kh~~lR~~~La~  440 (878)
T PRK09694        361 SPNLILAHGNSRFNHLFQSLKSRAATEQGQEEAWVQCCEWLSQSNKRVFLGQIGVCTIDQVLISVLPVKHRFIRGFGLGR  440 (878)
T ss_pred             CCceEeecCcchhhhhhhhhhcccccccccchhhhHHHHHHhhhhhhhhcCCEEEcCHHHHHHHHHccchHHHHHHhhcc
Confidence            2345555554321110                     01111   1   26899999999875433321 111112    


Q ss_pred             cEEEEechhHhhccCcHHHHHHHHhhCC-ccCcEEEEEeeCChhHHHHHHHhcCCC----------EEEEecC---cccc
Q 017573          140 KMFVLDEADEMLSRGFKDQIYDIFQLLP-AKVQVGVFSATMPPEALEITRKFMNKP----------VRILVKR---DELT  205 (369)
Q Consensus       140 ~~viiDE~H~~~~~~~~~~~~~~~~~~~-~~~~~i~~saT~~~~~~~~~~~~~~~~----------~~~~~~~---~~~~  205 (369)
                      ++||+||+|.+.. .....+..+++.+. ....+|+||||++....+.+...+...          .......   ....
T Consensus       441 svvIiDEVHAyD~-ym~~lL~~~L~~l~~~g~~vIllSATLP~~~r~~L~~a~~~~~~~~~~~~YPlvt~~~~~~~~~~~  519 (878)
T PRK09694        441 SVLIVDEVHAYDA-YMYGLLEAVLKAQAQAGGSVILLSATLPATLKQKLLDTYGGHDPVELSSAYPLITWRGVNGAQRFD  519 (878)
T ss_pred             CeEEEechhhCCH-HHHHHHHHHHHHHHhcCCcEEEEeCCCCHHHHHHHHHHhccccccccccccccccccccccceeee
Confidence            5899999998743 23344455554432 356799999999877655443322210          0000000   0000


Q ss_pred             ---c----cceeEEEEE-c--cchhhhHHHHHHHHHhc-cCCCeEEEeCCHhhHHHHHHHHhhCC---CeeEEecCCCCH
Q 017573          206 ---L----EGIKQFYVN-V--EKEEWKLETLCDLYETL-AITQSVIFVNTRRKVDWLTDKMRSRD---HTVSATHGDMDQ  271 (369)
Q Consensus       206 ---~----~~~~~~~~~-~--~~~~~~~~~l~~~~~~~-~~~k~lv~~~~~~~~~~~~~~l~~~~---~~~~~~~~~~~~  271 (369)
                         .    ......... .  .........+..+.+.. .+++++||||+++.++.+++.|++.+   .++..+|++++.
T Consensus       520 ~~~~~~~~~~~~~v~v~~~~~~~~~~~~~~l~~i~~~~~~g~~vLVf~NTV~~Aq~ly~~L~~~~~~~~~v~llHsrf~~  599 (878)
T PRK09694        520 LSAHPEQLPARFTIQLEPICLADMLPDLTLLQRMIAAANAGAQVCLICNLVDDAQKLYQRLKELNNTQVDIDLFHARFTL  599 (878)
T ss_pred             ccccccccCcceEEEEEeeccccccCHHHHHHHHHHHHhcCCEEEEEECCHHHHHHHHHHHHhhCCCCceEEEEeCCCCH
Confidence               0    000111110 1  11111223334444432 45689999999999999999999764   579999999999


Q ss_pred             HHH----HHHHHHH-hcCC---CcEEEEecCCcCCCCCCCCcEEEEecCCCCccchhhhhcccccCCC
Q 017573          272 NTR----DIIMREF-RSGS---SRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGR  331 (369)
Q Consensus       272 ~~r----~~~~~~f-~~~~---~~vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~  331 (369)
                      .+|    +++++.| ++|+   ..|||+|++++.|+|+ +++.+|....|  ...++||+||++|.+.
T Consensus       600 ~dR~~~E~~vl~~fgk~g~r~~~~ILVaTQViE~GLDI-d~DvlItdlaP--idsLiQRaGR~~R~~~  664 (878)
T PRK09694        600 NDRREKEQRVIENFGKNGKRNQGRILVATQVVEQSLDL-DFDWLITQLCP--VDLLFQRLGRLHRHHR  664 (878)
T ss_pred             HHHHHHHHHHHHHHHhcCCcCCCeEEEECcchhheeec-CCCeEEECCCC--HHHHHHHHhccCCCCC
Confidence            998    4567777 5555   4699999999999999 57888776555  6799999999999865

>TIGR00595 priA primosomal protein N'

Probab=100.00  E-value=4e-31  Score=238.26  Aligned_cols=304  Identities=21%  Similarity=0.295  Sum_probs=203.0

Q ss_pred             EEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHH----HHHHc
Q 017573           37 IQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVRED----QRILQ  112 (369)
Q Consensus        37 li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~----~~~~~  112 (369)
                      +++||||+|||.+++.++.+.+..+.   +++|++|+.+|+.|+.+.+++.+   +.++..++++.+..+.    .....
T Consensus         1 LL~g~TGsGKT~v~l~~i~~~l~~g~---~vLvlvP~i~L~~Q~~~~l~~~f---~~~v~vlhs~~~~~er~~~~~~~~~   74 (505)
T TIGR00595         1 LLFGVTGSGKTEVYLQAIEKVLALGK---SVLVLVPEIALTPQMIQRFKYRF---GSQVAVLHSGLSDSEKLQAWRKVKN   74 (505)
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHcCC---eEEEEeCcHHHHHHHHHHHHHHh---CCcEEEEECCCCHHHHHHHHHHHHc
Confidence            57899999999999877766665544   89999999999999999998754   4567788887665433    33344


Q ss_pred             cCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccC-----c-HHHHHHHHhhCCccCcEEEEEeeCChhHHHH
Q 017573          113 AGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRG-----F-KDQIYDIFQLLPAKVQVGVFSATMPPEALEI  186 (369)
Q Consensus       113 ~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~-----~-~~~~~~~~~~~~~~~~~i~~saT~~~~~~~~  186 (369)
                      ++++|+|+|+..++.       ...++++||+||.|....++     | .+.+..+... ..+.+++++||||+.+....
T Consensus        75 g~~~IVVGTrsalf~-------p~~~l~lIIVDEeh~~sykq~~~p~y~ar~~a~~ra~-~~~~~vil~SATPsles~~~  146 (505)
T TIGR00595        75 GEILVVIGTRSALFL-------PFKNLGLIIVDEEHDSSYKQEEGPRYHARDVAVYRAK-KFNCPVVLGSATPSLESYHN  146 (505)
T ss_pred             CCCCEEECChHHHcC-------cccCCCEEEEECCCccccccccCCCCcHHHHHHHHHH-hcCCCEEEEeCCCCHHHHHH
Confidence            678999999987752       34568999999999876333     1 1223333333 34677999999988655443


Q ss_pred             HHHhcCCCEEEEecCc--cccccceeEEEEEccchh---hhHHHHHHHH-Hhc-cCCCeEEEeCCHhh------------
Q 017573          187 TRKFMNKPVRILVKRD--ELTLEGIKQFYVNVEKEE---WKLETLCDLY-ETL-AITQSVIFVNTRRK------------  247 (369)
Q Consensus       187 ~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~---~~~~~l~~~~-~~~-~~~k~lv~~~~~~~------------  247 (369)
                      ...  +..........  ....+.+.  ........   ...+.+.+.+ +.. .++++|||+|.+..            
T Consensus       147 ~~~--g~~~~~~l~~r~~~~~~p~v~--vid~~~~~~~~~ls~~l~~~i~~~l~~g~qvLvflnrrGya~~~~C~~Cg~~  222 (505)
T TIGR00595       147 AKQ--KAYRLLVLTRRVSGRKPPEVK--LIDMRKEPRQSFLSPELITAIEQTLAAGEQSILFLNRRGYSKNLLCRSCGYI  222 (505)
T ss_pred             Hhc--CCeEEeechhhhcCCCCCeEE--EEecccccccCCccHHHHHHHHHHHHcCCcEEEEEeCCcCCCeeEhhhCcCc
Confidence            322  11111111111  11111111  11111111   1112233323 222 34578999776532            


Q ss_pred             ------------------------------------------------HHHHHHHHhhC--CCeeEEecCCCCHHHH--H
Q 017573          248 ------------------------------------------------VDWLTDKMRSR--DHTVSATHGDMDQNTR--D  275 (369)
Q Consensus       248 ------------------------------------------------~~~~~~~l~~~--~~~~~~~~~~~~~~~r--~  275 (369)
                                                                      .+.+.+.|++.  +.++..+|++++...+  +
T Consensus       223 ~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~~l~~~g~Gte~~~e~l~~~fp~~~v~~~d~d~~~~~~~~~  302 (505)
T TIGR00595       223 LCCPNCDVSLTYHKKEGKLRCHYCGYQEPIPKTCPQCGSEDLVYKGYGTEQVEEELAKLFPGARIARIDSDTTSRKGAHE  302 (505)
T ss_pred             cCCCCCCCceEEecCCCeEEcCCCcCcCCCCCCCCCCCCCeeEeecccHHHHHHHHHhhCCCCcEEEEecccccCccHHH
Confidence                                                            46777777776  5688999999876655  8


Q ss_pred             HHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCCC------------CccchhhhhcccccCCCceeEEEEecccc
Q 017573          276 IIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPT------------QPENYLHRIGRSGRFGRKGVAINFVTRDD  343 (369)
Q Consensus       276 ~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~------------~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~  343 (369)
                      ++++.|.+|+.+|||+|+++..|+|+|+++.|++++...            ....+.|++||+||.++.|.+++.....+
T Consensus       303 ~~l~~f~~g~~~ILVgT~~i~kG~d~~~v~lV~vl~aD~~l~~pd~ra~E~~~~ll~q~~GRagR~~~~g~viiqt~~p~  382 (505)
T TIGR00595       303 ALLNQFANGKADILIGTQMIAKGHHFPNVTLVGVLDADSGLHSPDFRAAERGFQLLTQVAGRAGRAEDPGQVIIQTYNPN  382 (505)
T ss_pred             HHHHHHhcCCCCEEEeCcccccCCCCCcccEEEEEcCcccccCcccchHHHHHHHHHHHHhccCCCCCCCEEEEEeCCCC
Confidence            899999999999999999999999999999987665432            13468999999999999999997776655


Q ss_pred             HHHHH-----HHHHHhcccc
Q 017573          344 ERMLF-----DIQKFYNVVI  358 (369)
Q Consensus       344 ~~~~~-----~~~~~~~~~~  358 (369)
                      ...++     ++..|++.++
T Consensus       383 ~~~~~~~~~~d~~~f~~~el  402 (505)
T TIGR00595       383 HPAIQAALTGDYEAFYEQEL  402 (505)
T ss_pred             CHHHHHHHhCCHHHHHHHHH
Confidence            54333     3445555544

All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

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

Probab=100.00  E-value=2.2e-31  Score=245.93  Aligned_cols=339  Identities=20%  Similarity=0.308  Sum_probs=249.3

Q ss_pred             CCHHHHHHHHhCCCCCCcHhhhhhhhccccC-CcEEEEcCCCChhhHHHHHHHHHhhhccCC--------CccEEEEcCC
Q 017573            3 LQENLLRGIYAYGFEKPSAIQQRGIVPFCKG-LDVIQQAQSGTGKTATFCSGILQQLDYGLV--------QCQALVLAPT   73 (369)
Q Consensus         3 l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~-~~~li~~~tG~GKT~~~~~~~~~~~~~~~~--------~~~~liv~P~   73 (369)
                      +|.|-+.++.  |..++.+.|.........+ .++++|||||+|||.++++.+++.+..+.+        ..+++|++|.
T Consensus       296 lP~Wnq~aF~--g~~sLNrIQS~v~daAl~~~EnmLlCAPTGaGKTNVAvLtiLqel~~h~r~dgs~nl~~fKIVYIAPm  373 (1674)
T KOG0951|consen  296 LPKWNQPAFF--GKQSLNRIQSKVYDAALRGDENMLLCAPTGAGKTNVAVLTILQELGNHLREDGSVNLAPFKIVYIAPM  373 (1674)
T ss_pred             Ccchhhhhcc--cchhhhHHHHHHHHHHhcCcCcEEEeccCCCCchHHHHHHHHHHHhcccccccceecccceEEEEeeH
Confidence            4555555554  5567999999999988876 789999999999999999999999866543        2379999999


Q ss_pred             HHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCC---CCccEEEEechhHh
Q 017573           74 RELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRP---DYIKMFVLDEADEM  150 (369)
Q Consensus        74 ~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~---~~~~~viiDE~H~~  150 (369)
                      ++|++.|...|.+....+|++|...+|+.......   .....|+|+||+.+-- +.++..+.   +-++++|+||.|.+
T Consensus       374 KaLvqE~VgsfSkRla~~GI~V~ElTgD~~l~~~q---ieeTqVIV~TPEK~Di-ITRk~gdraY~qlvrLlIIDEIHLL  449 (1674)
T KOG0951|consen  374 KALVQEMVGSFSKRLAPLGITVLELTGDSQLGKEQ---IEETQVIVTTPEKWDI-ITRKSGDRAYEQLVRLLIIDEIHLL  449 (1674)
T ss_pred             HHHHHHHHHHHHhhccccCcEEEEecccccchhhh---hhcceeEEeccchhhh-hhcccCchhHHHHHHHHhhhhhhhc
Confidence            99999999999999999999999999986633221   2357999999999943 33333232   33789999999987


Q ss_pred             hccCcHHHHHHHH-------hhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhh--
Q 017573          151 LSRGFKDQIYDIF-------QLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEW--  221 (369)
Q Consensus       151 ~~~~~~~~~~~~~-------~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--  221 (369)
                      -+. ....+.++.       ..-...++++++|||++ +-.+....+..++.........+.+..+.+-++.+.....  
T Consensus       450 hDd-RGpvLESIVaRt~r~ses~~e~~RlVGLSATLP-Ny~DV~~Fl~v~~~glf~fd~syRpvPL~qq~Igi~ek~~~~  527 (1674)
T KOG0951|consen  450 HDD-RGPVLESIVARTFRRSESTEEGSRLVGLSATLP-NYEDVASFLRVDPEGLFYFDSSYRPVPLKQQYIGITEKKPLK  527 (1674)
T ss_pred             ccc-cchHHHHHHHHHHHHhhhcccCceeeeecccCC-chhhhHHHhccCcccccccCcccCcCCccceEeccccCCchH
Confidence            432 123332222       22234788999999996 5555555444555555556667777777777776643222  


Q ss_pred             hH----HHH-HHHHHhccCCCeEEEeCCHhhHHHHHHHHhhC-------------------------------------C
Q 017573          222 KL----ETL-CDLYETLAITQSVIFVNTRRKVDWLTDKMRSR-------------------------------------D  259 (369)
Q Consensus       222 ~~----~~l-~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~-------------------------------------~  259 (369)
                      ..    +.. .++++.....++|||+-+++++-+.++.++..                                     .
T Consensus       528 ~~qamNe~~yeKVm~~agk~qVLVFVHsRkET~ktA~aIRd~~le~dtls~fmre~s~s~eilrtea~~~kn~dLkdLLp  607 (1674)
T KOG0951|consen  528 RFQAMNEACYEKVLEHAGKNQVLVFVHSRKETAKTARAIRDKALEEDTLSRFMREDSASREILRTEAGQAKNPDLKDLLP  607 (1674)
T ss_pred             HHHHHHHHHHHHHHHhCCCCcEEEEEEechHHHHHHHHHHHHHhhhhHHHHHHhcccchhhhhhhhhhcccChhHHHHhh
Confidence            22    222 23444445579999999999887777766522                                     3


Q ss_pred             CeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEE----ecC------CCCccchhhhhcccccC
Q 017573          260 HTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVIN----YDL------PTQPENYLHRIGRSGRF  329 (369)
Q Consensus       260 ~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~----~~~------~~~~~~~~Q~~GR~~R~  329 (369)
                      ..++..|++|+..+|....+.|.+|.++|+++|..++.|+|+|.-.++|-    +++      +.++.+..||.||+||.
T Consensus       608 ygfaIHhAGl~R~dR~~~EdLf~~g~iqvlvstatlawgvnlpahtViikgtqvy~pekg~w~elsp~dv~qmlgragrp  687 (1674)
T KOG0951|consen  608 YGFAIHHAGLNRKDRELVEDLFADGHIQVLVSTATLAWGVNLPAHTVIIKGTQVYDPEKGRWTELSPLDVMQMLGRAGRP  687 (1674)
T ss_pred             ccceeeccCCCcchHHHHHHHHhcCceeEEEeehhhhhhcCCCcceEEecCccccCcccCccccCCHHHHHHHHhhcCCC
Confidence            45889999999999999999999999999999999999999987666653    222      34678899999999998


Q ss_pred             CC--ceeEEEEeccccHHHHHH
Q 017573          330 GR--KGVAINFVTRDDERMLFD  349 (369)
Q Consensus       330 ~~--~~~~~~~~~~~~~~~~~~  349 (369)
                      +.  .|..+++.+..+...+.+
T Consensus       688 ~~D~~gegiiit~~se~qyyls  709 (1674)
T KOG0951|consen  688 QYDTCGEGIIITDHSELQYYLS  709 (1674)
T ss_pred             ccCcCCceeeccCchHhhhhHH
Confidence            64  477777777666555544

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=100.00  E-value=1.1e-30  Score=250.76  Aligned_cols=303  Identities=21%  Similarity=0.317  Sum_probs=203.4

Q ss_pred             cHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCH----HHHHHHHHHHHH-hccccCcE
Q 017573           20 SAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTR----ELAQQIEKVMRA-LGDYLGVK   94 (369)
Q Consensus        20 ~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~----~l~~q~~~~~~~-~~~~~~~~   94 (369)
                      +.+-.+++..+.+++.++++|+||||||+.. .-++.....+.. +.+++.-|++    +++.+.++++.. ++...|+.
T Consensus        76 ~~~r~~Il~ai~~~~VviI~GeTGSGKTTql-Pq~lle~g~g~~-g~I~~TQPRRlAArsLA~RVA~El~~~lG~~VGY~  153 (1294)
T PRK11131         76 SQKKQDILEAIRDHQVVIVAGETGSGKTTQL-PKICLELGRGVK-GLIGHTQPRRLAARTVANRIAEELETELGGCVGYK  153 (1294)
T ss_pred             HHHHHHHHHHHHhCCeEEEECCCCCCHHHHH-HHHHHHcCCCCC-CceeeCCCcHHHHHHHHHHHHHHHhhhhcceecee
Confidence            3445567777777888999999999999852 223322222221 1333344754    677777777764 33333333


Q ss_pred             EEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhH-hhccCcHH-HHHHHHhhCCccCcE
Q 017573           95 VHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADE-MLSRGFKD-QIYDIFQLLPAKVQV  172 (369)
Q Consensus        95 v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~-~~~~~~~~-~~~~~~~~~~~~~~~  172 (369)
                      +..    ..      ....+++|+++|+..|+..+.... .++.++++|+||+|+ ..+.++.- .+..++.. .+..|+
T Consensus       154 vrf----~~------~~s~~t~I~v~TpG~LL~~l~~d~-~Ls~~~~IIIDEAHERsLn~DfLLg~Lk~lL~~-rpdlKv  221 (1294)
T PRK11131        154 VRF----ND------QVSDNTMVKLMTDGILLAEIQQDR-LLMQYDTIIIDEAHERSLNIDFILGYLKELLPR-RPDLKV  221 (1294)
T ss_pred             ecC----cc------ccCCCCCEEEEChHHHHHHHhcCC-ccccCcEEEecCccccccccchHHHHHHHhhhc-CCCceE
Confidence            311    11      113457999999999999887654 478899999999995 55555442 22233222 235789


Q ss_pred             EEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccch-----hhhHHHHHHHHH---hccCCCeEEEeCC
Q 017573          173 GVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKE-----EWKLETLCDLYE---TLAITQSVIFVNT  244 (369)
Q Consensus       173 i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~l~~~~~---~~~~~k~lv~~~~  244 (369)
                      ++||||++.+  .+...+...++ +.+.....   .+...+......     ......+...+.   ....+++|||+++
T Consensus       222 ILmSATid~e--~fs~~F~~apv-I~V~Gr~~---pVei~y~p~~~~~~~~~~d~l~~ll~~V~~l~~~~~GdILVFLpg  295 (1294)
T PRK11131        222 IITSATIDPE--RFSRHFNNAPI-IEVSGRTY---PVEVRYRPIVEEADDTERDQLQAIFDAVDELGREGPGDILIFMSG  295 (1294)
T ss_pred             EEeeCCCCHH--HHHHHcCCCCE-EEEcCccc---cceEEEeecccccchhhHHHHHHHHHHHHHHhcCCCCCEEEEcCC
Confidence            9999999643  44444444453 33332221   234444443221     112222222221   2345789999999


Q ss_pred             HhhHHHHHHHHhhCCCe---eEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecC---------
Q 017573          245 RRKVDWLTDKMRSRDHT---VSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDL---------  312 (369)
Q Consensus       245 ~~~~~~~~~~l~~~~~~---~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~---------  312 (369)
                      ..+++.+++.|.+.+..   +..+||+++.++|.++++.  .|..+|+|+|+++++|+|+|++++||.++.         
T Consensus       296 ~~EIe~lae~L~~~~~~~~~VlpLhg~Ls~~eQ~~Vf~~--~g~rkIIVATNIAEtSITIpgI~yVID~Gl~k~~~Yd~~  373 (1294)
T PRK11131        296 EREIRDTADALNKLNLRHTEILPLYARLSNSEQNRVFQS--HSGRRIVLATNVAETSLTVPGIKYVIDPGTARISRYSYR  373 (1294)
T ss_pred             HHHHHHHHHHHHhcCCCcceEeecccCCCHHHHHHHhcc--cCCeeEEEeccHHhhccccCcceEEEECCCccccccccc
Confidence            99999999999987654   6789999999999999875  467899999999999999999999999863         


Q ss_pred             ------C---CCccchhhhhcccccCCCceeEEEEeccccHH
Q 017573          313 ------P---TQPENYLHRIGRSGRFGRKGVAINFVTRDDER  345 (369)
Q Consensus       313 ------~---~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~  345 (369)
                            |   .|..++.||.||+||. .+|.||.++++.+..
T Consensus       374 ~~~~~Lp~~~iSkasa~QRaGRAGR~-~~G~c~rLyte~d~~  414 (1294)
T PRK11131        374 TKVQRLPIEPISQASANQRKGRCGRV-SEGICIRLYSEDDFL  414 (1294)
T ss_pred             cCcccCCeeecCHhhHhhhccccCCC-CCcEEEEeCCHHHHH
Confidence                  2   3446899999999999 789999999976644

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

Probab=99.97  E-value=6.6e-30  Score=230.81  Aligned_cols=314  Identities=19%  Similarity=0.257  Sum_probs=232.4

Q ss_pred             HhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhcccc
Q 017573           12 YAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYL   91 (369)
Q Consensus        12 ~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~   91 (369)
                      ..++| +|-++|++|+-++..|.+++|.|+|.+|||++|-.++.-...+..   +++|-+|-++|-+|-+++|++.+.+.
T Consensus       292 ~~~pF-elD~FQk~Ai~~lerg~SVFVAAHTSAGKTvVAEYAialaq~h~T---R~iYTSPIKALSNQKfRDFk~tF~Dv  367 (1248)
T KOG0947|consen  292 LIYPF-ELDTFQKEAIYHLERGDSVFVAAHTSAGKTVVAEYAIALAQKHMT---RTIYTSPIKALSNQKFRDFKETFGDV  367 (1248)
T ss_pred             hhCCC-CccHHHHHHHHHHHcCCeEEEEecCCCCcchHHHHHHHHHHhhcc---ceEecchhhhhccchHHHHHHhcccc
Confidence            34566 899999999999999999999999999999998777665544443   89999999999999999999876554


Q ss_pred             CcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCccCc
Q 017573           92 GVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQ  171 (369)
Q Consensus        92 ~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~  171 (369)
                      |    .++|+..       +..++.++|+|.+.|.+++.++.-....+..||+||+|.+.+....-.+..++-.+|...+
T Consensus       368 g----LlTGDvq-------inPeAsCLIMTTEILRsMLYrgadliRDvE~VIFDEVHYiND~eRGvVWEEViIMlP~HV~  436 (1248)
T KOG0947|consen  368 G----LLTGDVQ-------INPEASCLIMTTEILRSMLYRGADLIRDVEFVIFDEVHYINDVERGVVWEEVIIMLPRHVN  436 (1248)
T ss_pred             c----eeeccee-------eCCCcceEeehHHHHHHHHhcccchhhccceEEEeeeeecccccccccceeeeeeccccce
Confidence            4    6777665       3456899999999999999998888888999999999999887777888889999999999


Q ss_pred             EEEEEeeCChhHHHHHHHhcC-CCEEEEecCccccccceeEEEEEccch-------------------------------
Q 017573          172 VGVFSATMPPEALEITRKFMN-KPVRILVKRDELTLEGIKQFYVNVEKE-------------------------------  219 (369)
Q Consensus       172 ~i~~saT~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~-------------------------------  219 (369)
                      +|++|||-+ +..++..+... +...+.+......+-.++++...-..-                               
T Consensus       437 ~IlLSATVP-N~~EFA~WIGRtK~K~IyViST~kRPVPLEh~l~t~~~l~kiidq~g~fl~~~~~~a~~~~~~~ak~~~~  515 (1248)
T KOG0947|consen  437 FILLSATVP-NTLEFADWIGRTKQKTIYVISTSKRPVPLEHYLYTKKSLFKIIDQNGIFLLKGIKDAKDSLKKEAKFVDV  515 (1248)
T ss_pred             EEEEeccCC-ChHHHHHHhhhccCceEEEEecCCCccceEEEEEeccceehhhcccchhhhhcchhhhhhhccccccccc
Confidence            999999986 44444443332 111122211111111111111100000                               


Q ss_pred             ---------------------------------h---hhHHHHHHHHHhccCCCeEEEeCCHhhHHHHHHHHhhCC----
Q 017573          220 ---------------------------------E---WKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRD----  259 (369)
Q Consensus       220 ---------------------------------~---~~~~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~~----  259 (369)
                                                       .   ...-.+...+....--+++|||-+++.|+..++.|...+    
T Consensus       516 ~~~~~~~~rgs~~~ggk~~~~~g~~r~~~~~~nrr~~~~~l~lin~L~k~~lLP~VvFvFSkkrCde~a~~L~~~nL~~~  595 (1248)
T KOG0947|consen  516 EKSDARGGRGSQKRGGKTNYHNGGSRGSGIGKNRRKQPTWLDLINHLRKKNLLPVVVFVFSKKRCDEYADYLTNLNLTDS  595 (1248)
T ss_pred             ccccccccccccccCCcCCCCCCCcccccccccccccchHHHHHHHHhhcccCceEEEEEccccHHHHHHHHhccCcccc
Confidence                                             0   001112222222233488999999999999998887552    


Q ss_pred             -----------------------------------CeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCC
Q 017573          260 -----------------------------------HTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQV  304 (369)
Q Consensus       260 -----------------------------------~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~  304 (369)
                                                         ..+++.||++=+--++-+.-.|..|-++||+||..+.+|+|+|. 
T Consensus       596 ~EKseV~lfl~k~~~rLk~~DR~LPQvl~m~~ll~RGiaVHH~GlLPivKE~VE~LFqrGlVKVLFATETFAMGVNMPA-  674 (1248)
T KOG0947|consen  596 KEKSEVHLFLSKAVARLKGEDRNLPQVLSMRSLLLRGIAVHHGGLLPIVKEVVELLFQRGLVKVLFATETFAMGVNMPA-  674 (1248)
T ss_pred             hhHHHHHHHHHHHHHhcChhhccchHHHHHHHHHhhcchhhcccchHHHHHHHHHHHhcCceEEEeehhhhhhhcCCCc-
Confidence                                               24888999998888899999999999999999999999999985 


Q ss_pred             cEEEEecCC---------CCccchhhhhcccccCCC--ceeEEEEeccc
Q 017573          305 SLVINYDLP---------TQPENYLHRIGRSGRFGR--KGVAINFVTRD  342 (369)
Q Consensus       305 ~~vi~~~~~---------~~~~~~~Q~~GR~~R~~~--~~~~~~~~~~~  342 (369)
                      +.|++....         -.+.+|.|+.|||||.|-  .|++++.....
T Consensus       675 RtvVF~Sl~KhDG~efR~L~PGEytQMAGRAGRRGlD~tGTVii~~~~~  723 (1248)
T KOG0947|consen  675 RTVVFSSLRKHDGNEFRELLPGEYTQMAGRAGRRGLDETGTVIIMCKDS  723 (1248)
T ss_pred             eeEEeeehhhccCcceeecCChhHHhhhccccccccCcCceEEEEecCC
Confidence            444444332         267899999999999984  48888777654

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=99.97  E-value=9.1e-29  Score=228.36  Aligned_cols=317  Identities=18%  Similarity=0.216  Sum_probs=222.3

Q ss_pred             cHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEE
Q 017573           20 SAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACV   99 (369)
Q Consensus        20 ~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~   99 (369)
                      +||=.+++-.+.-.+.-+..++||+|||+++.++++.....+.   .++|++|++.|+.|.++++..+...+|+++..+.
T Consensus        82 ~~ydvQliGg~~Lh~G~Iaem~TGeGKTL~a~Lpa~~~al~G~---~V~VvTpn~yLA~qd~e~m~~l~~~lGLtv~~i~  158 (896)
T PRK13104         82 RHFDVQLIGGMVLHEGNIAEMRTGEGKTLVATLPAYLNAISGR---GVHIVTVNDYLAKRDSQWMKPIYEFLGLTVGVIY  158 (896)
T ss_pred             CcchHHHhhhhhhccCccccccCCCCchHHHHHHHHHHHhcCC---CEEEEcCCHHHHHHHHHHHHHHhcccCceEEEEe
Confidence            3333344444444566799999999999999999987665543   7999999999999999999999999999999999


Q ss_pred             CCcchHHHHHHHccCCcEEEeccHHH-HHHHHcC-CCCC-----CCccEEEEechhHhhccC----------------cH
Q 017573          100 GGTSVREDQRILQAGVHVVVGTPGRV-FDMLRRQ-SLRP-----DYIKMFVLDEADEMLSRG----------------FK  156 (369)
Q Consensus       100 ~~~~~~~~~~~~~~~~~iiv~t~~~l-~~~~~~~-~~~~-----~~~~~viiDE~H~~~~~~----------------~~  156 (369)
                      ++..........  .++|+++||..| +.+++.+ .+..     ..+.++|+||+|.+.-..                ..
T Consensus       159 gg~~~~~r~~~y--~~dIvygT~grlgfDyLrd~~~~~~~~~v~r~l~~~IvDEaDsiLIDeArtPLIISg~~~~~~~~y  236 (896)
T PRK13104        159 PDMSHKEKQEAY--KADIVYGTNNEYGFDYLRDNMAFSLTDKVQRELNFAIVDEVDSILIDEARTPLIISGAAEDSSELY  236 (896)
T ss_pred             CCCCHHHHHHHh--CCCEEEECChhhhHHHHhcCCccchHhhhccccceEEeccHhhhhhhccCCceeeeCCCccchHHH
Confidence            987766554433  589999999999 8888776 2333     468999999999865100                00


Q ss_pred             HHHHHHHhhCCc--------------c-----------------------------------------------------
Q 017573          157 DQIYDIFQLLPA--------------K-----------------------------------------------------  169 (369)
Q Consensus       157 ~~~~~~~~~~~~--------------~-----------------------------------------------------  169 (369)
                      .....+...+..              +                                                     
T Consensus       237 ~~~~~~v~~l~~~~~~~~~~dy~idek~~~v~Lte~G~~~~e~~~~~~~il~~~~~l~~~~~~~~~~~i~~aL~A~~lf~  316 (896)
T PRK13104        237 IKINSLIPQLKKQEEEGDEGDYTIDEKQKQAHLTDAGHLHIEELLTKAKLLDPGESLYHASNIMLMHHVNAALKAHAMFH  316 (896)
T ss_pred             HHHHHHHHHHHhccccCCCCCEEEEcCCCceEEchHHHHHHHHHHHhCCccCCcccccCchhhhHHHHHHHHHHHHHHhc
Confidence            111111111000              0                                                     


Q ss_pred             ---------------------------------------------------------------CcEEEEEeeCChhHHHH
Q 017573          170 ---------------------------------------------------------------VQVGVFSATMPPEALEI  186 (369)
Q Consensus       170 ---------------------------------------------------------------~~~i~~saT~~~~~~~~  186 (369)
                                                                                     .++-+||+|...... .
T Consensus       317 ~d~dYiV~dg~V~iVDe~TGR~m~grr~s~GLHQaiEaKE~v~i~~e~~t~AsIT~Qn~Fr~Y~kLsGMTGTa~te~~-E  395 (896)
T PRK13104        317 RDIDYIVKDNQVVIVDEHTGRTMPGRRWSEGLHQAVEAKEGVPIQNENQTLASITFQNFFRMYNKLSGMTGTADTEAY-E  395 (896)
T ss_pred             CCCceEEECCEEEEEECCCCCcCCCCCcChHHHHHHHHHcCCCCCCCceeeeeehHHHHHHhcchhccCCCCChhHHH-H
Confidence                                                                           344556666543332 2


Q ss_pred             HHHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHH-Hhc-cCCCeEEEeCCHhhHHHHHHHHhhCCCeeEE
Q 017573          187 TRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLY-ETL-AITQSVIFVNTRRKVDWLTDKMRSRDHTVSA  264 (369)
Q Consensus       187 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~-~~~-~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~  264 (369)
                      ....++-++.......+.........++  .+...+...+.+.+ ..+ .+.++||||++++.++.+++.|.+.+++..+
T Consensus       396 f~~iY~l~Vv~IPtnkp~~R~d~~d~v~--~t~~~k~~av~~~i~~~~~~g~PVLVgt~Sie~sE~ls~~L~~~gi~h~v  473 (896)
T PRK13104        396 FQQIYNLEVVVIPTNRSMIRKDEADLVY--LTQADKFQAIIEDVRECGVRKQPVLVGTVSIEASEFLSQLLKKENIKHQV  473 (896)
T ss_pred             HHHHhCCCEEECCCCCCcceecCCCeEE--cCHHHHHHHHHHHHHHHHhCCCCEEEEeCcHHHHHHHHHHHHHcCCCeEe
Confidence            3333333332222221111111111111  22233444444444 333 5569999999999999999999999999999


Q ss_pred             ecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCC--------------------------------------CcE
Q 017573          265 THGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQ--------------------------------------VSL  306 (369)
Q Consensus       265 ~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~--------------------------------------~~~  306 (369)
                      +|+++...++..+.+.|+.|.  |+|||+++++|+|+.=                                      -=+
T Consensus       474 Lnak~~q~Ea~iia~Ag~~G~--VtIATNmAGRGtDI~Lggn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGL~  551 (896)
T PRK13104        474 LNAKFHEKEAQIIAEAGRPGA--VTIATNMAGRGTDIVLGGSLAADLANLPADASEQEKEAVKKEWQKRHDEVIAAGGLR  551 (896)
T ss_pred             ecCCCChHHHHHHHhCCCCCc--EEEeccCccCCcceecCCchhhhhhccccchhhHHHHHHHHHhhhhhhHHHHcCCCE
Confidence            999999999999999999995  9999999999999861                                      225


Q ss_pred             EEEecCCCCccchhhhhcccccCCCceeEEEEeccccHHH
Q 017573          307 VINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERM  346 (369)
Q Consensus       307 vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~  346 (369)
                      ||....+.|...=.|..||+||.|.+|.+-.|++-.|.-+
T Consensus       552 VIgTerhesrRID~QLrGRaGRQGDPGss~f~lSleD~l~  591 (896)
T PRK13104        552 IIGSERHESRRIDNQLRGRAGRQGDPGSSRFYLSLEDNLM  591 (896)
T ss_pred             EEeeccCchHHHHHHhccccccCCCCCceEEEEEcCcHHH
Confidence            6666777888888999999999999999999988766543

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

Probab=99.97  E-value=6.3e-30  Score=225.61  Aligned_cols=308  Identities=18%  Similarity=0.256  Sum_probs=232.9

Q ss_pred             CCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEE
Q 017573           18 KPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHA   97 (369)
Q Consensus        18 ~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~   97 (369)
                      ++-|+|..++..+-.+++++|.|.|.+|||.+|-.+|+..++.+.   +++|-.|-++|.+|-++++..-+++.|+    
T Consensus       129 ~LDpFQ~~aI~Cidr~eSVLVSAHTSAGKTVVAeYAIA~sLr~kQ---RVIYTSPIKALSNQKYREl~~EF~DVGL----  201 (1041)
T KOG0948|consen  129 TLDPFQSTAIKCIDRGESVLVSAHTSAGKTVVAEYAIAMSLREKQ---RVIYTSPIKALSNQKYRELLEEFKDVGL----  201 (1041)
T ss_pred             ccCchHhhhhhhhcCCceEEEEeecCCCcchHHHHHHHHHHHhcC---eEEeeChhhhhcchhHHHHHHHhcccce----
Confidence            788999999999999999999999999999999999998888766   8999999999999999999876555444    


Q ss_pred             EECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEEe
Q 017573           98 CVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSA  177 (369)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~sa  177 (369)
                      .+|+-+       ++..+..+|+|.+.|..++.++..-...+.-||+||+|.+.+....-.+...+-.+|++.+.+|+||
T Consensus       202 MTGDVT-------InP~ASCLVMTTEILRsMLYRGSEvmrEVaWVIFDEIHYMRDkERGVVWEETIIllP~~vr~VFLSA  274 (1041)
T KOG0948|consen  202 MTGDVT-------INPDASCLVMTTEILRSMLYRGSEVMREVAWVIFDEIHYMRDKERGVVWEETIILLPDNVRFVFLSA  274 (1041)
T ss_pred             eeccee-------eCCCCceeeeHHHHHHHHHhccchHhheeeeEEeeeehhccccccceeeeeeEEeccccceEEEEec
Confidence            445544       3445889999999999999988877777889999999999887766666677778899999999999


Q ss_pred             eCChhHHHHHHHhcC---CCEEEEecCccccccceeEEEEEccc---------h----hh--------------------
Q 017573          178 TMPPEALEITRKFMN---KPVRILVKRDELTLEGIKQFYVNVEK---------E----EW--------------------  221 (369)
Q Consensus       178 T~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~---------~----~~--------------------  221 (369)
                      |.+ +..+++++.+.   .|.++.  ...+.+..+.++.++...         .    +.                    
T Consensus       275 TiP-NA~qFAeWI~~ihkQPcHVV--YTdyRPTPLQHyifP~ggdGlylvVDek~~FrednF~~am~~l~~~~~~~~~~~  351 (1041)
T KOG0948|consen  275 TIP-NARQFAEWICHIHKQPCHVV--YTDYRPTPLQHYIFPAGGDGLYLVVDEKGKFREDNFQKAMSVLRKAGESDGKKK  351 (1041)
T ss_pred             cCC-CHHHHHHHHHHHhcCCceEE--eecCCCCcceeeeecCCCCeeEEEEecccccchHHHHHHHHHhhccCCCccccc
Confidence            996 66667666653   232221  122223333333222111         0    00                    


Q ss_pred             ------------------hHHHHHHHHHhccCCCeEEEeCCHhhHHHHHHHHhhCC------------------------
Q 017573          222 ------------------KLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRD------------------------  259 (369)
Q Consensus       222 ------------------~~~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~~------------------------  259 (369)
                                        .+..+...+......++|||+-++++|+.++-.+.+..                        
T Consensus       352 ~~~k~~kG~~~~~~~~~s~i~kiVkmi~~~~~~PVIvFSFSkkeCE~~Alqm~kldfN~deEk~~V~~iF~nAi~~Lsee  431 (1041)
T KOG0948|consen  352 ANKKGRKGGTGGKGPGDSDIYKIVKMIMERNYLPVIVFSFSKKECEAYALQMSKLDFNTDEEKELVETIFNNAIDQLSEE  431 (1041)
T ss_pred             cccccccCCcCCCCCCcccHHHHHHHHHhhcCCceEEEEecHhHHHHHHHhhccCcCCChhHHHHHHHHHHHHHHhcChh
Confidence                              11112222222234579999999999999877776552                        


Q ss_pred             ---------------CeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCC--------CCc
Q 017573          260 ---------------HTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLP--------TQP  316 (369)
Q Consensus       260 ---------------~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~--------~~~  316 (369)
                                     ..+++.|+++=+--++-+.-.|..|-+++|+||...+.|+|+|.-++|+..-.-        -|.
T Consensus       432 Dr~LPqie~iLPLL~RGIGIHHsGLLPIlKE~IEILFqEGLvKvLFATETFsiGLNMPAkTVvFT~~rKfDG~~fRwiss  511 (1041)
T KOG0948|consen  432 DRELPQIENILPLLRRGIGIHHSGLLPILKEVIEILFQEGLVKVLFATETFSIGLNMPAKTVVFTAVRKFDGKKFRWISS  511 (1041)
T ss_pred             hccchHHHHHHHHHHhccccccccchHHHHHHHHHHHhccHHHHHHhhhhhhhccCCcceeEEEeeccccCCcceeeecc
Confidence                           248899999988888889999999999999999999999999866666532211        156


Q ss_pred             cchhhhhcccccCCCc--eeEEEEeccc
Q 017573          317 ENYLHRIGRSGRFGRK--GVAINFVTRD  342 (369)
Q Consensus       317 ~~~~Q~~GR~~R~~~~--~~~~~~~~~~  342 (369)
                      .+|+|+.|||||.|.+  |.||+.++..
T Consensus       512 GEYIQMSGRAGRRG~DdrGivIlmiDek  539 (1041)
T KOG0948|consen  512 GEYIQMSGRAGRRGIDDRGIVILMIDEK  539 (1041)
T ss_pred             cceEEecccccccCCCCCceEEEEecCc
Confidence            7999999999999865  7777777754

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=99.97  E-value=6.8e-29  Score=228.00  Aligned_cols=317  Identities=18%  Similarity=0.201  Sum_probs=227.8

Q ss_pred             CCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEE
Q 017573           18 KPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHA   97 (369)
Q Consensus        18 ~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~   97 (369)
                      .|++.|.-+.-.+.+|+  +....||+|||+++.++++.....+.   .+-+++|+.-|+.+-++++..++..+|+++..
T Consensus        80 ~~~dvQlig~l~l~~G~--iaEm~TGEGKTLvA~l~a~l~al~G~---~v~vvT~neyLA~Rd~e~~~~~~~~LGl~vg~  154 (796)
T PRK12906         80 RPFDVQIIGGIVLHEGN--IAEMKTGEGKTLTATLPVYLNALTGK---GVHVVTVNEYLSSRDATEMGELYRWLGLTVGL  154 (796)
T ss_pred             CCchhHHHHHHHHhcCC--cccccCCCCCcHHHHHHHHHHHHcCC---CeEEEeccHHHHHhhHHHHHHHHHhcCCeEEE
Confidence            67777777665554444  99999999999999988887777666   89999999999999999999999999999999


Q ss_pred             EECCcchHHHHHHHccCCcEEEeccHHHH-HHHHcCC------CCCCCccEEEEechhHhh-ccC---------------
Q 017573           98 CVGGTSVREDQRILQAGVHVVVGTPGRVF-DMLRRQS------LRPDYIKMFVLDEADEML-SRG---------------  154 (369)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~iiv~t~~~l~-~~~~~~~------~~~~~~~~viiDE~H~~~-~~~---------------  154 (369)
                      +.++.+........  .++|+++|...|. ..++..-      .....+.+.|+||++.+. +..               
T Consensus       155 i~~~~~~~~r~~~y--~~dI~Y~t~~e~gfDyLRD~m~~~~~~~v~r~~~~aIvDEvDSiLiDeartPLiisg~~~~~~~  232 (796)
T PRK12906        155 NLNSMSPDEKRAAY--NCDITYSTNSELGFDYLRDNMVVYKEQMVQRPLNYAIVDEVDSILIDEARTPLIISGQAEKATD  232 (796)
T ss_pred             eCCCCCHHHHHHHh--cCCCeecCCccccccchhhccccchhhhhccCcceeeeccchheeeccCCCceecCCCCCcchH
Confidence            98887766555443  4799999998873 3343321      112457899999999754 100               


Q ss_pred             cHHHHHHHHhhCCc------------------------------------------------------------------
Q 017573          155 FKDQIYDIFQLLPA------------------------------------------------------------------  168 (369)
Q Consensus       155 ~~~~~~~~~~~~~~------------------------------------------------------------------  168 (369)
                      .......+...+..                                                                  
T Consensus       233 ~y~~~~~~v~~l~~~~~~~~~~~~~~~dy~id~~~k~v~lte~G~~~~e~~~~i~~l~~~~~~~~~~~i~~Al~A~~l~~  312 (796)
T PRK12906        233 LYIRADRFVKTLIKDEAEDGDDDEDTGDYKIDEKTKTISLTEQGIRKAEKLFGLDNLYDSENTALAHHIDQALRANYIML  312 (796)
T ss_pred             HHHHHHHHHHHHHhhhhccccccCCCCceEEEcccCceeecHHHHHHHHHHcCCccccCchhhhHHHHHHHHHHHHHHHh
Confidence            00000000000000                                                                  


Q ss_pred             --------------------------------------------------------------cCcEEEEEeeCChhHHHH
Q 017573          169 --------------------------------------------------------------KVQVGVFSATMPPEALEI  186 (369)
Q Consensus       169 --------------------------------------------------------------~~~~i~~saT~~~~~~~~  186 (369)
                                                                                    -.++.+||+|...... .
T Consensus       313 ~d~dYiV~d~~V~ivD~~TGR~~~gr~ws~GLHQaieaKe~v~i~~e~~t~a~It~qnfFr~Y~kl~GmTGTa~~e~~-E  391 (796)
T PRK12906        313 KDIDYVVQDGEVLIVDEFTGRVMEGRRYSDGLHQAIEAKEGVKIQEENQTLATITYQNFFRMYKKLSGMTGTAKTEEE-E  391 (796)
T ss_pred             cCCcEEEECCEEEEEeCCCCCcCCCCccChHHHHHHHHhcCCCcCCCceeeeeehHHHHHHhcchhhccCCCCHHHHH-H
Confidence                                                                          0456678888764433 3


Q ss_pred             HHHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHHHhc--cCCCeEEEeCCHhhHHHHHHHHhhCCCeeEE
Q 017573          187 TRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETL--AITQSVIFVNTRRKVDWLTDKMRSRDHTVSA  264 (369)
Q Consensus       187 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~--~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~  264 (369)
                      ....++-++.......+.........  ...+...+...+.+.+...  .+.++||||++++.++.+++.|.+.+.+...
T Consensus       392 f~~iY~l~vv~IPtnkp~~r~d~~d~--i~~t~~~K~~al~~~i~~~~~~g~pvLI~t~si~~se~ls~~L~~~gi~~~~  469 (796)
T PRK12906        392 FREIYNMEVITIPTNRPVIRKDSPDL--LYPTLDSKFNAVVKEIKERHAKGQPVLVGTVAIESSERLSHLLDEAGIPHAV  469 (796)
T ss_pred             HHHHhCCCEEEcCCCCCeeeeeCCCe--EEcCHHHHHHHHHHHHHHHHhCCCCEEEEeCcHHHHHHHHHHHHHCCCCeeE
Confidence            34444444333222221111111111  1123344666666666433  5679999999999999999999999999999


Q ss_pred             ecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCC---CCc-----EEEEecCCCCccchhhhhcccccCCCceeEE
Q 017573          265 THGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQ---QVS-----LVINYDLPTQPENYLHRIGRSGRFGRKGVAI  336 (369)
Q Consensus       265 ~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~---~~~-----~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~  336 (369)
                      +|+++...++..+.+.++.|.  |+|||+++++|.|++   ++.     +||..+.|.|...+.|+.||+||.|.+|.+.
T Consensus       470 Lna~~~~~Ea~ii~~ag~~g~--VtIATnmAGRGtDI~l~~~V~~~GGLhVI~te~pes~ri~~Ql~GRtGRqG~~G~s~  547 (796)
T PRK12906        470 LNAKNHAKEAEIIMNAGQRGA--VTIATNMAGRGTDIKLGPGVKELGGLAVIGTERHESRRIDNQLRGRSGRQGDPGSSR  547 (796)
T ss_pred             ecCCcHHHHHHHHHhcCCCce--EEEEeccccCCCCCCCCcchhhhCCcEEEeeecCCcHHHHHHHhhhhccCCCCcceE
Confidence            999988887777777777666  999999999999995   788     9999999999999999999999999999999


Q ss_pred             EEeccccHHH
Q 017573          337 NFVTRDDERM  346 (369)
Q Consensus       337 ~~~~~~~~~~  346 (369)
                      .|++..|.-+
T Consensus       548 ~~~sleD~l~  557 (796)
T PRK12906        548 FYLSLEDDLM  557 (796)
T ss_pred             EEEeccchHH
Confidence            9998775443

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=99.97  E-value=2.3e-28  Score=225.51  Aligned_cols=317  Identities=19%  Similarity=0.208  Sum_probs=230.8

Q ss_pred             CCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEE
Q 017573           18 KPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHA   97 (369)
Q Consensus        18 ~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~   97 (369)
                      .|++.|--..-.+.  +.-+..+.||+|||+++.++++-....+.   .+-+++|+..|+.|-++++..++..+|+++..
T Consensus        81 ~~~dvQlig~l~L~--~G~Iaem~TGeGKTLva~lpa~l~aL~G~---~V~IvTpn~yLA~rd~e~~~~l~~~LGlsv~~  155 (830)
T PRK12904         81 RHFDVQLIGGMVLH--EGKIAEMKTGEGKTLVATLPAYLNALTGK---GVHVVTVNDYLAKRDAEWMGPLYEFLGLSVGV  155 (830)
T ss_pred             CCCccHHHhhHHhc--CCchhhhhcCCCcHHHHHHHHHHHHHcCC---CEEEEecCHHHHHHHHHHHHHHHhhcCCeEEE
Confidence            66677766655444  44599999999999999998863333333   68899999999999999999999999999999


Q ss_pred             EECCcchHHHHHHHccCCcEEEeccHHH-HHHHHcCCC------CCCCccEEEEechhHhhccC----------------
Q 017573           98 CVGGTSVREDQRILQAGVHVVVGTPGRV-FDMLRRQSL------RPDYIKMFVLDEADEMLSRG----------------  154 (369)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~iiv~t~~~l-~~~~~~~~~------~~~~~~~viiDE~H~~~~~~----------------  154 (369)
                      +.++.+........  .++|+++|+..| +.+++....      ....+.++|+||++.+.=..                
T Consensus       156 i~~~~~~~er~~~y--~~dI~ygT~~elgfDyLrd~~~~~~~~~~~r~~~~aIvDEaDsiLIDeArtpLiiSg~~~~~~~  233 (830)
T PRK12904        156 ILSGMSPEERREAY--AADITYGTNNEFGFDYLRDNMVFSLEERVQRGLNYAIVDEVDSILIDEARTPLIISGPAEDSSE  233 (830)
T ss_pred             EcCCCCHHHHHHhc--CCCeEEECCcchhhhhhhcccccchhhhcccccceEEEechhhheeccCCCceeeECCCCcccH
Confidence            99988876665543  489999999999 777776542      24568899999999865100                


Q ss_pred             cHHHHHHHHhhCCc------------------------------------------------------------------
Q 017573          155 FKDQIYDIFQLLPA------------------------------------------------------------------  168 (369)
Q Consensus       155 ~~~~~~~~~~~~~~------------------------------------------------------------------  168 (369)
                      .......+...+..                                                                  
T Consensus       234 ~y~~~~~~v~~l~~~~dy~vde~~~~v~lte~G~~~~e~~~~~~~ly~~~~~~~~~~i~~AL~A~~l~~~d~dYiV~dg~  313 (830)
T PRK12904        234 LYKRANKIVPTLEKEGDYTVDEKSRTVGLTEEGIEKAEKLLGIENLYDPENIALVHHLNQALRAHELFKRDVDYIVKDGE  313 (830)
T ss_pred             HHHHHHHHHHhcCCCCCeEEEcCCCeeeECHHHHHHHHHHhCCccccChhhhHHHHHHHHHHHHHHHHhcCCcEEEECCE
Confidence            01111111111100                                                                  


Q ss_pred             ---------------------------------------------------cCcEEEEEeeCChhHHHHHHHhcCCCEEE
Q 017573          169 ---------------------------------------------------KVQVGVFSATMPPEALEITRKFMNKPVRI  197 (369)
Q Consensus       169 ---------------------------------------------------~~~~i~~saT~~~~~~~~~~~~~~~~~~~  197 (369)
                                                                         -.++.+||+|...... .....++-.+..
T Consensus       314 V~ivDe~TGR~~~gr~ws~GLHQaiEaKE~v~i~~e~~t~a~It~qn~Fr~Y~kl~GmTGTa~te~~-E~~~iY~l~vv~  392 (830)
T PRK12904        314 VVIVDEFTGRLMPGRRYSDGLHQAIEAKEGVKIQNENQTLASITFQNYFRMYEKLAGMTGTADTEAE-EFREIYNLDVVV  392 (830)
T ss_pred             EEEEECCCCccCCCCccchHHHHHHHHhcCCCCCCCceeeeeeeHHHHHHhcchhcccCCCcHHHHH-HHHHHhCCCEEE
Confidence                                                               0457788888865443 344444444433


Q ss_pred             EecCccccccceeEEEEEccchhhhHHHHHHHHHh--ccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHH
Q 017573          198 LVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYET--LAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRD  275 (369)
Q Consensus       198 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~--~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~  275 (369)
                      .....+.........+  ..+...+...+...+..  ..+.++||||++++.++.+++.|.+.+++...+|++  ..+|+
T Consensus       393 IPtnkp~~r~d~~d~i--~~t~~~K~~aI~~~I~~~~~~grpVLIft~Si~~se~Ls~~L~~~gi~~~vLnak--q~eRE  468 (830)
T PRK12904        393 IPTNRPMIRIDHPDLI--YKTEKEKFDAVVEDIKERHKKGQPVLVGTVSIEKSELLSKLLKKAGIPHNVLNAK--NHERE  468 (830)
T ss_pred             cCCCCCeeeeeCCCeE--EECHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHCCCceEeccCc--hHHHH
Confidence            3322222221111122  22334466677776654  456799999999999999999999999999999995  67888


Q ss_pred             HHHHHHhcCCCcEEEEecCCcCCCCCCC--------------------------------------CcEEEEecCCCCcc
Q 017573          276 IIMREFRSGSSRVLITTDLLARGIDVQQ--------------------------------------VSLVINYDLPTQPE  317 (369)
Q Consensus       276 ~~~~~f~~~~~~vli~t~~~~~G~d~~~--------------------------------------~~~vi~~~~~~~~~  317 (369)
                      ..+..|..+...|+|||+++++|+|++-                                      -=+||....+.|..
T Consensus       469 a~Iia~Ag~~g~VtIATNmAGRGtDI~LgGn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~GGLhVigTerhesrR  548 (830)
T PRK12904        469 AEIIAQAGRPGAVTIATNMAGRGTDIKLGGNPEMLAAALLEEETEEQIAKIKAEWQEEHEEVLEAGGLHVIGTERHESRR  548 (830)
T ss_pred             HHHHHhcCCCceEEEecccccCCcCccCCCchhhhhhhhhhhhhhHHHHHHHHHHhhhhhhHHHcCCCEEEecccCchHH
Confidence            9999999999999999999999999863                                      23566677788888


Q ss_pred             chhhhhcccccCCCceeEEEEeccccHHH
Q 017573          318 NYLHRIGRSGRFGRKGVAINFVTRDDERM  346 (369)
Q Consensus       318 ~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~  346 (369)
                      .-.|..||+||.|.+|.+-.|++-.|.-+
T Consensus       549 id~QlrGRagRQGdpGss~f~lSleD~l~  577 (830)
T PRK12904        549 IDNQLRGRSGRQGDPGSSRFYLSLEDDLM  577 (830)
T ss_pred             HHHHhhcccccCCCCCceeEEEEcCcHHH
Confidence            89999999999999999999988766543

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

Probab=99.97  E-value=7.9e-29  Score=231.39  Aligned_cols=315  Identities=21%  Similarity=0.265  Sum_probs=234.1

Q ss_pred             HhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhcccc
Q 017573           12 YAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYL   91 (369)
Q Consensus        12 ~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~   91 (369)
                      ..+|| .|-++|++++..+.++.+++++||||+|||.++..++..++..+.   +++|.+|.++|.+|.++++.....+.
T Consensus       114 ~~~~F-~LD~fQ~~a~~~Ler~esVlV~ApTssGKTvVaeyAi~~al~~~q---rviYTsPIKALsNQKyrdl~~~fgdv  189 (1041)
T COG4581         114 REYPF-ELDPFQQEAIAILERGESVLVCAPTSSGKTVVAEYAIALALRDGQ---RVIYTSPIKALSNQKYRDLLAKFGDV  189 (1041)
T ss_pred             HhCCC-CcCHHHHHHHHHHhCCCcEEEEccCCCCcchHHHHHHHHHHHcCC---ceEeccchhhhhhhHHHHHHHHhhhh
Confidence            44676 899999999999999999999999999999999988888887766   79999999999999999987765443


Q ss_pred             CcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCccCc
Q 017573           92 GVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQ  171 (369)
Q Consensus        92 ~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~  171 (369)
                      ...+...+|+..       ++.++.++|+|.+-|.+++.++......+..||+||+|.+.+......+..++-.+|+..+
T Consensus       190 ~~~vGL~TGDv~-------IN~~A~clvMTTEILRnMlyrg~~~~~~i~~ViFDEvHyi~D~eRG~VWEE~Ii~lP~~v~  262 (1041)
T COG4581         190 ADMVGLMTGDVS-------INPDAPCLVMTTEILRNMLYRGSESLRDIEWVVFDEVHYIGDRERGVVWEEVIILLPDHVR  262 (1041)
T ss_pred             hhhccceeccee-------eCCCCceEEeeHHHHHHHhccCcccccccceEEEEeeeeccccccchhHHHHHHhcCCCCc
Confidence            334566677666       4566899999999999999999888888999999999999988888899999999999999


Q ss_pred             EEEEEeeCChhHHHHHHHhc---CCCEEEEecCccccccceeEEEEEc-------cchh----h----------------
Q 017573          172 VGVFSATMPPEALEITRKFM---NKPVRILVKRDELTLEGIKQFYVNV-------EKEE----W----------------  221 (369)
Q Consensus       172 ~i~~saT~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~----~----------------  221 (369)
                      ++++|||.+ +..++..++.   ..+..+....  ..+....+++..-       +...    .                
T Consensus       263 ~v~LSATv~-N~~EF~~Wi~~~~~~~~~vv~t~--~RpvPL~~~~~~~~~l~~lvde~~~~~~~~~~~a~~~l~~~~~~~  339 (1041)
T COG4581         263 FVFLSATVP-NAEEFAEWIQRVHSQPIHVVSTE--HRPVPLEHFVYVGKGLFDLVDEKKKFNAENFPSANRSLSCFSEKV  339 (1041)
T ss_pred             EEEEeCCCC-CHHHHHHHHHhccCCCeEEEeec--CCCCCeEEEEecCCceeeeecccccchhhcchhhhhhhhccchhc
Confidence            999999986 4445554443   2232222211  1111111111111       0000    0                


Q ss_pred             --------------------------hHHHHHHHHHhccCCCeEEEeCCHhhHHHHHHHHhhC-----------------
Q 017573          222 --------------------------KLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSR-----------------  258 (369)
Q Consensus       222 --------------------------~~~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~-----------------  258 (369)
                                                ....+...+.....-++++|+-++..|+..+..+...                 
T Consensus       340 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~iv~~l~~~~~lP~I~F~FSr~~Ce~~a~~~~~ldl~~~~~~e~~i~~ii~  419 (1041)
T COG4581         340 RETDDGDVGRYARRTKALRGSAKGPAGRPEIVNKLDKDNLLPAIVFSFSRRGCEEAAQILSTLDLVLTEEKERAIREIID  419 (1041)
T ss_pred             cccCccccccccccccccCCcccccccchHHHhhhhhhcCCceEEEEEchhhHHHHHHHhcccccccCCcHHHHHHHHHH
Confidence                                      0011222222223347899999998888776666422                 


Q ss_pred             ------------------------CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecC--
Q 017573          259 ------------------------DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDL--  312 (369)
Q Consensus       259 ------------------------~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~--  312 (369)
                                              ...++..|+++=+..+..+...|..|-.+|+++|..++.|+|+|. +.|++...  
T Consensus       420 ~~i~~L~~ed~~lp~~~~~~~~~L~RGiavHH~GlLP~~K~~vE~Lfq~GLvkvvFaTeT~s~GiNmPa-rtvv~~~l~K  498 (1041)
T COG4581         420 HAIGDLAEEDRELPLQILEISALLLRGIAVHHAGLLPAIKELVEELFQEGLVKVVFATETFAIGINMPA-RTVVFTSLSK  498 (1041)
T ss_pred             HHHhhcChhhhcCcccHHHHHHHHhhhhhhhccccchHHHHHHHHHHhccceeEEeehhhhhhhcCCcc-cceeeeeeEE
Confidence                                    113568889999999999999999999999999999999999985 44444332  


Q ss_pred             -------CCCccchhhhhcccccCCCc--eeEEEEecc
Q 017573          313 -------PTQPENYLHRIGRSGRFGRK--GVAINFVTR  341 (369)
Q Consensus       313 -------~~~~~~~~Q~~GR~~R~~~~--~~~~~~~~~  341 (369)
                             .-++.+|.|+.||+||.|-+  |.+++...+
T Consensus       499 ~dG~~~r~L~~gEy~QmsGRAGRRGlD~~G~vI~~~~~  536 (1041)
T COG4581         499 FDGNGHRWLSPGEYTQMSGRAGRRGLDVLGTVIVIEPP  536 (1041)
T ss_pred             ecCCceeecChhHHHHhhhhhccccccccceEEEecCC
Confidence                   23678999999999999866  777777443

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=99.97  E-value=1.4e-28  Score=237.10  Aligned_cols=304  Identities=19%  Similarity=0.253  Sum_probs=204.9

Q ss_pred             hhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhc-cccCcEEEEEECCc
Q 017573           24 QRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALG-DYLGVKVHACVGGT  102 (369)
Q Consensus        24 ~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~-~~~~~~v~~~~~~~  102 (369)
                      .+++..+..++.++|+|+||||||...-..++. ...+. ..++++.-|++.-+...++.+.+.. ...|..|.+.....
T Consensus        73 ~~Il~~l~~~~vvii~g~TGSGKTTqlPq~lle-~~~~~-~~~I~~tQPRRlAA~svA~RvA~elg~~lG~~VGY~vR~~  150 (1283)
T TIGR01967        73 EDIAEAIAENQVVIIAGETGSGKTTQLPKICLE-LGRGS-HGLIGHTQPRRLAARTVAQRIAEELGTPLGEKVGYKVRFH  150 (1283)
T ss_pred             HHHHHHHHhCceEEEeCCCCCCcHHHHHHHHHH-cCCCC-CceEecCCccHHHHHHHHHHHHHHhCCCcceEEeeEEcCC
Confidence            467777777889999999999999864323332 22222 2256666688877777776665533 33344454433222


Q ss_pred             chHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhH-hhccCcHHH-HHHHHhhCCccCcEEEEEeeCC
Q 017573          103 SVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADE-MLSRGFKDQ-IYDIFQLLPAKVQVGVFSATMP  180 (369)
Q Consensus       103 ~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~-~~~~~~~~~-~~~~~~~~~~~~~~i~~saT~~  180 (369)
                      ..      ...+..|.++|+..|...+.... .+..+++||+||+|+ ..+.++.-. +..++... +..++++||||+.
T Consensus       151 ~~------~s~~T~I~~~TdGiLLr~l~~d~-~L~~~~~IIIDEaHERsL~~D~LL~lLk~il~~r-pdLKlIlmSATld  222 (1283)
T TIGR01967       151 DQ------VSSNTLVKLMTDGILLAETQQDR-FLSRYDTIIIDEAHERSLNIDFLLGYLKQLLPRR-PDLKIIITSATID  222 (1283)
T ss_pred             cc------cCCCceeeeccccHHHHHhhhCc-ccccCcEEEEcCcchhhccchhHHHHHHHHHhhC-CCCeEEEEeCCcC
Confidence            21      13457899999999998887654 467789999999995 555554432 34444333 4678999999996


Q ss_pred             hhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccch-----hhhHHHHHHHHH---hccCCCeEEEeCCHhhHHHHH
Q 017573          181 PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKE-----EWKLETLCDLYE---TLAITQSVIFVNTRRKVDWLT  252 (369)
Q Consensus       181 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~l~~~~~---~~~~~k~lv~~~~~~~~~~~~  252 (369)
                      .  ..+...+...++ +.+.....   .+...|......     ....+.+...+.   ....+.+|||+++..+++.++
T Consensus       223 ~--~~fa~~F~~apv-I~V~Gr~~---PVev~Y~~~~~~~~~~~~~~~~~i~~~I~~l~~~~~GdILVFLpg~~EI~~l~  296 (1283)
T TIGR01967       223 P--ERFSRHFNNAPI-IEVSGRTY---PVEVRYRPLVEEQEDDDLDQLEAILDAVDELFAEGPGDILIFLPGEREIRDAA  296 (1283)
T ss_pred             H--HHHHHHhcCCCE-EEECCCcc---cceeEEecccccccchhhhHHHHHHHHHHHHHhhCCCCEEEeCCCHHHHHHHH
Confidence            4  344444444443 33322221   223333322111     112232322222   124579999999999999999


Q ss_pred             HHHhhCC---CeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCCC---------------
Q 017573          253 DKMRSRD---HTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPT---------------  314 (369)
Q Consensus       253 ~~l~~~~---~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~---------------  314 (369)
                      +.|.+.+   ..+..+||+++.+++.++++.+  +..+|+++|+++++|+|+|++++||..+.+.               
T Consensus       297 ~~L~~~~~~~~~VlpLhg~Ls~~eQ~~vf~~~--~~rkIVLATNIAEtSLTIpgV~yVIDsGl~r~~~yd~~~~~~~L~~  374 (1283)
T TIGR01967       297 EILRKRNLRHTEILPLYARLSNKEQQRVFQPH--SGRRIVLATNVAETSLTVPGIHYVIDTGTARISRYSYRTKVQRLPI  374 (1283)
T ss_pred             HHHHhcCCCCcEEEeccCCCCHHHHHHHhCCC--CCceEEEeccHHHhccccCCeeEEEeCCCccccccccccCccccCC
Confidence            9998764   3588899999999999986543  2468999999999999999999999988432               


Q ss_pred             ---CccchhhhhcccccCCCceeEEEEeccccHHH
Q 017573          315 ---QPENYLHRIGRSGRFGRKGVAINFVTRDDERM  346 (369)
Q Consensus       315 ---~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~  346 (369)
                         |..++.||.||+||.+ +|.||.+++..+...
T Consensus       375 ~~ISkasa~QRaGRAGR~~-~G~cyRLyte~~~~~  408 (1283)
T TIGR01967       375 EPISQASANQRKGRCGRVA-PGICIRLYSEEDFNS  408 (1283)
T ss_pred             ccCCHHHHHHHhhhhCCCC-CceEEEecCHHHHHh
Confidence               4568999999999996 999999998776543

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.

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=99.96  E-value=2.9e-27  Score=218.19  Aligned_cols=146  Identities=23%  Similarity=0.314  Sum_probs=124.6

Q ss_pred             CCCCHHHHHHHH-----hCCCCCC---cHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcC
Q 017573            1 MGLQENLLRGIY-----AYGFEKP---SAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAP   72 (369)
Q Consensus         1 ~~l~~~i~~~l~-----~~~~~~~---~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P   72 (369)
                      |++.+++.+.+.     ..|+..|   +|+|.+++..+..+++++.+++||+|||++++++++..+..+.   .++||+|
T Consensus        67 fal~re~~~r~lg~~~~~~G~~~p~~~tp~qvQ~I~~i~l~~gvIAeaqTGeGKTLAf~LP~l~~aL~g~---~v~IVTp  143 (970)
T PRK12899         67 YGVVKNVCRRLAGTPVEVSGYHQQWDMVPYDVQILGAIAMHKGFITEMQTGEGKTLTAVMPLYLNALTGK---PVHLVTV  143 (970)
T ss_pred             hCCCHHHHHHHhccccccccccCCCCCChHHHHHhhhhhcCCCeEEEeCCCCChHHHHHHHHHHHHhhcC---CeEEEeC
Confidence            345666666665     5788888   9999999999999999999999999999999999997765443   5899999


Q ss_pred             CHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHH-HHHHHcCCCCCC-------CccEEEE
Q 017573           73 TRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRV-FDMLRRQSLRPD-------YIKMFVL  144 (369)
Q Consensus        73 ~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l-~~~~~~~~~~~~-------~~~~vii  144 (369)
                      ++.|+.|..+++..+...+++++..+.|+.....+....  .++|+|+||..| +.+++.+.+..+       .+.++|+
T Consensus       144 TrELA~Qdae~m~~L~k~lGLsV~~i~GG~~~~eq~~~y--~~DIVygTPgRLgfDyLrd~~~~~~~~~~vqr~~~~~II  221 (970)
T PRK12899        144 NDYLAQRDCEWVGSVLRWLGLTTGVLVSGSPLEKRKEIY--QCDVVYGTASEFGFDYLRDNSIATRKEEQVGRGFYFAII  221 (970)
T ss_pred             CHHHHHHHHHHHHHHHhhcCCeEEEEeCCCCHHHHHHHc--CCCEEEECCChhHHHHhhCCCCCcCHHHhhcccccEEEE
Confidence            999999999999999998999999999998877665444  489999999999 999988766655       4589999


Q ss_pred             echhHhh
Q 017573          145 DEADEML  151 (369)
Q Consensus       145 DE~H~~~  151 (369)
                      ||++++.
T Consensus       222 DEADsmL  228 (970)
T PRK12899        222 DEVDSIL  228 (970)
T ss_pred             echhhhh
Confidence            9999865

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

Probab=99.96  E-value=1.9e-26  Score=215.42  Aligned_cols=299  Identities=16%  Similarity=0.145  Sum_probs=183.1

Q ss_pred             CcHhhhhhhhcccc----------CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhc
Q 017573           19 PSAIQQRGIVPFCK----------GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALG   88 (369)
Q Consensus        19 ~~~~Q~~~~~~~~~----------~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~   88 (369)
                      ++++|.+|+..+.+          .++.+++++||||||++++..+...+. ....+++|+|+|+..|..|+.+.|..+.
T Consensus       239 ~r~~Q~~av~~~~~~~~~~~~~~~~~~gli~~~TGsGKT~t~~~la~~l~~-~~~~~~vl~lvdR~~L~~Q~~~~f~~~~  317 (667)
T TIGR00348       239 QRYMQYRAVKKIVESITRKTWGKDERGGLIWHTQGSGKTLTMLFAARKALE-LLKNPKVFFVVDRRELDYQLMKEFQSLQ  317 (667)
T ss_pred             hHHHHHHHHHHHHHHHHhcccCCCCceeEEEEecCCCccHHHHHHHHHHHh-hcCCCeEEEEECcHHHHHHHHHHHHhhC
Confidence            88999999987642          257999999999999998766655443 3344589999999999999999999875


Q ss_pred             cccCcEEEEEECCcchHHHHHHH-ccCCcEEEeccHHHHHHHHcC--CCCCCCc-cEEEEechhHhhccCcHHHHHHHHh
Q 017573           89 DYLGVKVHACVGGTSVREDQRIL-QAGVHVVVGTPGRVFDMLRRQ--SLRPDYI-KMFVLDEADEMLSRGFKDQIYDIFQ  164 (369)
Q Consensus        89 ~~~~~~v~~~~~~~~~~~~~~~~-~~~~~iiv~t~~~l~~~~~~~--~~~~~~~-~~viiDE~H~~~~~~~~~~~~~~~~  164 (369)
                      ...   +   ............+ .....|+|+|.++|...+...  ....... .+||+||||+.....+.   ..+..
T Consensus       318 ~~~---~---~~~~s~~~L~~~l~~~~~~iivtTiQk~~~~~~~~~~~~~~~~~~~lvIvDEaHrs~~~~~~---~~l~~  388 (667)
T TIGR00348       318 KDC---A---ERIESIAELKRLLEKDDGGIIITTIQKFDKKLKEEEEKFPVDRKEVVVIFDEAHRSQYGELA---KNLKK  388 (667)
T ss_pred             CCC---C---cccCCHHHHHHHHhCCCCCEEEEEhHHhhhhHhhhhhccCCCCCCEEEEEEcCccccchHHH---HHHHh
Confidence            321   1   1111222222222 234689999999998644321  1111111 38999999986433222   22224


Q ss_pred             hCCccCcEEEEEeeCChhHHHHHHHh----cCCCEEEEecCccccccceeEEEEEcc-------ch--------------
Q 017573          165 LLPAKVQVGVFSATMPPEALEITRKF----MNKPVRILVKRDELTLEGIKQFYVNVE-------KE--------------  219 (369)
Q Consensus       165 ~~~~~~~~i~~saT~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~--------------  219 (369)
                      .++ +...+++||||...........    ++.++......+......+..+.+...       ..              
T Consensus       389 ~~p-~a~~lGfTaTP~~~~d~~t~~~f~~~fg~~i~~Y~~~~AI~dG~~~~i~Y~~~~~~~~~~~~~l~~~~~~~~~~~~  467 (667)
T TIGR00348       389 ALK-NASFFGFTGTPIFKKDRDTSLTFAYVFGRYLHRYFITDAIRDGLTVKIDYEDRLPEDHLDRKKLDAFFDEIFELLP  467 (667)
T ss_pred             hCC-CCcEEEEeCCCcccccccccccccCCCCCeEEEeeHHHHhhcCCeeeEEEEecchhhccChHHHHHHHHHHHHhhh
Confidence            454 5679999999963211111111    122222221111111111111110000       00              


Q ss_pred             ----hh--------------------hHHHHH-HHH----Hhc--cCCCeEEEeCCHhhHHHHHHHHhhCC-----CeeE
Q 017573          220 ----EW--------------------KLETLC-DLY----ETL--AITQSVIFVNTRRKVDWLTDKMRSRD-----HTVS  263 (369)
Q Consensus       220 ----~~--------------------~~~~l~-~~~----~~~--~~~k~lv~~~~~~~~~~~~~~l~~~~-----~~~~  263 (369)
                          ..                    ..+.+. .++    ...  ...|++|+|.++.+|..+++.|.+..     ....
T Consensus       468 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~ia~~i~~h~~~~~~~~~~kamvv~~sr~~a~~~~~~l~~~~~~~~~~~~v  547 (667)
T TIGR00348       468 ERIREITKESLKEKLQKTKKILFNEDRLESIAKDIAEHYAKFKELFKFKAMVVAISRYACVEEKNALDEELNEKFEASAI  547 (667)
T ss_pred             ccccHHHHHHHHHHHHHHHhhhcChHHHHHHHHHHHHHHHHhhhcccCceeEEEecHHHHHHHHHHHHhhcccccCCeeE
Confidence                00                    001111 111    111  23799999999999999998886542     3445


Q ss_pred             EecCCCCHH---------------------HHHHHHHHHhc-CCCcEEEEecCCcCCCCCCCCcEEEEecCCCCccchhh
Q 017573          264 ATHGDMDQN---------------------TRDIIMREFRS-GSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLH  321 (369)
Q Consensus       264 ~~~~~~~~~---------------------~r~~~~~~f~~-~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q  321 (369)
                      .+++..+.+                     ....++++|++ ++++++|+++++.+|+|.|.++++++..+..+. .++|
T Consensus       548 v~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Fk~~~~~~ilIVvdmllTGFDaP~l~tLyldKplk~h-~LlQ  626 (667)
T TIGR00348       548 VMTGKESDDAEIRDYNKHIRTKFDKSDGFEIYYKDLERFKKEENPKLLIVVDMLLTGFDAPILNTLYLDKPLKYH-GLLQ  626 (667)
T ss_pred             EecCCccchhHHHHHHHHhccccccchhhhHHHHHHHHhcCCCCceEEEEEcccccccCCCccceEEEecccccc-HHHH
Confidence            555543322                     12468888876 678999999999999999999999988877754 6899


Q ss_pred             hhcccccC
Q 017573          322 RIGRSGRF  329 (369)
Q Consensus       322 ~~GR~~R~  329 (369)
                      ++||+.|.
T Consensus       627 ai~R~nR~  634 (667)
T TIGR00348       627 AIARTNRI  634 (667)
T ss_pred             HHHHhccc
Confidence            99999994

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

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

Probab=99.96  E-value=1.2e-27  Score=188.33  Aligned_cols=164  Identities=26%  Similarity=0.461  Sum_probs=140.1

Q ss_pred             cHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEE
Q 017573           20 SAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACV   99 (369)
Q Consensus        20 ~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~   99 (369)
                      +|+|.++++.+.+++++++.+|||+|||++++.+++..+..+ ...++++++|+++|++|..+.+.++....+.++..++
T Consensus         1 t~~Q~~~~~~i~~~~~~li~aptGsGKT~~~~~~~l~~~~~~-~~~~~lii~P~~~l~~q~~~~~~~~~~~~~~~~~~~~   79 (169)
T PF00270_consen    1 TPLQQEAIEAIISGKNVLISAPTGSGKTLAYILPALNRLQEG-KDARVLIIVPTRALAEQQFERLRKFFSNTNVRVVLLH   79 (169)
T ss_dssp             -HHHHHHHHHHHTTSEEEEECSTTSSHHHHHHHHHHHHHHTT-SSSEEEEEESSHHHHHHHHHHHHHHTTTTTSSEEEES
T ss_pred             CHHHHHHHHHHHcCCCEEEECCCCCccHHHHHHHHHhhhccC-CCceEEEEeeccccccccccccccccccccccccccc
Confidence            689999999999999999999999999999999999888776 4448999999999999999999999887778888888


Q ss_pred             CCcchH-HHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCc--cCcEEEEE
Q 017573          100 GGTSVR-EDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPA--KVQVGVFS  176 (369)
Q Consensus       100 ~~~~~~-~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~--~~~~i~~s  176 (369)
                      ++.... .....+.++++|+|+||++|...+........+++++|+||+|.+..+.+...+..+...+..  +.+++++|
T Consensus        80 ~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~iViDE~h~l~~~~~~~~~~~i~~~~~~~~~~~~i~~S  159 (169)
T PF00270_consen   80 GGQSISEDQREVLSNQADILVTTPEQLLDLISNGKINISRLSLIVIDEAHHLSDETFRAMLKSILRRLKRFKNIQIILLS  159 (169)
T ss_dssp             TTSCHHHHHHHHHHTTSSEEEEEHHHHHHHHHTTSSTGTTESEEEEETHHHHHHTTHHHHHHHHHHHSHTTTTSEEEEEE
T ss_pred             ccccccccccccccccccccccCcchhhccccccccccccceeeccCcccccccccHHHHHHHHHHHhcCCCCCcEEEEe
Confidence            888755 444445567999999999999999886666667999999999999987777788888777633  58899999


Q ss_pred             eeCChhHH
Q 017573          177 ATMPPEAL  184 (369)
Q Consensus       177 aT~~~~~~  184 (369)
                      ||++.+.+
T Consensus       160 AT~~~~~~  167 (169)
T PF00270_consen  160 ATLPSNVE  167 (169)
T ss_dssp             SSSTHHHH
T ss_pred             eCCChhHh
Confidence            99985543

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 ....

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

Probab=99.96  E-value=1.1e-26  Score=206.76  Aligned_cols=331  Identities=18%  Similarity=0.174  Sum_probs=225.2

Q ss_pred             CCCcHhhhhhhhccc----cCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccC
Q 017573           17 EKPSAIQQRGIVPFC----KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLG   92 (369)
Q Consensus        17 ~~~~~~Q~~~~~~~~----~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~   92 (369)
                      ..|.+||++.++.+.    ++...|+-..+|-|||...+..+......+.-..++|||||. .++.||.++|..|..  .
T Consensus       204 ~~Lf~yQreGV~WL~~L~~q~~GGILgDeMGLGKTIQiisFLaaL~~S~k~~~paLIVCP~-Tii~qW~~E~~~w~p--~  280 (923)
T KOG0387|consen  204 SKLFPYQREGVQWLWELYCQRAGGILGDEMGLGKTIQIISFLAALHHSGKLTKPALIVCPA-TIIHQWMKEFQTWWP--P  280 (923)
T ss_pred             HHhhHHHHHHHHHHHHHHhccCCCeecccccCccchhHHHHHHHHhhcccccCceEEEccH-HHHHHHHHHHHHhCc--c
Confidence            458899999998876    467899999999999966443333222222333489999997 788999999999876  4


Q ss_pred             cEEEEEECCcchHH---------HH----HHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHH
Q 017573           93 VKVHACVGGTSVRE---------DQ----RILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQI  159 (369)
Q Consensus        93 ~~v~~~~~~~~~~~---------~~----~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~  159 (369)
                      ++|.++++......         ..    +....+..|+++|++.|.-.  ...+....|+++|+||.|.+.+.+  ..+
T Consensus       281 ~rv~ilh~t~s~~r~~~~~~~~~~~~~L~r~~~~~~~ilitty~~~r~~--~d~l~~~~W~y~ILDEGH~IrNpn--s~i  356 (923)
T KOG0387|consen  281 FRVFILHGTGSGARYDASHSSHKKDKLLIRKVATDGGILITTYDGFRIQ--GDDLLGILWDYVILDEGHRIRNPN--SKI  356 (923)
T ss_pred             eEEEEEecCCcccccccchhhhhhhhhheeeecccCcEEEEehhhhccc--CcccccccccEEEecCcccccCCc--cHH
Confidence            67777776555211         11    11223567999999888532  223444558999999999996665  556


Q ss_pred             HHHHhhCCccCcEEEEEeeCChhHHHHHHHhcC--C----------------CEEEEec---------------------
Q 017573          160 YDIFQLLPAKVQVGVFSATMPPEALEITRKFMN--K----------------PVRILVK---------------------  200 (369)
Q Consensus       160 ~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~--~----------------~~~~~~~---------------------  200 (369)
                      ...+..++.. +.+.+|+||-.+.......++.  .                |+..=..                     
T Consensus       357 slackki~T~-~RiILSGTPiQNnL~ELwsLfDFv~PG~Lgt~~~F~~~f~~pI~~GgyaNAs~~qv~~aykca~~Lr~l  435 (923)
T KOG0387|consen  357 SLACKKIRTV-HRIILSGTPIQNNLTELWSLFDFVFPGKLGTLPVFQQNFEHPINRGGYANASPRQVQTAYKCAVALRDL  435 (923)
T ss_pred             HHHHHhcccc-ceEEeeCccccchHHHHHHHhhhccCCcccchHHHHhhhhhheeccccCCCCHHHHHHHHHHHHHHHHH
Confidence            6666666544 4567899997553332221110  0                0000000                     


Q ss_pred             ----------Cc--cccccceeEEEEEcc---------------------------------------------------
Q 017573          201 ----------RD--ELTLEGIKQFYVNVE---------------------------------------------------  217 (369)
Q Consensus       201 ----------~~--~~~~~~~~~~~~~~~---------------------------------------------------  217 (369)
                                .+  ....+.....++.+.                                                   
T Consensus       436 I~PylLRR~K~dv~~~~Lp~K~E~VlfC~LT~~QR~~Y~~fl~s~~v~~i~ng~~~~l~Gi~iLrkICnHPdll~~~~~~  515 (923)
T KOG0387|consen  436 ISPYLLRRMKSDVKGLKLPKKEEIVLFCRLTKLQRRLYQRFLNSSEVNKILNGKRNCLSGIDILRKICNHPDLLDRRDED  515 (923)
T ss_pred             hHHHHHHHHHHHhhhccCCCccceEEEEeccHHHHHHHHHHhhhHHHHHHHcCCccceechHHHHhhcCCcccccCcccc
Confidence                      00  000000001111100                                                   


Q ss_pred             -----------chhhhHHHHHHHHHhc--cCCCeEEEeCCHhhHHHHHHHHh-hCCCeeEEecCCCCHHHHHHHHHHHhc
Q 017573          218 -----------KEEWKLETLCDLYETL--AITQSVIFVNTRRKVDWLTDKMR-SRDHTVSATHGDMDQNTRDIIMREFRS  283 (369)
Q Consensus       218 -----------~~~~~~~~l~~~~~~~--~~~k~lv~~~~~~~~~~~~~~l~-~~~~~~~~~~~~~~~~~r~~~~~~f~~  283 (369)
                                 ...-++..+..++..+  .+.++|+|..++.....+...|. ..++.+..+.|..+...|..+++.|++
T Consensus       516 ~~~~~D~~g~~k~sGKm~vl~~ll~~W~kqg~rvllFsqs~~mLdilE~fL~~~~~ysylRmDGtT~~~~R~~lVd~Fne  595 (923)
T KOG0387|consen  516 EKQGPDYEGDPKRSGKMKVLAKLLKDWKKQGDRVLLFSQSRQMLDILESFLRRAKGYSYLRMDGTTPAALRQKLVDRFNE  595 (923)
T ss_pred             cccCCCcCCChhhcchHHHHHHHHHHHhhCCCEEEEehhHHHHHHHHHHHHHhcCCceEEEecCCCccchhhHHHHhhcC
Confidence                       0111566677766554  44599999999999999999998 578999999999999999999999998


Q ss_pred             CCC-c-EEEEecCCcCCCCCCCCcEEEEecCCCCccchhhhhcccccCCCcee--EEEEeccccHHHHHHHHHHhc
Q 017573          284 GSS-R-VLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGV--AINFVTRDDERMLFDIQKFYN  355 (369)
Q Consensus       284 ~~~-~-vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~--~~~~~~~~~~~~~~~~~~~~~  355 (369)
                      ++. . +|++|.+.+-|+|+.+++.||+++|.||+.+=.|+.-|+.|.|++..  +|-+.+....+....-.+.++
T Consensus       596 ~~s~~VFLLTTrvGGLGlNLTgAnRVIIfDPdWNPStD~QAreRawRiGQkkdV~VYRL~t~gTIEEkiY~rQI~K  671 (923)
T KOG0387|consen  596 DESIFVFLLTTRVGGLGLNLTGANRVIIFDPDWNPSTDNQARERAWRIGQKKDVVVYRLMTAGTIEEKIYHRQIFK  671 (923)
T ss_pred             CCceEEEEEEecccccccccccCceEEEECCCCCCccchHHHHHHHhhcCccceEEEEEecCCcHHHHHHHHHHHH
Confidence            764 4 55678899999999999999999999999999999999999998754  555566666655544444443

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

Probab=99.95  E-value=3.2e-27  Score=214.50  Aligned_cols=334  Identities=18%  Similarity=0.230  Sum_probs=234.1

Q ss_pred             HHHHHhCCCCCCcHhhhhhh--hccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHH
Q 017573            8 LRGIYAYGFEKPSAIQQRGI--VPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMR   85 (369)
Q Consensus         8 ~~~l~~~~~~~~~~~Q~~~~--~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~   85 (369)
                      .-.....|...++.+|.+.+  +.+.++++.+..+||+.|||+++-+.++..+....+  .++.+.|..+.+..-...+.
T Consensus       213 ~~~~~~kgi~~~fewq~ecls~~~~~e~~nliys~Pts~gktlvaeilml~~~l~~rr--~~llilp~vsiv~Ek~~~l~  290 (1008)
T KOG0950|consen  213 HLYAKDKGILKLFEWQAECLSLPRLLERKNLIYSLPTSAGKTLVAEILMLREVLCRRR--NVLLILPYVSIVQEKISALS  290 (1008)
T ss_pred             HHHHHhhhHHHHHHHHHHHhcchhhhcccceEEeCCCccchHHHHHHHHHHHHHHHhh--ceeEecceeehhHHHHhhhh
Confidence            33446678899999999987  567789999999999999999998888776554332  79999999999998889999


Q ss_pred             HhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHc--CCCCCCCccEEEEechhHhhccCcHHHHHHHH
Q 017573           86 ALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRR--QSLRPDYIKMFVLDEADEMLSRGFKDQIYDIF  163 (369)
Q Consensus        86 ~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~--~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~  163 (369)
                      .+....|+.+....|..++....    .+.++.|+|.|+-......  .......+++||+||.|.+.+.+....+..++
T Consensus       291 ~~~~~~G~~ve~y~g~~~p~~~~----k~~sv~i~tiEkanslin~lie~g~~~~~g~vvVdElhmi~d~~rg~~lE~~l  366 (1008)
T KOG0950|consen  291 PFSIDLGFPVEEYAGRFPPEKRR----KRESVAIATIEKANSLINSLIEQGRLDFLGMVVVDELHMIGDKGRGAILELLL  366 (1008)
T ss_pred             hhccccCCcchhhcccCCCCCcc----cceeeeeeehHhhHhHHHHHHhcCCccccCcEEEeeeeeeeccccchHHHHHH
Confidence            99999999998888766644432    3468999999987654433  11234457899999999998877666666555


Q ss_pred             hhC-----CccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccce--eEEEEEccchhhhHHHHH---------
Q 017573          164 QLL-----PAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGI--KQFYVNVEKEEWKLETLC---------  227 (369)
Q Consensus       164 ~~~-----~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~l~---------  227 (369)
                      ...     ....|+++||||.+ +. .+...++...+.....++....+.+  ....+... .......+.         
T Consensus       367 ~k~~y~~~~~~~~iIGMSATi~-N~-~lL~~~L~A~~y~t~fRPv~L~E~ik~G~~i~~~~-r~~~lr~ia~l~~~~~g~  443 (1008)
T KOG0950|consen  367 AKILYENLETSVQIIGMSATIP-NN-SLLQDWLDAFVYTTRFRPVPLKEYIKPGSLIYESS-RNKVLREIANLYSSNLGD  443 (1008)
T ss_pred             HHHHHhccccceeEeeeecccC-Ch-HHHHHHhhhhheecccCcccchhccCCCcccccch-hhHHHHHhhhhhhhhccc
Confidence            443     23467999999986 33 3344444432222211111111111  11111111 111111111         


Q ss_pred             -------HHHHh-ccC-CCeEEEeCCHhhHHHHHHHHhhC--------------------------------------CC
Q 017573          228 -------DLYET-LAI-TQSVIFVNTRRKVDWLTDKMRSR--------------------------------------DH  260 (369)
Q Consensus       228 -------~~~~~-~~~-~k~lv~~~~~~~~~~~~~~l~~~--------------------------------------~~  260 (369)
                             .+... .+. ..+||||++++.++.++..+...                                      ..
T Consensus       444 ~dpD~~v~L~tet~~e~~~~lvfc~sk~~ce~~a~~~~~~vpk~~~~e~~~~~~~~~s~s~~lr~~~~~ld~Vl~~ti~~  523 (1008)
T KOG0950|consen  444 EDPDHLVGLCTETAPEGSSVLVFCPSKKNCENVASLIAKKVPKHIKSEKRLGLWELLSISNLLRRIPGILDPVLAKTIPY  523 (1008)
T ss_pred             CCCcceeeehhhhhhcCCeEEEEcCcccchHHHHHHHHHHhhHhhhhhhhhhHHHHHHHHhHhhcCCcccchHHheeccc
Confidence                   11111 122 35999999999988876555322                                      23


Q ss_pred             eeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEec----CCCCccchhhhhcccccCCC--cee
Q 017573          261 TVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYD----LPTQPENYLHRIGRSGRFGR--KGV  334 (369)
Q Consensus       261 ~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~----~~~~~~~~~Q~~GR~~R~~~--~~~  334 (369)
                      .+++.|++++.++|+.+...|++|...|+.+|+.+..|+|.|.-++++-..    ...+..+|.||+||+||+|-  .|.
T Consensus       524 GvAyHhaGLT~eER~~iE~afr~g~i~vl~aTSTlaaGVNLPArRVIiraP~~g~~~l~~~~YkQM~GRAGR~gidT~Gd  603 (1008)
T KOG0950|consen  524 GVAYHHAGLTSEEREIIEAAFREGNIFVLVATSTLAAGVNLPARRVIIRAPYVGREFLTRLEYKQMVGRAGRTGIDTLGD  603 (1008)
T ss_pred             cceecccccccchHHHHHHHHHhcCeEEEEecchhhccCcCCcceeEEeCCccccchhhhhhHHhhhhhhhhcccccCcc
Confidence            588999999999999999999999999999999999999999777766432    23467799999999999974  499


Q ss_pred             EEEEeccccHHHHHHH
Q 017573          335 AINFVTRDDERMLFDI  350 (369)
Q Consensus       335 ~~~~~~~~~~~~~~~~  350 (369)
                      +++++.+.+.+....+
T Consensus       604 siLI~k~~e~~~~~~l  619 (1008)
T KOG0950|consen  604 SILIIKSSEKKRVREL  619 (1008)
T ss_pred             eEEEeeccchhHHHHH
Confidence            9999999998766533

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

Probab=99.95  E-value=3.3e-26  Score=202.96  Aligned_cols=318  Identities=19%  Similarity=0.195  Sum_probs=219.6

Q ss_pred             CCCcHhhhhhhhcccc----CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccC
Q 017573           17 EKPSAIQQRGIVPFCK----GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLG   92 (369)
Q Consensus        17 ~~~~~~Q~~~~~~~~~----~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~   92 (369)
                      ..+++||.+.++.+..    |-++|+...+|-|||+..+..+..........+..||+||...| .+|.+++++|++  +
T Consensus       166 g~lr~YQveGlnWLi~l~engingILaDEMGLGKTlQtIs~l~yl~~~~~~~GPfLVi~P~StL-~NW~~Ef~rf~P--~  242 (971)
T KOG0385|consen  166 GELRDYQLEGLNWLISLYENGINGILADEMGLGKTLQTISLLGYLKGRKGIPGPFLVIAPKSTL-DNWMNEFKRFTP--S  242 (971)
T ss_pred             CccchhhhccHHHHHHHHhcCcccEeehhcccchHHHHHHHHHHHHHhcCCCCCeEEEeeHhhH-HHHHHHHHHhCC--C
Confidence            4799999999988763    67899999999999977644333322223323389999998666 458889999987  5


Q ss_pred             cEEEEEECCcchHHH--HH-HHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCcc
Q 017573           93 VKVHACVGGTSVRED--QR-ILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAK  169 (369)
Q Consensus        93 ~~v~~~~~~~~~~~~--~~-~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~  169 (369)
                      +++...+|+......  ++ +.....+|+|||++.....  ...+..-.|.++||||+|++.+.  ...+..+++.+...
T Consensus       243 l~~~~~~Gdk~eR~~~~r~~~~~~~fdV~iTsYEi~i~d--k~~lk~~~W~ylvIDEaHRiKN~--~s~L~~~lr~f~~~  318 (971)
T KOG0385|consen  243 LNVVVYHGDKEERAALRRDIMLPGRFDVCITSYEIAIKD--KSFLKKFNWRYLVIDEAHRIKNE--KSKLSKILREFKTD  318 (971)
T ss_pred             cceEEEeCCHHHHHHHHHHhhccCCCceEeehHHHHHhh--HHHHhcCCceEEEechhhhhcch--hhHHHHHHHHhccc
Confidence            677888887753322  22 2335799999999998653  22233345899999999999654  45566777777654


Q ss_pred             CcEEEEEeeCChhHHHHHH------------------Hhc-----------------------------------CCC--
Q 017573          170 VQVGVFSATMPPEALEITR------------------KFM-----------------------------------NKP--  194 (369)
Q Consensus       170 ~~~i~~saT~~~~~~~~~~------------------~~~-----------------------------------~~~--  194 (369)
                      . .+++|+||-.+......                  .|+                                   .+.  
T Consensus       319 n-rLLlTGTPLQNNL~ELWaLLnFllPdiF~~~e~F~swF~~~~~~~~~e~v~~Lh~vL~pFlLRR~K~dVe~sLppKkE  397 (971)
T KOG0385|consen  319 N-RLLLTGTPLQNNLHELWALLNFLLPDIFNSAEDFDSWFDFTNCEGDQELVSRLHKVLRPFLLRRIKSDVEKSLPPKKE  397 (971)
T ss_pred             c-eeEeeCCcccccHHHHHHHHHhhchhhccCHHHHHHHHcccccccCHHHHHHHHhhhhHHHHHHHHHhHhhcCCCcce
Confidence            4 57789998533221110                  000                                   000  


Q ss_pred             EEEEecCc--------------------cc------------------cccceeEEEEE---------ccchhhhHHHHH
Q 017573          195 VRILVKRD--------------------EL------------------TLEGIKQFYVN---------VEKEEWKLETLC  227 (369)
Q Consensus       195 ~~~~~~~~--------------------~~------------------~~~~~~~~~~~---------~~~~~~~~~~l~  227 (369)
                      +.+.+.-.                    ..                  ..+.+....-.         +-....++..|.
T Consensus       398 ~~iyvgms~mQkk~Y~~iL~kdl~~~n~~~~~~k~kL~NI~mQLRKccnHPYLF~g~ePg~pyttdehLv~nSGKm~vLD  477 (971)
T KOG0385|consen  398 LIIYVGMSSMQKKWYKAILMKDLDALNGEGKGEKTKLQNIMMQLRKCCNHPYLFDGAEPGPPYTTDEHLVTNSGKMLVLD  477 (971)
T ss_pred             eeEeccchHHHHHHHHHHHHhcchhhcccccchhhHHHHHHHHHHHhcCCccccCCCCCCCCCCcchHHHhcCcceehHH
Confidence            00000000                    00                  00000000000         001122556666


Q ss_pred             HHHHhc--cCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCC---CcEEEEecCCcCCCCCC
Q 017573          228 DLYETL--AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGS---SRVLITTDLLARGIDVQ  302 (369)
Q Consensus       228 ~~~~~~--~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~---~~vli~t~~~~~G~d~~  302 (369)
                      .++...  .+.++|||..-.....-+..++.-+++....+.|.++.++|...++.|+..+   .-+|++|.+.+.|+|+.
T Consensus       478 kLL~~Lk~~GhRVLIFSQmt~mLDILeDyc~~R~y~ycRiDGSt~~eeR~~aI~~fn~~~s~~FiFlLSTRAGGLGINL~  557 (971)
T KOG0385|consen  478 KLLPKLKEQGHRVLIFSQMTRMLDILEDYCMLRGYEYCRLDGSTSHEEREDAIEAFNAPPSEKFIFLLSTRAGGLGINLT  557 (971)
T ss_pred             HHHHHHHhCCCeEEEeHHHHHHHHHHHHHHHhcCceeEeecCCCCcHHHHHHHHhcCCCCcceEEEEEeccccccccccc
Confidence            666554  4469999999999999999999888999999999999999999999998755   23678899999999999


Q ss_pred             CCcEEEEecCCCCccchhhhhcccccCCCceeEEE--Eeccc
Q 017573          303 QVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAIN--FVTRD  342 (369)
Q Consensus       303 ~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~--~~~~~  342 (369)
                      .+++||+++..||+..=.|+.-|++|.|+...|.+  +++.+
T Consensus       558 aADtVIlyDSDWNPQ~DLQAmDRaHRIGQ~K~V~V~RLiten  599 (971)
T KOG0385|consen  558 AADTVILYDSDWNPQVDLQAMDRAHRIGQKKPVVVYRLITEN  599 (971)
T ss_pred             cccEEEEecCCCCchhhhHHHHHHHhhCCcCceEEEEEeccc
Confidence            99999999999999999999999999998865555  45554

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=99.95  E-value=3.1e-26  Score=211.11  Aligned_cols=316  Identities=18%  Similarity=0.223  Sum_probs=221.5

Q ss_pred             CCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEE
Q 017573           18 KPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHA   97 (369)
Q Consensus        18 ~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~   97 (369)
                      .|++.|-  +-.+.-.+.-+..++||.|||+++.++++.....+.   .+.||+|+..|+.+-.+++..+...+|+++..
T Consensus        82 ~~ydVQl--iGgl~L~~G~IaEm~TGEGKTL~a~lp~~l~al~g~---~VhIvT~ndyLA~RD~e~m~~l~~~lGlsv~~  156 (908)
T PRK13107         82 RHFDVQL--LGGMVLDSNRIAEMRTGEGKTLTATLPAYLNALTGK---GVHVITVNDYLARRDAENNRPLFEFLGLTVGI  156 (908)
T ss_pred             CcCchHH--hcchHhcCCccccccCCCCchHHHHHHHHHHHhcCC---CEEEEeCCHHHHHHHHHHHHHHHHhcCCeEEE
Confidence            3444444  444444567799999999999999998886665554   69999999999999999999999999999999


Q ss_pred             EECCcchHHHHHHHccCCcEEEeccHHH-HHHHHcC-CCCC-----CCccEEEEechhHhhccC----------------
Q 017573           98 CVGGTSVREDQRILQAGVHVVVGTPGRV-FDMLRRQ-SLRP-----DYIKMFVLDEADEMLSRG----------------  154 (369)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~iiv~t~~~l-~~~~~~~-~~~~-----~~~~~viiDE~H~~~~~~----------------  154 (369)
                      +.++.......  ..-.++|+++|+..| +.+++.+ ....     ..+.++|+||++.+.-..                
T Consensus       157 i~~~~~~~~r~--~~Y~~dI~YgT~~e~gfDyLrdnm~~~~~~~vqr~~~~aIvDEvDsiLiDEArtPLIISg~~~~~~~  234 (908)
T PRK13107        157 NVAGLGQQEKK--AAYNADITYGTNNEFGFDYLRDNMAFSPQERVQRPLHYALIDEVDSILIDEARTPLIISGAAEDSSE  234 (908)
T ss_pred             ecCCCCHHHHH--hcCCCCeEEeCCCcccchhhhccCccchhhhhccccceeeecchhhhccccCCCceeecCCCccchH
Confidence            98877754332  223589999999999 7777765 3332     558899999999865211                


Q ss_pred             cHHHHHHHHhhCC-------------------cc----------------------------------------------
Q 017573          155 FKDQIYDIFQLLP-------------------AK----------------------------------------------  169 (369)
Q Consensus       155 ~~~~~~~~~~~~~-------------------~~----------------------------------------------  169 (369)
                      ....+..+...+.                   ..                                              
T Consensus       235 ~y~~~~~~v~~L~~~~~~~~~~~~~~~dy~idek~~~v~LTe~G~~~~e~~l~~~~~~~~~~~l~~~~~~~~~~~i~~aL  314 (908)
T PRK13107        235 LYIKINTLIPNLIRQDKEDTEEYVGEGDYSIDEKAKQVHFTERGQEKVENLLIERGMLAEGDSLYSAANISLLHHVNAAL  314 (908)
T ss_pred             HHHHHHHHHHHHHhhhhccccccCCCCCEEEecCCCeeeechHHHHHHHHHHHhCCcccCcccccCchhhHHHHHHHHHH
Confidence            0000000000000                   00                                              


Q ss_pred             ----------------------------------------------------------------------CcEEEEEeeC
Q 017573          170 ----------------------------------------------------------------------VQVGVFSATM  179 (369)
Q Consensus       170 ----------------------------------------------------------------------~~~i~~saT~  179 (369)
                                                                                            .++.+||+|.
T Consensus       315 ~A~~lf~~d~dYiV~dg~V~IVDe~TGRim~grrwsdGLHQaIEaKE~v~I~~e~~t~AsIT~QnfFr~Y~kL~GMTGTa  394 (908)
T PRK13107        315 RAHTLFEKDVDYIVQDNEVIIVDEHTGRTMPGRRWSEGLHQAVEAKEGVHIQNENQTLASITFQNYFRQYEKLAGMTGTA  394 (908)
T ss_pred             HHHHHHhcCCceEEECCEEEEEECCCCCCCCCCccchHHHHHHHHhcCCCCCCCceeeeeehHHHHHHhhhHhhcccCCC
Confidence                                                                                  3455666666


Q ss_pred             ChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHH-Hhc-cCCCeEEEeCCHhhHHHHHHHHhh
Q 017573          180 PPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLY-ETL-AITQSVIFVNTRRKVDWLTDKMRS  257 (369)
Q Consensus       180 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~-~~~-~~~k~lv~~~~~~~~~~~~~~l~~  257 (369)
                      .....+ ....++-.+.......+.........++  .+...+...+.+-+ ..+ .+.++||||.+++.++.+++.|..
T Consensus       395 ~te~~E-f~~iY~l~Vv~IPTnkp~~R~d~~d~iy--~t~~~K~~Aii~ei~~~~~~GrpVLV~t~sv~~se~ls~~L~~  471 (908)
T PRK13107        395 DTEAFE-FQHIYGLDTVVVPTNRPMVRKDMADLVY--LTADEKYQAIIKDIKDCRERGQPVLVGTVSIEQSELLARLMVK  471 (908)
T ss_pred             hHHHHH-HHHHhCCCEEECCCCCCccceeCCCcEE--eCHHHHHHHHHHHHHHHHHcCCCEEEEeCcHHHHHHHHHHHHH
Confidence            544332 3333333333322222222111111222  12223433443333 322 456999999999999999999999


Q ss_pred             CCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCC-----------------------------------
Q 017573          258 RDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQ-----------------------------------  302 (369)
Q Consensus       258 ~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~-----------------------------------  302 (369)
                      .+++...+|++.+..++..+.+.|+.|.  |+|||+++++|.|+.                                   
T Consensus       472 ~gi~~~vLnak~~~~Ea~ii~~Ag~~G~--VtIATnmAGRGTDIkLggn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~  549 (908)
T PRK13107        472 EKIPHEVLNAKFHEREAEIVAQAGRTGA--VTIATNMAGRGTDIVLGGNWNMEIEALENPTAEQKAKIKADWQIRHDEVV  549 (908)
T ss_pred             CCCCeEeccCcccHHHHHHHHhCCCCCc--EEEecCCcCCCcceecCCchHHhhhhhcchhhHHHHHHHHHHHhhHHHHH
Confidence            9999999999999999999999999988  999999999999986                                   


Q ss_pred             --CCcEEEEecCCCCccchhhhhcccccCCCceeEEEEeccccHH
Q 017573          303 --QVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDER  345 (369)
Q Consensus       303 --~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~  345 (369)
                        +-=+||....+.|...=.|..||+||.|.+|.+..|++-.|.-
T Consensus       550 ~~GGL~VIgTerheSrRID~QLrGRaGRQGDPGss~f~lSlED~L  594 (908)
T PRK13107        550 AAGGLHILGTERHESRRIDNQLRGRAGRQGDAGSSRFYLSMEDSL  594 (908)
T ss_pred             HcCCCEEEecccCchHHHHhhhhcccccCCCCCceeEEEEeCcHH
Confidence              2235777777888888899999999999999999999877653

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

Probab=99.95  E-value=9.6e-27  Score=209.30  Aligned_cols=295  Identities=19%  Similarity=0.249  Sum_probs=198.5

Q ss_pred             CCCcHhhhhhhhcccc----C-CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhcccc
Q 017573           17 EKPSAIQQRGIVPFCK----G-LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYL   91 (369)
Q Consensus        17 ~~~~~~Q~~~~~~~~~----~-~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~   91 (369)
                      ..+|.||..|+..+.+    | +.++++++||+|||.+|+..+...+..+ ..+++|+++-+++|++|....+..+... 
T Consensus       164 i~~RyyQ~~AI~rv~Eaf~~g~~raLlvMATGTGKTrTAiaii~rL~r~~-~~KRVLFLaDR~~Lv~QA~~af~~~~P~-  241 (875)
T COG4096         164 IGPRYYQIIAIRRVIEAFSKGQNRALLVMATGTGKTRTAIAIIDRLIKSG-WVKRVLFLADRNALVDQAYGAFEDFLPF-  241 (875)
T ss_pred             ccchHHHHHHHHHHHHHHhcCCceEEEEEecCCCcceeHHHHHHHHHhcc-hhheeeEEechHHHHHHHHHHHHHhCCC-
Confidence            5699999999987764    3 5699999999999999865555444444 4449999999999999999999888665 


Q ss_pred             CcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcC-----CCCCCCccEEEEechhHhhccCcHHHHHHHHhhC
Q 017573           92 GVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQ-----SLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLL  166 (369)
Q Consensus        92 ~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~-----~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~  166 (369)
                      +-....+.+...        .+.+.|+++|++++.......     .+....||+||+||||+-....+    ..++.++
T Consensus       242 ~~~~n~i~~~~~--------~~s~~i~lsTyqt~~~~~~~~~~~~~~f~~g~FDlIvIDEaHRgi~~~~----~~I~dYF  309 (875)
T COG4096         242 GTKMNKIEDKKG--------DTSSEIYLSTYQTMTGRIEQKEDEYRRFGPGFFDLIVIDEAHRGIYSEW----SSILDYF  309 (875)
T ss_pred             ccceeeeecccC--------CcceeEEEeehHHHHhhhhccccccccCCCCceeEEEechhhhhHHhhh----HHHHHHH
Confidence            223333322221        125799999999998877665     23334589999999998654443    3555555


Q ss_pred             CccCcEEEEEeeCChhHHHHHHHhc-CCCEEEEec----------------------Cccccccce-------------e
Q 017573          167 PAKVQVGVFSATMPPEALEITRKFM-NKPVRILVK----------------------RDELTLEGI-------------K  210 (369)
Q Consensus       167 ~~~~~~i~~saT~~~~~~~~~~~~~-~~~~~~~~~----------------------~~~~~~~~~-------------~  210 (369)
                      .+.  .+++||||..........++ +.|+..+..                      .+...+...             .
T Consensus       310 dA~--~~gLTATP~~~~d~~T~~~F~g~Pt~~YsleeAV~DGfLvpy~vi~i~~~~~~~G~~~~~~serek~~g~~i~~d  387 (875)
T COG4096         310 DAA--TQGLTATPKETIDRSTYGFFNGEPTYAYSLEEAVEDGFLVPYKVIRIDTDFDLDGWKPDAGSEREKLQGEAIDED  387 (875)
T ss_pred             HHH--HHhhccCcccccccccccccCCCcceeecHHHHhhccccCCCCceEEeeeccccCcCcCccchhhhhhccccCcc
Confidence            432  34559999765554444555 333222211                      111111110             0


Q ss_pred             -EEE---------EEccchhhhHHHHHHHHHhcc----CCCeEEEeCCHhhHHHHHHHHhhCCC-----eeEEecCCCCH
Q 017573          211 -QFY---------VNVEKEEWKLETLCDLYETLA----ITQSVIFVNTRRKVDWLTDKMRSRDH-----TVSATHGDMDQ  271 (369)
Q Consensus       211 -~~~---------~~~~~~~~~~~~l~~~~~~~~----~~k~lv~~~~~~~~~~~~~~l~~~~~-----~~~~~~~~~~~  271 (369)
                       +.+         ............+.+.+...+    .+|+||||.+..+|+.+...|.+...     -+..+.++...
T Consensus       388 d~~~~~~d~dr~~v~~~~~~~V~r~~~~~l~~~~~g~~~~KTIvFa~n~dHAe~i~~~~~~~ype~~~~~a~~IT~d~~~  467 (875)
T COG4096         388 DQNFEARDFDRTLVIPFRTETVARELTEYLKRGATGDEIGKTIVFAKNHDHAERIREALVNEYPEYNGRYAMKITGDAEQ  467 (875)
T ss_pred             cccccccccchhccccchHHHHHHHHHHHhccccCCCccCceEEEeeCcHHHHHHHHHHHHhCccccCceEEEEeccchh
Confidence             000         000011113344555555422    35999999999999999999987733     35667675333


Q ss_pred             HHHHHHHHHHhc--CCCcEEEEecCCcCCCCCCCCcEEEEecCCCCccchhhhhcccccC
Q 017573          272 NTRDIIMREFRS--GSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRF  329 (369)
Q Consensus       272 ~~r~~~~~~f~~--~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~  329 (369)
                        -...++.|..  .-.+|.++++++.+|+|+|.+.+++++....|...|.||+||+-|.
T Consensus       468 --~q~~Id~f~~ke~~P~IaitvdlL~TGiDvpev~nlVF~r~VrSktkF~QMvGRGTRl  525 (875)
T COG4096         468 --AQALIDNFIDKEKYPRIAITVDLLTTGVDVPEVVNLVFDRKVRSKTKFKQMVGRGTRL  525 (875)
T ss_pred             --hHHHHHHHHhcCCCCceEEehhhhhcCCCchheeeeeehhhhhhHHHHHHHhcCcccc
Confidence              3345555544  3356889999999999999999999999999999999999999996

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

Probab=99.95  E-value=2.2e-25  Score=202.92  Aligned_cols=318  Identities=19%  Similarity=0.158  Sum_probs=208.4

Q ss_pred             CCCcHhhhhhhhcccc----------CCcEEEEcCCCChhhHHHHHHHHHhhhccCCC----ccEEEEcCCHHHHHHHHH
Q 017573           17 EKPSAIQQRGIVPFCK----------GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQ----CQALVLAPTRELAQQIEK   82 (369)
Q Consensus        17 ~~~~~~Q~~~~~~~~~----------~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~----~~~liv~P~~~l~~q~~~   82 (369)
                      ..+||+|++++..+.+          ...+++...+|+|||+..+..+...+...+.+    .++|||+|. +|+..|.+
T Consensus       237 ~~LrPHQ~EG~~FL~knl~g~~~~~~~~GCImAd~~GlGKTlq~IsflwtlLrq~P~~~~~~~k~lVV~P~-sLv~nWkk  315 (776)
T KOG0390|consen  237 KILRPHQREGFEFLYKNLAGLIRPKNSGGCIMADEPGLGKTLQCISFIWTLLRQFPQAKPLINKPLVVAPS-SLVNNWKK  315 (776)
T ss_pred             hhcCchHHHHHHHHHhhhhcccccCCCCceEeeCCCCcchHHHHHHHHHHHHHhCcCccccccccEEEccH-HHHHHHHH
Confidence            3589999999988764          25689999999999999888888887776551    389999997 89999999


Q ss_pred             HHHHhccccCcEEEEEECCcch-HHH-HHHH-----ccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCc
Q 017573           83 VMRALGDYLGVKVHACVGGTSV-RED-QRIL-----QAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGF  155 (369)
Q Consensus        83 ~~~~~~~~~~~~v~~~~~~~~~-~~~-~~~~-----~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~  155 (369)
                      +|.+|.....+.....++.... ... ..++     .-..-|.+.+++.+......  +....++++|+||.|+..+.  
T Consensus       316 EF~KWl~~~~i~~l~~~~~~~~~w~~~~sil~~~~~~~~~~vli~sye~~~~~~~~--il~~~~glLVcDEGHrlkN~--  391 (776)
T KOG0390|consen  316 EFGKWLGNHRINPLDFYSTKKSSWIKLKSILFLGYKQFTTPVLIISYETASDYCRK--ILLIRPGLLVCDEGHRLKNS--  391 (776)
T ss_pred             HHHHhccccccceeeeecccchhhhhhHHHHHhhhhheeEEEEeccHHHHHHHHHH--HhcCCCCeEEECCCCCccch--
Confidence            9999987656666666666653 000 0111     11346888899999866665  44556899999999998544  


Q ss_pred             HHHHHHHHhhCCccCcEEEEEeeCChhHHHHHHHhcC--C----------------CE----------------------
Q 017573          156 KDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMN--K----------------PV----------------------  195 (369)
Q Consensus       156 ~~~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~--~----------------~~----------------------  195 (369)
                      ...+...+..+. ..+.|++|+||-.+.....-..+.  .                +.                      
T Consensus       392 ~s~~~kaL~~l~-t~rRVLLSGTp~QNdl~EyFnlL~fvrP~~Lgs~~sf~k~~~~~i~~~~~~~~s~e~~~~~~rl~eL  470 (776)
T KOG0390|consen  392 DSLTLKALSSLK-TPRRVLLTGTPIQNDLKEYFNLLDFVRPGFLGSISSFKKKFEIPILRGRDADASEEDREREERLQEL  470 (776)
T ss_pred             hhHHHHHHHhcC-CCceEEeeCCcccccHHHHHHHHhhcChhhccchHHHHHHhhcccccccCCCcchhhhhhHHHHHHH
Confidence            355556666665 344677899986432211100000  0                00                      


Q ss_pred             --------EEEec-CccccccceeEEEEEccchhh---------------------------------------------
Q 017573          196 --------RILVK-RDELTLEGIKQFYVNVEKEEW---------------------------------------------  221 (369)
Q Consensus       196 --------~~~~~-~~~~~~~~~~~~~~~~~~~~~---------------------------------------------  221 (369)
                              ..... .-....+....+.+.+.....                                             
T Consensus       471 ~~~t~~fi~rrt~~il~k~LP~k~e~vv~~n~t~~Q~~~~~~l~~~~~~~~~~~~~l~~~~~L~k~cnhP~L~~~~~~~~  550 (776)
T KOG0390|consen  471 RELTNKFILRRTGDILLKYLPGKYEYVVFCNPTPIQKELYKKLLDSMKMRTLKGYALELITKLKKLCNHPSLLLLCEKTE  550 (776)
T ss_pred             HHHHHhheeecccchhhhhCCCceeEEEEeCCcHHHHHHHHHHHHHHHhhhhhcchhhHHHHHHHHhcCHHhhccccccc
Confidence                    00000 000011122222222222111                                             


Q ss_pred             ----------------------------hHHHHHHHHHhc---cCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCC
Q 017573          222 ----------------------------KLETLCDLYETL---AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMD  270 (369)
Q Consensus       222 ----------------------------~~~~l~~~~~~~---~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~  270 (369)
                                                  ++..|..++...   ...++.+..|.....+-+...++-.|..+..++|.++
T Consensus       551 ~e~~~~~~~~~~~~~~~~~~~~~~~ks~kl~~L~~ll~~~~ek~~~~~v~Isny~~tldl~e~~~~~~g~~~~rLdG~~~  630 (776)
T KOG0390|consen  551 KEKAFKNPALLLDPGKLKLDAGDGSKSGKLLVLVFLLEVIREKLLVKSVLISNYTQTLDLFEQLCRWRGYEVLRLDGKTS  630 (776)
T ss_pred             ccccccChHhhhcccccccccccchhhhHHHHHHHHHHHHhhhcceEEEEeccHHHHHHHHHHHHhhcCceEEEEcCCCc
Confidence                                        111112221111   1112333334444444445555555899999999999


Q ss_pred             HHHHHHHHHHHhcCCC--cEE-EEecCCcCCCCCCCCcEEEEecCCCCccchhhhhcccccCCCceeEEEEec
Q 017573          271 QNTRDIIMREFRSGSS--RVL-ITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVT  340 (369)
Q Consensus       271 ~~~r~~~~~~f~~~~~--~vl-i~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~  340 (369)
                      ..+|..+++.|++...  .|+ .++.+.++|+++-+++.+|++|+.||++.-.|+++|+.|.|++..|++|--
T Consensus       631 ~~qRq~~vd~FN~p~~~~~vfLlSsKAgg~GinLiGAsRlil~D~dWNPa~d~QAmaR~~RdGQKk~v~iYrL  703 (776)
T KOG0390|consen  631 IKQRQKLVDTFNDPESPSFVFLLSSKAGGEGLNLIGASRLILFDPDWNPAVDQQAMARAWRDGQKKPVYIYRL  703 (776)
T ss_pred             hHHHHHHHHhccCCCCCceEEEEecccccCceeecccceEEEeCCCCCchhHHHHHHHhccCCCcceEEEEEe
Confidence            9999999999987432  444 566799999999999999999999999999999999999999988777654

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=99.95  E-value=3.9e-26  Score=215.51  Aligned_cols=323  Identities=18%  Similarity=0.228  Sum_probs=209.5

Q ss_pred             CCCcHhhhhhhhccccC---C-cEEEEcCCCChhhHHHHHHHHHhhhc-cCCCccEEEEcCCHHHHHHHHHHHHHhcccc
Q 017573           17 EKPSAIQQRGIVPFCKG---L-DVIQQAQSGTGKTATFCSGILQQLDY-GLVQCQALVLAPTRELAQQIEKVMRALGDYL   91 (369)
Q Consensus        17 ~~~~~~Q~~~~~~~~~~---~-~~li~~~tG~GKT~~~~~~~~~~~~~-~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~   91 (369)
                      ...++.|..+++.....   . .+++.||||+|||.+++.++...+.. .....+++++.|.+++++++.+.+.++....
T Consensus       194 ~~~~~~~~~~~~~~~~~~~~~~~~vl~aPTG~GKT~asl~~a~~~~~~~~~~~~r~i~vlP~~t~ie~~~~r~~~~~~~~  273 (733)
T COG1203         194 HEGYELQEKALELILRLEKRSLLVVLEAPTGYGKTEASLILALALLDEKIKLKSRVIYVLPFRTIIEDMYRRAKEIFGLF  273 (733)
T ss_pred             chhhHHHHHHHHHHHhcccccccEEEEeCCCCChHHHHHHHHHHHhhccccccceEEEEccHHHHHHHHHHHHHhhhccc
Confidence            34589999999887753   4 78999999999999999988888776 3345599999999999999999999876544


Q ss_pred             CcEEEEEECCcchHHHHHH--------------HccCCcEEEeccHHHHHH-HHcCCCC-C--CCccEEEEechhHhhcc
Q 017573           92 GVKVHACVGGTSVREDQRI--------------LQAGVHVVVGTPGRVFDM-LRRQSLR-P--DYIKMFVLDEADEMLSR  153 (369)
Q Consensus        92 ~~~v~~~~~~~~~~~~~~~--------------~~~~~~iiv~t~~~l~~~-~~~~~~~-~--~~~~~viiDE~H~~~~~  153 (369)
                      +......++..........              ...-..+.++++...... ....... .  -..+++|+||+|.+...
T Consensus       274 ~~~~~~~h~~~~~~~~~~~~~~~~~~~~~~ds~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~S~vIlDE~h~~~~~  353 (733)
T COG1203         274 SVIGKSLHSSSKEPLLLEPDQDILLTLTTNDSYKKLLLALIVVTPIQILIFSVKGFKFEFLALLLTSLVILDEVHLYADE  353 (733)
T ss_pred             ccccccccccccchhhhccccccceeEEecccccceeccccccCHhHhhhhhccccchHHHHHHHhhchhhccHHhhccc
Confidence            3333212322221111100              000122333333333321 1111111 0  11368999999998766


Q ss_pred             CcHHHHHHHHhhCC-ccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccc---ccccee-EEEEEccchhhhHHHHHH
Q 017573          154 GFKDQIYDIFQLLP-AKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDEL---TLEGIK-QFYVNVEKEEWKLETLCD  228 (369)
Q Consensus       154 ~~~~~~~~~~~~~~-~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~-~~~~~~~~~~~~~~~l~~  228 (369)
                      .....+..+...+. .+..+++||||+|+...+.....+.............   ...... .......... .......
T Consensus       354 ~~~~~l~~~i~~l~~~g~~ill~SATlP~~~~~~l~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~-~~~~~~~  432 (733)
T COG1203         354 TMLAALLALLEALAEAGVPVLLMSATLPPFLKEKLKKALGKGREVVENAKFCPKEDEPGLKRKERVDVEDGP-QEELIEL  432 (733)
T ss_pred             chHHHHHHHHHHHHhCCCCEEEEecCCCHHHHHHHHHHHhcccceeccccccccccccccccccchhhhhhh-hHhhhhc
Confidence            33444444443332 3677999999999988887777776654433321100   000000 0000000000 0011112


Q ss_pred             HHHh-ccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHh----cCCCcEEEEecCCcCCCCCCC
Q 017573          229 LYET-LAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFR----SGSSRVLITTDLLARGIDVQQ  303 (369)
Q Consensus       229 ~~~~-~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~----~~~~~vli~t~~~~~G~d~~~  303 (369)
                      .... ..+++++|.||++..|.++++.|+..+.++..+|+.+...+|.++++...    .++..|+|+|++++.|+|+ +
T Consensus       433 ~~~~~~~~~kvlvI~NTV~~Aie~Y~~Lk~~~~~v~LlHSRf~~~dR~~ke~~l~~~~~~~~~~IvVaTQVIEagvDi-d  511 (733)
T COG1203         433 ISEEVKEGKKVLVIVNTVDRAIELYEKLKEKGPKVLLLHSRFTLKDREEKERELKKLFKQNEGFIVVATQVIEAGVDI-D  511 (733)
T ss_pred             chhhhccCCcEEEEEecHHHHHHHHHHHHhcCCCEEEEecccchhhHHHHHHHHHHHHhccCCeEEEEeeEEEEEecc-c
Confidence            2222 24579999999999999999999999888999999999999988888654    4567899999999999999 4


Q ss_pred             CcEEEEecCCCCccchhhhhcccccCC--CceeEEEEecccc
Q 017573          304 VSLVINYDLPTQPENYLHRIGRSGRFG--RKGVAINFVTRDD  343 (369)
Q Consensus       304 ~~~vi~~~~~~~~~~~~Q~~GR~~R~~--~~~~~~~~~~~~~  343 (369)
                      .+.+|--  +.....++||+||++|.|  ..|.++++.....
T Consensus       512 fd~mITe--~aPidSLIQR~GRv~R~g~~~~~~~~v~~~~~~  551 (733)
T COG1203         512 FDVLITE--LAPIDSLIQRAGRVNRHGKKENGKIYVYNDEER  551 (733)
T ss_pred             cCeeeec--CCCHHHHHHHHHHHhhcccccCCceeEeecccC
Confidence            6666533  233788999999999999  5677777777553

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

Probab=99.94  E-value=6.5e-25  Score=200.85  Aligned_cols=286  Identities=21%  Similarity=0.300  Sum_probs=202.3

Q ss_pred             HHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhc
Q 017573            9 RGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALG   88 (369)
Q Consensus         9 ~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~   88 (369)
                      +-+.+.....|+..|+-....+..|+++-+.||||.|||...++..+....+++   ++++|+||+.|+.|..+.+.++.
T Consensus        73 ~fF~k~~G~~~ws~QR~WakR~~rg~SFaiiAPTGvGKTTfg~~~sl~~a~kgk---r~yii~PT~~Lv~Q~~~kl~~~~  149 (1187)
T COG1110          73 EFFKKATGFRPWSAQRVWAKRLVRGKSFAIIAPTGVGKTTFGLLMSLYLAKKGK---RVYIIVPTTTLVRQVYERLKKFA  149 (1187)
T ss_pred             HHHHHhhCCCchHHHHHHHHHHHcCCceEEEcCCCCchhHHHHHHHHHHHhcCC---eEEEEecCHHHHHHHHHHHHHHH
Confidence            334343334999999999999999999999999999999776655554444443   89999999999999999999987


Q ss_pred             cccC-cEEEE-EECCcchHHH----HHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccC--------
Q 017573           89 DYLG-VKVHA-CVGGTSVRED----QRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRG--------  154 (369)
Q Consensus        89 ~~~~-~~v~~-~~~~~~~~~~----~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~--------  154 (369)
                      ...+ ..+.. .|+..+....    .++..++.||+|+|.+.+...+..-  ...+||++++|++|.+...+        
T Consensus       150 e~~~~~~~~~~yh~~l~~~ekee~le~i~~gdfdIlitTs~FL~k~~e~L--~~~kFdfifVDDVDA~LkaskNvDriL~  227 (1187)
T COG1110         150 EDAGSLDVLVVYHSALPTKEKEEALERIESGDFDILITTSQFLSKRFEEL--SKLKFDFIFVDDVDAILKASKNVDRLLR  227 (1187)
T ss_pred             hhcCCcceeeeeccccchHHHHHHHHHHhcCCccEEEEeHHHHHhhHHHh--cccCCCEEEEccHHHHHhccccHHHHHH
Confidence            6655 44444 4444333332    3444568999999999888776662  23468999999999876322        


Q ss_pred             ---cHHH-----------------------HHHHHhh--------CCccCcEEEEEeeCChh--HHHHHHHhcCCCEEEE
Q 017573          155 ---FKDQ-----------------------IYDIFQL--------LPAKVQVGVFSATMPPE--ALEITRKFMNKPVRIL  198 (369)
Q Consensus       155 ---~~~~-----------------------~~~~~~~--------~~~~~~~i~~saT~~~~--~~~~~~~~~~~~~~~~  198 (369)
                         +.+.                       ..+....        -.+..++++.|||..+.  -..+.+.+++-.    
T Consensus       228 LlGf~eE~i~~a~~~~~lr~~~~~~~~~~~~~e~~~~~e~~~~~~r~k~g~LvvsSATg~~rg~R~~LfReLlgFe----  303 (1187)
T COG1110         228 LLGFSEEVIESAYELIKLRRKLYGEKRAERVREELREVEREREKKRRKLGILVVSSATGKPRGSRLKLFRELLGFE----  303 (1187)
T ss_pred             HcCCCHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHhccCCceEEEeeccCCCCCchHHHHHHHhCCc----
Confidence               1110                       0011000        12346788999997643  233444544422    


Q ss_pred             ecCccccccceeEEEEEccchhhhHHHHHHHHHhccCCCeEEEeCC---HhhHHHHHHHHhhCCCeeEEecCCCCHHHHH
Q 017573          199 VKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNT---RRKVDWLTDKMRSRDHTVSATHGDMDQNTRD  275 (369)
Q Consensus       199 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lv~~~~---~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~  275 (369)
                      +........++...+...    .....+.++++... ..+|||++.   .+.++.++++|+..|+++..+++.     +.
T Consensus       304 vG~~~~~LRNIvD~y~~~----~~~e~~~elvk~lG-~GgLIfV~~d~G~e~aeel~e~Lr~~Gi~a~~~~a~-----~~  373 (1187)
T COG1110         304 VGSGGEGLRNIVDIYVES----ESLEKVVELVKKLG-DGGLIFVPIDYGREKAEELAEYLRSHGINAELIHAE-----KE  373 (1187)
T ss_pred             cCccchhhhheeeeeccC----ccHHHHHHHHHHhC-CCeEEEEEcHHhHHHHHHHHHHHHhcCceEEEeecc-----ch
Confidence            122233334444444433    34555666666654 378999999   999999999999999999999884     37


Q ss_pred             HHHHHHhcCCCcEEEEec----CCcCCCCCC-CCcEEEEecCC
Q 017573          276 IIMREFRSGSSRVLITTD----LLARGIDVQ-QVSLVINYDLP  313 (369)
Q Consensus       276 ~~~~~f~~~~~~vli~t~----~~~~G~d~~-~~~~vi~~~~~  313 (369)
                      +.++.|..|++++||++.    .+.+|+|+| .++.+|+++.|
T Consensus       374 ~~le~F~~GeidvLVGvAsyYG~lVRGlDLP~rirYaIF~GvP  416 (1187)
T COG1110         374 EALEDFEEGEVDVLVGVASYYGVLVRGLDLPHRIRYAVFYGVP  416 (1187)
T ss_pred             hhhhhhccCceeEEEEecccccceeecCCchhheeEEEEecCC
Confidence            789999999999999864    889999999 48889988866

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

Probab=99.94  E-value=2.9e-26  Score=194.33  Aligned_cols=314  Identities=17%  Similarity=0.171  Sum_probs=216.5

Q ss_pred             CCCCCcHhhhhhhhccccC---CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhcccc
Q 017573           15 GFEKPSAIQQRGIVPFCKG---LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYL   91 (369)
Q Consensus        15 ~~~~~~~~Q~~~~~~~~~~---~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~   91 (369)
                      +-.++||||++.+..+.-+   ++.+|+.|||+|||++.+-++.. +     ++.+|++|.+...++||..+|..|...-
T Consensus       299 Pst~iRpYQEksL~KMFGNgRARSGiIVLPCGAGKtLVGvTAa~t-i-----kK~clvLcts~VSVeQWkqQfk~wsti~  372 (776)
T KOG1123|consen  299 PSTQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKTLVGVTAACT-I-----KKSCLVLCTSAVSVEQWKQQFKQWSTIQ  372 (776)
T ss_pred             cccccCchHHHHHHHHhCCCcccCceEEEecCCCCceeeeeeeee-e-----cccEEEEecCccCHHHHHHHHHhhcccC
Confidence            5578999999999998865   67899999999999886544332 1     2279999999999999999999998766


Q ss_pred             CcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHc--------CCCCCCCccEEEEechhHhhccCcHHHHHHHH
Q 017573           92 GVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRR--------QSLRPDYIKMFVLDEADEMLSRGFKDQIYDIF  163 (369)
Q Consensus        92 ~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~--------~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~  163 (369)
                      +..+...+.+.+     .....++.|+|+|+.++..--.+        ..+....|+++++||+|.+....|.+.+.-+.
T Consensus       373 d~~i~rFTsd~K-----e~~~~~~gvvvsTYsMva~t~kRS~eaek~m~~l~~~EWGllllDEVHvvPA~MFRRVlsiv~  447 (776)
T KOG1123|consen  373 DDQICRFTSDAK-----ERFPSGAGVVVTTYSMVAYTGKRSHEAEKIMDFLRGREWGLLLLDEVHVVPAKMFRRVLSIVQ  447 (776)
T ss_pred             ccceEEeecccc-----ccCCCCCcEEEEeeehhhhcccccHHHHHHHHHHhcCeeeeEEeehhccchHHHHHHHHHHHH
Confidence            677777776554     22356789999999877321111        01223448999999999887777776666666


Q ss_pred             hhCCccCcEEEEEeeCChhHHHHHH------------Hhc---CCC--E------EEEecCc----cccc---cceeEEE
Q 017573          164 QLLPAKVQVGVFSATMPPEALEITR------------KFM---NKP--V------RILVKRD----ELTL---EGIKQFY  213 (369)
Q Consensus       164 ~~~~~~~~~i~~saT~~~~~~~~~~------------~~~---~~~--~------~~~~~~~----~~~~---~~~~~~~  213 (369)
                      ..+     .+++|||+-.+......            .|+   .+.  .      ++.....    ++..   ......+
T Consensus       448 aHc-----KLGLTATLvREDdKI~DLNFLIGPKlYEAnWmdL~~kGhIA~VqCaEVWCpMt~eFy~eYL~~~t~kr~lLy  522 (776)
T KOG1123|consen  448 AHC-----KLGLTATLVREDDKITDLNFLIGPKLYEANWMDLQKKGHIAKVQCAEVWCPMTPEFYREYLRENTRKRMLLY  522 (776)
T ss_pred             HHh-----hccceeEEeeccccccccceeecchhhhccHHHHHhCCceeEEeeeeeecCCCHHHHHHHHhhhhhhhheee
Confidence            665     48999997433221110            000   000  0      0100000    0000   1112233


Q ss_pred             EEccchhhhHHHHHHHHHhccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcC-CCcEEEEe
Q 017573          214 VNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSG-SSRVLITT  292 (369)
Q Consensus       214 ~~~~~~~~~~~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~-~~~vli~t  292 (369)
                      +..+..-...+.|.++..+ .++|+|||..+.--...++-.|.+     -+++|..++.+|.+|++.|+.. .++.++.+
T Consensus       523 vMNP~KFraCqfLI~~HE~-RgDKiIVFsDnvfALk~YAikl~K-----pfIYG~Tsq~ERm~ILqnFq~n~~vNTIFlS  596 (776)
T KOG1123|consen  523 VMNPNKFRACQFLIKFHER-RGDKIIVFSDNVFALKEYAIKLGK-----PFIYGPTSQNERMKILQNFQTNPKVNTIFLS  596 (776)
T ss_pred             ecCcchhHHHHHHHHHHHh-cCCeEEEEeccHHHHHHHHHHcCC-----ceEECCCchhHHHHHHHhcccCCccceEEEe
Confidence            3333333345777777766 668999999999888888877644     4788999999999999999854 57889999


Q ss_pred             cCCcCCCCCCCCcEEEEecCC-CCccchhhhhcccccCCCc------eeEEEEeccccHHHHHHH
Q 017573          293 DLLARGIDVQQVSLVINYDLP-TQPENYLHRIGRSGRFGRK------GVAINFVTRDDERMLFDI  350 (369)
Q Consensus       293 ~~~~~G~d~~~~~~vi~~~~~-~~~~~~~Q~~GR~~R~~~~------~~~~~~~~~~~~~~~~~~  350 (369)
                      .+....+|+|.++++|..... .|-.+-.||.||..|..+.      .--+.+++.+..+++.+-
T Consensus       597 KVgDtSiDLPEAnvLIQISSH~GSRRQEAQRLGRILRAKk~~de~fnafFYSLVS~DTqEM~YSt  661 (776)
T KOG1123|consen  597 KVGDTSIDLPEANVLIQISSHGGSRRQEAQRLGRILRAKKRNDEEFNAFFYSLVSKDTQEMYYST  661 (776)
T ss_pred             eccCccccCCcccEEEEEcccccchHHHHHHHHHHHHHhhcCccccceeeeeeeecchHHHHhhh
Confidence            999999999999999977654 4667889999999986322      234555556666655443

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

Probab=99.94  E-value=1.9e-24  Score=200.86  Aligned_cols=309  Identities=17%  Similarity=0.261  Sum_probs=216.4

Q ss_pred             cHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHH-hccccCcEEEEE
Q 017573           20 SAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRA-LGDYLGVKVHAC   98 (369)
Q Consensus        20 ~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~-~~~~~~~~v~~~   98 (369)
                      +....+++.++.+++-++|.||||+|||...-..+++.-.  ..+.++.+.=|++--+...++.+.+ +....|-.|.+.
T Consensus        52 ~~~~~~i~~ai~~~~vvii~getGsGKTTqlP~~lle~g~--~~~g~I~~tQPRRlAArsvA~RvAeel~~~~G~~VGY~  129 (845)
T COG1643          52 TAVRDEILKAIEQNQVVIIVGETGSGKTTQLPQFLLEEGL--GIAGKIGCTQPRRLAARSVAERVAEELGEKLGETVGYS  129 (845)
T ss_pred             HHHHHHHHHHHHhCCEEEEeCCCCCChHHHHHHHHHhhhc--ccCCeEEecCchHHHHHHHHHHHHHHhCCCcCceeeEE
Confidence            4556677788888999999999999999876555554432  2223777778999777777766654 333345555554


Q ss_pred             ECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhh-cc-CcHHHHHHHHhhCCccCcEEEEE
Q 017573           99 VGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEML-SR-GFKDQIYDIFQLLPAKVQVGVFS  176 (369)
Q Consensus        99 ~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~-~~-~~~~~~~~~~~~~~~~~~~i~~s  176 (369)
                      ...+.      ....+..|-++|...|.+.+..... ++.+++||+||+|+=+ +. -....+..+....++..++|.||
T Consensus       130 iRfe~------~~s~~Trik~mTdGiLlrei~~D~~-Ls~ys~vIiDEaHERSl~tDilLgllk~~~~~rr~DLKiIimS  202 (845)
T COG1643         130 IRFES------KVSPRTRIKVMTDGILLREIQNDPL-LSGYSVVIIDEAHERSLNTDILLGLLKDLLARRRDDLKLIIMS  202 (845)
T ss_pred             EEeec------cCCCCceeEEeccHHHHHHHhhCcc-cccCCEEEEcchhhhhHHHHHHHHHHHHHHhhcCCCceEEEEe
Confidence            43322      1234578999999999999887664 6778999999999722 11 12234445556666678899999


Q ss_pred             eeCChhHHHHHHHhcC-CCEEEEecCccccccceeEEEEEccchhh-hHHHHHHHH---HhccCCCeEEEeCCHhhHHHH
Q 017573          177 ATMPPEALEITRKFMN-KPVRILVKRDELTLEGIKQFYVNVEKEEW-KLETLCDLY---ETLAITQSVIFVNTRRKVDWL  251 (369)
Q Consensus       177 aT~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~l~~~~---~~~~~~k~lv~~~~~~~~~~~  251 (369)
                      ||...+  .+. .+++ -|+.... ...+   .++..|........ ..+.+...+   .....+.+|||.+...+.+..
T Consensus       203 ATld~~--rfs-~~f~~apvi~i~-GR~f---PVei~Y~~~~~~d~~l~~ai~~~v~~~~~~~~GdILvFLpG~~EI~~~  275 (845)
T COG1643         203 ATLDAE--RFS-AYFGNAPVIEIE-GRTY---PVEIRYLPEAEADYILLDAIVAAVDIHLREGSGSILVFLPGQREIERT  275 (845)
T ss_pred             cccCHH--HHH-HHcCCCCEEEec-CCcc---ceEEEecCCCCcchhHHHHHHHHHHHhccCCCCCEEEECCcHHHHHHH
Confidence            998543  333 4444 4443332 2211   22333322222222 333333333   334568999999999999999


Q ss_pred             HHHHhh----CCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecC---------------
Q 017573          252 TDKMRS----RDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDL---------------  312 (369)
Q Consensus       252 ~~~l~~----~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~---------------  312 (369)
                      ++.|.+    ....+..+||.++.+++.++++-...|.-+|+++|+++++++.+|+++.||.-+.               
T Consensus       276 ~~~L~~~~l~~~~~i~PLy~~L~~~eQ~rvF~p~~~~~RKVVlATNIAETSLTI~gIr~VIDsG~ak~~~y~~~~g~~~L  355 (845)
T COG1643         276 AEWLEKAELGDDLEILPLYGALSAEEQVRVFEPAPGGKRKVVLATNIAETSLTIPGIRYVIDSGLAKEKRYDPRTGLTRL  355 (845)
T ss_pred             HHHHHhccccCCcEEeeccccCCHHHHHhhcCCCCCCcceEEEEccccccceeeCCeEEEecCCcccccccccccCceee
Confidence            999997    3467999999999999999888777776669999999999999999999997654               


Q ss_pred             ---CCCccchhhhhcccccCCCceeEEEEeccccHH
Q 017573          313 ---PTQPENYLHRIGRSGRFGRKGVAINFVTRDDER  345 (369)
Q Consensus       313 ---~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~  345 (369)
                         +-|-.+..||.||+||. .+|.||-+++..+..
T Consensus       356 ~~~~ISqAsA~QRaGRAGR~-~pGicyRLyse~~~~  390 (845)
T COG1643         356 ETEPISKASADQRAGRAGRT-GPGICYRLYSEEDFL  390 (845)
T ss_pred             eEEEechhhhhhhccccccC-CCceEEEecCHHHHH
Confidence               23567789999999999 689999999985443

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

Probab=99.93  E-value=4.4e-24  Score=182.78  Aligned_cols=174  Identities=23%  Similarity=0.253  Sum_probs=130.0

Q ss_pred             cCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHHHhc-cCCCeEEEeCCHhh
Q 017573          169 KVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETL-AITQSVIFVNTRRK  247 (369)
Q Consensus       169 ~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~~~k~lv~~~~~~~  247 (369)
                      ..|++++||||.+-..+..   -+.-+..........    .+.....+.....-+.+.++.... .+.++||-+-+++.
T Consensus       386 ~~q~i~VSATPg~~E~e~s---~~~vveQiIRPTGLl----DP~ievRp~~~QvdDL~~EI~~r~~~~eRvLVTtLTKkm  458 (663)
T COG0556         386 IPQTIYVSATPGDYELEQS---GGNVVEQIIRPTGLL----DPEIEVRPTKGQVDDLLSEIRKRVAKNERVLVTTLTKKM  458 (663)
T ss_pred             cCCEEEEECCCChHHHHhc---cCceeEEeecCCCCC----CCceeeecCCCcHHHHHHHHHHHHhcCCeEEEEeehHHH
Confidence            4789999999975322211   111121222222221    112222222233344445554433 45799999999999


Q ss_pred             HHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecC-----CCCccchhhh
Q 017573          248 VDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDL-----PTQPENYLHR  322 (369)
Q Consensus       248 ~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~-----~~~~~~~~Q~  322 (369)
                      |+.+.++|...|+++..+|++.+.-+|.+++...+.|.++|||+.+.+-+|+|+|.++.|.+++.     ..|..+++|.
T Consensus       459 AEdLT~Yl~e~gikv~YlHSdidTlER~eIirdLR~G~~DvLVGINLLREGLDiPEVsLVAIlDADKeGFLRse~SLIQt  538 (663)
T COG0556         459 AEDLTEYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQT  538 (663)
T ss_pred             HHHHHHHHHhcCceEEeeeccchHHHHHHHHHHHhcCCccEEEeehhhhccCCCcceeEEEEeecCccccccccchHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999875     5688999999


Q ss_pred             hcccccCCCceeEEEEeccccHHHHHHH
Q 017573          323 IGRSGRFGRKGVAINFVTRDDERMLFDI  350 (369)
Q Consensus       323 ~GR~~R~~~~~~~~~~~~~~~~~~~~~~  350 (369)
                      +|||.|. -.|.++.|.+.-...+-+.+
T Consensus       539 IGRAARN-~~GkvIlYAD~iT~sM~~Ai  565 (663)
T COG0556         539 IGRAARN-VNGKVILYADKITDSMQKAI  565 (663)
T ss_pred             HHHHhhc-cCCeEEEEchhhhHHHHHHH
Confidence            9999996 56999999998766655444

>KOG1000 consensus Chromatin remodeling protein HARP/SMARCAL1, DEAD-box superfamily [Chromatin structure and dynamics]

Probab=99.93  E-value=2.9e-23  Score=175.93  Aligned_cols=326  Identities=14%  Similarity=0.164  Sum_probs=221.5

Q ss_pred             CCCcHhhhhhhhccc-cCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEE
Q 017573           17 EKPSAIQQRGIVPFC-KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKV   95 (369)
Q Consensus        17 ~~~~~~Q~~~~~~~~-~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v   95 (369)
                      ..+-|+|++.+...+ .|+++++..++|-|||..++..+......+    ..|||||. ++...|++.+.+|.....- +
T Consensus       197 s~LlPFQreGv~faL~RgGR~llADeMGLGKTiQAlaIA~yyraEw----plliVcPA-svrftWa~al~r~lps~~p-i  270 (689)
T KOG1000|consen  197 SRLLPFQREGVIFALERGGRILLADEMGLGKTIQALAIARYYRAEW----PLLIVCPA-SVRFTWAKALNRFLPSIHP-I  270 (689)
T ss_pred             HhhCchhhhhHHHHHhcCCeEEEecccccchHHHHHHHHHHHhhcC----cEEEEecH-HHhHHHHHHHHHhcccccc-e
Confidence            457799999998765 578999999999999998765444443333    69999997 6778899999999876533 4


Q ss_pred             EEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEE
Q 017573           96 HACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVF  175 (369)
Q Consensus        96 ~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~  175 (369)
                      .+..++.....   .+.....|.|.+++.+..+-..  +....+.++|+||+|++.+.. ......+...+....++|++
T Consensus       271 ~vv~~~~D~~~---~~~t~~~v~ivSye~ls~l~~~--l~~~~~~vvI~DEsH~Lk~sk-tkr~Ka~~dllk~akhvILL  344 (689)
T KOG1000|consen  271 FVVDKSSDPLP---DVCTSNTVAIVSYEQLSLLHDI--LKKEKYRVVIFDESHMLKDSK-TKRTKAATDLLKVAKHVILL  344 (689)
T ss_pred             EEEecccCCcc---ccccCCeEEEEEHHHHHHHHHH--HhcccceEEEEechhhhhccc-hhhhhhhhhHHHHhhheEEe
Confidence            44444333221   1344567999999998654332  233347999999999987654 34455555666667789999


Q ss_pred             EeeCC-------------------hhHHHHHHHhcCCC-EEEEecCc--------------------------cccccce
Q 017573          176 SATMP-------------------PEALEITRKFMNKP-VRILVKRD--------------------------ELTLEGI  209 (369)
Q Consensus       176 saT~~-------------------~~~~~~~~~~~~~~-~~~~~~~~--------------------------~~~~~~~  209 (369)
                      |+||.                   ++..++..++|... ..+..+..                          .-.++.-
T Consensus       345 SGTPavSRP~elytqi~avd~tlfp~f~efa~rYCd~k~vr~~~Dykg~tnl~EL~~lL~k~lMIRRlK~dvL~qLPpKr  424 (689)
T KOG1000|consen  345 SGTPAVSRPSELYTQIRAVDHTLFPNFHEFAIRYCDGKQVRFCFDYKGCTNLEELAALLFKRLMIRRLKADVLKQLPPKR  424 (689)
T ss_pred             cCCcccCCchhhhhhhhhhcccccccHHHHHHHhcCccccceeeecCCCCCHHHHHHHHHHHHHHHHHHHHHHhhCCccc
Confidence            99984                   11222333333211 11110000                          0001111


Q ss_pred             eEEEEEccch------------------------------------hhhHHHHHHHHHhc------cCCCeEEEeCCHhh
Q 017573          210 KQFYVNVEKE------------------------------------EWKLETLCDLYETL------AITQSVIFVNTRRK  247 (369)
Q Consensus       210 ~~~~~~~~~~------------------------------------~~~~~~l~~~~~~~------~~~k~lv~~~~~~~  247 (369)
                      +...+.....                                    ..+...+.+.+..+      +..|.+||+-...-
T Consensus       425 r~Vv~~~~gr~da~~~~lv~~a~~~t~~~~~e~~~~~l~l~y~~tgiaK~~av~eyi~~~~~l~d~~~~KflVFaHH~~v  504 (689)
T KOG1000|consen  425 REVVYVSGGRIDARMDDLVKAAADYTKVNSMERKHESLLLFYSLTGIAKAAAVCEYILENYFLPDAPPRKFLVFAHHQIV  504 (689)
T ss_pred             eEEEEEcCCccchHHHHHHHHhhhcchhhhhhhhhHHHHHHHHHhcccccHHHHHHHHhCcccccCCCceEEEEehhHHH
Confidence            1111111110                                    01334444444431      44589999999999


Q ss_pred             HHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcC-CCcEE-EEecCCcCCCCCCCCcEEEEecCCCCccchhhhhcc
Q 017573          248 VDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSG-SSRVL-ITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGR  325 (369)
Q Consensus       248 ~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~-~~~vl-i~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR  325 (369)
                      .+.+...+.+.++....+.|..++.+|....++|+.+ +..|- ++..+.++|+++..++.|++...+|++.-++|+--|
T Consensus       505 Ld~Iq~~~~~r~vg~IRIDGst~s~~R~ll~qsFQ~seev~VAvlsItA~gvGLt~tAa~~VVFaEL~wnPgvLlQAEDR  584 (689)
T KOG1000|consen  505 LDTIQVEVNKRKVGSIRIDGSTPSHRRTLLCQSFQTSEEVRVAVLSITAAGVGLTLTAASVVVFAELHWNPGVLLQAEDR  584 (689)
T ss_pred             HHHHHHHHHHcCCCeEEecCCCCchhHHHHHHHhccccceEEEEEEEeecccceeeeccceEEEEEecCCCceEEechhh
Confidence            9999999999999999999999999999999999864 45544 456788999999999999999999999999999999


Q ss_pred             cccCCCceeEEEEe--ccc--cHHHHHHHHHHh
Q 017573          326 SGRFGRKGVAINFV--TRD--DERMLFDIQKFY  354 (369)
Q Consensus       326 ~~R~~~~~~~~~~~--~~~--~~~~~~~~~~~~  354 (369)
                      +.|.|+.+.+.+++  ..+  |+..+..+.+.+
T Consensus       585 aHRiGQkssV~v~ylvAKgT~Ddy~Wp~l~~KL  617 (689)
T KOG1000|consen  585 AHRIGQKSSVFVQYLVAKGTADDYMWPMLQQKL  617 (689)
T ss_pred             hhhccccceeeEEEEEecCchHHHHHHHHHHHH
Confidence            99999886554444  333  555555555444

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

Probab=99.93  E-value=6.2e-24  Score=194.62  Aligned_cols=328  Identities=21%  Similarity=0.281  Sum_probs=221.6

Q ss_pred             CCCcHhhhhhhhccccC----CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccC
Q 017573           17 EKPSAIQQRGIVPFCKG----LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLG   92 (369)
Q Consensus        17 ~~~~~~Q~~~~~~~~~~----~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~   92 (369)
                      ..+++-|+.+++.+...    ..+++.+.||||||.+++-++...+.+++   .+|+++|-.+|..|+.+.|+..+   +
T Consensus       197 ~~Ln~~Q~~a~~~i~~~~~~~~~~Ll~GvTGSGKTEvYl~~i~~~L~~Gk---qvLvLVPEI~Ltpq~~~rf~~rF---g  270 (730)
T COG1198         197 LALNQEQQAAVEAILSSLGGFAPFLLDGVTGSGKTEVYLEAIAKVLAQGK---QVLVLVPEIALTPQLLARFKARF---G  270 (730)
T ss_pred             cccCHHHHHHHHHHHHhcccccceeEeCCCCCcHHHHHHHHHHHHHHcCC---EEEEEeccccchHHHHHHHHHHh---C
Confidence            36788899999998765    67899999999999999999999998876   89999999999999999998765   4


Q ss_pred             cEEEEEECCcch----HHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccC-----cHHHHHHHH
Q 017573           93 VKVHACVGGTSV----REDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRG-----FKDQIYDIF  163 (369)
Q Consensus        93 ~~v~~~~~~~~~----~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~-----~~~~~~~~~  163 (369)
                      .++.+++++.+.    ..+.+...++..|+|+|-..++--+.+       +++||+||=|.-...+     |...-..++
T Consensus       271 ~~v~vlHS~Ls~~er~~~W~~~~~G~~~vVIGtRSAlF~Pf~~-------LGLIIvDEEHD~sYKq~~~prYhARdvA~~  343 (730)
T COG1198         271 AKVAVLHSGLSPGERYRVWRRARRGEARVVIGTRSALFLPFKN-------LGLIIVDEEHDSSYKQEDGPRYHARDVAVL  343 (730)
T ss_pred             CChhhhcccCChHHHHHHHHHHhcCCceEEEEechhhcCchhh-------ccEEEEeccccccccCCcCCCcCHHHHHHH
Confidence            566666666543    445566678899999998888754444       8999999999765322     222222333


Q ss_pred             hhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecC--ccccccceeEEEEEccchhh---hHHHHHHHH-Hhc-cCC
Q 017573          164 QLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKR--DELTLEGIKQFYVNVEKEEW---KLETLCDLY-ETL-AIT  236 (369)
Q Consensus       164 ~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~---~~~~l~~~~-~~~-~~~  236 (369)
                      ..-..++++++-||||+-+........  .........  ....++.+.-.-........   -...+.+.+ +.. .++
T Consensus       344 Ra~~~~~pvvLgSATPSLES~~~~~~g--~y~~~~L~~R~~~a~~p~v~iiDmr~e~~~~~~~lS~~Ll~~i~~~l~~ge  421 (730)
T COG1198         344 RAKKENAPVVLGSATPSLESYANAESG--KYKLLRLTNRAGRARLPRVEIIDMRKEPLETGRSLSPALLEAIRKTLERGE  421 (730)
T ss_pred             HHHHhCCCEEEecCCCCHHHHHhhhcC--ceEEEEccccccccCCCcceEEeccccccccCccCCHHHHHHHHHHHhcCC
Confidence            333346779999999976554444222  111222111  11112222221111111111   112233322 222 345


Q ss_pred             CeEEEeCCHhh------------------------------------------------------------HHHHHHHHh
Q 017573          237 QSVIFVNTRRK------------------------------------------------------------VDWLTDKMR  256 (369)
Q Consensus       237 k~lv~~~~~~~------------------------------------------------------------~~~~~~~l~  256 (369)
                      .+|+|.|.+-.                                                            .+.+.+.|+
T Consensus       422 Q~llflnRRGys~~l~C~~Cg~v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~~L~~~G~GterieeeL~  501 (730)
T COG1198         422 QVLLFLNRRGYAPLLLCRDCGYIAECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSEHLRAVGPGTERIEEELK  501 (730)
T ss_pred             eEEEEEccCCccceeecccCCCcccCCCCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCCCeeEEecccHHHHHHHHH
Confidence            77777777633                                                            234455554


Q ss_pred             hC--CCeeEEecCCCCHH--HHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCCC------------Cccchh
Q 017573          257 SR--DHTVSATHGDMDQN--TRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPT------------QPENYL  320 (369)
Q Consensus       257 ~~--~~~~~~~~~~~~~~--~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~------------~~~~~~  320 (369)
                      +.  +.++..+.++....  .-+..+.+|.+|+.+|||+|+++..|.|+|+++.|.+++...            ....+.
T Consensus       502 ~~FP~~rv~r~d~Dtt~~k~~~~~~l~~~~~ge~dILiGTQmiaKG~~fp~vtLVgvl~aD~~L~~~DfRA~Er~fqll~  581 (730)
T COG1198         502 RLFPGARIIRIDSDTTRRKGALEDLLDQFANGEADILIGTQMIAKGHDFPNVTLVGVLDADTGLGSPDFRASERTFQLLM  581 (730)
T ss_pred             HHCCCCcEEEEccccccchhhHHHHHHHHhCCCCCeeecchhhhcCCCcccceEEEEEechhhhcCCCcchHHHHHHHHH
Confidence            44  34566777765433  346789999999999999999999999999999987765421            234569


Q ss_pred             hhhcccccCCCceeEEEEeccccHHHHHHH-----HHHhccccc
Q 017573          321 HRIGRSGRFGRKGVAINFVTRDDERMLFDI-----QKFYNVVIE  359 (369)
Q Consensus       321 Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~  359 (369)
                      |..||+||.+++|.+++-....+...++.+     ..|++.+++
T Consensus       582 QvaGRAgR~~~~G~VvIQT~~P~hp~i~~~~~~dy~~F~~~El~  625 (730)
T COG1198         582 QVAGRAGRAGKPGEVVIQTYNPDHPAIQALKRGDYEAFYEQELA  625 (730)
T ss_pred             HHHhhhccCCCCCeEEEEeCCCCcHHHHHHHhcCHHHHHHHHHH
Confidence            999999999999999999998886666443     555555553

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

Probab=99.93  E-value=8.7e-23  Score=196.87  Aligned_cols=332  Identities=14%  Similarity=0.142  Sum_probs=202.1

Q ss_pred             HHHHHHHHhCCCCCCcHhhhhhhh----ccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHH
Q 017573            5 ENLLRGIYAYGFEKPSAIQQRGIV----PFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQI   80 (369)
Q Consensus         5 ~~i~~~l~~~~~~~~~~~Q~~~~~----~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~   80 (369)
                      +.+.+.+...|| ++|+.|.++.+    .+.+++++++.||||+|||++++++++.....   +.+++|.+||++|..|+
T Consensus       233 ~~~~~~~~~~~~-~~r~~Q~~~~~~i~~~~~~~~~~~~eA~TG~GKT~ayLlp~~~~~~~---~~~vvi~t~t~~Lq~Ql  308 (850)
T TIGR01407       233 SLFSKNIDRLGL-EYRPEQLKLAELVLDQLTHSEKSLIEAPTGTGKTLGYLLPALYYAIT---EKPVVISTNTKVLQSQL  308 (850)
T ss_pred             HHHHHhhhhcCC-ccCHHHHHHHHHHHHHhccCCcEEEECCCCCchhHHHHHHHHHHhcC---CCeEEEEeCcHHHHHHH
Confidence            456677777777 58999998666    55568999999999999999999998876652   23899999999999998


Q ss_pred             HH-HHHHhccccC--cEEEEEECCcch-----------------H---------------------H----------HH-
Q 017573           81 EK-VMRALGDYLG--VKVHACVGGTSV-----------------R---------------------E----------DQ-  108 (369)
Q Consensus        81 ~~-~~~~~~~~~~--~~v~~~~~~~~~-----------------~---------------------~----------~~-  108 (369)
                      .. ++..+...++  +++..+.|....                 .                     +          +. 
T Consensus       309 ~~~~~~~l~~~~~~~~~~~~~kG~~~ylcl~k~~~~l~~~~~~~~~~~~~~~~~~wl~~T~tGD~~el~~~~~~~~~~~~  388 (850)
T TIGR01407       309 LEKDIPLLNEILNFKINAALIKGKSNYLSLGKFSQILKDNTDNYEFNIFKMQVLVWLTETETGDLDELNLKGGNKMFFAQ  388 (850)
T ss_pred             HHHHHHHHHHHcCCCceEEEEEcchhhccHHHHHHHHhcCCCcHHHHHHHHHHHHHhccCCccCHhhccCCCcchhhHHH
Confidence            65 4443332222  444433332110                 0                     0          00 


Q ss_pred             ----------------------HHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccC-------c----
Q 017573          109 ----------------------RILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRG-------F----  155 (369)
Q Consensus       109 ----------------------~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~-------~----  155 (369)
                                            +.....++|+|+++..|+..+..........+.+|+||||++.+..       .    
T Consensus       389 i~~~~~l~~~c~~~~~Cf~~~ar~~a~~AdivItNHa~L~~~~~~~~~ilp~~~~lIiDEAH~L~d~a~~~~~~~ls~~~  468 (850)
T TIGR01407       389 VRHDGNLSKKDLFYEVDFYNRAQKNAEQAQILITNHAYLITRLVDNPELFPSFRDLIIDEAHHLPDIAENQLQEELDYAD  468 (850)
T ss_pred             hhcCCCCCCCCCCccccHHHHHHHHHhcCCEEEecHHHHHHHhhcccccCCCCCEEEEECcchHHHHHHHHhcceeCHHH
Confidence                                  0012357999999999887764433223345899999999876310       0    


Q ss_pred             -HH---H-------------------------------------------------------------HHHHHhh-----
Q 017573          156 -KD---Q-------------------------------------------------------------IYDIFQL-----  165 (369)
Q Consensus       156 -~~---~-------------------------------------------------------------~~~~~~~-----  165 (369)
                       ..   .                                                             +......     
T Consensus       469 ~~~~l~~l~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~l~~~~~~~~~~~~~l~~~~~~~~~~~  548 (850)
T TIGR01407       469 IKYQIDLIGKGENEQLLKRIQQLEKQEILEKLFDFETKDILKDLQAILDKLNKLLQIFSELSHKTVDQLRKFDLALKDDF  548 (850)
T ss_pred             HHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHH
Confidence             00   0                                                             0000000     


Q ss_pred             ------C-------------------------------------CccCcEEEEEeeCChh-HHHHHHHhcCCC-EE-EEe
Q 017573          166 ------L-------------------------------------PAKVQVGVFSATMPPE-ALEITRKFMNKP-VR-ILV  199 (369)
Q Consensus       166 ------~-------------------------------------~~~~~~i~~saT~~~~-~~~~~~~~~~~~-~~-~~~  199 (369)
                            +                                     +....+|++|||+..+ ..+.....++-+ .. ...
T Consensus       549 ~~l~~~~~~~~~~wi~~~~~~~~~~~~l~~~pl~~~~~l~~~~~~~~~~~il~SATL~~~~~~~~~~~~lGl~~~~~~~~  628 (850)
T TIGR01407       549 KNIEQSLKEGHTSWISIENLQQKSTIRLYIKDYEVGDVLTKRLLPKFKSLIFTSATLKFSHSFESFPQLLGLTDVHFNTI  628 (850)
T ss_pred             HHHHHHhccCCeEEEEecCCCCCceEEEEeeeCcHHHHHHHHHhccCCeEEEEecccccCCChHHHHHhcCCCcccccee
Confidence                  0                                     1124578899998743 233333333322 11 111


Q ss_pred             cCccccccceeEEEEEc--c-----chhhhH----HHHHHHHHhccCCCeEEEeCCHhhHHHHHHHHhhC--CCeeEEec
Q 017573          200 KRDELTLEGIKQFYVNV--E-----KEEWKL----ETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSR--DHTVSATH  266 (369)
Q Consensus       200 ~~~~~~~~~~~~~~~~~--~-----~~~~~~----~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~--~~~~~~~~  266 (369)
                      .........-...+...  +     ......    +.+.+++.. ..+++|||++|.+.++.++..|...  .....++.
T Consensus       629 ~~spf~~~~~~~l~v~~d~~~~~~~~~~~~~~~ia~~i~~l~~~-~~g~~LVlftS~~~l~~v~~~L~~~~~~~~~~~l~  707 (850)
T TIGR01407       629 EPTPLNYAENQRVLIPTDAPAIQNKSLEEYAQEIASYIIEITAI-TSPKILVLFTSYEMLHMVYDMLNELPEFEGYEVLA  707 (850)
T ss_pred             cCCCCCHHHcCEEEecCCCCCCCCCChHHHHHHHHHHHHHHHHh-cCCCEEEEeCCHHHHHHHHHHHhhhccccCceEEe
Confidence            11112211112222211  1     111122    223333332 4479999999999999999999752  11222333


Q ss_pred             CCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCc--EEEEecCCCCc----------------------------
Q 017573          267 GDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVS--LVINYDLPTQP----------------------------  316 (369)
Q Consensus       267 ~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~--~vi~~~~~~~~----------------------------  316 (369)
                      .+.+ ..|.++++.|++++..||++|+.+.+|+|+|+..  .||+.+.|...                            
T Consensus       708 q~~~-~~r~~ll~~F~~~~~~iLlgt~sf~EGVD~~g~~l~~viI~~LPf~~p~dp~~~a~~~~~~~~g~~~f~~~~lP~  786 (850)
T TIGR01407       708 QGIN-GSRAKIKKRFNNGEKAILLGTSSFWEGVDFPGNGLVCLVIPRLPFANPKHPLTKKYWQKLEQEGKNPFYDYVLPM  786 (850)
T ss_pred             cCCC-ccHHHHHHHHHhCCCeEEEEcceeecccccCCCceEEEEEeCCCCCCCCCHHHHHHHHHHHHhcCCchHHhhHHH
Confidence            3323 5688899999999999999999999999999754  56777766421                            


Q ss_pred             --cchhhhhcccccCCCceeEEEEeccc
Q 017573          317 --ENYLHRIGRSGRFGRKGVAINFVTRD  342 (369)
Q Consensus       317 --~~~~Q~~GR~~R~~~~~~~~~~~~~~  342 (369)
                        ..+.|.+||+.|..++.-++++.++.
T Consensus       787 A~~~l~Qa~GRlIRs~~D~G~v~ilD~R  814 (850)
T TIGR01407       787 AIIRLRQALGRLIRRENDRGSIVILDRR  814 (850)
T ss_pred             HHHHHHHhhccccccCCceEEEEEEccc
Confidence              23589999999997765556666654

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=99.93  E-value=8.7e-24  Score=195.81  Aligned_cols=328  Identities=21%  Similarity=0.249  Sum_probs=221.8

Q ss_pred             CCcHhhhhhhhccc----cCCcEEEEcCCCChhhHHHHHHHHHhhhccC------CCccEEEEcCCHHHHHHHHHHHHHh
Q 017573           18 KPSAIQQRGIVPFC----KGLDVIQQAQSGTGKTATFCSGILQQLDYGL------VQCQALVLAPTRELAQQIEKVMRAL   87 (369)
Q Consensus        18 ~~~~~Q~~~~~~~~----~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~------~~~~~liv~P~~~l~~q~~~~~~~~   87 (369)
                      .+|.||++.++.+.    .+=+.|++..+|-|||+..+..++....+.+      .....|||||+ +|+.-|..++.+|
T Consensus       975 ~LRkYQqEGVnWLaFLnky~LHGILcDDMGLGKTLQticilAsd~y~r~s~~~e~~~~PSLIVCPs-TLtGHW~~E~~kf 1053 (1549)
T KOG0392|consen  975 KLRKYQQEGVNWLAFLNKYKLHGILCDDMGLGKTLQTICILASDHYKRRSESSEFNRLPSLIVCPS-TLTGHWKSEVKKF 1053 (1549)
T ss_pred             HHHHHHHhccHHHHHHHHhcccceeeccccccHHHHHHHHHHHHHHhhcccchhhccCCeEEECCc-hhhhHHHHHHHHh
Confidence            48999999998765    2467899999999999887655554433321      11248999998 7899999999999


Q ss_pred             ccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCC
Q 017573           88 GDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLP  167 (369)
Q Consensus        88 ~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~  167 (369)
                      +..  +++....|........+..-++++|+|++|+.+.+-+..  +....|.+.|+||.|-+.+.  ...+.+..+.+.
T Consensus      1054 ~pf--L~v~~yvg~p~~r~~lR~q~~~~~iiVtSYDv~RnD~d~--l~~~~wNYcVLDEGHVikN~--ktkl~kavkqL~ 1127 (1549)
T KOG0392|consen 1054 FPF--LKVLQYVGPPAERRELRDQYKNANIIVTSYDVVRNDVDY--LIKIDWNYCVLDEGHVIKNS--KTKLTKAVKQLR 1127 (1549)
T ss_pred             cch--hhhhhhcCChHHHHHHHhhccccceEEeeHHHHHHHHHH--HHhcccceEEecCcceecch--HHHHHHHHHHHh
Confidence            876  555555666555555444556689999999999754433  22334789999999988443  456666666666


Q ss_pred             ccCcEEEEEeeCChhHH-HHHH-----------------HhcCCCEEEEec-----------------------------
Q 017573          168 AKVQVGVFSATMPPEAL-EITR-----------------KFMNKPVRILVK-----------------------------  200 (369)
Q Consensus       168 ~~~~~i~~saT~~~~~~-~~~~-----------------~~~~~~~~~~~~-----------------------------  200 (369)
                      .+. .+.+|+||..+.. ++..                 .-+.+|+.-...                             
T Consensus      1128 a~h-RLILSGTPIQNnvleLWSLFdFLMPGfLGtEKqFqsrf~kpI~asRd~K~Sske~EaG~lAleaLHKqVLPF~LRR 1206 (1549)
T KOG0392|consen 1128 ANH-RLILSGTPIQNNVLELWSLFDFLMPGFLGTEKQFQSRFGKPILASRDPKSSSKEQEAGVLALEALHKQVLPFLLRR 1206 (1549)
T ss_pred             hcc-eEEeeCCCcccCHHHHHHHHHHhcccccCcHHHHHHHhcchhhhhcCcccchhHHHhhHHHHHHHHHHHHHHHHHH
Confidence            555 4557999863321 1110                 000000000000                             


Q ss_pred             -----CccccccceeEEEEEccc---------------------------------------------------------
Q 017573          201 -----RDELTLEGIKQFYVNVEK---------------------------------------------------------  218 (369)
Q Consensus       201 -----~~~~~~~~~~~~~~~~~~---------------------------------------------------------  218 (369)
                           -...++..+..++....+                                                         
T Consensus      1207 lKedVL~DLPpKIIQDyyCeLs~lQ~kLY~df~~~~k~~~~~~~d~~~~S~gt~~~HvFqaLqYlrKLcnHpaLvlt~~h 1286 (1549)
T KOG0392|consen 1207 LKEDVLKDLPPKIIQDYYCELSPLQKKLYRDFVKKAKQCVSSQIDGGEESLGTDKTHVFQALQYLRKLCNHPALVLTPVH 1286 (1549)
T ss_pred             HHHHHHhhCChhhhhheeeccCHHHHHHHHHHHHHhccccccccccchhccCcchHHHHHHHHHHHHhcCCcceeeCCCc
Confidence                 000011111111111111                                                         


Q ss_pred             ---------------------hhhhHHHHHHHHHhccC----------------CCeEEEeCCHhhHHHHHHHHhhCC--
Q 017573          219 ---------------------EEWKLETLCDLYETLAI----------------TQSVIFVNTRRKVDWLTDKMRSRD--  259 (369)
Q Consensus       219 ---------------------~~~~~~~l~~~~~~~~~----------------~k~lv~~~~~~~~~~~~~~l~~~~--  259 (369)
                                           ...|+.++.+++.....                -++||||.-+..+..+.+.|.+..  
T Consensus      1287 p~la~i~~~l~~~~~~LHdi~hspKl~AL~qLL~eCGig~~~~~~~g~~s~vsqHRiLIFcQlK~mlDlVekDL~k~~mp 1366 (1549)
T KOG0392|consen 1287 PDLAAIVSHLAHFNSSLHDIQHSPKLSALKQLLSECGIGNNSDSEVGTPSDVSQHRILIFCQLKSMLDLVEKDLFKKYMP 1366 (1549)
T ss_pred             chHHHHHHHHHHhhhhHHHhhhchhHHHHHHHHHHhCCCCCCcccccCcchhccceeEEeeeHHHHHHHHHHHHhhhhcC
Confidence                                 01156667777755421                278999999999998888776552  


Q ss_pred             -CeeEEecCCCCHHHHHHHHHHHhcC-CCcEEE-EecCCcCCCCCCCCcEEEEecCCCCccchhhhhcccccCCCc--ee
Q 017573          260 -HTVSATHGDMDQNTRDIIMREFRSG-SSRVLI-TTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRK--GV  334 (369)
Q Consensus       260 -~~~~~~~~~~~~~~r~~~~~~f~~~-~~~vli-~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~--~~  334 (369)
                       +....+.|..++.+|.++.++|+++ .++||+ +|.+.+-|+|+.+++.||+++-.||+..=.|++-||+|.|++  -.
T Consensus      1367 sVtymRLDGSVpp~~R~kiV~~FN~DptIDvLlLTThVGGLGLNLTGADTVVFvEHDWNPMrDLQAMDRAHRIGQKrvVN 1446 (1549)
T KOG0392|consen 1367 SVTYMRLDGSVPPGDRQKIVERFNEDPTIDVLLLTTHVGGLGLNLTGADTVVFVEHDWNPMRDLQAMDRAHRIGQKRVVN 1446 (1549)
T ss_pred             ceeEEEecCCCCcHHHHHHHHHhcCCCceeEEEEeeeccccccccCCCceEEEEecCCCchhhHHHHHHHHhhcCceeee
Confidence             3455899999999999999999998 678775 567999999999999999999999999999999999999988  46


Q ss_pred             EEEEecccc-HHHHHHHHHH
Q 017573          335 AINFVTRDD-ERMLFDIQKF  353 (369)
Q Consensus       335 ~~~~~~~~~-~~~~~~~~~~  353 (369)
                      +|-+++.+. ++.+.++++|
T Consensus      1447 VyRlItrGTLEEKVMgLQkF 1466 (1549)
T KOG0392|consen 1447 VYRLITRGTLEEKVMGLQKF 1466 (1549)
T ss_pred             eeeehhcccHHHHHhhHHHH
Confidence            777777764 3334445544

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

Probab=99.92  E-value=2.1e-23  Score=183.60  Aligned_cols=310  Identities=15%  Similarity=0.217  Sum_probs=209.8

Q ss_pred             cHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHH-hccccCcEEEEE
Q 017573           20 SAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRA-LGDYLGVKVHAC   98 (369)
Q Consensus        20 ~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~-~~~~~~~~v~~~   98 (369)
                      +.+-.+++..+.+++-++|.|+||+|||...--.+.++--. ..+ ++.+--|++.-+..+++...+ ....+|-.|.+.
T Consensus        53 ~~~r~~il~~ve~nqvlIviGeTGsGKSTQipQyL~eaG~~-~~g-~I~~TQPRRVAavslA~RVAeE~~~~lG~~VGY~  130 (674)
T KOG0922|consen   53 YKYRDQILYAVEDNQVLIVIGETGSGKSTQIPQYLAEAGFA-SSG-KIACTQPRRVAAVSLAKRVAEEMGCQLGEEVGYT  130 (674)
T ss_pred             HHHHHHHHHHHHHCCEEEEEcCCCCCccccHhHHHHhcccc-cCC-cEEeecCchHHHHHHHHHHHHHhCCCcCceeeeE
Confidence            34445677777888999999999999997754444433221 122 566777998766666655533 333445555444


Q ss_pred             ECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhh--ccCcHHHHHHHHhhCCccCcEEEEE
Q 017573           99 VGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEML--SRGFKDQIYDIFQLLPAKVQVGVFS  176 (369)
Q Consensus        99 ~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~--~~~~~~~~~~~~~~~~~~~~~i~~s  176 (369)
                      ..-...      ...+..|.++|-..|++....... ++.+++||+||||+=.  ..-....+.++.+.- +..++|.+|
T Consensus       131 IRFed~------ts~~TrikymTDG~LLRE~l~Dp~-LskYsvIIlDEAHERsl~TDiLlGlLKki~~~R-~~LklIimS  202 (674)
T KOG0922|consen  131 IRFEDS------TSKDTRIKYMTDGMLLREILKDPL-LSKYSVIILDEAHERSLHTDILLGLLKKILKKR-PDLKLIIMS  202 (674)
T ss_pred             EEeccc------CCCceeEEEecchHHHHHHhcCCc-cccccEEEEechhhhhhHHHHHHHHHHHHHhcC-CCceEEEEe
Confidence            432221      123478999999999987776653 5568999999999721  111112222333332 356799999


Q ss_pred             eeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhh---HHHHHHHHHhccCCCeEEEeCCHhhHHHHHH
Q 017573          177 ATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWK---LETLCDLYETLAITQSVIFVNTRRKVDWLTD  253 (369)
Q Consensus       177 aT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~  253 (369)
                      ||...   +....++..-..+.+....   ..++.+|..-+..+..   ...+.++....+.+.+|||..+.++.+..++
T Consensus       203 ATlda---~kfS~yF~~a~i~~i~GR~---fPVei~y~~~p~~dYv~a~~~tv~~Ih~~E~~GDILvFLtGqeEIe~~~~  276 (674)
T KOG0922|consen  203 ATLDA---EKFSEYFNNAPILTIPGRT---FPVEILYLKEPTADYVDAALITVIQIHLTEPPGDILVFLTGQEEIEAACE  276 (674)
T ss_pred             eeecH---HHHHHHhcCCceEeecCCC---CceeEEeccCCchhhHHHHHHHHHHHHccCCCCCEEEEeCCHHHHHHHHH
Confidence            99863   3344555542233332222   2234444443333333   3444455555677899999999999999999


Q ss_pred             HHhhC----CC----eeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecC-------------
Q 017573          254 KMRSR----DH----TVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDL-------------  312 (369)
Q Consensus       254 ~l~~~----~~----~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~-------------  312 (369)
                      .|.+.    ..    -+..+||.++.+++.++++.-..|.-+|+++|+++++.+.+|++..||.-+.             
T Consensus       277 ~l~e~~~~~~~~~~~~~lply~aL~~e~Q~rvF~p~p~g~RKvIlsTNIAETSlTI~GI~YVVDsG~vK~~~y~p~~g~~  356 (674)
T KOG0922|consen  277 LLRERAKSLPEDCPELILPLYGALPSEEQSRVFDPAPPGKRKVILSTNIAETSLTIDGIRYVVDSGFVKQKKYNPRTGLD  356 (674)
T ss_pred             HHHHHhhhccccCcceeeeecccCCHHHhhccccCCCCCcceEEEEcceeeeeEEecceEEEEcCCceEEEeeccccCcc
Confidence            99766    11    2467999999999999988888888899999999999999999999996553             


Q ss_pred             -----CCCccchhhhhcccccCCCceeEEEEeccccHHH
Q 017573          313 -----PTQPENYLHRIGRSGRFGRKGVAINFVTRDDERM  346 (369)
Q Consensus       313 -----~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~  346 (369)
                           |-|.....||.||+||+ .+|.|+-+++..+...
T Consensus       357 ~L~v~~ISkasA~QRaGRAGRt-~pGkcyRLYte~~~~~  394 (674)
T KOG0922|consen  357 SLIVVPISKASANQRAGRAGRT-GPGKCYRLYTESAYDK  394 (674)
T ss_pred             ceeEEechHHHHhhhcccCCCC-CCceEEEeeeHHHHhh
Confidence                 33667889999999999 5799999999876643

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=99.92  E-value=5.6e-23  Score=185.44  Aligned_cols=316  Identities=20%  Similarity=0.237  Sum_probs=216.9

Q ss_pred             CCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcE
Q 017573           15 GFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVK   94 (369)
Q Consensus        15 ~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~   94 (369)
                      |. .|++.|--+.-.+.+|  -+....||.|||+++.++++.....+.   .+.+++|+.-|+.+-++++..++..+|++
T Consensus        76 g~-r~ydvQlig~l~Ll~G--~VaEM~TGEGKTLvA~l~a~l~AL~G~---~VhvvT~NdyLA~RDae~m~~ly~~LGLs  149 (764)
T PRK12326         76 GL-RPFDVQLLGALRLLAG--DVIEMATGEGKTLAGAIAAAGYALQGR---RVHVITVNDYLARRDAEWMGPLYEALGLT  149 (764)
T ss_pred             CC-CcchHHHHHHHHHhCC--CcccccCCCCHHHHHHHHHHHHHHcCC---CeEEEcCCHHHHHHHHHHHHHHHHhcCCE
Confidence            44 7888888777777655  488999999999999888886666555   89999999999999999999999999999


Q ss_pred             EEEEECCcchHHHHHHHccCCcEEEeccHHHH-HHHHcCC------CCCCCccEEEEechhHhhccC-------------
Q 017573           95 VHACVGGTSVREDQRILQAGVHVVVGTPGRVF-DMLRRQS------LRPDYIKMFVLDEADEMLSRG-------------  154 (369)
Q Consensus        95 v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~-~~~~~~~------~~~~~~~~viiDE~H~~~~~~-------------  154 (369)
                      +..+.++.+....+...  .+||+++|...|- ..++.+-      .....+.++|+||++.+.-..             
T Consensus       150 vg~i~~~~~~~err~aY--~~DItYgTn~e~gFDyLRDnm~~~~~~~v~R~~~faIVDEvDSiLIDeArtPLiISg~~~~  227 (764)
T PRK12326        150 VGWITEESTPEERRAAY--ACDVTYASVNEIGFDVLRDQLVTDVADLVSPNPDVAIIDEADSVLVDEALVPLVLAGSTPG  227 (764)
T ss_pred             EEEECCCCCHHHHHHHH--cCCCEEcCCcccccccchhhhccChHhhcCCccceeeecchhhheeccccCceeeeCCCcc
Confidence            99998887766555444  4799999998873 3333321      122447899999999754100             


Q ss_pred             --cHHHHHHHHhhCCc----------------------------------------------------------------
Q 017573          155 --FKDQIYDIFQLLPA----------------------------------------------------------------  168 (369)
Q Consensus       155 --~~~~~~~~~~~~~~----------------------------------------------------------------  168 (369)
                        ....+..+...+.+                                                                
T Consensus       228 ~~~y~~~~~~v~~L~~~~dy~ide~~k~v~LTe~G~~~~e~~l~~~~ly~~~~~~~~~~~i~~AL~A~~l~~~d~dYiV~  307 (764)
T PRK12326        228 EAPRGEIAELVRRLREGKDYEIDDDGRNVHLTDKGARKVEKALGGIDLYSEEHVGTTLTQVNVALHAHALLQRDVHYIVR  307 (764)
T ss_pred             hhHHHHHHHHHHhcCcCCcEEEEcCCCeeEecHHHHHHHHHHcCCccccCcchhHHHHHHHHHHHHHHHHHhcCCcEEEE
Confidence              00111111111100                                                                


Q ss_pred             ------------------------------------------------------cCcEEEEEeeCChhHHHHHHHhcCCC
Q 017573          169 ------------------------------------------------------KVQVGVFSATMPPEALEITRKFMNKP  194 (369)
Q Consensus       169 ------------------------------------------------------~~~~i~~saT~~~~~~~~~~~~~~~~  194 (369)
                                                                            -.++.+||+|...... .....++-+
T Consensus       308 dgeV~iVDe~TGRvm~grrwsdGLHQaIEaKE~v~i~~e~~t~AsIT~QnfFr~Y~kLsGMTGTa~t~~~-Ef~~iY~l~  386 (764)
T PRK12326        308 DGKVHLINASRGRIAQLQRWPDGLQAAVEAKEGLETTETGEVLDTITVQALIGRYPTVCGMTGTAVAAGE-QLRQFYDLG  386 (764)
T ss_pred             CCEEEEEECCCCCcCCCCccChHHHHHHHHHcCCCCCCCceeeehhhHHHHHHhcchheeecCCChhHHH-HHHHHhCCc
Confidence                                                                  0457788888865443 344444444


Q ss_pred             EEEEecCcccccc-ceeEEEEEccchhhhHHHHHH-HHHhc-cCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCH
Q 017573          195 VRILVKRDELTLE-GIKQFYVNVEKEEWKLETLCD-LYETL-AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQ  271 (369)
Q Consensus       195 ~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~l~~-~~~~~-~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~  271 (369)
                      +.......+.... .....|.   +...+...+.+ +...+ .+.++||.+.+++..+.+.+.|.+.+++..++++....
T Consensus       387 Vv~IPtnkp~~R~d~~d~iy~---t~~~k~~Aii~ei~~~~~~GrPVLVgt~sI~~SE~ls~~L~~~gI~h~vLNAk~~~  463 (764)
T PRK12326        387 VSVIPPNKPNIREDEADRVYA---TAAEKNDAIVEHIAEVHETGQPVLVGTHDVAESEELAERLRAAGVPAVVLNAKNDA  463 (764)
T ss_pred             EEECCCCCCceeecCCCceEe---CHHHHHHHHHHHHHHHHHcCCCEEEEeCCHHHHHHHHHHHHhCCCcceeeccCchH
Confidence            3333222222111 1112222   22334444444 33333 55699999999999999999999999999999998554


Q ss_pred             HHHHHHHHHHhcCC-CcEEEEecCCcCCCCCC---------------CCcEEEEecCCCCccchhhhhcccccCCCceeE
Q 017573          272 NTRDIIMREFRSGS-SRVLITTDLLARGIDVQ---------------QVSLVINYDLPTQPENYLHRIGRSGRFGRKGVA  335 (369)
Q Consensus       272 ~~r~~~~~~f~~~~-~~vli~t~~~~~G~d~~---------------~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~  335 (369)
                      .+ .+++.  ..|. -.|.|||+++++|.||.               +-=+||....+.|...-.|..||+||.|.+|.+
T Consensus       464 ~E-A~IIa--~AG~~gaVTIATNMAGRGTDIkLg~~~~~~~~~V~~~GGLhVIgTerheSrRID~QLrGRaGRQGDpGss  540 (764)
T PRK12326        464 EE-ARIIA--EAGKYGAVTVSTQMAGRGTDIRLGGSDEADRDRVAELGGLHVIGTGRHRSERLDNQLRGRAGRQGDPGSS  540 (764)
T ss_pred             hH-HHHHH--hcCCCCcEEEEecCCCCccCeecCCCcccchHHHHHcCCcEEEeccCCchHHHHHHHhcccccCCCCCce
Confidence            44 33333  2343 34999999999999986               233677778888999999999999999999999


Q ss_pred             EEEeccccHH
Q 017573          336 INFVTRDDER  345 (369)
Q Consensus       336 ~~~~~~~~~~  345 (369)
                      ..|++-.|.-
T Consensus       541 ~f~lSleDdl  550 (764)
T PRK12326        541 VFFVSLEDDV  550 (764)
T ss_pred             eEEEEcchhH
Confidence            9888866544

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

Probab=99.92  E-value=1.3e-23  Score=187.16  Aligned_cols=321  Identities=17%  Similarity=0.180  Sum_probs=216.7

Q ss_pred             CCcHhhhhhhhccc----cCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCc
Q 017573           18 KPSAIQQRGIVPFC----KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGV   93 (369)
Q Consensus        18 ~~~~~Q~~~~~~~~----~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~   93 (369)
                      ++.+||.-.++.+.    ++=+.|+..++|-|||..++..+......+. .+.-|||||+.. .++|.++|.+||+.  +
T Consensus       399 ~LkdYQlvGvNWL~Llyk~~l~gILADEMGLGKTiQvIaFlayLkq~g~-~gpHLVVvPsST-leNWlrEf~kwCPs--l  474 (941)
T KOG0389|consen  399 QLKDYQLVGVNWLLLLYKKKLNGILADEMGLGKTIQVIAFLAYLKQIGN-PGPHLVVVPSST-LENWLREFAKWCPS--L  474 (941)
T ss_pred             cccchhhhhHHHHHHHHHccccceehhhccCcchhHHHHHHHHHHHcCC-CCCcEEEecchh-HHHHHHHHHHhCCc--e
Confidence            58999999987764    3557799999999999776544443334444 448999999965 46799999999975  6


Q ss_pred             EEEEEECCcchHHHHH-HH-c--cCCcEEEeccHHHHHHH-HcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCc
Q 017573           94 KVHACVGGTSVREDQR-IL-Q--AGVHVVVGTPGRVFDML-RRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPA  168 (369)
Q Consensus        94 ~v~~~~~~~~~~~~~~-~~-~--~~~~iiv~t~~~l~~~~-~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~  168 (369)
                      +|...+|+.......+ .+ .  .+++|+++||+.+..-- .+.-+...+|+++|+||+|.+.+.. ...+..++.- + 
T Consensus       475 ~Ve~YyGSq~ER~~lR~~i~~~~~~ydVllTTY~la~~~kdDRsflk~~~~n~viyDEgHmLKN~~-SeRy~~LM~I-~-  551 (941)
T KOG0389|consen  475 KVEPYYGSQDERRELRERIKKNKDDYDVLLTTYNLAASSKDDRSFLKNQKFNYVIYDEGHMLKNRT-SERYKHLMSI-N-  551 (941)
T ss_pred             EEEeccCcHHHHHHHHHHHhccCCCccEEEEEeecccCChHHHHHHHhccccEEEecchhhhhccc-hHHHHHhccc-c-
Confidence            7777888775433322 22 2  27899999998773211 1111223447999999999997765 4444444433 3 


Q ss_pred             cCcEEEEEeeCChh-HHHHHHHhc---CC-----------------------------------------CEEEEecCc-
Q 017573          169 KVQVGVFSATMPPE-ALEITRKFM---NK-----------------------------------------PVRILVKRD-  202 (369)
Q Consensus       169 ~~~~i~~saT~~~~-~~~~~~~~~---~~-----------------------------------------~~~~~~~~~-  202 (369)
                      ....+++|+||-.+ +.+++..+.   .+                                         |........ 
T Consensus       552 An~RlLLTGTPLQNNL~ELiSLL~FvlP~vF~~~~~dl~~if~~k~~~d~d~e~~~l~qerIsrAK~im~PFILRR~K~q  631 (941)
T KOG0389|consen  552 ANFRLLLTGTPLQNNLKELISLLAFVLPKVFDSSMEDLDVIFKAKKTSDGDIENALLSQERISRAKTIMKPFILRRLKSQ  631 (941)
T ss_pred             ccceEEeeCCcccccHHHHHHHHHHHhhHhhhccchHHHHHHhccCCccchhhHHHHHHHHHHHHHHhhhHHHHHHHHHH
Confidence            44568889998643 222211100   00                                         000000000 


Q ss_pred             --cccccceeEEE-EEccchh-----------------------------------------------------------
Q 017573          203 --ELTLEGIKQFY-VNVEKEE-----------------------------------------------------------  220 (369)
Q Consensus       203 --~~~~~~~~~~~-~~~~~~~-----------------------------------------------------------  220 (369)
                        ...++.+.++. +......                                                           
T Consensus       632 VL~~LPpK~~~Ie~c~mse~Q~~~Y~~~~~~~~~~~~~~~~ns~~~~~~vlmqlRK~AnHPLL~R~~Y~de~L~~mak~i  711 (941)
T KOG0389|consen  632 VLKQLPPKIQRIEYCEMSEKQKQLYDELIELYDVKLNEVSKNSELKSGNVLMQLRKAANHPLLFRSIYTDEKLRKMAKRI  711 (941)
T ss_pred             HHHhcCCccceeEeeecchHHHHHHHHHHHHHhhhccccccccccccchHHHHHHHHhcChhHHHHhccHHHHHHHHHHH
Confidence              00000000000 0000000                                                           


Q ss_pred             -------------------------------------------------hhHHHHHHHHHhc--cCCCeEEEeCCHhhHH
Q 017573          221 -------------------------------------------------WKLETLCDLYETL--AITQSVIFVNTRRKVD  249 (369)
Q Consensus       221 -------------------------------------------------~~~~~l~~~~~~~--~~~k~lv~~~~~~~~~  249 (369)
                                                                       .+...|..++...  .+.++|+|........
T Consensus       712 l~e~ay~~~n~qyIfEDm~~msDfelHqLc~~f~~~~~f~L~d~~~mdSgK~r~L~~LLp~~k~~G~RVLiFSQFTqmLD  791 (941)
T KOG0389|consen  712 LNEPAYKKANEQYIFEDMEVMSDFELHQLCCQFRHLSKFQLKDDLWMDSGKCRKLKELLPKIKKKGDRVLIFSQFTQMLD  791 (941)
T ss_pred             hCchhhhhcCHHHHHHHHHhhhHHHHHHHHHhcCCCcccccCCchhhhhhhHhHHHHHHHHHhhcCCEEEEeeHHHHHHH
Confidence                                                             0566666666554  3368999999999999


Q ss_pred             HHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCC-Cc-EEEEecCCcCCCCCCCCcEEEEecCCCCccchhhhhcccc
Q 017573          250 WLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGS-SR-VLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSG  327 (369)
Q Consensus       250 ~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~-~~-vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~  327 (369)
                      -+.-.|...++....+.|...-.+|..++++|..++ +. +|++|.+.+.|+|+..+++||+++...++..=.|+--|++
T Consensus       792 ILE~~L~~l~~~ylRLDGsTqV~~RQ~lId~Fn~d~difVFLLSTKAGG~GINLt~An~VIihD~dFNP~dD~QAEDRcH  871 (941)
T KOG0389|consen  792 ILEVVLDTLGYKYLRLDGSTQVNDRQDLIDEFNTDKDIFVFLLSTKAGGFGINLTCANTVIIHDIDFNPYDDKQAEDRCH  871 (941)
T ss_pred             HHHHHHHhcCceEEeecCCccchHHHHHHHhhccCCceEEEEEeeccCcceecccccceEEEeecCCCCcccchhHHHHH
Confidence            999999999999999999999999999999998764 44 6678999999999999999999999999999999999999


Q ss_pred             cCCCc--eeEEEEeccccHH
Q 017573          328 RFGRK--GVAINFVTRDDER  345 (369)
Q Consensus       328 R~~~~--~~~~~~~~~~~~~  345 (369)
                      |.|+.  ..++-+++.+..+
T Consensus       872 RvGQtkpVtV~rLItk~TIE  891 (941)
T KOG0389|consen  872 RVGQTKPVTVYRLITKSTIE  891 (941)
T ss_pred             hhCCcceeEEEEEEecCcHH
Confidence            99976  5666677766544

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=99.91  E-value=6.8e-23  Score=190.07  Aligned_cols=124  Identities=19%  Similarity=0.228  Sum_probs=107.3

Q ss_pred             hhhHHHHHHHHHhc--cCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcC
Q 017573          220 EWKLETLCDLYETL--AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLAR  297 (369)
Q Consensus       220 ~~~~~~l~~~~~~~--~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~  297 (369)
                      ..+...+...+...  .+.++||||++++.++.+.+.|...+++...+|+  ...+|+..+..|..+...|+|||+++++
T Consensus       581 ~eK~~Ali~~I~~~~~~grpVLIft~Sve~sE~Ls~~L~~~gI~h~vLna--kq~~REa~Iia~AG~~g~VtIATNMAGR  658 (1025)
T PRK12900        581 REKYNAIVLKVEELQKKGQPVLVGTASVEVSETLSRMLRAKRIAHNVLNA--KQHDREAEIVAEAGQKGAVTIATNMAGR  658 (1025)
T ss_pred             HHHHHHHHHHHHHHhhCCCCEEEEeCcHHHHHHHHHHHHHcCCCceeecC--CHHHhHHHHHHhcCCCCeEEEeccCcCC
Confidence            44667777766443  5679999999999999999999999999999997  5778899999999999999999999999


Q ss_pred             CCCCC---CCcE-----EEEecCCCCccchhhhhcccccCCCceeEEEEeccccHH
Q 017573          298 GIDVQ---QVSL-----VINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDER  345 (369)
Q Consensus       298 G~d~~---~~~~-----vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~  345 (369)
                      |+||+   .+..     ||....|.|...+.|+.||+||.|.+|.+++|++..|.-
T Consensus       659 GtDIkl~~~V~~vGGL~VIgterhes~Rid~Ql~GRtGRqGdpGsS~ffvSleD~L  714 (1025)
T PRK12900        659 GTDIKLGEGVRELGGLFILGSERHESRRIDRQLRGRAGRQGDPGESVFYVSLEDEL  714 (1025)
T ss_pred             CCCcCCccchhhhCCceeeCCCCCchHHHHHHHhhhhhcCCCCcceEEEechhHHH
Confidence            99999   3433     377778888899999999999999999999999876654

>COG4889 Predicted helicase [General function prediction only]

Probab=99.91  E-value=1.3e-24  Score=195.35  Aligned_cols=317  Identities=18%  Similarity=0.212  Sum_probs=191.1

Q ss_pred             HHHHHHhCCCCCCcHhhhhhhhccccC----CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHH
Q 017573            7 LLRGIYAYGFEKPSAIQQRGIVPFCKG----LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEK   82 (369)
Q Consensus         7 i~~~l~~~~~~~~~~~Q~~~~~~~~~~----~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~   82 (369)
                      +..+|.-..=..|||+|++|+++..++    .+.-+.+.||+|||++++- +.+++..    .++|+++|+.+|..|..+
T Consensus       150 ~~~nl~l~~~kk~R~hQq~Aid~a~~~F~~n~RGkLIMAcGTGKTfTsLk-isEala~----~~iL~LvPSIsLLsQTlr  224 (1518)
T COG4889         150 LQDNLPLKKPKKPRPHQQTAIDAAKEGFSDNDRGKLIMACGTGKTFTSLK-ISEALAA----ARILFLVPSISLLSQTLR  224 (1518)
T ss_pred             cccccccCCCCCCChhHHHHHHHHHhhcccccCCcEEEecCCCccchHHH-HHHHHhh----hheEeecchHHHHHHHHH
Confidence            334443334457999999999988764    5667788999999999754 3444443    389999999999999988


Q ss_pred             HHHHhccccCcEEEEEECCcchHHH-----------------H--------HHHccCCcEEEeccHHHHHHHHcCCCCCC
Q 017573           83 VMRALGDYLGVKVHACVGGTSVRED-----------------Q--------RILQAGVHVVVGTPGRVFDMLRRQSLRPD  137 (369)
Q Consensus        83 ~~~~~~~~~~~~v~~~~~~~~~~~~-----------------~--------~~~~~~~~iiv~t~~~l~~~~~~~~~~~~  137 (369)
                      +|..-.. +.++.....++......                 .        .....+--|+++|++++...-.....-..
T Consensus       225 ew~~~~~-l~~~a~aVcSD~kvsrs~eDik~sdl~~p~sT~~~~il~~~~~~~k~~~~~vvFsTYQSl~~i~eAQe~G~~  303 (1518)
T COG4889         225 EWTAQKE-LDFRASAVCSDDKVSRSAEDIKASDLPIPVSTDLEDILSEMEHRQKANGLTVVFSTYQSLPRIKEAQEAGLD  303 (1518)
T ss_pred             HHhhccC-ccceeEEEecCccccccccccccccCCCCCcccHHHHHHHHHHhhccCCcEEEEEcccchHHHHHHHHcCCC
Confidence            8876422 23333333322221110                 0        11123456999999999888777666777


Q ss_pred             CccEEEEechhHhhccCcHHHHHHHHhhCC-----ccCcEEEEEeeCChhHHHHHHH-----------------------
Q 017573          138 YIKMFVLDEADEMLSRGFKDQIYDIFQLLP-----AKVQVGVFSATMPPEALEITRK-----------------------  189 (369)
Q Consensus       138 ~~~~viiDE~H~~~~~~~~~~~~~~~~~~~-----~~~~~i~~saT~~~~~~~~~~~-----------------------  189 (369)
                      .|++||+||+|+.........-.+.+.++.     +..+.+.|||||.--.+....+                       
T Consensus       304 ~fDliicDEAHRTtGa~~a~dd~saFt~vHs~~niKa~kRlYmTATPkiy~eS~K~kAkd~s~~l~SMDDe~~fGeef~r  383 (1518)
T COG4889         304 EFDLIICDEAHRTTGATLAGDDKSAFTRVHSDQNIKAAKRLYMTATPKIYSESSKAKAKDHSAELSSMDDELTFGEEFHR  383 (1518)
T ss_pred             CccEEEecchhccccceecccCcccceeecCcchhHHHHhhhcccCchhhchhhhhhhhhccceeeccchhhhhchhhhc
Confidence            899999999999764332222112222221     1345678999985211111000                       


Q ss_pred             ----------hcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHHHhc---------------------cCCCe
Q 017573          190 ----------FMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETL---------------------AITQS  238 (369)
Q Consensus       190 ----------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~---------------------~~~k~  238 (369)
                                ++....+.....+........+....-+......+....++-.+                     +..+.
T Consensus       384 l~FgeAv~rdlLTDYKVmvlaVd~~~i~~~~~~~~~~~~~~L~~dd~~kIvG~wnGlakr~g~~n~~~~~~~d~ap~~RA  463 (1518)
T COG4889         384 LGFGEAVERDLLTDYKVMVLAVDKEVIAGVLQSVLSGPSKGLALDDVSKIVGCWNGLAKRNGEDNDLKNIKADTAPMQRA  463 (1518)
T ss_pred             ccHHHHHHhhhhccceEEEEEechhhhhhhhhhhccCcccccchhhhhhhhhhhhhhhhhccccccccCCcCCchHHHHH
Confidence                      01111111111111000000111111111122333333322111                     11256


Q ss_pred             EEEeCCHhhHHHHHHHHhh---------------CCCeeEEecCCCCHHHHHHHHH---HHhcCCCcEEEEecCCcCCCC
Q 017573          239 VIFVNTRRKVDWLTDKMRS---------------RDHTVSATHGDMDQNTRDIIMR---EFRSGSSRVLITTDLLARGID  300 (369)
Q Consensus       239 lv~~~~~~~~~~~~~~l~~---------------~~~~~~~~~~~~~~~~r~~~~~---~f~~~~~~vli~t~~~~~G~d  300 (369)
                      +-||.++++.+.+++.+..               ....+..+.|.|+-.+|...+.   .|...+++||-....+++|+|
T Consensus       464 IaF~k~I~tSK~i~~sFe~Vve~Y~~Elk~d~~nL~iSi~HvDGtmNal~R~~l~~l~~~~~~neckIlSNaRcLSEGVD  543 (1518)
T COG4889         464 IAFAKDIKTSKQIAESFETVVEAYDEELKKDFKNLKISIDHVDGTMNALERLDLLELKNTFEPNECKILSNARCLSEGVD  543 (1518)
T ss_pred             HHHHHhhHHHHHHHHHHHHHHHHHHHHHHhcCCCceEEeecccccccHHHHHHHHhccCCCCcchheeeccchhhhcCCC
Confidence            8889888877766655532               1345667788888888844433   234456788888889999999


Q ss_pred             CCCCcEEEEecCCCCccchhhhhcccccC
Q 017573          301 VQQVSLVINYDLPTQPENYLHRIGRSGRF  329 (369)
Q Consensus       301 ~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~  329 (369)
                      +|.++.||++++..+..+.+|.+||+.|.
T Consensus       544 VPaLDsViFf~pr~smVDIVQaVGRVMRK  572 (1518)
T COG4889         544 VPALDSVIFFDPRSSMVDIVQAVGRVMRK  572 (1518)
T ss_pred             ccccceEEEecCchhHHHHHHHHHHHHHh
Confidence            99999999999999999999999999996

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=99.91  E-value=2.7e-22  Score=185.37  Aligned_cols=314  Identities=19%  Similarity=0.226  Sum_probs=211.6

Q ss_pred             CCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEE
Q 017573           18 KPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHA   97 (369)
Q Consensus        18 ~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~   97 (369)
                      .|++.|-  +-.+.-.+.-+..+.||+|||+++.++++-....+.   .+.+++|+.-|+.+-++++..++..+|+++..
T Consensus        82 ~~ydVQl--iGg~~Lh~G~iaEM~TGEGKTLvA~l~a~l~al~G~---~VhvvT~ndyLA~RD~e~m~~l~~~lGl~v~~  156 (913)
T PRK13103         82 RHFDVQL--IGGMTLHEGKIAEMRTGEGKTLVGTLAVYLNALSGK---GVHVVTVNDYLARRDANWMRPLYEFLGLSVGI  156 (913)
T ss_pred             CcchhHH--HhhhHhccCccccccCCCCChHHHHHHHHHHHHcCC---CEEEEeCCHHHHHHHHHHHHHHhcccCCEEEE
Confidence            4455554  444444677899999999999999888876666555   89999999999999999999999999999999


Q ss_pred             EECCcchHHHHHHHccCCcEEEeccHHH-HHHHHcCCCC-------CCCccEEEEechhHhh-ccC--------------
Q 017573           98 CVGGTSVREDQRILQAGVHVVVGTPGRV-FDMLRRQSLR-------PDYIKMFVLDEADEML-SRG--------------  154 (369)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~iiv~t~~~l-~~~~~~~~~~-------~~~~~~viiDE~H~~~-~~~--------------  154 (369)
                      +.++.+....+....  ++|+++|...| +.+++.. ..       ...++++|+||+|.+. +..              
T Consensus       157 i~~~~~~~err~~Y~--~dI~YGT~~e~gFDYLrD~-~~~~~~~~vqr~l~~aIVDEvDsiLIDEArtPLIISg~~~~~~  233 (913)
T PRK13103        157 VTPFQPPEEKRAAYA--ADITYGTNNEFGFDYLRDN-MAFSLDDKFQRELNFAVIDEVDSILIDEARTPLIISGQAEDSS  233 (913)
T ss_pred             ECCCCCHHHHHHHhc--CCEEEEcccccccchhhcc-ceechhhhcccccceeEechhhheeccccCCceeecCCCccch
Confidence            988877666555444  89999999887 3333332 22       2568999999999754 100              


Q ss_pred             -cHHHHHHHHhhCC-------------------cc---------------------------------------------
Q 017573          155 -FKDQIYDIFQLLP-------------------AK---------------------------------------------  169 (369)
Q Consensus       155 -~~~~~~~~~~~~~-------------------~~---------------------------------------------  169 (369)
                       .......+...+.                   .+                                             
T Consensus       234 ~~y~~~~~~v~~L~~~~~~~~~~~~~~~~y~idek~~~v~LTe~G~~~~e~~~~~~~i~~~~~~ly~~~~~~~~~~i~~A  313 (913)
T PRK13103        234 KLYIEINRLIPRLKQHIEEVEGQVTQEGHFTIDEKTRQVELNEAGHQFIEEMLTQAGLLAEGESLYSAHNLGLLTHVYAG  313 (913)
T ss_pred             HHHHHHHHHHHHHHhhhhccccccCCCCCeEEEcCCCeeeechHHHHHHHHHhhhCCCcccchhccChhhhHHHHHHHHH
Confidence             0000000000000                   00                                             


Q ss_pred             -----------------------------------------------------------------------CcEEEEEee
Q 017573          170 -----------------------------------------------------------------------VQVGVFSAT  178 (369)
Q Consensus       170 -----------------------------------------------------------------------~~~i~~saT  178 (369)
                                                                                             .++.+||+|
T Consensus       314 L~A~~lf~~d~dYiV~dg~V~IVDe~TGR~m~grrwsdGLHQaIEaKE~v~I~~e~~t~AsIT~QnfFr~Y~kLsGMTGT  393 (913)
T PRK13103        314 LRAHKLFHRNVEYIVQDGQVLLIDEHTGRTMPGRRLSEGLHQAIEAKENLNIQAESQTLASTTFQNYFRLYNKLSGMTGT  393 (913)
T ss_pred             HHHHHHHhcCCcEEEECCEEEEEECCCCCcCCCCccchHHHHHHHHHcCCCcCCCceeEEeehHHHHHHhcchhccCCCC
Confidence                                                                                   345667777


Q ss_pred             CChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHH-Hhc-cCCCeEEEeCCHhhHHHHHHHHh
Q 017573          179 MPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLY-ETL-AITQSVIFVNTRRKVDWLTDKMR  256 (369)
Q Consensus       179 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~-~~~-~~~k~lv~~~~~~~~~~~~~~l~  256 (369)
                      ...... .....++-++.......+.........++  .+...+...+.+-+ ..+ .+.++||-+.|++..+.+++.|.
T Consensus       394 a~te~~-Ef~~iY~l~Vv~IPTnkP~~R~D~~d~vy--~t~~eK~~Ai~~ei~~~~~~GrPVLVGT~SVe~SE~ls~~L~  470 (913)
T PRK13103        394 ADTEAF-EFRQIYGLDVVVIPPNKPLARKDFNDLVY--LTAEEKYAAIITDIKECMALGRPVLVGTATIETSEHMSNLLK  470 (913)
T ss_pred             CHHHHH-HHHHHhCCCEEECCCCCCcccccCCCeEE--cCHHHHHHHHHHHHHHHHhCCCCEEEEeCCHHHHHHHHHHHH
Confidence            754443 33344444433333222222222222222  22233444444433 333 46799999999999999999999


Q ss_pred             hCCCeeEEecCCCCHHHHHHHHHHHhcCC-CcEEEEecCCcCCCCCC---------------------------------
Q 017573          257 SRDHTVSATHGDMDQNTRDIIMREFRSGS-SRVLITTDLLARGIDVQ---------------------------------  302 (369)
Q Consensus       257 ~~~~~~~~~~~~~~~~~r~~~~~~f~~~~-~~vli~t~~~~~G~d~~---------------------------------  302 (369)
                      +.+++..++++.....+...+ .  ..|. -.|.|||+++++|.||.                                 
T Consensus       471 ~~gi~h~VLNAk~~~~EA~II-a--~AG~~GaVTIATNMAGRGTDIkLg~n~~~~~~~~~~~~~~~~~~~~~~~~~~~e~  547 (913)
T PRK13103        471 KEGIEHKVLNAKYHEKEAEII-A--QAGRPGALTIATNMAGRGTDILLGGNWEVEVAALENPTPEQIAQIKADWQKRHQQ  547 (913)
T ss_pred             HcCCcHHHhccccchhHHHHH-H--cCCCCCcEEEeccCCCCCCCEecCCchHHHHHhhhhhhHHHHHHHHHHHHhHHHH
Confidence            999999888887654443333 3  3343 35999999999999984                                 


Q ss_pred             ----CCcEEEEecCCCCccchhhhhcccccCCCceeEEEEeccccHH
Q 017573          303 ----QVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDER  345 (369)
Q Consensus       303 ----~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~  345 (369)
                          +-=+||....+.|...=.|..||+||.|.+|.+-.|++-.|.-
T Consensus       548 V~e~GGLhVIgTerheSrRID~QLrGRaGRQGDPGsS~f~lSlED~L  594 (913)
T PRK13103        548 VIEAGGLHVIASERHESRRIDNQLRGRAGRQGDPGSSRFYLSLEDSL  594 (913)
T ss_pred             HHHcCCCEEEeeccCchHHHHHHhccccccCCCCCceEEEEEcCcHH
Confidence                2335777778888888899999999999999999998875543

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=99.90  E-value=3.2e-22  Score=162.13  Aligned_cols=188  Identities=35%  Similarity=0.516  Sum_probs=149.7

Q ss_pred             hCCCCCCcHhhhhhhhccccC-CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhcccc
Q 017573           13 AYGFEKPSAIQQRGIVPFCKG-LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYL   91 (369)
Q Consensus        13 ~~~~~~~~~~Q~~~~~~~~~~-~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~   91 (369)
                      .+++.+++++|.++++.+... +.+++.+|||+|||.+++.+++..+..... .++++++|+.+++.|+.+.+.+.....
T Consensus         3 ~~~~~~~~~~Q~~~~~~~~~~~~~~~i~~~~GsGKT~~~~~~~~~~~~~~~~-~~~l~~~p~~~~~~~~~~~~~~~~~~~   81 (201)
T smart00487        3 KFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGKG-KRVLVLVPTRELAEQWAEELKKLGPSL   81 (201)
T ss_pred             ccCCCCCCHHHHHHHHHHHcCCCcEEEECCCCCchhHHHHHHHHHHhcccCC-CcEEEEeCCHHHHHHHHHHHHHHhccC
Confidence            457789999999999999998 999999999999999888888887766532 389999999999999999999876554


Q ss_pred             C-cEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCccC
Q 017573           92 G-VKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKV  170 (369)
Q Consensus        92 ~-~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~  170 (369)
                      . .......+...............+++++|++.+.............++++|+||+|.+....+...+..+...+++..
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~t~~~l~~~~~~~~~~~~~~~~iIiDE~h~~~~~~~~~~~~~~~~~~~~~~  161 (201)
T smart00487       82 GLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDLLELSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNV  161 (201)
T ss_pred             CeEEEEEeCCcchHHHHHHHhcCCCCEEEeChHHHHHHHHcCCcCHhHCCEEEEECHHHHhcCCcHHHHHHHHHhCCccc
Confidence            4 333334443333333333344449999999999998888776667789999999999986567788888888887888


Q ss_pred             cEEEEEeeCChhHHHHHHHhcCCCEEEEecC
Q 017573          171 QVGVFSATMPPEALEITRKFMNKPVRILVKR  201 (369)
Q Consensus       171 ~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~  201 (369)
                      +++++||||+.+.......++.....+....
T Consensus       162 ~~v~~saT~~~~~~~~~~~~~~~~~~~~~~~  192 (201)
T smart00487      162 QLLLLSATPPEEIENLLELFLNDPVFIDVGP  192 (201)
T ss_pred             eEEEEecCCchhHHHHHHHhcCCCEEEeCCc
Confidence            9999999999888888878777666555443

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=99.90  E-value=8.1e-21  Score=175.77  Aligned_cols=131  Identities=24%  Similarity=0.354  Sum_probs=113.7

Q ss_pred             hHHHHHHHHHhc--cCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCC
Q 017573          222 KLETLCDLYETL--AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGI  299 (369)
Q Consensus       222 ~~~~l~~~~~~~--~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~  299 (369)
                      ..+.+...+...  .+.+++|||++.+.++.+++.|...+.++..+|++++..+|.++++.|++|++.|+|+|+.+.+|+
T Consensus       427 qi~~Ll~eI~~~~~~g~~vLIf~~tk~~ae~L~~~L~~~gi~~~~lh~~~~~~eR~~~l~~fr~G~i~VLV~t~~L~rGf  506 (655)
T TIGR00631       427 QVDDLLSEIRQRVARNERVLVTTLTKKMAEDLTDYLKELGIKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGINLLREGL  506 (655)
T ss_pred             hHHHHHHHHHHHHcCCCEEEEEECCHHHHHHHHHHHhhhccceeeeeCCCCHHHHHHHHHHHhcCCceEEEEcChhcCCe
Confidence            444444444432  456899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCcEEEEec-----CCCCccchhhhhcccccCCCceeEEEEeccccHHHHHHHHHH
Q 017573          300 DVQQVSLVINYD-----LPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKF  353 (369)
Q Consensus       300 d~~~~~~vi~~~-----~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~  353 (369)
                      |+|.+++|++++     .|.+...|+|++||+||. ..|.+++|.+..+..+...+.+.
T Consensus       507 DiP~v~lVvi~DadifG~p~~~~~~iqriGRagR~-~~G~vi~~~~~~~~~~~~ai~~~  564 (655)
T TIGR00631       507 DLPEVSLVAILDADKEGFLRSERSLIQTIGRAARN-VNGKVIMYADKITDSMQKAIEET  564 (655)
T ss_pred             eeCCCcEEEEeCcccccCCCCHHHHHHHhcCCCCC-CCCEEEEEEcCCCHHHHHHHHHH
Confidence            999999999887     688999999999999998 67999999998776665555443

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

>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]

Probab=99.90  E-value=3.4e-22  Score=185.89  Aligned_cols=318  Identities=18%  Similarity=0.208  Sum_probs=216.4

Q ss_pred             CCCcHhhhhhhhccc----cCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccC
Q 017573           17 EKPSAIQQRGIVPFC----KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLG   92 (369)
Q Consensus        17 ~~~~~~Q~~~~~~~~----~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~   92 (369)
                      .++|.||-+.++.++    .++++|+...+|.|||+..+..+.........-+..|+|+|...+ ..|.++|..+.   .
T Consensus       369 ~~LRdyQLeGlNWl~~~W~~~~n~ILADEmgLgktvqti~fl~~l~~~~~~~gpflvvvplst~-~~W~~ef~~w~---~  444 (1373)
T KOG0384|consen  369 NELRDYQLEGLNWLLYSWYKRNNCILADEMGLGKTVQTITFLSYLFHSLQIHGPFLVVVPLSTI-TAWEREFETWT---D  444 (1373)
T ss_pred             chhhhhhcccchhHHHHHHhcccceehhhcCCCcchHHHHHHHHHHHhhhccCCeEEEeehhhh-HHHHHHHHHHh---h
Confidence            689999999998876    579999999999999976544333333333233379999999655 45777788775   6


Q ss_pred             cEEEEEECCcchHHHHHH----Hcc-----CCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHH
Q 017573           93 VKVHACVGGTSVREDQRI----LQA-----GVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIF  163 (369)
Q Consensus        93 ~~v~~~~~~~~~~~~~~~----~~~-----~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~  163 (369)
                      +++.+.+|+.......+.    ...     ..+++++|++.++.-...  +..-.|.++++||||++.+..  ..+...+
T Consensus       445 mn~i~y~g~~~sr~~i~~ye~~~~~~~~~lkf~~lltTye~~LkDk~~--L~~i~w~~~~vDeahrLkN~~--~~l~~~l  520 (1373)
T KOG0384|consen  445 MNVIVYHGNLESRQLIRQYEFYHSSNTKKLKFNALLTTYEIVLKDKAE--LSKIPWRYLLVDEAHRLKNDE--SKLYESL  520 (1373)
T ss_pred             hceeeeecchhHHHHHHHHHheecCCccccccceeehhhHHHhccHhh--hccCCcceeeecHHhhcCchH--HHHHHHH
Confidence            788888887765544322    112     478999999988653322  333447899999999996543  3333445


Q ss_pred             hhCCccCcEEEEEeeCChhHHHHHHHhcC--CCEEEEe---------------------------------cCccccccc
Q 017573          164 QLLPAKVQVGVFSATMPPEALEITRKFMN--KPVRILV---------------------------------KRDELTLEG  208 (369)
Q Consensus       164 ~~~~~~~~~i~~saT~~~~~~~~~~~~~~--~~~~~~~---------------------------------~~~~~~~~~  208 (369)
                      ..+..+ ..+++|+||-.+.......++.  .|..+..                                 +.+...++.
T Consensus       521 ~~f~~~-~rllitgTPlQNsikEL~sLl~Fl~P~kf~~~~~f~~~~~~~~e~~~~~L~~~L~P~~lRr~kkdvekslp~k  599 (1373)
T KOG0384|consen  521 NQFKMN-HRLLITGTPLQNSLKELWSLLHFLMPGKFDSWDEFLEEFDEETEEQVRKLQQILKPFLLRRLKKDVEKSLPPK  599 (1373)
T ss_pred             HHhccc-ceeeecCCCccccHHHHHHHhcccCCCCCCcHHHHHHhhcchhHHHHHHHHHHhhHHHHHHHHhhhccCCCCC
Confidence            555433 3577899996543332221110  1100000                                 000001111


Q ss_pred             eeEEE-EEccc------------------------------------------------hhhh---H------HHHHHHH
Q 017573          209 IKQFY-VNVEK------------------------------------------------EEWK---L------ETLCDLY  230 (369)
Q Consensus       209 ~~~~~-~~~~~------------------------------------------------~~~~---~------~~l~~~~  230 (369)
                      .+.+. +....                                                .+..   .      ..+..++
T Consensus       600 ~E~IlrVels~lQk~yYk~ILtkN~~~LtKG~~g~~~~lLNimmELkKccNHpyLi~gaee~~~~~~~~~~~d~~L~~lI  679 (1373)
T KOG0384|consen  600 EETILRVELSDLQKQYYKAILTKNFSALTKGAKGSTPSLLNIMMELKKCCNHPYLIKGAEEKILGDFRDKMRDEALQALI  679 (1373)
T ss_pred             cceEEEeehhHHHHHHHHHHHHhhHHHHhccCCCCCchHHHHHHHHHHhcCCccccCcHHHHHHHhhhhcchHHHHHHHH
Confidence            11110 00000                                                0000   0      1222222


Q ss_pred             -------------Hhc--cCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcC---CCcEEEEe
Q 017573          231 -------------ETL--AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSG---SSRVLITT  292 (369)
Q Consensus       231 -------------~~~--~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~---~~~vli~t  292 (369)
                                   -+.  .+-++|||..-+....-++++|...+++...+.|....+.|..+++.|+..   +..+|++|
T Consensus       680 ~sSGKlVLLDKLL~rLk~~GHrVLIFSQMVRmLDIL~eYL~~r~ypfQRLDGsvrgelRq~AIDhFnap~SddFvFLLST  759 (1373)
T KOG0384|consen  680 QSSGKLVLLDKLLPRLKEGGHRVLIFSQMVRMLDILAEYLSLRGYPFQRLDGSVRGELRQQAIDHFNAPDSDDFVFLLST  759 (1373)
T ss_pred             HhcCcEEeHHHHHHHHhcCCceEEEhHHHHHHHHHHHHHHHHcCCcceeccCCcchHHHHHHHHhccCCCCCceEEEEec
Confidence                         222  234899999999999999999999999999999999999999999999864   46689999


Q ss_pred             cCCcCCCCCCCCcEEEEecCCCCccchhhhhcccccCCCc--eeEEEEecccc
Q 017573          293 DLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRK--GVAINFVTRDD  343 (369)
Q Consensus       293 ~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~--~~~~~~~~~~~  343 (369)
                      .+.+-|||+..++.||+++..||+..=.|+..|++|.|++  ..+|-+++.+.
T Consensus       760 RAGGLGINLatADTVIIFDSDWNPQNDLQAqARaHRIGQkk~VnVYRLVTk~T  812 (1373)
T KOG0384|consen  760 RAGGLGINLATADTVIIFDSDWNPQNDLQAQARAHRIGQKKHVNVYRLVTKNT  812 (1373)
T ss_pred             ccCcccccccccceEEEeCCCCCcchHHHHHHHHHhhcccceEEEEEEecCCc
Confidence            9999999999999999999999999999999999999977  56777777763

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

Probab=99.88  E-value=3.5e-20  Score=176.47  Aligned_cols=315  Identities=18%  Similarity=0.199  Sum_probs=189.1

Q ss_pred             CCCcHhhhhhhhccc----cCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHH-HHHHHHhcccc
Q 017573           17 EKPSAIQQRGIVPFC----KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQI-EKVMRALGDYL   91 (369)
Q Consensus        17 ~~~~~~Q~~~~~~~~----~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~-~~~~~~~~~~~   91 (369)
                      -++|+-|.+....+.    +++.++++|+||+|||++++++++....    +.+++|.+||++|.+|. .+.+..+....
T Consensus       244 ~e~R~~Q~~ma~~V~~~l~~~~~~~~eA~tGtGKT~ayllp~l~~~~----~~~vvI~t~T~~Lq~Ql~~~~i~~l~~~~  319 (820)
T PRK07246        244 LEERPKQESFAKLVGEDFHDGPASFIEAQTGIGKTYGYLLPLLAQSD----QRQIIVSVPTKILQDQIMAEEVKAIQEVF  319 (820)
T ss_pred             CccCHHHHHHHHHHHHHHhCCCcEEEECCCCCcHHHHHHHHHHHhcC----CCcEEEEeCcHHHHHHHHHHHHHHHHHhc
Confidence            379999999665554    4688999999999999999999886542    33899999999999999 45566555445


Q ss_pred             CcEEEEEECCcchH-----------------H-------------------------------HH---------------
Q 017573           92 GVKVHACVGGTSVR-----------------E-------------------------------DQ---------------  108 (369)
Q Consensus        92 ~~~v~~~~~~~~~~-----------------~-------------------------------~~---------------  108 (369)
                      ++++..+.|+...-                 .                               +.               
T Consensus       320 ~~~~~~~kg~~~ylcl~k~~~~l~~~~~~~~~~~~~~~il~Wl~~T~tGD~~El~~~~~~~~~w~~i~~~~~~~~~cp~~  399 (820)
T PRK07246        320 HIDCHSLKGPQNYLKLDAFYDSLQQNDDNRLVNRYKMQLLVWLTETETGDLDEIKQKQRYAAYFDQLKHDGNLSQSSLFY  399 (820)
T ss_pred             CCcEEEEECCcccccHHHHHHHhhccCcchHHHHHHHHHHHHHhcCCCCCHhhccCCccccHHHHHhhccCCCCCCCCcc
Confidence            55555444321100                 0                               00               


Q ss_pred             --------HHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccC-----c-------HHH----------
Q 017573          109 --------RILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRG-----F-------KDQ----------  158 (369)
Q Consensus       109 --------~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~-----~-------~~~----------  158 (369)
                              +.....++|+|+++..|...+..... ....+.+|+||||++.+..     .       ...          
T Consensus       400 ~~cf~~~ar~~a~~AdivItNHall~~~~~~~~~-~p~~~~lIiDEAH~l~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  478 (820)
T PRK07246        400 DYDFWKRSYEKAKTARLLITNHAYFLTRVQDDKD-FARNKVLVFDEAQKLMLQLEQLSRHQLNITSFLQTIQKALSGPLP  478 (820)
T ss_pred             hhhHHHHHHHHHHhCCEEEEchHHHHHHHhhccC-CCCCCEEEEECcchhHHHHHHHhcceecHHHHHHHHHHHHHHHHH
Confidence                    00022479999999988876654432 3457999999999875211     0       000          


Q ss_pred             ---------------------------------H------------------HHHHhh----------------------
Q 017573          159 ---------------------------------I------------------YDIFQL----------------------  165 (369)
Q Consensus       159 ---------------------------------~------------------~~~~~~----------------------  165 (369)
                                                       +                  ..++..                      
T Consensus       479 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~l~~l~~~~~~~~~~~~~~~~~~~W~e~~~~~~~~~~~l~~  558 (820)
T PRK07246        479 LLQKRLLESISFELLQLSEQFYQGKERQLIHDSLSRLHQYFSELEVAGFQELQAFFATAEGDYWLESEKQSEKRVTYLNS  558 (820)
T ss_pred             HHhhhhHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCeEEEEecCCCCcceeEEEe
Confidence                                             0                  000000                      


Q ss_pred             -----------CCccCcEEEEEeeCChh-HHHHHHHhcCCC-EEEEecCccccccceeEEEEE--ccc-----hhhhHHH
Q 017573          166 -----------LPAKVQVGVFSATMPPE-ALEITRKFMNKP-VRILVKRDELTLEGIKQFYVN--VEK-----EEWKLET  225 (369)
Q Consensus       166 -----------~~~~~~~i~~saT~~~~-~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~--~~~-----~~~~~~~  225 (369)
                                 ++....+|++|||+..+ ...+ ...++-. .......  .....-...+..  .+.     .....+.
T Consensus       559 ~pl~v~~~~~~~~~~~~~i~tSATL~v~~~f~~-~~~lGl~~~~~~~~~--~~~~~~~~~~i~~~~p~~~~~~~~~~~~~  635 (820)
T PRK07246        559 ASKAFTHFSQLLPETCKTYFVSATLQISPRVSL-ADLLGFEEYLFHKIE--KDKKQDQLVVVDQDMPLVTETSDEVYAEE  635 (820)
T ss_pred             eeCcHHHHHHHHhcCCeEEEEecccccCCCCcH-HHHcCCCccceecCC--CChHHccEEEeCCCCCCCCCCChHHHHHH
Confidence                       01113567888887521 1122 2222211 1111110  111111111111  111     1112222


Q ss_pred             HHHHHHh--ccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCC
Q 017573          226 LCDLYET--LAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQ  303 (369)
Q Consensus       226 l~~~~~~--~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~  303 (369)
                      +.+.+..  ..+++++|+++|.+..+.+++.|......+ ...|...  .+.+++++|++++..||++|..+.+|+|+|+
T Consensus       636 ~~~~i~~~~~~~g~~LVLFtS~~~l~~v~~~l~~~~~~~-l~Qg~~~--~~~~l~~~F~~~~~~vLlG~~sFwEGVD~p~  712 (820)
T PRK07246        636 IAKRLEELKQLQQPILVLFNSKKHLLAVSDLLDQWQVSH-LAQEKNG--TAYNIKKRFDRGEQQILLGLGSFWEGVDFVQ  712 (820)
T ss_pred             HHHHHHHHHhcCCCEEEEECcHHHHHHHHHHHhhcCCcE-EEeCCCc--cHHHHHHHHHcCCCeEEEecchhhCCCCCCC
Confidence            2222211  345899999999999999999997654443 4444322  3566899999988889999999999999974


Q ss_pred             --CcEEEEecCCCC-c-----------------------------cchhhhhcccccCCCceeEEEEeccc
Q 017573          304 --VSLVINYDLPTQ-P-----------------------------ENYLHRIGRSGRFGRKGVAINFVTRD  342 (369)
Q Consensus       304 --~~~vi~~~~~~~-~-----------------------------~~~~Q~~GR~~R~~~~~~~~~~~~~~  342 (369)
                        ...+|+...|.. +                             ..+.|.+||+.|..++.-+++++++.
T Consensus       713 ~~~~~viI~kLPF~~P~dP~~~a~~~~~~~~g~~~F~~~~lP~A~iklkQg~GRLIRs~~D~Gvv~ilD~R  783 (820)
T PRK07246        713 ADRMIEVITRLPFDNPEDPFVKKMNQYLLQEGKNPFYDYFLPMTILRLKQAIGRTMRREDQKSAVLILDRR  783 (820)
T ss_pred             CCeEEEEEecCCCCCCCCHHHHHHHHHHHHhCCCchhheeHHHHHHHHHHHhcccccCCCCcEEEEEECCc
Confidence              555677776532 1                             23689999999997654455566654

>KOG0923 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.88  E-value=9.6e-21  Score=166.04  Aligned_cols=311  Identities=16%  Similarity=0.221  Sum_probs=207.0

Q ss_pred             CCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHH-HhccccCcEE
Q 017573           17 EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMR-ALGDYLGVKV   95 (369)
Q Consensus        17 ~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~-~~~~~~~~~v   95 (369)
                      ...+++-.+.+.++.+++-++|.|+||||||...-..+.+. .-...+.++-.--|++.-+...+.... ++...+|-.|
T Consensus       264 LPVy~ykdell~av~e~QVLiI~GeTGSGKTTQiPQyL~Ea-Gytk~gk~IgcTQPRRVAAmSVAaRVA~EMgvkLG~eV  342 (902)
T KOG0923|consen  264 LPVYPYKDELLKAVKEHQVLIIVGETGSGKTTQIPQYLYEA-GYTKGGKKIGCTQPRRVAAMSVAARVAEEMGVKLGHEV  342 (902)
T ss_pred             CCchhhHHHHHHHHHhCcEEEEEcCCCCCccccccHHHHhc-ccccCCceEeecCcchHHHHHHHHHHHHHhCccccccc
Confidence            34577788889999999999999999999997653333322 112222245555688877766655543 3443444444


Q ss_pred             EEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhh--ccCcHHHHHHHHhhCCccCcEE
Q 017573           96 HACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEML--SRGFKDQIYDIFQLLPAKVQVG  173 (369)
Q Consensus        96 ~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~--~~~~~~~~~~~~~~~~~~~~~i  173 (369)
                      .+.+.-...      .....-+=++|-.+|++.+... .++..++++|+||+|.=.  ..-....+..+. .+.+..+++
T Consensus       343 GYsIRFEdc------TSekTvlKYMTDGmLlREfL~e-pdLasYSViiiDEAHERTL~TDILfgLvKDIa-r~RpdLKll  414 (902)
T KOG0923|consen  343 GYSIRFEDC------TSEKTVLKYMTDGMLLREFLSE-PDLASYSVIIVDEAHERTLHTDILFGLVKDIA-RFRPDLKLL  414 (902)
T ss_pred             ceEEEeccc------cCcceeeeeecchhHHHHHhcc-ccccceeEEEeehhhhhhhhhhHHHHHHHHHH-hhCCcceEE
Confidence            333221110      1123567799999998877665 456668999999999721  111122222333 334677899


Q ss_pred             EEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHH---HhccCCCeEEEeCCHhhHHH
Q 017573          174 VFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLY---ETLAITQSVIFVNTRRKVDW  250 (369)
Q Consensus       174 ~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~---~~~~~~k~lv~~~~~~~~~~  250 (369)
                      ..|||+..  ..+...+-.-|+.....+.    ..+..+|...+........+..++   ..-+.+.+|||....++.+.
T Consensus       415 IsSAT~DA--ekFS~fFDdapIF~iPGRR----yPVdi~Yt~~PEAdYldAai~tVlqIH~tqp~GDILVFltGQeEIEt  488 (902)
T KOG0923|consen  415 ISSATMDA--EKFSAFFDDAPIFRIPGRR----YPVDIFYTKAPEADYLDAAIVTVLQIHLTQPLGDILVFLTGQEEIET  488 (902)
T ss_pred             eeccccCH--HHHHHhccCCcEEeccCcc----cceeeecccCCchhHHHHHHhhheeeEeccCCccEEEEeccHHHHHH
Confidence            99999853  3333333334444333222    233445554444443333333333   33466899999999999888


Q ss_pred             HHHHHhhC---------CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecC---------
Q 017573          251 LTDKMRSR---------DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDL---------  312 (369)
Q Consensus       251 ~~~~l~~~---------~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~---------  312 (369)
                      ..+.|...         ..-+..+++.++.+.+.++++--.+|.-+|++||+++++.+.|+++..||.-+.         
T Consensus       489 ~~e~l~~~~~~LGski~eliv~PiYaNLPselQakIFePtP~gaRKVVLATNIAETSlTIdgI~yViDpGf~K~nsynpr  568 (902)
T KOG0923|consen  489 VKENLKERCRRLGSKIRELIVLPIYANLPSELQAKIFEPTPPGARKVVLATNIAETSLTIDGIKYVIDPGFVKQNSYNPR  568 (902)
T ss_pred             HHHHHHHHHHHhccccceEEEeeccccCChHHHHhhcCCCCCCceeEEEeecchhhceeecCeEEEecCccccccCcCCC
Confidence            77777544         345788999999999999988888888899999999999999999999996443         


Q ss_pred             ---------CCCccchhhhhcccccCCCceeEEEEecccc
Q 017573          313 ---------PTQPENYLHRIGRSGRFGRKGVAINFVTRDD  343 (369)
Q Consensus       313 ---------~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~  343 (369)
                               |-|.+...||.||+||+| +|.|+-+++.-.
T Consensus       569 tGmesL~v~piSKAsA~QRaGRAGRtg-PGKCfRLYt~~a  607 (902)
T KOG0923|consen  569 TGMESLLVTPISKASANQRAGRAGRTG-PGKCFRLYTAWA  607 (902)
T ss_pred             cCceeEEEeeechhhhhhhccccCCCC-CCceEEeechhh
Confidence                     346677899999999995 799999998543

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

Probab=99.88  E-value=1.2e-20  Score=171.95  Aligned_cols=159  Identities=18%  Similarity=0.138  Sum_probs=112.6

Q ss_pred             CCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccC-cEEE
Q 017573           18 KPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLG-VKVH   96 (369)
Q Consensus        18 ~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~-~~v~   96 (369)
                      .|-.+|++.+..+-.+...+|.|||.+|||++..-++-..++....+ -++++.|+++|+.|....+........ ..-.
T Consensus       511 ~Pd~WQ~elLDsvDr~eSavIVAPTSaGKTfisfY~iEKVLResD~~-VVIyvaPtKaLVnQvsa~VyaRF~~~t~~rg~  589 (1330)
T KOG0949|consen  511 CPDEWQRELLDSVDRNESAVIVAPTSAGKTFISFYAIEKVLRESDSD-VVIYVAPTKALVNQVSANVYARFDTKTFLRGV  589 (1330)
T ss_pred             CCcHHHHHHhhhhhcccceEEEeeccCCceeccHHHHHHHHhhcCCC-EEEEecchHHHhhhhhHHHHHhhccCccccch
Confidence            57889999999999999999999999999998766666666555444 899999999999999887765432211 1112


Q ss_pred             EEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcC---CCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCccCcEE
Q 017573           97 ACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQ---SLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVG  173 (369)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~---~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i  173 (369)
                      .+.|...  .+.++-.-.|+|.|+-|+.+...+...   .....+++++|+||+|.+.+..-.-.+..+....  .+.++
T Consensus       590 sl~g~lt--qEYsinp~nCQVLITvPecleslLlspp~~q~~cerIRyiIfDEVH~iG~~ed~l~~Eqll~li--~CP~L  665 (1330)
T KOG0949|consen  590 SLLGDLT--QEYSINPWNCQVLITVPECLESLLLSPPHHQKFCERIRYIIFDEVHLIGNEEDGLLWEQLLLLI--PCPFL  665 (1330)
T ss_pred             hhHhhhh--HHhcCCchhceEEEEchHHHHHHhcCchhhhhhhhcceEEEechhhhccccccchHHHHHHHhc--CCCee
Confidence            2222222  111111225899999999998887763   3345568999999999987655444555555544  34589


Q ss_pred             EEEeeCCh
Q 017573          174 VFSATMPP  181 (369)
Q Consensus       174 ~~saT~~~  181 (369)
                      ++|||..+
T Consensus       666 ~LSATigN  673 (1330)
T KOG0949|consen  666 VLSATIGN  673 (1330)
T ss_pred             EEecccCC
Confidence            99999864

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=99.87  E-value=1.8e-20  Score=171.87  Aligned_cols=314  Identities=17%  Similarity=0.230  Sum_probs=209.1

Q ss_pred             CCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEE
Q 017573           18 KPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHA   97 (369)
Q Consensus        18 ~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~   97 (369)
                      .|++.|--.--.+  .++-+....||-|||+++.++++-....+.   .+-||+.+.-|+..=++++..++..+|+.|.+
T Consensus        78 r~ydVQliGglvL--h~G~IAEMkTGEGKTLvAtLpayLnAL~Gk---gVhVVTvNdYLA~RDae~mg~vy~fLGLsvG~  152 (925)
T PRK12903         78 RPYDVQIIGGIIL--DLGSVAEMKTGEGKTITSIAPVYLNALTGK---GVIVSTVNEYLAERDAEEMGKVFNFLGLSVGI  152 (925)
T ss_pred             CcCchHHHHHHHH--hcCCeeeecCCCCccHHHHHHHHHHHhcCC---ceEEEecchhhhhhhHHHHHHHHHHhCCceee
Confidence            5666666555444  345689999999999999887764444443   79999999999999999999999999999998


Q ss_pred             EECCcchHHHHHHHccCCcEEEeccHHH-HHHHHcCCC------CCCCccEEEEechhHhh-ccC---------------
Q 017573           98 CVGGTSVREDQRILQAGVHVVVGTPGRV-FDMLRRQSL------RPDYIKMFVLDEADEML-SRG---------------  154 (369)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~iiv~t~~~l-~~~~~~~~~------~~~~~~~viiDE~H~~~-~~~---------------  154 (369)
                      ...+......+...  .+||.++|...| +.+++..-.      ....+.+.|+||++.+. +..               
T Consensus       153 i~~~~~~~~rr~aY--~~DItYgTn~E~gFDYLRDnm~~~~~~~vqR~~~faIVDEVDSILIDEArTPLIISg~~~~~~~  230 (925)
T PRK12903        153 NKANMDPNLKREAY--ACDITYSVHSELGFDYLRDNMVSSKEEKVQRGLNFCLIDEVDSILIDEAKTPLIISGGQSNDSN  230 (925)
T ss_pred             eCCCCChHHHHHhc--cCCCeeecCcccchhhhhhcccccHHHhcCcccceeeeccchheeecccCCcccccCCCccchH
Confidence            88766655544433  489999999887 344443211      12447899999999754 100               


Q ss_pred             cHHHHHHHHhhCCc------------------------------------------------------------------
Q 017573          155 FKDQIYDIFQLLPA------------------------------------------------------------------  168 (369)
Q Consensus       155 ~~~~~~~~~~~~~~------------------------------------------------------------------  168 (369)
                      .......+...+..                                                                  
T Consensus       231 ~Y~~~~~~v~~L~~~dy~iDek~k~v~LTe~G~~~~E~~l~i~nLy~~~n~~l~h~i~~AL~A~~lf~rd~dYiV~dg~V  310 (925)
T PRK12903        231 LYLAADQFVRTLKEDDYKIDEETKAISLTEKGIKKANKFFKLKNLYDIENSELVHRIQNALRAHKVMKEDVEYIVRDGKI  310 (925)
T ss_pred             HHHHHHHHHHhccccceEEecccceEEECHhHHHHHHHHcCCCcccChhhHHHHHHHHHHHHHHHHHhcCCceEEECCEE
Confidence            01111111111100                                                                  


Q ss_pred             --------------------------------------------------cCcEEEEEeeCChhHHHHHHHhcCCCEEEE
Q 017573          169 --------------------------------------------------KVQVGVFSATMPPEALEITRKFMNKPVRIL  198 (369)
Q Consensus       169 --------------------------------------------------~~~~i~~saT~~~~~~~~~~~~~~~~~~~~  198 (369)
                                                                        -.++.+||+|......++. ..++-.+...
T Consensus       311 ~IVDefTGR~m~gRrwsdGLHQaIEAKEgv~I~~e~~TlAsIT~QnfFr~Y~kLsGMTGTA~te~~Ef~-~iY~l~Vv~I  389 (925)
T PRK12903        311 ELVDQFTGRIMEGRSYSEGLQQAIQAKEMVEIEPETKTLATITYQNFFRLFKKLSGMTGTAKTEEQEFI-DIYNMRVNVV  389 (925)
T ss_pred             EEEECCCCCCCCCCccchHHHHHHHHHcCCCCCCCceeeeeehHHHHHHhcchhhccCCCCHHHHHHHH-HHhCCCEEEC
Confidence                                                              0456778888765544443 3444333333


Q ss_pred             ecCccccc-cceeEEEEEccchhhhHHHHHH-HHHhc-cCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHH
Q 017573          199 VKRDELTL-EGIKQFYVNVEKEEWKLETLCD-LYETL-AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRD  275 (369)
Q Consensus       199 ~~~~~~~~-~~~~~~~~~~~~~~~~~~~l~~-~~~~~-~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~  275 (369)
                      ....+... .....+|.   +...+...+.+ +...+ .+.++||.|.+++..+.+++.|.+.+++..++++.....+..
T Consensus       390 PTnkP~~R~D~~d~iy~---t~~~K~~Aii~ei~~~~~~gqPVLVgT~SIe~SE~ls~~L~~~gi~h~vLNAk~~e~EA~  466 (925)
T PRK12903        390 PTNKPVIRKDEPDSIFG---TKHAKWKAVVKEVKRVHKKGQPILIGTAQVEDSETLHELLLEANIPHTVLNAKQNAREAE  466 (925)
T ss_pred             CCCCCeeeeeCCCcEEE---cHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHCCCCceeecccchhhHHH
Confidence            22222111 11112222   22233444444 33333 456999999999999999999999999999999975544433


Q ss_pred             HHHHHHhcCC-CcEEEEecCCcCCCCCCCCc--------EEEEecCCCCccchhhhhcccccCCCceeEEEEeccccHH
Q 017573          276 IIMREFRSGS-SRVLITTDLLARGIDVQQVS--------LVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDER  345 (369)
Q Consensus       276 ~~~~~f~~~~-~~vli~t~~~~~G~d~~~~~--------~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~  345 (369)
                       ++.  ..|. -.|.|||+++++|.||.--.        +||....+.|...-.|..||+||.|.+|.+-.|.+-.|.-
T Consensus       467 -IIa--~AG~~GaVTIATNMAGRGTDI~Lg~~V~~~GGLhVIgTerheSrRIDnQLrGRaGRQGDpGss~f~lSLeD~L  542 (925)
T PRK12903        467 -IIA--KAGQKGAITIATNMAGRGTDIKLSKEVLELGGLYVLGTDKAESRRIDNQLRGRSGRQGDVGESRFFISLDDQL  542 (925)
T ss_pred             -HHH--hCCCCCeEEEecccccCCcCccCchhHHHcCCcEEEecccCchHHHHHHHhcccccCCCCCcceEEEecchHH
Confidence             333  3453 45999999999999986322        7888888888888899999999999999999888876544

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

Probab=99.87  E-value=2.8e-20  Score=172.79  Aligned_cols=318  Identities=17%  Similarity=0.209  Sum_probs=217.4

Q ss_pred             CcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHh-ccccCcEEEE
Q 017573           19 PSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRAL-GDYLGVKVHA   97 (369)
Q Consensus        19 ~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~-~~~~~~~v~~   97 (369)
                      .+..++++++++.+++-+++.++||+|||...-..+++........++++.--|++--+...+++..+- +...|-.|.+
T Consensus       174 a~~~r~~Il~~i~~~qVvvIsGeTGcGKTTQvpQfiLd~~~~~~~~~~IicTQPRRIsAIsvAeRVa~ER~~~~g~~VGY  253 (924)
T KOG0920|consen  174 AYKMRDTILDAIEENQVVVISGETGCGKTTQVPQFILDEAIESGAACNIICTQPRRISAISVAERVAKERGESLGEEVGY  253 (924)
T ss_pred             cHHHHHHHHHHHHhCceEEEeCCCCCCchhhhhHHHHHHHHhcCCCCeEEecCCchHHHHHHHHHHHHHhccccCCeeeE
Confidence            467788999999999999999999999999988888887655555557777779987777777766432 2333444443


Q ss_pred             EECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhh-ccCcHHHHHHHHhhCCccCcEEEEE
Q 017573           98 CVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEML-SRGFKDQIYDIFQLLPAKVQVGVFS  176 (369)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~-~~~~~~~~~~~~~~~~~~~~~i~~s  176 (369)
                      -.+.....      .....+.+||...|++.+.. ......+..+|+||+|+=. +..+.-.+.+.+-...+..++|+||
T Consensus       254 qvrl~~~~------s~~t~L~fcTtGvLLr~L~~-~~~l~~vthiivDEVHER~i~~DflLi~lk~lL~~~p~LkvILMS  326 (924)
T KOG0920|consen  254 QVRLESKR------SRETRLLFCTTGVLLRRLQS-DPTLSGVTHIIVDEVHERSINTDFLLILLKDLLPRNPDLKVILMS  326 (924)
T ss_pred             EEeeeccc------CCceeEEEecHHHHHHHhcc-CcccccCceeeeeeEEEccCCcccHHHHHHHHhhhCCCceEEEee
Confidence            33322211      22368999999999998887 3456668999999999732 2223333333333344788999999


Q ss_pred             eeCChhHHHHHHHhcCCCEEEEecCcccc----------------ccceeEEE-----------E---Ec-cchhhhHHH
Q 017573          177 ATMPPEALEITRKFMNKPVRILVKRDELT----------------LEGIKQFY-----------V---NV-EKEEWKLET  225 (369)
Q Consensus       177 aT~~~~~~~~~~~~~~~~~~~~~~~~~~~----------------~~~~~~~~-----------~---~~-~~~~~~~~~  225 (369)
                      ||..   .+....+++....+.......+                .....+..           .   .. -......+.
T Consensus       327 AT~d---ae~fs~YF~~~pvi~i~grtfpV~~~fLEDil~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~id~~Li~~l  403 (924)
T KOG0920|consen  327 ATLD---AELFSDYFGGCPVITIPGRTFPVKEYFLEDILSKTGYVSEDDSARSGPERSQLRLARLKLWEPEIDYDLIEDL  403 (924)
T ss_pred             eecc---hHHHHHHhCCCceEeecCCCcchHHHHHHHHHHHhcccccccccccccccCccccccchhccccccHHHHHHH
Confidence            9986   2344444443322222111000                00000000           0   00 001112233


Q ss_pred             HHHHHHhccCCCeEEEeCCHhhHHHHHHHHhhC-------CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCC
Q 017573          226 LCDLYETLAITQSVIFVNTRRKVDWLTDKMRSR-------DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARG  298 (369)
Q Consensus       226 l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~-------~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G  298 (369)
                      +..+......+.+|||.++.++...+.+.|...       ..-+..+|+.++..++..+......|..+|+++|.+++.+
T Consensus       404 i~~I~~~~~~GaILVFLPG~~eI~~~~~~L~~~~~f~~~~~~~ilplHs~~~s~eQ~~VF~~pp~g~RKIIlaTNIAETS  483 (924)
T KOG0920|consen  404 IEYIDEREFEGAILVFLPGWEEILQLKELLEVNLPFADSLKFAILPLHSSIPSEEQQAVFKRPPKGTRKIILATNIAETS  483 (924)
T ss_pred             HHhcccCCCCceEEEEcCCHHHHHHHHHHhhhccccccccceEEEeccccCChHHHHHhcCCCCCCcchhhhhhhhHhhc
Confidence            333334444678999999999999999999753       2457889999999999999999889999999999999999


Q ss_pred             CCCCCCcEEEEecCC------------------CCccchhhhhcccccCCCceeEEEEeccccHHHH
Q 017573          299 IDVQQVSLVINYDLP------------------TQPENYLHRIGRSGRFGRKGVAINFVTRDDERML  347 (369)
Q Consensus       299 ~d~~~~~~vi~~~~~------------------~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~  347 (369)
                      +.|+++-.||..+..                  -|.....||.||+||. ..|.||-+++....+.+
T Consensus       484 ITIdDVvyVIDsG~~Ke~~yD~~~~~s~l~~~wvSkAna~QR~GRAGRv-~~G~cy~L~~~~~~~~~  549 (924)
T KOG0920|consen  484 ITIDDVVYVIDSGLVKEKSYDPERKVSCLLLSWVSKANAKQRRGRAGRV-RPGICYHLYTRSRYEKL  549 (924)
T ss_pred             ccccCeEEEEecCeeeeeeecccCCcchhheeeccccchHHhcccccCc-cCCeeEEeechhhhhhc
Confidence            999999999976532                  1456779999999998 88999999997654433

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=99.87  E-value=1.8e-19  Score=168.15  Aligned_cols=143  Identities=27%  Similarity=0.359  Sum_probs=122.6

Q ss_pred             hHHHHHHHHHhc--cCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCC
Q 017573          222 KLETLCDLYETL--AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGI  299 (369)
Q Consensus       222 ~~~~l~~~~~~~--~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~  299 (369)
                      ..+.+...+...  .+.+++|||++.+.++.+++.|...+.++..+|++++..+|..+++.|+.|...|+|+|+.+++|+
T Consensus       431 q~~~L~~~L~~~~~~g~~viIf~~t~~~ae~L~~~L~~~gi~~~~~h~~~~~~~R~~~l~~f~~g~i~vlV~t~~L~rGf  510 (652)
T PRK05298        431 QVDDLLSEIRKRVAKGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLREGL  510 (652)
T ss_pred             cHHHHHHHHHHHHhCCCEEEEEeCCHHHHHHHHHHHhhcceeEEEEECCCCHHHHHHHHHHHHcCCceEEEEeCHHhCCc
Confidence            344444444332  456899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCcEEEEecC-----CCCccchhhhhcccccCCCceeEEEEecc---------ccHHHHHHHHHHhccccccCCcch
Q 017573          300 DVQQVSLVINYDL-----PTQPENYLHRIGRSGRFGRKGVAINFVTR---------DDERMLFDIQKFYNVVIEELPSNV  365 (369)
Q Consensus       300 d~~~~~~vi~~~~-----~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~---------~~~~~~~~~~~~~~~~~~~~~~~~  365 (369)
                      |+|+++.|++++.     |.+...|+|++||+||. ..|.++.|++.         .+....+.++..++.....+|..+
T Consensus       511 dlp~v~lVii~d~eifG~~~~~~~yiqr~GR~gR~-~~G~~i~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~  589 (652)
T PRK05298        511 DIPEVSLVAILDADKEGFLRSERSLIQTIGRAARN-VNGKVILYADKITDSMQKAIDETERRREIQIAYNEEHGITPKTI  589 (652)
T ss_pred             cccCCcEEEEeCCcccccCCCHHHHHHHhccccCC-CCCEEEEEecCCCHHHHHHHHHHHHHHHHHHHhhhccCCCChhH
Confidence            9999999998874     67889999999999996 78999999995         456666777888888887777655

>KOG0926 consensus DEAH-box RNA helicase [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.86  E-value=1.1e-20  Score=168.86  Aligned_cols=326  Identities=17%  Similarity=0.200  Sum_probs=204.9

Q ss_pred             hhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhh---ccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEEC
Q 017573           24 QRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLD---YGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVG  100 (369)
Q Consensus        24 ~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~---~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~  100 (369)
                      +++.+++.++.-++|+|.||||||...-..++++=-   ....++-+-|--|++.-+..++++...-...++-.|.+...
T Consensus       262 q~IMEaIn~n~vvIIcGeTGsGKTTQvPQFLYEAGf~s~~~~~~gmIGITqPRRVAaiamAkRVa~EL~~~~~eVsYqIR  341 (1172)
T KOG0926|consen  262 QRIMEAINENPVVIICGETGSGKTTQVPQFLYEAGFASEQSSSPGMIGITQPRRVAAIAMAKRVAFELGVLGSEVSYQIR  341 (1172)
T ss_pred             HHHHHHhhcCCeEEEecCCCCCccccchHHHHHcccCCccCCCCCeeeecCchHHHHHHHHHHHHHHhccCccceeEEEE
Confidence            455667777888999999999999775444444311   11112246666688876666666554333333444443332


Q ss_pred             CcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhcc-----CcHHHHHHHHhhCCc------c
Q 017573          101 GTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSR-----GFKDQIYDIFQLLPA------K  169 (369)
Q Consensus       101 ~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~-----~~~~~~~~~~~~~~~------~  169 (369)
                      -..      .......|-++|-.-|++.+.+. +.+..+++||+||||.=+-.     +....+-.+.+....      .
T Consensus       342 fd~------ti~e~T~IkFMTDGVLLrEi~~D-flL~kYSvIIlDEAHERSvnTDILiGmLSRiV~LR~k~~ke~~~~kp  414 (1172)
T KOG0926|consen  342 FDG------TIGEDTSIKFMTDGVLLREIEND-FLLTKYSVIILDEAHERSVNTDILIGMLSRIVPLRQKYYKEQCQIKP  414 (1172)
T ss_pred             ecc------ccCCCceeEEecchHHHHHHHHh-HhhhhceeEEechhhhccchHHHHHHHHHHHHHHHHHHhhhhcccCc
Confidence            111      12335789999999999888775 45666899999999972100     111222233333322      5


Q ss_pred             CcEEEEEeeCChhHHHHHHHhcC-CCEEEEecCccccccceeEEEEEccc---hhhhHHHHHHHHHhccCCCeEEEeCCH
Q 017573          170 VQVGVFSATMPPEALEITRKFMN-KPVRILVKRDELTLEGIKQFYVNVEK---EEWKLETLCDLYETLAITQSVIFVNTR  245 (369)
Q Consensus       170 ~~~i~~saT~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~l~~~~~~~~~~k~lv~~~~~  245 (369)
                      .+.|.||||+.-+......+++. .|-.+.++..+++   +...+.....   -....+....++++.+.+.+|||+...
T Consensus       415 LKLIIMSATLRVsDFtenk~LFpi~pPlikVdARQfP---VsIHF~krT~~DYi~eAfrKtc~IH~kLP~G~ILVFvTGQ  491 (1172)
T KOG0926|consen  415 LKLIIMSATLRVSDFTENKRLFPIPPPLIKVDARQFP---VSIHFNKRTPDDYIAEAFRKTCKIHKKLPPGGILVFVTGQ  491 (1172)
T ss_pred             eeEEEEeeeEEecccccCceecCCCCceeeeecccCc---eEEEeccCCCchHHHHHHHHHHHHhhcCCCCcEEEEEeCh
Confidence            67899999997554333333433 2334444444332   1222222222   223456667788889999999999999


Q ss_pred             hhHHHHHHHHhhCCCe----------------------------------------------------------------
Q 017573          246 RKVDWLTDKMRSRDHT----------------------------------------------------------------  261 (369)
Q Consensus       246 ~~~~~~~~~l~~~~~~----------------------------------------------------------------  261 (369)
                      .++..+++.|++...-                                                                
T Consensus       492 qEV~qL~~kLRK~~p~~f~~~k~~k~~k~~~e~k~~~s~~~~~~k~~dfe~Ed~~~~~ed~d~~~~~~~~~~~raa~~~~  571 (1172)
T KOG0926|consen  492 QEVDQLCEKLRKRFPESFGGVKMKKNVKAFKELKENPSDIGDSNKTDDFEEEDMYESDEDIDQELVDSGFASLRAAFNAL  571 (1172)
T ss_pred             HHHHHHHHHHHhhCccccccchhhhhhhhccccccchhhhccCcccccchhcccccchhhhhhhhhcccchhhhhhhhcc
Confidence            9999999998866110                                                                


Q ss_pred             -----------------------------------eEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcE
Q 017573          262 -----------------------------------VSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSL  306 (369)
Q Consensus       262 -----------------------------------~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~  306 (369)
                                                         +..+++-++.+.+.++++.-..|.-=++|+|+++++.+.||++..
T Consensus       572 ~De~~~~nge~e~d~~e~~~E~~~~~~~~~~~pLyvLPLYSLLs~~~Q~RVF~~~p~g~RLcVVaTNVAETSLTIPgIkY  651 (1172)
T KOG0926|consen  572 ADENGSVNGEPEKDESEEGQEAEQGKGKFSPGPLYVLPLYSLLSTEKQMRVFDEVPKGERLCVVATNVAETSLTIPGIKY  651 (1172)
T ss_pred             ccccccccCCcccchhhhchhhhhccCCCCCCceEEeehhhhcCHHHhhhhccCCCCCceEEEEeccchhcccccCCeeE
Confidence                                               333334455666666666666676668999999999999999999


Q ss_pred             EEEecCC------------------CCccchhhhhcccccCCCceeEEEEeccccHHHHHHHHHHhccccccCC
Q 017573          307 VINYDLP------------------TQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELP  362 (369)
Q Consensus       307 vi~~~~~------------------~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  362 (369)
                      |+..+..                  -|.+..-||.|||||.| +|.||-++++.-..  ..++++...++...|
T Consensus       652 VVD~Gr~K~R~Yd~~TGV~~FeV~wiSkASadQRAGRAGRtg-pGHcYRLYSSAVf~--~~Fe~fS~PEIlk~P  722 (1172)
T KOG0926|consen  652 VVDCGRVKERLYDSKTGVSSFEVDWISKASADQRAGRAGRTG-PGHCYRLYSSAVFS--NDFEEFSLPEILKKP  722 (1172)
T ss_pred             EEeccchhhhccccccCceeEEEEeeeccccchhccccCCCC-CCceeehhhhHHhh--cchhhhccHHHhhCc
Confidence            9976642                  14566799999999995 69999999865333  234444444444333

>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated

Probab=99.85  E-value=3.3e-18  Score=166.01  Aligned_cols=109  Identities=14%  Similarity=0.224  Sum_probs=82.8

Q ss_pred             cCCCeEEEeCCHhhHHHHHHHHhhCCC--eeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCC--CcEEEE
Q 017573          234 AITQSVIFVNTRRKVDWLTDKMRSRDH--TVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQ--VSLVIN  309 (369)
Q Consensus       234 ~~~k~lv~~~~~~~~~~~~~~l~~~~~--~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~--~~~vi~  309 (369)
                      .+++++|+++|.+..+.+++.|.....  ...++.-+++...|.++++.|++++-.||++|..+.+|+|+|+  ++.||+
T Consensus       751 ~~g~~LVLFtSy~~l~~v~~~l~~~~~~~~~~ll~Qg~~~~~r~~l~~~F~~~~~~iLlG~~sFwEGVD~pg~~l~~viI  830 (928)
T PRK08074        751 TKGRMLVLFTSYEMLKKTYYNLKNEEELEGYVLLAQGVSSGSRARLTKQFQQFDKAILLGTSSFWEGIDIPGDELSCLVI  830 (928)
T ss_pred             CCCCEEEEECCHHHHHHHHHHHhhcccccCceEEecCCCCCCHHHHHHHHHhcCCeEEEecCcccCccccCCCceEEEEE
Confidence            457999999999999999999975432  1223333334456788999999888889999999999999996  588888


Q ss_pred             ecCCCC-c-----------------------------cchhhhhcccccCCCceeEEEEeccc
Q 017573          310 YDLPTQ-P-----------------------------ENYLHRIGRSGRFGRKGVAINFVTRD  342 (369)
Q Consensus       310 ~~~~~~-~-----------------------------~~~~Q~~GR~~R~~~~~~~~~~~~~~  342 (369)
                      ...|.. +                             ..+.|.+||+.|..++.-++++.++.
T Consensus       831 ~kLPF~~p~dp~~~a~~~~~~~~g~~~F~~~~lP~A~~~lkQg~GRlIRs~~D~G~v~ilD~R  893 (928)
T PRK08074        831 VRLPFAPPDQPVMEAKSEWAKEQGENPFQELSLPQAVLRFKQGFGRLIRTETDRGTVFVLDRR  893 (928)
T ss_pred             ecCCCCCCCCHHHHHHHHHHHHhCCCchhhhhhHHHHHHHHhhhhhhcccCCceEEEEEecCc
Confidence            887642 2                             22489999999997664456666654

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

Probab=99.85  E-value=9.8e-18  Score=153.03  Aligned_cols=115  Identities=14%  Similarity=0.124  Sum_probs=82.0

Q ss_pred             HHHHHHHhccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhc----CCCcEEEEecCCcCCCC
Q 017573          225 TLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRS----GSSRVLITTDLLARGID  300 (369)
Q Consensus       225 ~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~----~~~~vli~t~~~~~G~d  300 (369)
                      .+..++.. ..++++|.+.|...++.+++.|...-.-..++.|+.  ..+..++++|+.    |...||++|..+.+|+|
T Consensus       461 ~~~~~~~~-~~G~~lvLfTS~~~~~~~~~~l~~~l~~~~l~qg~~--~~~~~l~~~f~~~~~~~~~~vL~gt~sfweGvD  537 (636)
T TIGR03117       461 STAAILRK-AQGGTLVLTTAFSHISAIGQLVELGIPAEIVIQSEK--NRLASAEQQFLALYANGIQPVLIAAGGAWTGID  537 (636)
T ss_pred             HHHHHHHH-cCCCEEEEechHHHHHHHHHHHHhhcCCCEEEeCCC--ccHHHHHHHHHHhhcCCCCcEEEeCCccccccc
Confidence            33344333 457999999999999999999976433334555533  245668888876    46789999999999999


Q ss_pred             C--------CC--CcEEEEecCCCCc-------------------------cchhhhhcccccCCCc--eeEEEEeccc
Q 017573          301 V--------QQ--VSLVINYDLPTQP-------------------------ENYLHRIGRSGRFGRK--GVAINFVTRD  342 (369)
Q Consensus       301 ~--------~~--~~~vi~~~~~~~~-------------------------~~~~Q~~GR~~R~~~~--~~~~~~~~~~  342 (369)
                      +        |+  ++.||+...|+.+                         ..+.|.+||..|...+  --++.+.++.
T Consensus       538 v~~~~~~p~~G~~Ls~ViI~kLPF~~~dp~a~~~~~~~~g~~~f~~~p~a~i~lkQg~GRLIR~~~D~~~G~i~ilD~R  616 (636)
T TIGR03117       538 LTHKPVSPDKDNLLTDLIITCAPFGLNRSLSMLKRIRKTSVRPWEIINESLMMLRQGLGRLVRHPDMPQNRRIHMLDGR  616 (636)
T ss_pred             cCCccCCCCCCCcccEEEEEeCCCCcCChHHHHHHHHhcCCChHhhhHHHHHHHHHhcCceeecCCCcCceEEEEEeCC
Confidence            9        33  8889988877432                         2368999999998765  3344444544

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.

>KOG0924 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.84  E-value=2.3e-19  Score=157.98  Aligned_cols=305  Identities=18%  Similarity=0.257  Sum_probs=196.6

Q ss_pred             cHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCc-cEEEEcCCHHHHHHHHHHHH-HhccccCcEEEE
Q 017573           20 SAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQC-QALVLAPTRELAQQIEKVMR-ALGDYLGVKVHA   97 (369)
Q Consensus        20 ~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~-~~liv~P~~~l~~q~~~~~~-~~~~~~~~~v~~   97 (369)
                      -.++.+++..+.+++-++|.++||||||......++.   .+.... -+-.--|++.-+...++... ++...+|..|.+
T Consensus       358 f~~R~~ll~~ir~n~vvvivgETGSGKTTQl~QyL~e---dGY~~~GmIGcTQPRRvAAiSVAkrVa~EM~~~lG~~VGY  434 (1042)
T KOG0924|consen  358 FACRDQLLSVIRENQVVVIVGETGSGKTTQLAQYLYE---DGYADNGMIGCTQPRRVAAISVAKRVAEEMGVTLGDTVGY  434 (1042)
T ss_pred             HHHHHHHHHHHhhCcEEEEEecCCCCchhhhHHHHHh---cccccCCeeeecCchHHHHHHHHHHHHHHhCCccccccce
Confidence            3456666777778899999999999999875443332   222221 23333488877777766654 343444545544


Q ss_pred             EECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhC---CccCcEEE
Q 017573           98 CVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLL---PAKVQVGV  174 (369)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~---~~~~~~i~  174 (369)
                      ...-....      .....|=++|-..|++...... .+.++++||+||||+=.-.  ...+.-+++..   ....++|.
T Consensus       435 sIRFEdvT------~~~T~IkymTDGiLLrEsL~d~-~L~kYSviImDEAHERslN--tDilfGllk~~larRrdlKliV  505 (1042)
T KOG0924|consen  435 SIRFEDVT------SEDTKIKYMTDGILLRESLKDR-DLDKYSVIIMDEAHERSLN--TDILFGLLKKVLARRRDLKLIV  505 (1042)
T ss_pred             EEEeeecC------CCceeEEEeccchHHHHHhhhh-hhhheeEEEechhhhcccc--hHHHHHHHHHHHHhhccceEEE
Confidence            33222111      1235678899888876544433 3455799999999973211  12222222221   23667999


Q ss_pred             EEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHH---HhccCCCeEEEeCCHhhHHHH
Q 017573          175 FSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLY---ETLAITQSVIFVNTRRKVDWL  251 (369)
Q Consensus       175 ~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~---~~~~~~k~lv~~~~~~~~~~~  251 (369)
                      +|||+.  ...+...+.+-|......+..    .+...+...+-.+.....+...+   ...+.+.+|||....+..+..
T Consensus       506 tSATm~--a~kf~nfFgn~p~f~IpGRTy----PV~~~~~k~p~eDYVeaavkq~v~Ihl~~~~GdilIfmtGqediE~t  579 (1042)
T KOG0924|consen  506 TSATMD--AQKFSNFFGNCPQFTIPGRTY----PVEIMYTKTPVEDYVEAAVKQAVQIHLSGPPGDILIFMTGQEDIECT  579 (1042)
T ss_pred             eecccc--HHHHHHHhCCCceeeecCCcc----ceEEEeccCchHHHHHHHHhhheEeeccCCCCCEEEecCCCcchhHH
Confidence            999985  334444444355444332221    22333333333333334444433   334567899999998877665


Q ss_pred             HHHHhhC----------CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecC---------
Q 017573          252 TDKMRSR----------DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDL---------  312 (369)
Q Consensus       252 ~~~l~~~----------~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~---------  312 (369)
                      +..+...          +..+..+++.++..-+.++++.-..|.-+++|+|+++++.+.+|++..||..+.         
T Consensus       580 ~~~i~~~l~ql~~~~~~~L~vlpiYSQLp~dlQ~kiFq~a~~~vRK~IvATNIAETSLTi~gI~yVID~Gy~K~kvyn~~  659 (1042)
T KOG0924|consen  580 CDIIKEKLEQLDSAPTTDLAVLPIYSQLPADLQAKIFQKAEGGVRKCIVATNIAETSLTIPGIRYVIDTGYCKLKVYNPR  659 (1042)
T ss_pred             HHHHHHHHHhhhcCCCCceEEEeehhhCchhhhhhhcccCCCCceeEEEeccchhhceeecceEEEEecCceeeeecccc
Confidence            5554322          567889999999999999988777788889999999999999999999997653         


Q ss_pred             ---------CCCccchhhhhcccccCCCceeEEEEecccc
Q 017573          313 ---------PTQPENYLHRIGRSGRFGRKGVAINFVTRDD  343 (369)
Q Consensus       313 ---------~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~  343 (369)
                               |-|-+...||.|||||+ .+|.||-+++...
T Consensus       660 ~G~D~L~~~pIS~AnA~QRaGRAGRt-~pG~cYRlYTe~a  698 (1042)
T KOG0924|consen  660 IGMDALQIVPISQANADQRAGRAGRT-GPGTCYRLYTEDA  698 (1042)
T ss_pred             cccceeEEEechhccchhhccccCCC-CCcceeeehhhhH
Confidence                     44667789999999999 4799999998753

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=99.84  E-value=6.2e-19  Score=162.69  Aligned_cols=273  Identities=15%  Similarity=0.133  Sum_probs=175.4

Q ss_pred             CCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEE
Q 017573           18 KPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHA   97 (369)
Q Consensus        18 ~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~   97 (369)
                      .|++.|.-+.  +.-.++-+..+.||.|||+++.++++-....+.   .+.||+++.-|+.+-++++..++..+|+.+..
T Consensus        76 r~ydvQlig~--l~L~~G~IaEm~TGEGKTL~a~l~ayl~aL~G~---~VhVvT~NdyLA~RD~e~m~pvy~~LGLsvg~  150 (870)
T CHL00122         76 RHFDVQLIGG--LVLNDGKIAEMKTGEGKTLVATLPAYLNALTGK---GVHIVTVNDYLAKRDQEWMGQIYRFLGLTVGL  150 (870)
T ss_pred             CCCchHhhhh--HhhcCCccccccCCCCchHHHHHHHHHHHhcCC---ceEEEeCCHHHHHHHHHHHHHHHHHcCCceee
Confidence            4666665554  444677899999999999999887754333333   79999999999999999999999999999998


Q ss_pred             EECCcchHHHHHHHccCCcEEEeccHHHH-HHHHcCCC------CCCCccEEEEechhHhh-ccC---------------
Q 017573           98 CVGGTSVREDQRILQAGVHVVVGTPGRVF-DMLRRQSL------RPDYIKMFVLDEADEML-SRG---------------  154 (369)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~iiv~t~~~l~-~~~~~~~~------~~~~~~~viiDE~H~~~-~~~---------------  154 (369)
                      ..++.+....+...  .+||+++|...|- ..++..-.      ....+.++|+||++.+. +..               
T Consensus       151 i~~~~~~~err~aY--~~DItYgTn~e~gFDyLRDnm~~~~~~~v~r~~~faIVDEvDSiLIDeArTPLiISg~~~~~~~  228 (870)
T CHL00122        151 IQEGMSSEERKKNY--LKDITYVTNSELGFDYLRDNMALSLSDVVQRPFNYCIIDEVDSILIDEARTPLIISGQSKTNID  228 (870)
T ss_pred             eCCCCChHHHHHhc--CCCCEecCCccccccchhhccCcChHHhhccccceeeeecchhheeccCCCceeccCCCccchH
Confidence            88777765554433  4789999998763 34433211      23457899999999754 100               


Q ss_pred             cHHHHHHHHhhCCc------------------------------------------------------------------
Q 017573          155 FKDQIYDIFQLLPA------------------------------------------------------------------  168 (369)
Q Consensus       155 ~~~~~~~~~~~~~~------------------------------------------------------------------  168 (369)
                      .......+...+..                                                                  
T Consensus       229 ~y~~~~~~v~~L~~~~dy~vdek~k~v~LTe~G~~~~e~~l~i~~ly~~~~~~~~~i~~AL~A~~lf~~d~dYiV~dgeV  308 (870)
T CHL00122        229 KYIVADELAKYLEKNVHYEVDEKNKNVILTEQGILFIEKILKIEDLYSANDPWIPYILNALKAKELFFKNVHYIVRNNEI  308 (870)
T ss_pred             HHHHHHHHHHhcCcCCCeEEEcCCCceEecHHHHHHHHHHcCCccccccccHHHHHHHHHHHHHHHHhcCCcEEEECCEE
Confidence            00000000000000                                                                  


Q ss_pred             --------------------------------------------------cCcEEEEEeeCChhHHHHHHHhcCCCEEEE
Q 017573          169 --------------------------------------------------KVQVGVFSATMPPEALEITRKFMNKPVRIL  198 (369)
Q Consensus       169 --------------------------------------------------~~~~i~~saT~~~~~~~~~~~~~~~~~~~~  198 (369)
                                                                        -.++.+||+|..... ......++-.+...
T Consensus       309 ~iVDe~TGR~m~grrws~GLHQaiEaKEgv~It~e~~tlAsIT~QnfFr~Y~kL~GMTGTa~te~-~Ef~~iY~l~vv~I  387 (870)
T CHL00122        309 IIVDEFTGRIMPGRRWSDGLHQAIEAKENLPIRQETETLASITYQNFFLLYPKLSGMTGTAKTEE-LEFEKIYNLEVVCI  387 (870)
T ss_pred             EEEECCCCcCCCCCccchHHHHHHHhhcCCCCCCCceeeeeeeHHHHHHhCchhcccCCCCHHHH-HHHHHHhCCCEEEC
Confidence                                                              046778999986544 34445555444443


Q ss_pred             ecCccccccceeEEEEEccchhhhHHHHHHHHHhc-cCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCC-C-HHHHH
Q 017573          199 VKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETL-AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDM-D-QNTRD  275 (369)
Q Consensus       199 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~-~-~~~r~  275 (369)
                      ....+.........++. .........+.++...+ .+.++||-+.+++..+.+++.|.+.+.+..++++.. . ..+ .
T Consensus       388 Ptnkp~~R~d~~d~v~~-t~~~K~~AI~~ei~~~~~~grPVLIgT~SIe~SE~ls~~L~~~gi~h~vLNAk~~~~~~E-A  465 (870)
T CHL00122        388 PTHRPMLRKDLPDLIYK-DELSKWRAIADECLQMHQTGRPILIGTTTIEKSELLSQLLKEYRLPHQLLNAKPENVRRE-S  465 (870)
T ss_pred             CCCCCccceeCCCeEEe-CHHHHHHHHHHHHHHHHhcCCCEEEeeCCHHHHHHHHHHHHHcCCccceeeCCCccchhH-H
Confidence            33222222222222221 22222223344444443 456999999999999999999999999999999973 2 333 3


Q ss_pred             HHHHHHhcCC-CcEEEEecCCcCCCCCC
Q 017573          276 IIMREFRSGS-SRVLITTDLLARGIDVQ  302 (369)
Q Consensus       276 ~~~~~f~~~~-~~vli~t~~~~~G~d~~  302 (369)
                      +++.+  .|. -.|.|||+++++|.||.
T Consensus       466 ~IIA~--AG~~G~VTIATNMAGRGTDI~  491 (870)
T CHL00122        466 EIVAQ--AGRKGSITIATNMAGRGTDII  491 (870)
T ss_pred             HHHHh--cCCCCcEEEeccccCCCcCee
Confidence            34443  343 35999999999999974

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=99.84  E-value=3.6e-19  Score=136.01  Aligned_cols=144  Identities=40%  Similarity=0.560  Sum_probs=112.8

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHcc
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQA  113 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~  113 (369)
                      +++++.+|||+|||.+++..+........ .+++++++|++.++.|+.+.+...... +..+....+.............
T Consensus         1 ~~~~i~~~~G~GKT~~~~~~~~~~~~~~~-~~~~lv~~p~~~l~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~   78 (144)
T cd00046           1 RDVLLAAPTGSGKTLAALLPILELLDSLK-GGQVLVLAPTRELANQVAERLKELFGE-GIKVGYLIGGTSIKQQEKLLSG   78 (144)
T ss_pred             CCEEEECCCCCchhHHHHHHHHHHHhccc-CCCEEEEcCcHHHHHHHHHHHHHHhhC-CcEEEEEecCcchhHHHHHhcC
Confidence            46899999999999998888887766533 338999999999999999999887654 6777777777665555445566


Q ss_pred             CCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEEeeC
Q 017573          114 GVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATM  179 (369)
Q Consensus       114 ~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~saT~  179 (369)
                      ..+++++|++.+.............++++|+||+|.+....................+++++||||
T Consensus        79 ~~~i~i~t~~~~~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~~~~~~~~~~~~i~~saTp  144 (144)
T cd00046          79 KTDIVVGTPGRLLDELERLKLSLKKLDLLILDEAHRLLNQGFGLLGLKILLKLPKDRQVLLLSATP  144 (144)
T ss_pred             CCCEEEECcHHHHHHHHcCCcchhcCCEEEEeCHHHHhhcchHHHHHHHHhhCCccceEEEEeccC
Confidence            789999999999888877655556689999999999876664443333344456678899999997

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

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

Probab=99.84  E-value=3.3e-19  Score=157.47  Aligned_cols=106  Identities=19%  Similarity=0.240  Sum_probs=91.1

Q ss_pred             cCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhc--CCCcEEEE-ecCCcCCCCCCCCcEEEEe
Q 017573          234 AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRS--GSSRVLIT-TDLLARGIDVQQVSLVINY  310 (369)
Q Consensus       234 ~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~--~~~~vli~-t~~~~~G~d~~~~~~vi~~  310 (369)
                      ...|++|...-.+...-+...|.+.|.....++|.....+|.++++.|+.  |..+|++. -.+.+.|+|+-+.+|+|++
T Consensus       745 skeK~viVSQwtsvLniv~~hi~~~g~~y~si~Gqv~vK~Rq~iv~~FN~~k~~~rVmLlSLtAGGVGLNL~GaNHlilv  824 (901)
T KOG4439|consen  745 SKEKVVIVSQWTSVLNIVRKHIQKGGHIYTSITGQVLVKDRQEIVDEFNQEKGGARVMLLSLTAGGVGLNLIGANHLILV  824 (901)
T ss_pred             ccceeeehhHHHHHHHHHHHHHhhCCeeeeeecCccchhHHHHHHHHHHhccCCceEEEEEEccCcceeeecccceEEEE
Confidence            44567777777777788889999999999999999999999999999974  44666654 4688999999999999999


Q ss_pred             cCCCCccchhhhhcccccCCCceeEEEEe
Q 017573          311 DLPTQPENYLHRIGRSGRFGRKGVAINFV  339 (369)
Q Consensus       311 ~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~  339 (369)
                      +..|++.--.|++.|..|.|++..++++-
T Consensus       825 DlHWNPaLEqQAcDRIYR~GQkK~V~IhR  853 (901)
T KOG4439|consen  825 DLHWNPALEQQACDRIYRMGQKKDVFIHR  853 (901)
T ss_pred             ecccCHHHHHHHHHHHHHhcccCceEEEE
Confidence            99999999999999999999988777653

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

Probab=99.83  E-value=4.4e-20  Score=147.45  Aligned_cols=151  Identities=18%  Similarity=0.178  Sum_probs=103.0

Q ss_pred             CCcHhhhhhhhcccc-------CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccc
Q 017573           18 KPSAIQQRGIVPFCK-------GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDY   90 (369)
Q Consensus        18 ~~~~~Q~~~~~~~~~-------~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~   90 (369)
                      .||++|.+++..+.+       .+++++.+|||+|||.+++..+.....      ++++++|+.+|..|+.+.+..+...
T Consensus         3 ~lr~~Q~~ai~~i~~~~~~~~~~~~~ll~~~tGsGKT~~~~~~~~~l~~------~~l~~~p~~~l~~Q~~~~~~~~~~~   76 (184)
T PF04851_consen    3 KLRPYQQEAIARIINSLENKKEERRVLLNAPTGSGKTIIALALILELAR------KVLIVAPNISLLEQWYDEFDDFGSE   76 (184)
T ss_dssp             EE-HHHHHHHHHHHHHHHTTSGCSEEEEEESTTSSHHHHHHHHHHHHHC------EEEEEESSHHHHHHHHHHHHHHSTT
T ss_pred             CCCHHHHHHHHHHHHHHHhcCCCCCEEEEECCCCCcChhhhhhhhcccc------ceeEecCHHHHHHHHHHHHHHhhhh
Confidence            589999999999884       689999999999999998765555443      7999999999999999999766443


Q ss_pred             cCcEEEE------------EECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCC-----------CCCCCccEEEEech
Q 017573           91 LGVKVHA------------CVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQS-----------LRPDYIKMFVLDEA  147 (369)
Q Consensus        91 ~~~~v~~------------~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~-----------~~~~~~~~viiDE~  147 (369)
                      . .....            ..................+++++|++.+........           .....++++|+|||
T Consensus        77 ~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~vI~DEa  155 (184)
T PF04851_consen   77 K-YNFFEKSIKPAYDSKEFISIQDDISDKSESDNNDKDIILTTYQSLQSDIKEEKKIDESARRSYKLLKNKFDLVIIDEA  155 (184)
T ss_dssp             S-EEEEE--GGGCCE-SEEETTTTEEEHHHHHCBSS-SEEEEEHHHHHHHHHH---------GCHHGGGGSESEEEEETG
T ss_pred             h-hhhcccccccccccccccccccccccccccccccccchhhHHHHHHhhcccccccccchhhhhhhccccCCEEEEehh
Confidence            2 11111            111111112223345578999999999987765422           12234789999999


Q ss_pred             hHhhccCcHHHHHHHHhhCCccCcEEEEEeeCC
Q 017573          148 DEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMP  180 (369)
Q Consensus       148 H~~~~~~~~~~~~~~~~~~~~~~~~i~~saT~~  180 (369)
                      |++.....   ...+..  .+...+++|||||.
T Consensus       156 H~~~~~~~---~~~i~~--~~~~~~l~lTATp~  183 (184)
T PF04851_consen  156 HHYPSDSS---YREIIE--FKAAFILGLTATPF  183 (184)
T ss_dssp             GCTHHHHH---HHHHHH--SSCCEEEEEESS-S
T ss_pred             hhcCCHHH---HHHHHc--CCCCeEEEEEeCcc
Confidence            99865442   333333  45667899999985

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 ....

>KOG0386 consensus Chromatin remodeling complex SWI/SNF, component SWI2 and related ATPases (DNA/RNA helicase superfamily) [Chromatin structure and dynamics; Transcription]

Probab=99.82  E-value=2.4e-20  Score=170.54  Aligned_cols=321  Identities=18%  Similarity=0.189  Sum_probs=215.3

Q ss_pred             CCCCCcHhhhhhhhcccc----CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccc
Q 017573           15 GFEKPSAIQQRGIVPFCK----GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDY   90 (369)
Q Consensus        15 ~~~~~~~~Q~~~~~~~~~----~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~   90 (369)
                      ...++.+||.+.++.+..    +-+.++..+||.|||...+..+...+......+..+|+||+..|.. |..+|.+|...
T Consensus       391 ~GG~Lk~YQl~GLqWmVSLyNNnLNGILADEMGLGKTIQtIsLitYLmE~K~~~GP~LvivPlstL~N-W~~Ef~kWaPS  469 (1157)
T KOG0386|consen  391 QGGELKEYQLHGLQWMVSLYNNNLNGILADEMGLGKTIQTISLITYLMEHKQMQGPFLIIVPLSTLVN-WSSEFPKWAPS  469 (1157)
T ss_pred             cCCCCchhhhhhhHHHhhccCCCcccccchhcccchHHHHHHHHHHHHHHcccCCCeEEeccccccCC-chhhccccccc
Confidence            335899999999988763    4678999999999998888777777776666668999999988875 67777777543


Q ss_pred             cCcEEEEEECCcchH--HHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCc
Q 017573           91 LGVKVHACVGGTSVR--EDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPA  168 (369)
Q Consensus        91 ~~~~v~~~~~~~~~~--~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~  168 (369)
                        +......|.....  ....+.....+|+++|++....  ....+..-.|.++||||.|++.+.  ...+...++..-.
T Consensus       470 --v~~i~YkGtp~~R~~l~~qir~gKFnVLlTtyEyiik--dk~lLsKI~W~yMIIDEGHRmKNa--~~KLt~~L~t~y~  543 (1157)
T KOG0386|consen  470 --VQKIQYKGTPQQRSGLTKQQRHGKFNVLLTTYEYIIK--DKALLSKISWKYMIIDEGHRMKNA--ICKLTDTLNTHYR  543 (1157)
T ss_pred             --eeeeeeeCCHHHHhhHHHHHhcccceeeeeeHHHhcC--CHHHHhccCCcceeecccccccch--hhHHHHHhhcccc
Confidence              3333333322211  1122334689999999988754  222222334789999999999544  3445555553333


Q ss_pred             cCcEEEEEeeCChhHHH------------------HHHHhcCCCEEEEec-----C------------------------
Q 017573          169 KVQVGVFSATMPPEALE------------------ITRKFMNKPVRILVK-----R------------------------  201 (369)
Q Consensus       169 ~~~~i~~saT~~~~~~~------------------~~~~~~~~~~~~~~~-----~------------------------  201 (369)
                      ....+++|+||..+...                  .+..|+..|..-...     .                        
T Consensus       544 ~q~RLLLTGTPLQN~LpELWaLLNFlLP~IFnS~~~FeqWFN~PFantGek~eLteEEtlLIIrRLHkVLRPFlLRRlKk  623 (1157)
T KOG0386|consen  544 AQRRLLLTGTPLQNNLPELWALLNFLLPNIFNSCKAFEQWFNQPFANTGEKVELTEEETLLIIRRLHKVLRPFLLRRLKK  623 (1157)
T ss_pred             chhhhhhcCChhhhccHHHHHHHHHhccchhhhHhHHHHHhhhhhhhcCCcccccchHHHHHHHHHHHhhhHHHHHhhhH
Confidence            44467789998533211                  112222211100000     0                        


Q ss_pred             --ccccccc-----------------------------------------------------------eeEEEE------
Q 017573          202 --DELTLEG-----------------------------------------------------------IKQFYV------  214 (369)
Q Consensus       202 --~~~~~~~-----------------------------------------------------------~~~~~~------  214 (369)
                        +...|..                                                           +...+.      
T Consensus       624 eVE~~LPdKve~viKC~mSalQq~lY~~m~~~g~l~~d~~~g~~g~k~L~N~imqLRKiCNHP~lf~~ve~~~~~~~~~~  703 (1157)
T KOG0386|consen  624 EVEQELPDKVEDVIKCDMSALQQSLYKQMQNKGQLLKDTAKGKKGYKPLFNTIMQLRKLCNHPYLFANVENSYTLHYDIK  703 (1157)
T ss_pred             HHhhhCchhhhHhhheehhhhhHhhhHHHHhCCCCCcCchhccccchhhhhHhHHHHHhcCCchhhhhhccccccccChh
Confidence              0000000                                                           000000      


Q ss_pred             EccchhhhHHHHHHHHHhc--cCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCC---cEE
Q 017573          215 NVEKEEWKLETLCDLYETL--AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSS---RVL  289 (369)
Q Consensus       215 ~~~~~~~~~~~l~~~~~~~--~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~---~vl  289 (369)
                      .+-+...+.+.+..++-+.  .+.+++.|+.-..-...+..+|.-.+++...+.|....++|...++.|+..+.   .+|
T Consensus       704 dL~R~sGKfELLDRiLPKLkatgHRVLlF~qMTrlmdimEdyL~~~~~kYlRLDG~TK~~eRg~ll~~FN~Pds~yf~Fl  783 (1157)
T KOG0386|consen  704 DLVRVSGKFELLDRILPKLKATGHRVLLFSQMTRLMDILEDYLQIREYKYLRLDGQTKVEERGDLLEIFNAPDSPYFIFL  783 (1157)
T ss_pred             HHHHhccHHHHHHhhhHHHHhcCcchhhHHHHHHHHHHHHHHHhhhhhheeeecCCcchhhHHHHHHHhcCCCCceeeee
Confidence            0000111455555655433  45688999998888899999999889999999999999999999999987553   467


Q ss_pred             EEecCCcCCCCCCCCcEEEEecCCCCccchhhhhcccccCCCceeEEEEeccc
Q 017573          290 ITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRD  342 (369)
Q Consensus       290 i~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~  342 (369)
                      ++|.+.+.|+|+.-++.||+++..|++....|+.-|+.|.|+...+-++.-..
T Consensus       784 lstragglglNlQtadtviifdsdwnp~~d~qaqdrahrigq~~evRv~rl~t  836 (1157)
T KOG0386|consen  784 LSTRAGGLGLNLQTADTVIIFDSDWNPHQDLQAQDRAHRIGQKKEVRVLRLIT  836 (1157)
T ss_pred             eeecccccccchhhcceEEEecCCCCchhHHHHHHHHHHhhchhheeeeeeeh
Confidence            78999999999999999999999999999999999999999876666555544

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

Probab=99.82  E-value=1.7e-19  Score=156.01  Aligned_cols=357  Identities=15%  Similarity=0.118  Sum_probs=236.3

Q ss_pred             HHHH-HHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHH
Q 017573            7 LLRG-IYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMR   85 (369)
Q Consensus         7 i~~~-l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~   85 (369)
                      +.+. ++.+..+..+.+|.++++.+-+|++.++.-.+.+||++++.++........... ..+++.|+.+++++..+-+.
T Consensus       274 ~~~~~~~~~~~E~~~~~~~~~~~~~~~G~~~~~~~~~~~GK~~~~~~~s~~~~~~~~~s-~~~~~~~~~~~~~~~~~~~~  352 (1034)
T KOG4150|consen  274 SIRSLLNKNTGESGIAISLELLKFASEGRADGGNEARQAGKGTCPTSGSRKFQTLCHAT-NSLLPSEMVEHLRNGSKGQV  352 (1034)
T ss_pred             HHHHHHhcccccchhhhhHHHHhhhhhcccccccchhhcCCccCcccchhhhhhcCccc-ceecchhHHHHhhccCCceE
Confidence            3444 466777889999999999999999999999999999999988877666554433 78999999998876655332


Q ss_pred             Hhcccc---CcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCC----ccEEEEechhHhhccC--c-
Q 017573           86 ALGDYL---GVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDY----IKMFVLDEADEMLSRG--F-  155 (369)
Q Consensus        86 ~~~~~~---~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~----~~~viiDE~H~~~~~~--~-  155 (369)
                      -.....   .--+.-...+........+...+.+++++.+.........+......    ..+++.||+|.+....  . 
T Consensus       353 V~~~~I~~~K~A~V~~~D~~sE~~~~A~~R~~~~~~~s~~~~~~s~~L~~~~~~~~~~~~~~~~~~~~~~~Y~~~~~~~~  432 (1034)
T KOG4150|consen  353 VHVEVIKARKSAYVEMSDKLSETTKSALKRIGLNTLYSHQAEAISAALAKSLCYNVPVFEELCKDTNSCALYLFPTKALA  432 (1034)
T ss_pred             EEEEehhhhhcceeecccCCCchhHHHHHhcCcceeecCHHHHHHHHhhhccccccHHHHHHHhcccceeeeecchhhHH
Confidence            111100   11122222333334455555667899999998887655443333222    4578999999765322  1 


Q ss_pred             H---HHHHHHHhhC--CccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCc-cccccceeEEEEEccc------hhhhH
Q 017573          156 K---DQIYDIFQLL--PAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRD-ELTLEGIKQFYVNVEK------EEWKL  223 (369)
Q Consensus       156 ~---~~~~~~~~~~--~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~------~~~~~  223 (369)
                      .   +.+..+...+  ..+.+++-.++|..... .....+.+-.....+..+ ........-.|.....      .+.++
T Consensus       433 ~~~~R~L~~L~~~F~~~~~~~~~~~~~~~K~~~-~~~~~~~~~~E~~Li~~DGSPs~~K~~V~WNP~~~P~~~~~~~~~i  511 (1034)
T KOG4150|consen  433 QDQLRALSDLIKGFEASINMGVYDGDTPYKDRT-RLRSELANLSELELVTIDGSPSSEKLFVLWNPSAPPTSKSEKSSKV  511 (1034)
T ss_pred             HHHHHHHHHHHHHHHhhcCcceEeCCCCcCCHH-HHHHHhcCCcceEEEEecCCCCccceEEEeCCCCCCcchhhhhhHH
Confidence            1   1222222222  23677887788775444 444455444333332222 2222222222221111      12233


Q ss_pred             HHHHHHHHhc--cCCCeEEEeCCHhhHHHHHHHHhhC----CC----eeEEecCCCCHHHHHHHHHHHhcCCCcEEEEec
Q 017573          224 ETLCDLYETL--AITQSVIFVNTRRKVDWLTDKMRSR----DH----TVSATHGDMDQNTRDIIMREFRSGSSRVLITTD  293 (369)
Q Consensus       224 ~~l~~~~~~~--~~~k~lv~~~~~~~~~~~~~~l~~~----~~----~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~  293 (369)
                      ....+++...  .+-++|.||++++-++-+....+..    +.    .+..+.|+.+.++|.++....-.|+..-+|+|.
T Consensus       512 ~E~s~~~~~~i~~~~R~IAFC~~R~~CEL~~~~~R~I~~ET~~~LV~~i~SYRGGY~A~DRRKIE~~~F~G~L~giIaTN  591 (1034)
T KOG4150|consen  512 VEVSHLFAEMVQHGLRCIAFCPSRKLCELVLCLTREILAETAPHLVEAITSYRGGYIAEDRRKIESDLFGGKLCGIIATN  591 (1034)
T ss_pred             HHHHHHHHHHHHcCCcEEEeccHHHHHHHHHHHHHHHHHHhhHHHHHHHHhhcCccchhhHHHHHHHhhCCeeeEEEecc
Confidence            3344444332  3458999999999888665544322    22    466788999999999999999999999999999


Q ss_pred             CCcCCCCCCCCcEEEEecCCCCccchhhhhcccccCCCceeEEEEec--cccHHHHHHHHHHhccccccCCcch
Q 017573          294 LLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVT--RDDERMLFDIQKFYNVVIEELPSNV  365 (369)
Q Consensus       294 ~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~  365 (369)
                      +++-|+|+..++.|+..+.|.|...+.|..||+||.++++.++.+..  +-|..++..-...+...+.++.-++
T Consensus       592 ALELGIDIG~LDAVl~~GFP~S~aNl~QQ~GRAGRRNk~SLavyva~~~PVDQ~Y~~HP~~l~~~pN~EL~LD~  665 (1034)
T KOG4150|consen  592 ALELGIDIGHLDAVLHLGFPGSIANLWQQAGRAGRRNKPSLAVYVAFLGPVDQYYMSHPDKLFGSPNEELHLDS  665 (1034)
T ss_pred             hhhhccccccceeEEEccCchhHHHHHHHhccccccCCCceEEEEEeccchhhHhhcCcHHHhCCCcceeEEec
Confidence            99999999999999999999999999999999999988865554443  5577777777777777777665444

>cd00079 HELICc Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process

Probab=99.82  E-value=3e-19  Score=134.22  Aligned_cols=118  Identities=44%  Similarity=0.721  Sum_probs=109.0

Q ss_pred             hhHHHHHHHHHhcc--CCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCC
Q 017573          221 WKLETLCDLYETLA--ITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARG  298 (369)
Q Consensus       221 ~~~~~l~~~~~~~~--~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G  298 (369)
                      .+...+..++....  ++++|||+++.+.++.+++.|.+.+..+..+||++++.+|..+++.|.++...++++|+++++|
T Consensus        12 ~k~~~i~~~i~~~~~~~~~~lvf~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~ili~t~~~~~G   91 (131)
T cd00079          12 EKLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAALHGDGSQEEREEVLKDFREGEIVVLVATDVIARG   91 (131)
T ss_pred             HHHHHHHHHHHhcccCCCcEEEEeCcHHHHHHHHHHHHhcCCcEEEEECCCCHHHHHHHHHHHHcCCCcEEEEcChhhcC
Confidence            56677777776653  6799999999999999999999888899999999999999999999999999999999999999


Q ss_pred             CCCCCCcEEEEecCCCCccchhhhhcccccCCCceeEEEE
Q 017573          299 IDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINF  338 (369)
Q Consensus       299 ~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~  338 (369)
                      +|+|.+++|++++++++..++.|++||++|.|+.|.++++
T Consensus        92 ~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~  131 (131)
T cd00079          92 IDLPNVSVVINYDLPWSPSSYLQRIGRAGRAGQKGTAILL  131 (131)
T ss_pred             cChhhCCEEEEeCCCCCHHHheecccccccCCCCceEEeC
Confidence            9999999999999999999999999999999998887764

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

Probab=99.82  E-value=1.1e-18  Score=161.60  Aligned_cols=121  Identities=20%  Similarity=0.265  Sum_probs=104.3

Q ss_pred             hHHHHHHHHHhc--cCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCC--CcEEEEecCCcC
Q 017573          222 KLETLCDLYETL--AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGS--SRVLITTDLLAR  297 (369)
Q Consensus       222 ~~~~l~~~~~~~--~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~--~~vli~t~~~~~  297 (369)
                      |++.|.-+++..  .+.++|||+.-.+....+..+|.-+|+....+.|..+.++|...++.|+.+.  .++|++|...+.
T Consensus      1261 KLQtLAiLLqQLk~eghRvLIfTQMtkmLDVLeqFLnyHgylY~RLDg~t~vEqRQaLmerFNaD~RIfcfILSTrSggv 1340 (1958)
T KOG0391|consen 1261 KLQTLAILLQQLKSEGHRVLIFTQMTKMLDVLEQFLNYHGYLYVRLDGNTSVEQRQALMERFNADRRIFCFILSTRSGGV 1340 (1958)
T ss_pred             hHHHHHHHHHHHHhcCceEEehhHHHHHHHHHHHHHhhcceEEEEecCCccHHHHHHHHHHhcCCCceEEEEEeccCCcc
Confidence            667777777654  3458999999999999999999999999999999999999999999999865  467788999999


Q ss_pred             CCCCCCCcEEEEecCCCCccchhhhhcccccCCCceeEEE--Eeccc
Q 017573          298 GIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAIN--FVTRD  342 (369)
Q Consensus       298 G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~--~~~~~  342 (369)
                      |+|+.+++.||+||..||+..=.|+--|..|.|+...+.+  +++..
T Consensus      1341 GiNLtgADTVvFYDsDwNPtMDaQAQDrChRIGqtRDVHIYRLISe~ 1387 (1958)
T KOG0391|consen 1341 GINLTGADTVVFYDSDWNPTMDAQAQDRCHRIGQTRDVHIYRLISER 1387 (1958)
T ss_pred             ccccccCceEEEecCCCCchhhhHHHHHHHhhcCccceEEEEeeccc
Confidence            9999999999999999999999999999999887655544  45544

>KOG0953 consensus Mitochondrial RNA helicase SUV3, DEAD-box superfamily [RNA processing and modification]

Probab=99.82  E-value=7.1e-19  Score=151.61  Aligned_cols=284  Identities=18%  Similarity=0.186  Sum_probs=184.9

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHcc
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQA  113 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~  113 (369)
                      +=++-+|||.||||.-|    ++++....   +.+|.-|.+-|+.+.++.+++.    |+.+..++|.+......+  .+
T Consensus       192 kIi~H~GPTNSGKTy~A----Lqrl~~ak---sGvycGPLrLLA~EV~~r~na~----gipCdL~TGeE~~~~~~~--~~  258 (700)
T KOG0953|consen  192 KIIMHVGPTNSGKTYRA----LQRLKSAK---SGVYCGPLRLLAHEVYDRLNAL----GIPCDLLTGEERRFVLDN--GN  258 (700)
T ss_pred             eEEEEeCCCCCchhHHH----HHHHhhhc---cceecchHHHHHHHHHHHhhhc----CCCccccccceeeecCCC--CC
Confidence            33677899999999765    34444333   7899999999999999998876    666767777554322211  23


Q ss_pred             CCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCC
Q 017573          114 GVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNK  193 (369)
Q Consensus       114 ~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~  193 (369)
                      .++.+=+|.|+..        ....+++.|+||++++.+.+..-.+.+.+-.+...-  +-+.+-|  ...++.+..+..
T Consensus       259 ~a~hvScTVEM~s--------v~~~yeVAViDEIQmm~Dp~RGwAWTrALLGl~AdE--iHLCGep--svldlV~~i~k~  326 (700)
T KOG0953|consen  259 PAQHVSCTVEMVS--------VNTPYEVAVIDEIQMMRDPSRGWAWTRALLGLAADE--IHLCGEP--SVLDLVRKILKM  326 (700)
T ss_pred             cccceEEEEEEee--------cCCceEEEEehhHHhhcCcccchHHHHHHHhhhhhh--hhccCCc--hHHHHHHHHHhh
Confidence            4677778876653        223479999999999987665444444433332211  2223333  344455555442


Q ss_pred             CEEEEecCccccccceeEEEEEccchhhhHHHHHHHHHhccCCCeEEEeCCHhhHHHHHHHHhhCCCe-eEEecCCCCHH
Q 017573          194 PVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHT-VSATHGDMDQN  272 (369)
Q Consensus       194 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~~~~-~~~~~~~~~~~  272 (369)
                      ..           ..+....+..-......+.+..-++....+.|+| |-|++....+.+.+++.+.. +++++|.++++
T Consensus       327 TG-----------d~vev~~YeRl~pL~v~~~~~~sl~nlk~GDCvV-~FSkk~I~~~k~kIE~~g~~k~aVIYGsLPPe  394 (700)
T KOG0953|consen  327 TG-----------DDVEVREYERLSPLVVEETALGSLSNLKPGDCVV-AFSKKDIFTVKKKIEKAGNHKCAVIYGSLPPE  394 (700)
T ss_pred             cC-----------CeeEEEeecccCcceehhhhhhhhccCCCCCeEE-EeehhhHHHHHHHHHHhcCcceEEEecCCCCc
Confidence            11           0111111111111112223333444555566655 45677888899999888665 99999999999


Q ss_pred             HHHHHHHHHhc--CCCcEEEEecCCcCCCCCCCCcEEEEecCC---------CCccchhhhhcccccCCCc---eeEEEE
Q 017573          273 TRDIIMREFRS--GSSRVLITTDLLARGIDVQQVSLVINYDLP---------TQPENYLHRIGRSGRFGRK---GVAINF  338 (369)
Q Consensus       273 ~r~~~~~~f~~--~~~~vli~t~~~~~G~d~~~~~~vi~~~~~---------~~~~~~~Q~~GR~~R~~~~---~~~~~~  338 (369)
                      .|......|++  ++.+|||||+++++|+|+ +++.||++...         .+..+..|..|||||.|..   |.+-++
T Consensus       395 Tr~aQA~~FNd~~~e~dvlVAsDAIGMGLNL-~IrRiiF~sl~Kysg~e~~~it~sqikQIAGRAGRf~s~~~~G~vTtl  473 (700)
T KOG0953|consen  395 TRLAQAALFNDPSNECDVLVASDAIGMGLNL-NIRRIIFYSLIKYSGRETEDITVSQIKQIAGRAGRFGSKYPQGEVTTL  473 (700)
T ss_pred             hhHHHHHHhCCCCCccceEEeeccccccccc-ceeEEEEeecccCCcccceeccHHHHHHHhhcccccccCCcCceEEEe
Confidence            99999999987  789999999999999998 78888888753         3556789999999998643   544444


Q ss_pred             eccccHHHHHHHHHHhccccc
Q 017573          339 VTRDDERMLFDIQKFYNVVIE  359 (369)
Q Consensus       339 ~~~~~~~~~~~~~~~~~~~~~  359 (369)
                      .    .+.+..+.+.++...+
T Consensus       474 ~----~eDL~~L~~~l~~p~e  490 (700)
T KOG0953|consen  474 H----SEDLKLLKRILKRPVE  490 (700)
T ss_pred             e----HhhHHHHHHHHhCCch
Confidence            3    3444555555554443

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=99.80  E-value=1.5e-17  Score=153.50  Aligned_cols=273  Identities=17%  Similarity=0.180  Sum_probs=172.6

Q ss_pred             CCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEE
Q 017573           18 KPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHA   97 (369)
Q Consensus        18 ~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~   97 (369)
                      .|++.|  ++-.+.-.+.-+..+.||.|||+++.++++-....+.   .+-||+++.-|+..=++++..+...+|+.|..
T Consensus        85 r~ydVQ--liGgl~Lh~G~IAEM~TGEGKTL~atlpaylnAL~Gk---gVhVVTvNdYLA~RDae~m~~vy~~LGLtvg~  159 (939)
T PRK12902         85 RHFDVQ--LIGGMVLHEGQIAEMKTGEGKTLVATLPSYLNALTGK---GVHVVTVNDYLARRDAEWMGQVHRFLGLSVGL  159 (939)
T ss_pred             CcchhH--HHhhhhhcCCceeeecCCCChhHHHHHHHHHHhhcCC---CeEEEeCCHHHHHhHHHHHHHHHHHhCCeEEE
Confidence            344444  4444444677899999999999999887776555444   79999999999999999999999999999999


Q ss_pred             EECCcchHHHHHHHccCCcEEEeccHHH-HHHHHcC------CCCCCCccEEEEechhHhh-ccC---------------
Q 017573           98 CVGGTSVREDQRILQAGVHVVVGTPGRV-FDMLRRQ------SLRPDYIKMFVLDEADEML-SRG---------------  154 (369)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~iiv~t~~~l-~~~~~~~------~~~~~~~~~viiDE~H~~~-~~~---------------  154 (369)
                      ..++......+.  .-.+||+++|...| +..++..      ......+.+.|+||++.+. +..               
T Consensus       160 i~~~~~~~err~--aY~~DItYgTn~e~gFDYLRDnm~~~~~~~vqR~~~faIVDEvDSILIDEArTPLIISg~~~~~~~  237 (939)
T PRK12902        160 IQQDMSPEERKK--NYACDITYATNSELGFDYLRDNMATDISEVVQRPFNYCVIDEVDSILIDEARTPLIISGQVERPQE  237 (939)
T ss_pred             ECCCCChHHHHH--hcCCCeEEecCCcccccchhhhhcccccccccCccceEEEecccceeeccCCCcccccCCCccchH
Confidence            877666554443  33689999999887 2333221      1223557899999999754 100               


Q ss_pred             cHHHHHHHHhhCCc--------------c---------------------------------------------------
Q 017573          155 FKDQIYDIFQLLPA--------------K---------------------------------------------------  169 (369)
Q Consensus       155 ~~~~~~~~~~~~~~--------------~---------------------------------------------------  169 (369)
                      .......+...+..              .                                                   
T Consensus       238 ~y~~~~~~~~~L~~~~~~~~~~dy~idek~~~v~LTe~G~~~~e~~~~i~nLy~~~~~~~~~i~~AL~A~~lf~~d~dYi  317 (939)
T PRK12902        238 KYQKAAEVAAALQRKDGIDPEGDYEVDEKQRNVLLTDEGFAKAEQLLGVSDLFDPQDPWAHYIFNALKAKELFIKDVNYI  317 (939)
T ss_pred             HHHHHHHHHHHhhhhcccCCCCCeEEecCCCeeeEcHHHHHHHHHHhCchhhcCcccHHHHHHHHHHHHHHHHhcCCeEE
Confidence            00000111100000              0                                                   


Q ss_pred             ---------------------------------------------------------CcEEEEEeeCChhHHHHHHHhcC
Q 017573          170 ---------------------------------------------------------VQVGVFSATMPPEALEITRKFMN  192 (369)
Q Consensus       170 ---------------------------------------------------------~~~i~~saT~~~~~~~~~~~~~~  192 (369)
                                                                               .++.+||+|......+ ....++
T Consensus       318 V~dg~V~IVDe~TGR~m~grrws~GLHQaIEaKE~v~it~e~~tlAsIT~QnfFr~Y~kLsGMTGTa~te~~E-f~~iY~  396 (939)
T PRK12902        318 VRNGEVVIVDEFTGRVMPGRRWSDGLHQAIEAKEGVEIQPETQTLASITYQNFFLLYPKLAGMTGTAKTEEVE-FEKTYK  396 (939)
T ss_pred             EECCEEEEEECCCCCCCCCCccchHHHHHHHhhcCCCCCCCceeeeeeeHHHHHhhCchhcccCCCCHHHHHH-HHHHhC
Confidence                                                                     4566777777544433 334444


Q ss_pred             CCEEEEecCccccccceeEEEEEccchhhhHHHHH-HHHHhc-cCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCC-
Q 017573          193 KPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLC-DLYETL-AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDM-  269 (369)
Q Consensus       193 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~-~~~~~~-~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~-  269 (369)
                      -++.......+.........++  .+...+...+. ++...+ .+.++||-+.|++..+.+++.|.+.+++..++++.. 
T Consensus       397 l~Vv~IPTnkP~~R~d~~d~vy--~t~~~K~~Ai~~ei~~~~~~GrPVLIgT~SVe~SE~ls~~L~~~gi~h~vLNAk~~  474 (939)
T PRK12902        397 LEVTVIPTNRPRRRQDWPDQVY--KTEIAKWRAVANETAEMHKQGRPVLVGTTSVEKSELLSALLQEQGIPHNLLNAKPE  474 (939)
T ss_pred             CcEEEcCCCCCeeeecCCCeEE--cCHHHHHHHHHHHHHHHHhCCCCEEEeeCCHHHHHHHHHHHHHcCCchheeeCCCc
Confidence            4433332222222211111121  12223333443 444433 467999999999999999999999999999999972 


Q ss_pred             CHHHHHHHHHHHhcCC-CcEEEEecCCcCCCCCC
Q 017573          270 DQNTRDIIMREFRSGS-SRVLITTDLLARGIDVQ  302 (369)
Q Consensus       270 ~~~~r~~~~~~f~~~~-~~vli~t~~~~~G~d~~  302 (369)
                      ..+.-.+++.+  .|. -.|.|||+++++|.||.
T Consensus       475 ~~~~EA~IIa~--AG~~GaVTIATNMAGRGTDIk  506 (939)
T PRK12902        475 NVEREAEIVAQ--AGRKGAVTIATNMAGRGTDII  506 (939)
T ss_pred             chHhHHHHHHh--cCCCCcEEEeccCCCCCcCEe
Confidence            22222334432  444 34999999999999974

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=99.79  E-value=2.1e-16  Score=150.15  Aligned_cols=75  Identities=24%  Similarity=0.218  Sum_probs=64.0

Q ss_pred             hCCCCCCcHhhhhhhhccc----cCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHh
Q 017573           13 AYGFEKPSAIQQRGIVPFC----KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRAL   87 (369)
Q Consensus        13 ~~~~~~~~~~Q~~~~~~~~----~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~   87 (369)
                      .|+|..+||.|.+....+.    +++++++.+|||+|||++.+.+++......+...+++|.+.+.+=..|..+++++.
T Consensus         5 ~FPy~~~y~~Q~~~m~~v~~~l~~~~~~llEsPTGtGKTlslL~~aL~~~~~~~~~~kIiy~sRThsQl~q~i~Elk~~   83 (705)
T TIGR00604         5 YFPYEKIYPEQRSYMRDLKRSLDRGDEAILEMPSGTGKTISLLSLILAYQQEKPEVRKIIYASRTHSQLEQATEELRKL   83 (705)
T ss_pred             ecCCCCCCHHHHHHHHHHHHHhccCCceEEeCCCCCCccHHHHHHHHHHHHhccccccEEEEcccchHHHHHHHHHHhh
Confidence            4889888999999887765    57999999999999999999999987764443458999999999999999999884

All proteins in this family for which funcitons are known are DNA-DNA helicases that funciton in the initiation of transcription and nucleotide excision repair as part of the TFIIH complex. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

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

Probab=99.78  E-value=7.8e-17  Score=152.98  Aligned_cols=113  Identities=15%  Similarity=0.299  Sum_probs=82.1

Q ss_pred             HHHHHHhccCCCeEEEeCCHhhHHHHHHHHhhCCCe-eEEecCCCCHHHHHHHHHHHhcCCC-cEEEEecCCcCCCCCCC
Q 017573          226 LCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHT-VSATHGDMDQNTRDIIMREFRSGSS-RVLITTDLLARGIDVQQ  303 (369)
Q Consensus       226 l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~~~~-~~~~~~~~~~~~r~~~~~~f~~~~~-~vli~t~~~~~G~d~~~  303 (369)
                      +..++...+ ++++||++|.+.++.+.+.+...... .....+.   ..+.+.++.|..+.- -+++++..+.+|+|+|+
T Consensus       471 i~~~~~~~~-~~~lvlF~Sy~~l~~~~~~~~~~~~~~~v~~q~~---~~~~~~l~~f~~~~~~~~lv~~gsf~EGVD~~g  546 (654)
T COG1199         471 LREILKASP-GGVLVLFPSYEYLKRVAERLKDERSTLPVLTQGE---DEREELLEKFKASGEGLILVGGGSFWEGVDFPG  546 (654)
T ss_pred             HHHHHhhcC-CCEEEEeccHHHHHHHHHHHhhcCccceeeecCC---CcHHHHHHHHHHhcCCeEEEeeccccCcccCCC
Confidence            333444334 59999999999999999999876553 2333333   334478888876554 79999999999999996


Q ss_pred             --CcEEEEecCCCC------------------------------ccchhhhhcccccCCCceeEEEEeccc
Q 017573          304 --VSLVINYDLPTQ------------------------------PENYLHRIGRSGRFGRKGVAINFVTRD  342 (369)
Q Consensus       304 --~~~vi~~~~~~~------------------------------~~~~~Q~~GR~~R~~~~~~~~~~~~~~  342 (369)
                        ++.|++.+.|.-                              ...+.|.+||+.|..++.-++++++..
T Consensus       547 ~~l~~vvI~~lPfp~p~dp~~~~r~~~~~~~g~~~f~~~~l~~A~~~l~QavGRlIR~~~D~G~ivllD~R  617 (654)
T COG1199         547 DALRLVVIVGLPFPNPDDPLLKARLEFLKRLGGDPFEEFYLPPAVIKLRQAVGRLIRSEDDRGVIVLLDKR  617 (654)
T ss_pred             CCeeEEEEEecCCCCCCCHHHHHHHHHHHHhcCCCceEeehHHHHHHHHHhhccccccCCCceEEEEeccc
Confidence              688888887642                              234699999999986665555555553

>KOG0388 consensus SNF2 family DNA-dependent ATPase [Replication, recombination and repair]

Probab=99.78  E-value=4e-18  Score=150.84  Aligned_cols=124  Identities=21%  Similarity=0.316  Sum_probs=103.3

Q ss_pred             hHHHHHHHHHhc--cCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCc-EEEEecCCcCC
Q 017573          222 KLETLCDLYETL--AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSR-VLITTDLLARG  298 (369)
Q Consensus       222 ~~~~l~~~~~~~--~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~-vli~t~~~~~G  298 (369)
                      ++..+.+++.+.  .+-++|+|+.-.+...-+.++|.-.++....+.|...-.+|..++..|+..++- +|++|.+.+-|
T Consensus      1029 KL~~LDeLL~kLkaegHRvL~yfQMTkM~dl~EdYl~yr~Y~ylRLDGSsk~~dRrd~vrDwQ~sdiFvFLLSTRAGGLG 1108 (1185)
T KOG0388|consen 1029 KLVVLDELLPKLKAEGHRVLMYFQMTKMIDLIEDYLVYRGYTYLRLDGSSKASDRRDVVRDWQASDIFVFLLSTRAGGLG 1108 (1185)
T ss_pred             ceeeHHHHHHHhhcCCceEEehhHHHHHHHHHHHHHHhhccceEEecCcchhhHHHHHHhhccCCceEEEEEecccCccc
Confidence            344455555443  234788999888889999999999999999999999999999999999987765 56788999999


Q ss_pred             CCCCCCcEEEEecCCCCccchhhhhcccccCCCc--eeEEEEeccccHH
Q 017573          299 IDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRK--GVAINFVTRDDER  345 (369)
Q Consensus       299 ~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~--~~~~~~~~~~~~~  345 (369)
                      +|+..++.||+++..|++..-.|++.|+.|.|+.  .+++-+......+
T Consensus      1109 INLTAADTViFYdSDWNPT~D~QAMDRAHRLGQTrdvtvyrl~~rgTvE 1157 (1185)
T KOG0388|consen 1109 INLTAADTVIFYDSDWNPTADQQAMDRAHRLGQTRDVTVYRLITRGTVE 1157 (1185)
T ss_pred             ccccccceEEEecCCCCcchhhHHHHHHHhccCccceeeeeecccccHH
Confidence            9999999999999999999999999999999976  4566677766444

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

Probab=99.78  E-value=2.7e-17  Score=153.84  Aligned_cols=312  Identities=16%  Similarity=0.191  Sum_probs=208.5

Q ss_pred             CCcHhhhhhhhcccc-CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHH-HhccccCcEE
Q 017573           18 KPSAIQQRGIVPFCK-GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMR-ALGDYLGVKV   95 (369)
Q Consensus        18 ~~~~~Q~~~~~~~~~-~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~-~~~~~~~~~v   95 (369)
                      ...+.|.+.++-+.+ ++++++.+|+|||||.++-++++.   .. ...+++++.|.-+.+..+++.|. ++....|..+
T Consensus      1143 ~~n~iqtqVf~~~y~~nd~v~vga~~gsgkt~~ae~a~l~---~~-~~~~~vyi~p~~~i~~~~~~~w~~~f~~~~G~~~ 1218 (1674)
T KOG0951|consen 1143 DFNPIQTQVFTSLYNTNDNVLVGAPNGSGKTACAELALLR---PD-TIGRAVYIAPLEEIADEQYRDWEKKFSKLLGLRI 1218 (1674)
T ss_pred             ccCCceEEEEeeeecccceEEEecCCCCchhHHHHHHhcC---Cc-cceEEEEecchHHHHHHHHHHHHHhhccccCceE
Confidence            348899999998886 478999999999999999888876   22 22389999999999887777664 4555568888


Q ss_pred             EEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcH------HHHHHHHhhCCcc
Q 017573           96 HACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFK------DQIYDIFQLLPAK  169 (369)
Q Consensus        96 ~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~------~~~~~~~~~~~~~  169 (369)
                      ..+.|....+..   +....+++|+||++|-.. .    ..+..++.|.||.|.+.+.. .      -....+...+-++
T Consensus      1219 ~~l~ge~s~~lk---l~~~~~vii~tpe~~d~l-q----~iQ~v~l~i~d~lh~igg~~-g~v~evi~S~r~ia~q~~k~ 1289 (1674)
T KOG0951|consen 1219 VKLTGETSLDLK---LLQKGQVIISTPEQWDLL-Q----SIQQVDLFIVDELHLIGGVY-GAVYEVICSMRYIASQLEKK 1289 (1674)
T ss_pred             EecCCccccchH---HhhhcceEEechhHHHHH-h----hhhhcceEeeehhhhhcccC-CceEEEEeeHHHHHHHHHhh
Confidence            888887764432   234568999999999654 2    44558999999999876322 1      1145556666677


Q ss_pred             CcEEEEEeeCChhHHHHHHHhcCCCEEEEecC-ccccccceeEEEEEccchhh----hHHHHHHHHHhc--cCCCeEEEe
Q 017573          170 VQVGVFSATMPPEALEITRKFMNKPVRILVKR-DELTLEGIKQFYVNVEKEEW----KLETLCDLYETL--AITQSVIFV  242 (369)
Q Consensus       170 ~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~----~~~~l~~~~~~~--~~~k~lv~~  242 (369)
                      .+++++|.... +..++  ..+.....+.... ....|..+....+.......    +.+-...-+.++  ..++.+||+
T Consensus      1290 ir~v~ls~~la-na~d~--ig~s~~~v~Nf~p~~R~~Pl~i~i~~~~~~~~~~~~~am~~~~~~ai~~~a~~~k~~~vf~ 1366 (1674)
T KOG0951|consen 1290 IRVVALSSSLA-NARDL--IGASSSGVFNFSPSVRPVPLEIHIQSVDISHFESRMLAMTKPTYTAIVRHAGNRKPAIVFL 1366 (1674)
T ss_pred             eeEEEeehhhc-cchhh--ccccccceeecCcccCCCceeEEEEEeccchhHHHHHHhhhhHHHHHHHHhcCCCCeEEEe
Confidence            78898887764 44444  1222222222221 11222222222222211111    111122222222  446899999


Q ss_pred             CCHhhHHHHHHHHhhC----------------------CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCC
Q 017573          243 NTRRKVDWLTDKMRSR----------------------DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID  300 (369)
Q Consensus       243 ~~~~~~~~~~~~l~~~----------------------~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d  300 (369)
                      ++++++..++..|-..                      ..+.++-|.+++..+...+-..|..|.+.|+|.+.. ..|+-
T Consensus      1367 p~rk~~~~~a~~~~~~s~~~~~~~l~~~~e~~~~~l~e~l~~gvg~e~~s~~d~~iv~~l~e~g~i~v~v~s~~-~~~~~ 1445 (1674)
T KOG0951|consen 1367 PTRKHARLVAVDLVTFSHADEPDYLLSELEECDETLRESLKHGVGHEGLSSNDQEIVQQLFEAGAIQVCVMSRD-CYGTK 1445 (1674)
T ss_pred             ccchhhhhhhhccchhhccCcHHHHHHHHhcchHhhhhcccccccccccCcchHHHHHHHHhcCcEEEEEEEcc-ccccc
Confidence            9999988664433211                      233444488899999999999999999999998887 77877


Q ss_pred             CCCCcEEEEec-----------CCCCccchhhhhcccccCCCceeEEEEeccccHHHHHHH
Q 017573          301 VQQVSLVINYD-----------LPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDI  350 (369)
Q Consensus       301 ~~~~~~vi~~~-----------~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~  350 (369)
                      .. .+.|+..+           .+.+.....|+.|++.|   .|.|+++.+.++.++++++
T Consensus      1446 ~~-~~lVvvmgt~~ydg~e~~~~~y~i~~ll~m~G~a~~---~~k~vi~~~~~~k~yykkf 1502 (1674)
T KOG0951|consen 1446 LK-AHLVVVMGTQYYDGKEHSYEDYPIAELLQMVGLASG---AGKCVIMCHTPKKEYYKKF 1502 (1674)
T ss_pred             cc-ceEEEEecceeecccccccccCchhHHHHHhhhhcC---CccEEEEecCchHHHHHHh
Confidence            63 44455443           24567788999999998   5889999999988877654

>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]

Probab=99.77  E-value=5.7e-17  Score=138.20  Aligned_cols=109  Identities=17%  Similarity=0.256  Sum_probs=91.9

Q ss_pred             CCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcC-CCcEEE-EecCCcCCCCCCCCcEEEEecCC
Q 017573          236 TQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSG-SSRVLI-TTDLLARGIDVQQVSLVINYDLP  313 (369)
Q Consensus       236 ~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~-~~~vli-~t~~~~~G~d~~~~~~vi~~~~~  313 (369)
                      -|.|||........-+.=.|.+.|+.+..+.|.|++..|...++.|.++ +++|++ +-.+.+..+|+..+++|++.+|=
T Consensus       639 ~KsIVFSQFTSmLDLi~~rL~kaGfscVkL~GsMs~~ardatik~F~nd~~c~vfLvSLkAGGVALNLteASqVFmmDPW  718 (791)
T KOG1002|consen  639 AKSIVFSQFTSMLDLIEWRLGKAGFSCVKLVGSMSPAARDATIKYFKNDIDCRVFLVSLKAGGVALNLTEASQVFMMDPW  718 (791)
T ss_pred             hhhhhHHHHHHHHHHHHHHhhccCceEEEeccCCChHHHHHHHHHhccCCCeEEEEEEeccCceEeeechhceeEeeccc
Confidence            4778888877777777777888899999999999999999999999886 455554 55688888999999999999999


Q ss_pred             CCccchhhhhcccccCCCc--eeEEEEeccccH
Q 017573          314 TQPENYLHRIGRSGRFGRK--GVAINFVTRDDE  344 (369)
Q Consensus       314 ~~~~~~~Q~~GR~~R~~~~--~~~~~~~~~~~~  344 (369)
                      |++..-.|+..|..|.|+.  -.++.|+-++..
T Consensus       719 WNpaVe~Qa~DRiHRIGQ~rPvkvvrf~iEnsi  751 (791)
T KOG1002|consen  719 WNPAVEWQAQDRIHRIGQYRPVKVVRFCIENSI  751 (791)
T ss_pred             ccHHHHhhhhhhHHhhcCccceeEEEeehhccH
Confidence            9999999999999999865  567777776543

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

Probab=99.77  E-value=1.7e-16  Score=153.29  Aligned_cols=285  Identities=15%  Similarity=0.161  Sum_probs=170.9

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHcc
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQA  113 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~  113 (369)
                      +..+||+.+|||||++++..+- .+......+++++||-++.|..|+.+.+..+........    ...+....++.+..
T Consensus       274 ~~G~IWHtqGSGKTlTm~~~A~-~l~~~~~~~~v~fvvDR~dLd~Q~~~~f~~~~~~~~~~~----~~~s~~~Lk~~l~~  348 (962)
T COG0610         274 KGGYIWHTQGSGKTLTMFKLAR-LLLELPKNPKVLFVVDRKDLDDQTSDEFQSFGKVAFNDP----KAESTSELKELLED  348 (962)
T ss_pred             CceEEEeecCCchHHHHHHHHH-HHHhccCCCeEEEEechHHHHHHHHHHHHHHHHhhhhcc----cccCHHHHHHHHhc
Confidence            5799999999999998654444 444446666999999999999999999998865432222    34444455555553


Q ss_pred             -CCcEEEeccHHHHHHHHcCC-C-CCCCccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEEeeCChhHHHH-HHH
Q 017573          114 -GVHVVVGTPGRVFDMLRRQS-L-RPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMPPEALEI-TRK  189 (369)
Q Consensus       114 -~~~iiv~t~~~l~~~~~~~~-~-~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~saT~~~~~~~~-~~~  189 (369)
                       ...|+|||.++|........ . ....--++|+||||+.   ++......+...++ +...+++|+||....... ...
T Consensus       349 ~~~~ii~TTIQKf~~~~~~~~~~~~~~~~ivvI~DEaHRS---Q~G~~~~~~~~~~~-~a~~~gFTGTPi~~~d~~tt~~  424 (962)
T COG0610         349 GKGKIIVTTIQKFNKAVKEDELELLKRKNVVVIIDEAHRS---QYGELAKLLKKALK-KAIFIGFTGTPIFKEDKDTTKD  424 (962)
T ss_pred             CCCcEEEEEecccchhhhcccccccCCCcEEEEEechhhc---cccHHHHHHHHHhc-cceEEEeeCCccccccccchhh
Confidence             34899999999987776541 1 1112248999999984   44444445555554 366899999996433222 244


Q ss_pred             hcCCCEEEEecCccccccceeEEEEEcc-chhh-------------------------------------------hHHH
Q 017573          190 FMNKPVRILVKRDELTLEGIKQFYVNVE-KEEW-------------------------------------------KLET  225 (369)
Q Consensus       190 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~-------------------------------------------~~~~  225 (369)
                      .++.........+......+-..++... ..+.                                           ..+.
T Consensus       425 ~fg~ylh~Y~i~daI~Dg~vl~i~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~r~~~~  504 (962)
T COG0610         425 VFGDYLHTYTITDAIRDGAVLPVYYENRVELELIEESIKEEAEELDERIEEITEDILEKIKKKTKNLEFLAMLAVRLIRA  504 (962)
T ss_pred             hhcceeEEEecchhhccCceeeEEEeecccccccccchhhhhhhhHHHHhhhHHHHHHHHHHHHhhhhHHhcchHHHHHH
Confidence            4555544444433333333222222221 0000                                           0011


Q ss_pred             HHHHH----H-hccCCCeEEEeCCHhhHHHHHHHHhhCCCe----------eEEe-------------cCCCCHHHHHHH
Q 017573          226 LCDLY----E-TLAITQSVIFVNTRRKVDWLTDKMRSRDHT----------VSAT-------------HGDMDQNTRDII  277 (369)
Q Consensus       226 l~~~~----~-~~~~~k~lv~~~~~~~~~~~~~~l~~~~~~----------~~~~-------------~~~~~~~~r~~~  277 (369)
                      ..++.    . .....++.+.++++.-+..+.+........          +..+             +.. ....+...
T Consensus       505 a~~i~~~f~~~~~~~~kam~V~~sr~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~-~~~~~~~~  583 (962)
T COG0610         505 AKDIYDHFKKEEVFDLKAMVVASSRKVAVELYEAEIAARLDWHSKESLEGAIKDYNTEFETDFDKKQSHAK-LKDEKKDL  583 (962)
T ss_pred             HHHHHHHHHhhcccCceEEEEEechHHHHHhHHHHhhhhhhhhhhhhhhhHHHHHHhhcccchhhhhhhHH-HHHHHhhh
Confidence            11111    1 112347778888877444444333222000          0000             011 12223334


Q ss_pred             HHHH--hcCCCcEEEEecCCcCCCCCCCCcEEEEecCCCCccchhhhhcccccC
Q 017573          278 MREF--RSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRF  329 (369)
Q Consensus       278 ~~~f--~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~  329 (369)
                      ...|  .+.+.++||.++++-+|+|.|.++.+++.. |.-.-.++|++.|+.|.
T Consensus       584 ~~r~~~~~d~~kilIV~dmlLTGFDaP~L~TmYvDK-~Lk~H~L~QAisRtNR~  636 (962)
T COG0610         584 IKRFKLKDDPLDLLIVVDMLLTGFDAPCLNTLYVDK-PLKYHNLIQAISRTNRV  636 (962)
T ss_pred             hhhhcCcCCCCCEEEEEccccccCCccccceEEecc-ccccchHHHHHHHhccC
Confidence            4443  345789999999999999999999998555 46677999999999996

>PF00271 Helicase_C: Helicase conserved C-terminal domain; InterPro: IPR001650 The domain, which defines this group of proteins is found in a wide variety of helicases and helicase related proteins

Probab=99.77  E-value=1.3e-18  Score=117.45  Aligned_cols=78  Identities=47%  Similarity=0.814  Sum_probs=75.3

Q ss_pred             HHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCCCCccchhhhhcccccCC
Q 017573          253 DKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFG  330 (369)
Q Consensus       253 ~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~  330 (369)
                      ++|+..++++..+||+++..+|.++++.|++++..+|++|+++++|+|+|.+++|+++++|+|...|.|++||++|.|
T Consensus         1 ~~L~~~~~~~~~i~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~Gid~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~g   78 (78)
T PF00271_consen    1 KFLEKKGIKVAIIHGDMSQKERQEILKKFNSGEIRVLIATDILGEGIDLPDASHVIFYDPPWSPEEYIQRIGRAGRIG   78 (78)
T ss_dssp             HHHHHTTSSEEEESTTSHHHHHHHHHHHHHTTSSSEEEESCGGTTSSTSTTESEEEESSSESSHHHHHHHHTTSSTTT
T ss_pred             CChHHCCCcEEEEECCCCHHHHHHHHHHhhccCceEEEeeccccccccccccccccccccCCCHHHHHHHhhcCCCCC
Confidence            467888999999999999999999999999999999999999999999999999999999999999999999999986

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 ....

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=99.76  E-value=3.5e-15  Score=140.67  Aligned_cols=106  Identities=20%  Similarity=0.354  Sum_probs=77.8

Q ss_pred             cCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHh----cCCCcEEEEecCCcCCCCCCC--CcEE
Q 017573          234 AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFR----SGSSRVLITTDLLARGIDVQQ--VSLV  307 (369)
Q Consensus       234 ~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~----~~~~~vli~t~~~~~G~d~~~--~~~v  307 (369)
                      ..+.++|+++|.+..+.+++.|......-....+.   ..+.++++.|+    .++..||++|..+.+|+|+|+  ++.|
T Consensus       533 ~~gg~LVlFtSy~~l~~v~~~l~~~~~~~ll~Q~~---~~~~~ll~~f~~~~~~~~~~VL~g~~sf~EGVD~pGd~l~~v  609 (697)
T PRK11747        533 KHKGSLVLFASRRQMQKVADLLPRDLRLMLLVQGD---QPRQRLLEKHKKRVDEGEGSVLFGLQSFAEGLDLPGDYLTQV  609 (697)
T ss_pred             cCCCEEEEeCcHHHHHHHHHHHHHhcCCcEEEeCC---chHHHHHHHHHHHhccCCCeEEEEeccccccccCCCCceEEE
Confidence            34568999999999999999987532222344443   24667887776    466779999999999999996  7889


Q ss_pred             EEecCCCC-c-----------------------------cchhhhhcccccCCCceeEEEEeccc
Q 017573          308 INYDLPTQ-P-----------------------------ENYLHRIGRSGRFGRKGVAINFVTRD  342 (369)
Q Consensus       308 i~~~~~~~-~-----------------------------~~~~Q~~GR~~R~~~~~~~~~~~~~~  342 (369)
                      |+.+.|.. +                             ..+.|.+||+.|..++.-++++.++.
T Consensus       610 II~kLPF~~p~dp~~~ar~~~~~~~g~~~F~~~~lP~A~~kl~Qg~GRlIRs~~D~G~i~ilD~R  674 (697)
T PRK11747        610 IITKIPFAVPDSPVEATLAEWLKSRGGNPFMEISVPDASFKLIQAVGRLIRSEQDRGRVTILDRR  674 (697)
T ss_pred             EEEcCCCCCCCCHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhccccccCCceEEEEEEccc
Confidence            99887642 1                             13589999999997664455566654

>KOG0925 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.76  E-value=1.3e-16  Score=135.74  Aligned_cols=298  Identities=17%  Similarity=0.240  Sum_probs=179.0

Q ss_pred             hhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHH-hccccCcEEEEEECC
Q 017573           23 QQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRA-LGDYLGVKVHACVGG  101 (369)
Q Consensus        23 Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~-~~~~~~~~v~~~~~~  101 (369)
                      +.+-.+.+.+++-+++.++||+|||...-.+.+........  .+.---|++.-+.+.+.+..+ +.-.+|-.|.....-
T Consensus        52 k~~F~~~l~~nQ~~v~vGetgsGKttQiPq~~~~~~~~~~~--~v~CTQprrvaamsva~RVadEMDv~lG~EVGysIrf  129 (699)
T KOG0925|consen   52 KEEFLKLLLNNQIIVLVGETGSGKTTQIPQFVLEYELSHLT--GVACTQPRRVAAMSVAQRVADEMDVTLGEEVGYSIRF  129 (699)
T ss_pred             HHHHHHHHhcCceEEEEecCCCCccccCcHHHHHHHHhhcc--ceeecCchHHHHHHHHHHHHHHhccccchhccccccc
Confidence            33344455567889999999999997765555555443331  344444787777766665543 222223333332222


Q ss_pred             cchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhh--ccCcHHHHHHHHhhCCccCcEEEEEeeC
Q 017573          102 TSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEML--SRGFKDQIYDIFQLLPAKVQVGVFSATM  179 (369)
Q Consensus       102 ~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~--~~~~~~~~~~~~~~~~~~~~~i~~saT~  179 (369)
                      ......      +.-.-++|-.+|++....... +..++++|+||+|+=.  .......+..+...- +..+++.||||.
T Consensus       130 EdC~~~------~T~Lky~tDgmLlrEams~p~-l~~y~viiLDeahERtlATDiLmGllk~v~~~r-pdLk~vvmSatl  201 (699)
T KOG0925|consen  130 EDCTSP------NTLLKYCTDGMLLREAMSDPL-LGRYGVIILDEAHERTLATDILMGLLKEVVRNR-PDLKLVVMSATL  201 (699)
T ss_pred             cccCCh------hHHHHHhcchHHHHHHhhCcc-cccccEEEechhhhhhHHHHHHHHHHHHHHhhC-CCceEEEeeccc
Confidence            111111      111224566666665555443 4557999999999722  121223333444443 478899999998


Q ss_pred             ChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccch---hhhHHHHHHHHHhccCCCeEEEeCCHhhHHHHHHHHh
Q 017573          180 PPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKE---EWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMR  256 (369)
Q Consensus       180 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~  256 (369)
                      ...  .+-..+.+.|. ..+..    ....+.+|..-...   +..++.+.++...-..+.+++|..+.++.+..++.+.
T Consensus       202 ~a~--Kfq~yf~n~Pl-l~vpg----~~PvEi~Yt~e~erDylEaairtV~qih~~ee~GDilvFLtgeeeIe~aC~~i~  274 (699)
T KOG0925|consen  202 DAE--KFQRYFGNAPL-LAVPG----THPVEIFYTPEPERDYLEAAIRTVLQIHMCEEPGDILVFLTGEEEIEDACRKIS  274 (699)
T ss_pred             chH--HHHHHhCCCCe-eecCC----CCceEEEecCCCChhHHHHHHHHHHHHHhccCCCCEEEEecCHHHHHHHHHHHH
Confidence            543  33333334443 22221    11222233322222   2334555555555567899999999999999988887


Q ss_pred             hC---------CCeeEEecCCCCHHHHHHHHHHHh---cCC--CcEEEEecCCcCCCCCCCCcEEEEec-----------
Q 017573          257 SR---------DHTVSATHGDMDQNTRDIIMREFR---SGS--SRVLITTDLLARGIDVQQVSLVINYD-----------  311 (369)
Q Consensus       257 ~~---------~~~~~~~~~~~~~~~r~~~~~~f~---~~~--~~vli~t~~~~~G~d~~~~~~vi~~~-----------  311 (369)
                      +.         ..++..++    +..+..+++--.   +|.  -+|+|+|.+++..+.++++.+||.-+           
T Consensus       275 re~~~L~~~~g~l~v~PLy----P~~qq~iFep~p~~~~~~~~RkvVvstniaetsltidgiv~VIDpGf~kqkVYNPRI  350 (699)
T KOG0925|consen  275 REVDNLGPQVGPLKVVPLY----PAQQQRIFEPAPEKRNGAYGRKVVVSTNIAETSLTIDGIVFVIDPGFSKQKVYNPRI  350 (699)
T ss_pred             HHHHhhccccCCceEEecC----chhhccccCCCCcccCCCccceEEEEecchheeeeeccEEEEecCchhhhcccCcce
Confidence            55         23455555    333333322221   222  36999999999999999999998654           


Q ss_pred             -------CCCCccchhhhhcccccCCCceeEEEEeccc
Q 017573          312 -------LPTQPENYLHRIGRSGRFGRKGVAINFVTRD  342 (369)
Q Consensus       312 -------~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~  342 (369)
                             .|-|..+..||.||+||+ .+|.|+.++++.
T Consensus       351 Rvesllv~PISkasA~qR~gragrt-~pGkcfrLYte~  387 (699)
T KOG0925|consen  351 RVESLLVSPISKASAQQRAGRAGRT-RPGKCFRLYTEE  387 (699)
T ss_pred             eeeeeeeccchHhHHHHHhhhccCC-CCCceEEeecHH
Confidence                   255778889999999998 789999999864

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=99.74  E-value=1.7e-16  Score=148.10  Aligned_cols=122  Identities=18%  Similarity=0.248  Sum_probs=94.7

Q ss_pred             hHHHHHH-HHHhc-cCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCC
Q 017573          222 KLETLCD-LYETL-AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGI  299 (369)
Q Consensus       222 ~~~~l~~-~~~~~-~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~  299 (369)
                      +...+.+ +...+ .+.++||-+.|++..+.+++.|...+++..++++.....+...+-+.-+.  -.|.|||+++++|.
T Consensus       613 K~~Aii~ei~~~~~~GrPVLVGT~SVe~SE~lS~~L~~~gI~H~VLNAK~h~~EAeIVA~AG~~--GaVTIATNMAGRGT  690 (1112)
T PRK12901        613 KYNAVIEEITELSEAGRPVLVGTTSVEISELLSRMLKMRKIPHNVLNAKLHQKEAEIVAEAGQP--GTVTIATNMAGRGT  690 (1112)
T ss_pred             HHHHHHHHHHHHHHCCCCEEEEeCcHHHHHHHHHHHHHcCCcHHHhhccchhhHHHHHHhcCCC--CcEEEeccCcCCCc
Confidence            4444443 33333 55799999999999999999999999999999888665554444333222  34999999999999


Q ss_pred             CCC--------CCcEEEEecCCCCccchhhhhcccccCCCceeEEEEeccccHH
Q 017573          300 DVQ--------QVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDER  345 (369)
Q Consensus       300 d~~--------~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~  345 (369)
                      ||.        +-=+||....+.|...-.|..||+||.|.+|.+..|++-.|.-
T Consensus       691 DIkLg~~V~e~GGL~VIgTerheSrRID~QLrGRaGRQGDPGsS~f~lSLEDdL  744 (1112)
T PRK12901        691 DIKLSPEVKAAGGLAIIGTERHESRRVDRQLRGRAGRQGDPGSSQFYVSLEDNL  744 (1112)
T ss_pred             CcccchhhHHcCCCEEEEccCCCcHHHHHHHhcccccCCCCCcceEEEEcccHH
Confidence            986        3456777788889999999999999999999999888866543

>KOG1015 consensus Transcription regulator XNP/ATRX, DEAD-box superfamily [Transcription]

Probab=99.74  E-value=4.5e-16  Score=141.98  Aligned_cols=118  Identities=19%  Similarity=0.210  Sum_probs=97.1

Q ss_pred             HHHHHHHHHhc--cCCCeEEEeCCHhhHHHHHHHHhhC----------------------CCeeEEecCCCCHHHHHHHH
Q 017573          223 LETLCDLYETL--AITQSVIFVNTRRKVDWLTDKMRSR----------------------DHTVSATHGDMDQNTRDIIM  278 (369)
Q Consensus       223 ~~~l~~~~~~~--~~~k~lv~~~~~~~~~~~~~~l~~~----------------------~~~~~~~~~~~~~~~r~~~~  278 (369)
                      +-.|.++++..  -+.|.|||..+.....-+..+|...                      |.....+.|......|.+..
T Consensus      1128 miLLleIL~mceeIGDKlLVFSQSL~SLdLIe~fLe~v~r~gk~~~d~~~~~~~eGkW~~GkDyyriDGst~s~~R~k~~ 1207 (1567)
T KOG1015|consen 1128 MILLLEILRMCEEIGDKLLVFSQSLISLDLIEDFLELVSREGKEDKDKPLIYKGEGKWLRGKDYYRLDGSTTSQSRKKWA 1207 (1567)
T ss_pred             eehHHHHHHHHHHhcceeEEeecccchhHHHHHHHHhhcccCccccccccccccccceecCCceEEecCcccHHHHHHHH
Confidence            33445555443  3468999999998888887777532                      45678889999999999999


Q ss_pred             HHHhcCC-C---cEEEEecCCcCCCCCCCCcEEEEecCCCCccchhhhhcccccCCCceeEEEEec
Q 017573          279 REFRSGS-S---RVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVT  340 (369)
Q Consensus       279 ~~f~~~~-~---~vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~  340 (369)
                      ++|++.. .   ..||+|.+.+-|+|+-.++.||+++..|++.-=.|.+=|+.|.|+...||+|-.
T Consensus      1208 ~~FNdp~NlRaRl~LISTRAGsLGiNLvAANRVIIfDasWNPSyDtQSIFRvyRfGQtKPvyiYRf 1273 (1567)
T KOG1015|consen 1208 EEFNDPTNLRARLFLISTRAGSLGINLVAANRVIIFDASWNPSYDTQSIFRVYRFGQTKPVYIYRF 1273 (1567)
T ss_pred             HHhcCcccceeEEEEEeeccCccccceeecceEEEEecccCCccchHHHHHHHhhcCcCceeehhh
Confidence            9998743 2   388999999999999999999999999999999999999999999888877654

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

Probab=99.71  E-value=3.8e-15  Score=136.44  Aligned_cols=290  Identities=13%  Similarity=0.133  Sum_probs=183.1

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHcc
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQA  113 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~  113 (369)
                      .-.+|.+|+|+|||....-++.+.+..  ...++++|+.+++|+.++.+.++...-. ++.......+.      .+...
T Consensus        50 ~V~vVRSpMGTGKTtaLi~wLk~~l~~--~~~~VLvVShRrSL~~sL~~rf~~~~l~-gFv~Y~d~~~~------~i~~~  120 (824)
T PF02399_consen   50 GVLVVRSPMGTGKTTALIRWLKDALKN--PDKSVLVVSHRRSLTKSLAERFKKAGLS-GFVNYLDSDDY------IIDGR  120 (824)
T ss_pred             CeEEEECCCCCCcHHHHHHHHHHhccC--CCCeEEEEEhHHHHHHHHHHHHhhcCCC-cceeeeccccc------ccccc
Confidence            446999999999998876666655432  2338999999999999999999865221 22211111111      11112


Q ss_pred             CCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHH-------HHHHHhhCCccCcEEEEEeeCChhHHHH
Q 017573          114 GVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQ-------IYDIFQLLPAKVQVGVFSATMPPEALEI  186 (369)
Q Consensus       114 ~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~-------~~~~~~~~~~~~~~i~~saT~~~~~~~~  186 (369)
                      .++-+++..+++.+....   ...++|+||+||+-...+.-+...       ...+...+.....+|++-|+......++
T Consensus       121 ~~~rLivqIdSL~R~~~~---~l~~yDvVIIDEv~svL~qL~S~Tm~~~~~v~~~L~~lI~~ak~VI~~DA~ln~~tvdF  197 (824)
T PF02399_consen  121 PYDRLIVQIDSLHRLDGS---LLDRYDVVIIDEVMSVLNQLFSPTMRQREEVDNLLKELIRNAKTVIVMDADLNDQTVDF  197 (824)
T ss_pred             ccCeEEEEehhhhhcccc---cccccCEEEEehHHHHHHHHhHHHHhhHHHHHHHHHHHHHhCCeEEEecCCCCHHHHHH
Confidence            467888999998765422   344589999999998765433322       2233444566778999999999988888


Q ss_pred             HHHhcCCC-EEEEecCcccc-ccceeEEEE---------------------------------EccchhhhHHHHHHHHH
Q 017573          187 TRKFMNKP-VRILVKRDELT-LEGIKQFYV---------------------------------NVEKEEWKLETLCDLYE  231 (369)
Q Consensus       187 ~~~~~~~~-~~~~~~~~~~~-~~~~~~~~~---------------------------------~~~~~~~~~~~l~~~~~  231 (369)
                      +..+.+.. +.+....-... ..+-.-.+.                                 ..............+..
T Consensus       198 l~~~Rp~~~i~vI~n~y~~~~fs~R~~~~~~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~tF~~~L~~  277 (824)
T PF02399_consen  198 LASCRPDENIHVIVNTYASPGFSNRRCTFLRSLGTDTLAAALNPEDENADTSPTPKHSPDPTATAAISNDETTFFSELLA  277 (824)
T ss_pred             HHHhCCCCcEEEEEeeeecCCcccceEEEecccCcHHHHHHhCCcccccccCCCcCCCCccccccccccchhhHHHHHHH
Confidence            88865532 22222110000 000000000                                 00000112334444554


Q ss_pred             hc-cCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCC--CcEEE
Q 017573          232 TL-AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQ--VSLVI  308 (369)
Q Consensus       232 ~~-~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~--~~~vi  308 (369)
                      +. .++++.||+++...++.+++..+....++..+++..+..+.    +.|  ++++|++-|+.+..|+++..  .+.|+
T Consensus       278 ~L~~gknIcvfsSt~~~~~~v~~~~~~~~~~Vl~l~s~~~~~dv----~~W--~~~~VviYT~~itvG~Sf~~~HF~~~f  351 (824)
T PF02399_consen  278 RLNAGKNICVFSSTVSFAEIVARFCARFTKKVLVLNSTDKLEDV----ESW--KKYDVVIYTPVITVGLSFEEKHFDSMF  351 (824)
T ss_pred             HHhCCCcEEEEeChHHHHHHHHHHHHhcCCeEEEEcCCCCcccc----ccc--cceeEEEEeceEEEEeccchhhceEEE
Confidence            44 34577789999999999999999988899999887655532    223  45789999999999999864  34455


Q ss_pred             EecCC----CCccchhhhhcccccCCCceeEEEEeccc
Q 017573          309 NYDLP----TQPENYLHRIGRSGRFGRKGVAINFVTRD  342 (369)
Q Consensus       309 ~~~~~----~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~  342 (369)
                      .+--|    .+..+..|++||+ |.-.....+++++..
T Consensus       352 ~yvk~~~~gpd~~s~~Q~lgRv-R~l~~~ei~v~~d~~  388 (824)
T PF02399_consen  352 AYVKPMSYGPDMVSVYQMLGRV-RSLLDNEIYVYIDAS  388 (824)
T ss_pred             EEecCCCCCCcHHHHHHHHHHH-HhhccCeEEEEEecc
Confidence            44222    2334579999999 444667788887765

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

>PRK14873 primosome assembly protein PriA; Provisional

Probab=99.70  E-value=3.9e-15  Score=137.96  Aligned_cols=299  Identities=12%  Similarity=0.078  Sum_probs=173.7

Q ss_pred             EEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHH----HHHHHc
Q 017573           37 IQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVRE----DQRILQ  112 (369)
Q Consensus        37 li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~----~~~~~~  112 (369)
                      +..+.+|||||.+++-.+.+.+..++   .+|+++|..+|..|+.+.|++.+.  +..+..++++.+..+    +.....
T Consensus       164 i~~~~~GSGKTevyl~~i~~~l~~Gk---~vLvLvPEi~lt~q~~~rl~~~f~--~~~v~~lhS~l~~~~R~~~w~~~~~  238 (665)
T PRK14873        164 VWQALPGEDWARRLAAAAAATLRAGR---GALVVVPDQRDVDRLEAALRALLG--AGDVAVLSAGLGPADRYRRWLAVLR  238 (665)
T ss_pred             HhhcCCCCcHHHHHHHHHHHHHHcCC---eEEEEecchhhHHHHHHHHHHHcC--CCcEEEECCCCCHHHHHHHHHHHhC
Confidence            44444699999999888888887765   899999999999999999998763  246777887766543    344456


Q ss_pred             cCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccC-----cH-HHHHHHHhhCCccCcEEEEEeeCChhHHHH
Q 017573          113 AGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRG-----FK-DQIYDIFQLLPAKVQVGVFSATMPPEALEI  186 (369)
Q Consensus       113 ~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~-----~~-~~~~~~~~~~~~~~~~i~~saT~~~~~~~~  186 (369)
                      +...|+|+|...++-       -..++++||+||=|.-+..+     |. +.+...... ..+..+++.||||+-+....
T Consensus       239 G~~~IViGtRSAvFa-------P~~~LgLIIvdEEhd~sykq~~~p~yhaRdvA~~Ra~-~~~~~lvLgSaTPSles~~~  310 (665)
T PRK14873        239 GQARVVVGTRSAVFA-------PVEDLGLVAIWDDGDDLLAEPRAPYPHAREVALLRAH-QHGCALLIGGHARTAEAQAL  310 (665)
T ss_pred             CCCcEEEEcceeEEe-------ccCCCCEEEEEcCCchhhcCCCCCCccHHHHHHHHHH-HcCCcEEEECCCCCHHHHHH
Confidence            778999999877763       34458999999999755322     11 233333333 34677899999998766544


Q ss_pred             HHHhcCCCEEEEecCccccccceeEEEEE---c-----cch-hhhHHHHHHHHHhccCCCeEEEeCCHhhHHH-------
Q 017573          187 TRKFMNKPVRILVKRDELTLEGIKQFYVN---V-----EKE-EWKLETLCDLYETLAITQSVIFVNTRRKVDW-------  250 (369)
Q Consensus       187 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~-----~~~-~~~~~~l~~~~~~~~~~k~lv~~~~~~~~~~-------  250 (369)
                      ....................+.+.-.-..   .     ... ..-...+..+-+....+++|+|.|.+-.+-.       
T Consensus       311 ~~~g~~~~~~~~~~~~~~~~P~v~~vd~~~~~~~~~~~~~g~~ls~~l~~~i~~~L~~gqvll~lnRrGyap~l~C~~Cg  390 (665)
T PRK14873        311 VESGWAHDLVAPRPVVRARAPRVRALGDSGLALERDPAARAARLPSLAFRAARDALEHGPVLVQVPRRGYVPSLACARCR  390 (665)
T ss_pred             HhcCcceeeccccccccCCCCeEEEEeCchhhhccccccccCccCHHHHHHHHHHHhcCcEEEEecCCCCCCeeEhhhCc
Confidence            43221111100000000111111111000   0     000 0011223333333334488888887754332       


Q ss_pred             ----------------------------------------------------HHHHHhhCCC--eeEEecCCCCHHHHHH
Q 017573          251 ----------------------------------------------------LTDKMRSRDH--TVSATHGDMDQNTRDI  276 (369)
Q Consensus       251 ----------------------------------------------------~~~~l~~~~~--~~~~~~~~~~~~~r~~  276 (369)
                                                                          +.+.|.+...  ++...       +++.
T Consensus       391 ~~~~C~~C~~~L~~h~~~~~l~Ch~CG~~~~p~~Cp~Cgs~~l~~~g~Gter~eeeL~~~FP~~~V~r~-------d~d~  463 (665)
T PRK14873        391 TPARCRHCTGPLGLPSAGGTPRCRWCGRAAPDWRCPRCGSDRLRAVVVGARRTAEELGRAFPGVPVVTS-------GGDQ  463 (665)
T ss_pred             CeeECCCCCCceeEecCCCeeECCCCcCCCcCccCCCCcCCcceeeeccHHHHHHHHHHHCCCCCEEEE-------ChHH
Confidence                                                                2222222211  12221       2345


Q ss_pred             HHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCCC------------CccchhhhhcccccCCCceeEEEEeccccH
Q 017573          277 IMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPT------------QPENYLHRIGRSGRFGRKGVAINFVTRDDE  344 (369)
Q Consensus       277 ~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~------------~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~  344 (369)
                      +++.|. ++.+|||+|+.++.=+. ++...|.+++...            ....+.|..||+||..+.|.+++.. ..+.
T Consensus       464 ~l~~~~-~~~~IlVGTqgaepm~~-g~~~lV~ildaD~~L~~pDfRA~Er~~qll~qvagragr~~~~G~V~iq~-~p~~  540 (665)
T PRK14873        464 VVDTVD-AGPALVVATPGAEPRVE-GGYGAALLLDAWALLGRQDLRAAEDTLRRWMAAAALVRPRADGGQVVVVA-ESSL  540 (665)
T ss_pred             HHHhhc-cCCCEEEECCCCccccc-CCceEEEEEcchhhhcCCCcChHHHHHHHHHHHHHhhcCCCCCCEEEEEe-CCCC
Confidence            778886 48999999993221122 3567776665321            2344589999999998999999886 4444


Q ss_pred             HHHHHH-----HHHhcccc
Q 017573          345 RMLFDI-----QKFYNVVI  358 (369)
Q Consensus       345 ~~~~~~-----~~~~~~~~  358 (369)
                      ..++.+     ..|++.++
T Consensus       541 ~~~~~l~~~d~~~F~~~EL  559 (665)
T PRK14873        541 PTVQALIRWDPVGHAEREL  559 (665)
T ss_pred             HHHHHHHhCCHHHHHHHHH
Confidence            444433     34555444

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3

Probab=99.69  E-value=3.6e-15  Score=140.12  Aligned_cols=309  Identities=17%  Similarity=0.145  Sum_probs=180.8

Q ss_pred             CCcHhhhhhhhcccc--------CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhcc
Q 017573           18 KPSAIQQRGIVPFCK--------GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGD   89 (369)
Q Consensus        18 ~~~~~Q~~~~~~~~~--------~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~   89 (369)
                      .-..+|.+|++.+..        |--++--|.||+|||++= .-|+..+.....+.++.|..-.++|.-|+-+.+++-..
T Consensus       408 ~rF~WQdkA~d~a~~~r~~~~~~GfF~vNMASTGcGKT~aN-ARImyaLsd~~~g~RfsiALGLRTLTLQTGda~r~rL~  486 (1110)
T TIGR02562       408 PRFRWQNKAFNLAQKLRQKSPEQGAFGVNMASTGCGKTLAN-ARAMYALRDDKQGARFAIALGLRSLTLQTGHALKTRLN  486 (1110)
T ss_pred             CCcchHHHHHHHHHHHHhhcccCCeEEEEecCCCcchHHHH-HHHHHHhCCCCCCceEEEEccccceeccchHHHHHhcC
Confidence            456789999987763        223577899999999874 34455566656666788888888888888777776543


Q ss_pred             ccCcEEEEEECCcchHHH-------------------------------------------HHHHcc--------CCcEE
Q 017573           90 YLGVKVHACVGGTSVRED-------------------------------------------QRILQA--------GVHVV  118 (369)
Q Consensus        90 ~~~~~v~~~~~~~~~~~~-------------------------------------------~~~~~~--------~~~ii  118 (369)
                      -...+..++.|+....+.                                           ...+..        .+.+.
T Consensus       487 L~~ddLAVlIGs~Av~~L~e~~~~~~~~~~~~GSeS~e~l~~e~~~~~~~~~~g~l~~~~l~~~l~~~~k~~rll~apv~  566 (1110)
T TIGR02562       487 LSDDDLAVLIGGTAVQTLFDLSKEKIEQVDEDGSESAPIFLAEGQDCNLPDWDGPLDTIELLGRLSLDDKEKTLLAAPVL  566 (1110)
T ss_pred             CCccceEEEECHHHHHHHHHHHhhhccccccCCCccchhhhcccCcCCeeeccCCccchhhhhhhccChhhhhhhcCCeE
Confidence            333334444433221110                                           001110        25799


Q ss_pred             EeccHHHHHHHHc--CCC------CCCCccEEEEechhHhhccCcHHHHHHHHhhCC-ccCcEEEEEeeCChhHHHHHHH
Q 017573          119 VGTPGRVFDMLRR--QSL------RPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLP-AKVQVGVFSATMPPEALEITRK  189 (369)
Q Consensus       119 v~t~~~l~~~~~~--~~~------~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~-~~~~~i~~saT~~~~~~~~~~~  189 (369)
                      |+|++.++.....  .+.      .+. -+.+|+||+|.+.... ...+..++.... -+.++++||||+++.....+..
T Consensus       567 V~TIDQlL~a~~~~r~~~~~l~ll~La-~svlVlDEVHaYD~~~-~~~L~rlL~w~~~lG~~VlLmSATLP~~l~~~L~~  644 (1110)
T TIGR02562       567 VCTIDHLIPATESHRGGHHIAPMLRLM-SSDLILDEPDDYEPED-LPALLRLVQLAGLLGSRVLLSSATLPPALVKTLFR  644 (1110)
T ss_pred             EecHHHHHHHhhhcccchhHHHHHHhc-CCCEEEECCccCCHHH-HHHHHHHHHHHHHcCCCEEEEeCCCCHHHHHHHHH
Confidence            9999999876532  111      112 2689999999875333 334444444322 2567899999999776553322


Q ss_pred             h-----------cC---CCEEEEec--Ccc-c----------------------------cccceeEEEEEccchh----
Q 017573          190 F-----------MN---KPVRILVK--RDE-L----------------------------TLEGIKQFYVNVEKEE----  220 (369)
Q Consensus       190 ~-----------~~---~~~~~~~~--~~~-~----------------------------~~~~~~~~~~~~~~~~----  220 (369)
                      .           .+   .+..+...  .+. .                            .+..-.-....++...    
T Consensus       645 Ay~~G~~~~q~~~g~~~~~~~i~CaW~DE~~~~~~~~~~~~~F~~~H~~Fv~~R~~~L~~~p~~R~a~i~~~~~~~~~~~  724 (1110)
T TIGR02562       645 AYEAGRQMYQALYGQPKKPLNICCAWVDEPQVWQADCNQKSEFIQRHQDFLRDRAVQLAKKPVRRLAELLSLSSLPRENE  724 (1110)
T ss_pred             HHHHHHHHHHHhcCCCCCCcceeEEeecccCchhhhhcCHHHHHHHHHHHHHHHHHHHhcCcccceEEEeecCCcccchh
Confidence            2           12   11111110  000 0                            0000001111121110    


Q ss_pred             h--------hHHHHHHHHHhc----c-CC-C---eEEEeCCHhhHHHHHHHHhhC------CCeeEEecCCCCHHHHHHH
Q 017573          221 W--------KLETLCDLYETL----A-IT-Q---SVIFVNTRRKVDWLTDKMRSR------DHTVSATHGDMDQNTRDII  277 (369)
Q Consensus       221 ~--------~~~~l~~~~~~~----~-~~-k---~lv~~~~~~~~~~~~~~l~~~------~~~~~~~~~~~~~~~r~~~  277 (369)
                      .        ..+.+..+.+.+    + .+ +   .+|-+++++.+-.+++.|...      .+.+..||+......|..+
T Consensus       725 ~~~~~~a~~i~~~~~~LH~~h~~~~~~sgk~VSfGliR~anI~p~V~~A~~L~~~~~~~~~~i~~~~yHSr~~l~~Rs~~  804 (1110)
T TIGR02562       725 STYLALAQSLLEGALRLHQAHAQTDPKSEKKVSVGLIRVANIDPLIRLAQFLYALLAEEKYQIHLCCYHAQDPLLLRSYI  804 (1110)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCccCCCCCeEEEEEEEEEcCchHHHHHHHHHHhhccccCCceeEEEecccChHHHHHHH
Confidence            0        112223333332    1 12 2   388888888888888877655      2358889999887777666


Q ss_pred             HHHH----------------------hc----CCCcEEEEecCCcCCCCCCCCcEEEEecCCCCccchhhhhcccccCCC
Q 017573          278 MREF----------------------RS----GSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGR  331 (369)
Q Consensus       278 ~~~f----------------------~~----~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~  331 (369)
                      .+..                      .+    +...|+|+|++++.|+|+ +.+.+|.-  +.+...++|++||+.|.+.
T Consensus       805 E~~Ld~~L~R~~~~~~~~~~~i~~~l~~~~~~~~~~i~v~Tqv~E~g~D~-dfd~~~~~--~~~~~sliQ~aGR~~R~~~  881 (1110)
T TIGR02562       805 ERRLDQLLTRHKPEQLFQDDEIIDLMQNSPALNHLFIVLATPVEEVGRDH-DYDWAIAD--PSSMRSIIQLAGRVNRHRL  881 (1110)
T ss_pred             HHHHHHHhcccChhhhhchHHHHHHHhcccccCCCeEEEEeeeEEEEecc-cCCeeeec--cCcHHHHHHHhhccccccc
Confidence            6553                      12    356799999999999998 56666533  4557899999999999764


Q ss_pred             c
Q 017573          332 K  332 (369)
Q Consensus       332 ~  332 (369)
                      .
T Consensus       882 ~  882 (1110)
T TIGR02562       882 E  882 (1110)
T ss_pred             C
Confidence            3

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.

>COG0553 HepA Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]

Probab=99.65  E-value=4.1e-14  Score=139.88  Aligned_cols=322  Identities=21%  Similarity=0.225  Sum_probs=207.3

Q ss_pred             CCCcHhhhhhhhcccc-----CCcEEEEcCCCChhhHHHHHHHHHhhhccCC-CccEEEEcCCHHHHHHHHHHHHHhccc
Q 017573           17 EKPSAIQQRGIVPFCK-----GLDVIQQAQSGTGKTATFCSGILQQLDYGLV-QCQALVLAPTRELAQQIEKVMRALGDY   90 (369)
Q Consensus        17 ~~~~~~Q~~~~~~~~~-----~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~-~~~~liv~P~~~l~~q~~~~~~~~~~~   90 (369)
                      ..++++|.+.++.+..     +.+.++..++|.|||+..+..+......... .++.+++||. +++.+|.+++.++...
T Consensus       337 ~~lr~yq~~g~~wl~~~l~~~~~~~ilaD~mglGKTiq~i~~l~~~~~~~~~~~~~~liv~p~-s~~~nw~~e~~k~~~~  415 (866)
T COG0553         337 AELRPYQLEGVNWLSELLRSNLLGGILADDMGLGKTVQTIALLLSLLESIKVYLGPALIVVPA-SLLSNWKREFEKFAPD  415 (866)
T ss_pred             hhhHHHHHHHHHHHHHHHHhccCCCcccccccchhHHHHHHHHHhhhhcccCCCCCeEEEecH-HHHHHHHHHHhhhCcc
Confidence            5789999999977652     5788899999999998887776653333332 3489999998 6778899999888765


Q ss_pred             cCcEEEEEECCcc-----hHHHHHHHcc----CCcEEEeccHHHHHHH-HcCCCCCCCccEEEEechhHhhccCcHHHHH
Q 017573           91 LGVKVHACVGGTS-----VREDQRILQA----GVHVVVGTPGRVFDML-RRQSLRPDYIKMFVLDEADEMLSRGFKDQIY  160 (369)
Q Consensus        91 ~~~~v~~~~~~~~-----~~~~~~~~~~----~~~iiv~t~~~l~~~~-~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~  160 (369)
                      ... +...+|...     ..........    ..+++++|++.+.... ....+....++.+|+||+|.+.+... ....
T Consensus       416 ~~~-~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~v~itty~~l~~~~~~~~~l~~~~~~~~v~DEa~~ikn~~s-~~~~  493 (866)
T COG0553         416 LRL-VLVYHGEKSELDKKREALRDLLKLHLVIIFDVVITTYELLRRFLVDHGGLKKIEWDRVVLDEAHRIKNDQS-SEGK  493 (866)
T ss_pred             ccc-eeeeeCCcccccHHHHHHHHHhhhcccceeeEEechHHHHHHhhhhHHHHhhceeeeeehhhHHHHhhhhh-HHHH
Confidence            543 555666553     1222222222    2789999999997632 22334445589999999999765441 1122


Q ss_pred             HHHhhCCccCcEEEEEeeCChhHH-H---HHH----------------HhcCCCEE------------------------
Q 017573          161 DIFQLLPAKVQVGVFSATMPPEAL-E---ITR----------------KFMNKPVR------------------------  196 (369)
Q Consensus       161 ~~~~~~~~~~~~i~~saT~~~~~~-~---~~~----------------~~~~~~~~------------------------  196 (369)
                      .+ ..+.... .+.+|+||-.+.. +   +..                .++..+..                        
T Consensus       494 ~l-~~~~~~~-~~~LtgTPlen~l~eL~sl~~~f~~p~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~  571 (866)
T COG0553         494 AL-QFLKALN-RLDLTGTPLENRLGELWSLLQEFLNPGLLGTSFAIFTRLFEKPIQAEEDIGPLEARELGIELLRKLLSP  571 (866)
T ss_pred             HH-HHHhhcc-eeeCCCChHhhhHHHHHHHHHHHhCCccccchHHHHHHHHhhhhhhcccccchhhHHHHHHHHHHHHHH
Confidence            22 2332222 3556666621100 0   000                00000000                        


Q ss_pred             -------EE--ec----------------C----------c----------cc-ccc---------------------ce
Q 017573          197 -------IL--VK----------------R----------D----------EL-TLE---------------------GI  209 (369)
Q Consensus       197 -------~~--~~----------------~----------~----------~~-~~~---------------------~~  209 (369)
                             ..  +.                .          .          .. ...                     .+
T Consensus       572 f~lrr~k~~~~v~~~Lp~k~e~~~~~~l~~~q~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~lr~~  651 (866)
T COG0553         572 FILRRTKEDVEVLKELPPKIEKVLECELSEEQRELYEALLEGAEKNQQLLEDLEKADSDENRIGDSELNILALLTRLRQI  651 (866)
T ss_pred             HhhcccccchhHHHhCChhhhhhhhhcccHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccccchhhHHHHHHHHHHHh
Confidence                   00  00                0          0          00 000                     00


Q ss_pred             eEEEEEcc----------------------------chh-hhHHHHHHHH-Hh--ccCC--CeEEEeCCHhhHHHHHHHH
Q 017573          210 KQFYVNVE----------------------------KEE-WKLETLCDLY-ET--LAIT--QSVIFVNTRRKVDWLTDKM  255 (369)
Q Consensus       210 ~~~~~~~~----------------------------~~~-~~~~~l~~~~-~~--~~~~--k~lv~~~~~~~~~~~~~~l  255 (369)
                      ........                            ... .+...+.+++ ..  ..+.  ++++|++.......+...+
T Consensus       652 ~~~p~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~k~~~l~~ll~~~~~~~~~~~kvlifsq~t~~l~il~~~l  731 (866)
T COG0553         652 CNHPALVDEGLEATFDRIVLLLREDKDFDYLKKPLIQLSKGKLQALDELLLDKLLEEGHYHKVLIFSQFTPVLDLLEDYL  731 (866)
T ss_pred             ccCccccccccccccchhhhhhhcccccccccchhhhccchHHHHHHHHHHHHHHhhcccccEEEEeCcHHHHHHHHHHH
Confidence            00000000                            000 3455565666 22  2334  8999999999999999999


Q ss_pred             hhCCCeeEEecCCCCHHHHHHHHHHHhcC--CCcEEEEecCCcCCCCCCCCcEEEEecCCCCccchhhhhcccccCCCce
Q 017573          256 RSRDHTVSATHGDMDQNTRDIIMREFRSG--SSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKG  333 (369)
Q Consensus       256 ~~~~~~~~~~~~~~~~~~r~~~~~~f~~~--~~~vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~  333 (369)
                      ...+.....++|.++.+.|...++.|.++  ...+++++.+.+.|+|+..+++||++++.|++....|+..|+.|.|++.
T Consensus       732 ~~~~~~~~~ldG~~~~~~r~~~i~~f~~~~~~~v~lls~kagg~glnLt~a~~vi~~d~~wnp~~~~Qa~dRa~RigQ~~  811 (866)
T COG0553         732 KALGIKYVRLDGSTPAKRRQELIDRFNADEEEKVFLLSLKAGGLGLNLTGADTVILFDPWWNPAVELQAIDRAHRIGQKR  811 (866)
T ss_pred             HhcCCcEEEEeCCCChhhHHHHHHHhhcCCCCceEEEEecccccceeecccceEEEeccccChHHHHHHHHHHHHhcCcc
Confidence            99988899999999999999999999986  3345667779999999999999999999999999999999999999876


Q ss_pred             eEEEE--ecccc
Q 017573          334 VAINF--VTRDD  343 (369)
Q Consensus       334 ~~~~~--~~~~~  343 (369)
                      .+.++  ...+.
T Consensus       812 ~v~v~r~i~~~t  823 (866)
T COG0553         812 PVKVYRLITRGT  823 (866)
T ss_pred             eeEEEEeecCCc
Confidence            55444  44444

>smart00490 HELICc helicase superfamily c-terminal domain

Probab=99.64  E-value=7.6e-16  Score=105.33  Aligned_cols=81  Identities=41%  Similarity=0.749  Sum_probs=76.6

Q ss_pred             HHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCCCCccchhhhhcccccC
Q 017573          250 WLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRF  329 (369)
Q Consensus       250 ~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~  329 (369)
                      .+.+.|+..+..+..+||++++++|.++++.|.++...++++|+++++|+|+|.+++|++++++++...+.|++||++|.
T Consensus         2 ~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~Gi~~~~~~~vi~~~~~~~~~~~~Q~~gR~~R~   81 (82)
T smart00490        2 ELAELLKELGIKVARLHGGLSQEEREEILEKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRAGRA   81 (82)
T ss_pred             HHHHHHHHCCCeEEEEECCCCHHHHHHHHHHHHcCCCeEEEECChhhCCcChhcCCEEEEeCCCCCHHHHHHhhcccccC
Confidence            46677888889999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             C
Q 017573          330 G  330 (369)
Q Consensus       330 ~  330 (369)
                      |
T Consensus        82 g   82 (82)
T smart00490       82 G   82 (82)
T ss_pred             C
Confidence            5

>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=99.64  E-value=9.5e-13  Score=114.78  Aligned_cols=292  Identities=15%  Similarity=0.209  Sum_probs=203.1

Q ss_pred             ccCCCccEEEEcCCHHHHHHHHHHHHHhcccc-------------CcE-------EEEEECCcchHHHHHHHc-------
Q 017573           60 YGLVQCQALVLAPTRELAQQIEKVMRALGDYL-------------GVK-------VHACVGGTSVREDQRILQ-------  112 (369)
Q Consensus        60 ~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~-------------~~~-------v~~~~~~~~~~~~~~~~~-------  112 (369)
                      +|-..+++||++|++..+.++.+.+.++....             ++.       .........+.+....+.       
T Consensus        33 QGftRPkVLIL~P~R~~A~~~V~~Li~l~~~~~~~~nk~RF~~efg~~~~~~~~~~~~~~~~~kP~D~~~~F~GN~DD~F  112 (442)
T PF06862_consen   33 QGFTRPKVLILLPFRNSALRIVETLISLLPPGKQVENKKRFEEEFGLPEDEDDDEEPPEFKKSKPEDFKALFSGNNDDCF  112 (442)
T ss_pred             cCCCCceEEEEcccHHHHHHHHHHHHHHcCccchHHHHHHHHHHcCCCccccchhhhccccCCCchhHHHhcCCCccceE
Confidence            45556799999999999999998887765441             100       000001122223332221       


Q ss_pred             -----------------cCCcEEEeccHHHHHHHHc------CCCCCCCccEEEEechhHhhc--cCcHHHHHHHHhhCC
Q 017573          113 -----------------AGVHVVVGTPGRVFDMLRR------QSLRPDYIKMFVLDEADEMLS--RGFKDQIYDIFQLLP  167 (369)
Q Consensus       113 -----------------~~~~iiv~t~~~l~~~~~~------~~~~~~~~~~viiDE~H~~~~--~~~~~~~~~~~~~~~  167 (369)
                                       ..+||||+||=.|...+..      ..-.++.+.++|+|.+|.+.-  |.....+...++..|
T Consensus       113 rlGik~trk~ikLys~Fy~SDIIiASPLGLr~~i~~~~~~~~d~DFLSSIEv~iiD~ad~l~MQNW~Hv~~v~~~lN~~P  192 (442)
T PF06862_consen  113 RLGIKFTRKSIKLYSDFYSSDIIIASPLGLRMIIGEEGEKKRDYDFLSSIEVLIIDQADVLLMQNWEHVLHVFEHLNLQP  192 (442)
T ss_pred             EEeEEEecCeeeeecccccCCEEEEChHHHHHHhccccccccccchhheeeeEeechhhHHHHhhHHHHHHHHHHhccCC
Confidence                             2479999999999877764      223356688999999998874  433444444455544


Q ss_pred             cc---------------------CcEEEEEeeCChhHHHHHHHhcCCC---EEEEecCc-----cccccceeEEEEEccc
Q 017573          168 AK---------------------VQVGVFSATMPPEALEITRKFMNKP---VRILVKRD-----ELTLEGIKQFYVNVEK  218 (369)
Q Consensus       168 ~~---------------------~~~i~~saT~~~~~~~~~~~~~~~~---~~~~~~~~-----~~~~~~~~~~~~~~~~  218 (369)
                      ..                     .|.+++|+...++...+....+.+.   +.+.....     ......+.+.+...+.
T Consensus       193 ~~~~~~DfsRVR~w~Ldg~a~~~RQtii~S~~~~pe~~slf~~~~~N~~G~v~~~~~~~~~g~i~~v~~~v~Q~F~r~~~  272 (442)
T PF06862_consen  193 KKSHDTDFSRVRPWYLDGQAKYYRQTIIFSSFQTPEINSLFNRHCQNYAGKVRLKPPYEASGVISQVVVQVRQVFQRFDC  272 (442)
T ss_pred             CCCCCCCHHHHHHHHHcCcchheeEeEEecCCCCHHHHHHHHhhCcCccceEEEeeccccceeeeccccCCceEEEEecC
Confidence            32                     6999999999999888888866543   22222222     2334566777776543


Q ss_pred             hhh------hHH-----HHHHHHHhccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCc
Q 017573          219 EEW------KLE-----TLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSR  287 (369)
Q Consensus       219 ~~~------~~~-----~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~  287 (369)
                      ...      ..+     .+-.+......+++|||++|.-+--.+.++|++.+...+.++...+..+..++-..|.+|+.+
T Consensus       273 ~s~~~~~d~Rf~yF~~~iLP~l~~~~~~~~~LIfIPSYfDfVRlRN~lk~~~~sF~~i~EYts~~~isRAR~~F~~G~~~  352 (442)
T PF06862_consen  273 SSPADDPDARFKYFTKKILPQLKRDSKMSGTLIFIPSYFDFVRLRNYLKKENISFVQISEYTSNSDISRARSQFFHGRKP  352 (442)
T ss_pred             CCcchhhhHHHHHHHHHHHHHhhhccCCCcEEEEecchhhhHHHHHHHHhcCCeEEEecccCCHHHHHHHHHHHHcCCce
Confidence            221      111     122222234457999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEecCC--cCCCCCCCCcEEEEecCCCCccchhhhhcccccCC------CceeEEEEeccccHHHHHHHH
Q 017573          288 VLITTDLL--ARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFG------RKGVAINFVTRDDERMLFDIQ  351 (369)
Q Consensus       288 vli~t~~~--~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~------~~~~~~~~~~~~~~~~~~~~~  351 (369)
                      +|+.|.-+  -.-..+.++++||++++|..+.-|...+.-.....      ....|.++++.-|.-.++.+.
T Consensus       353 iLL~TER~HFfrRy~irGi~~viFY~~P~~p~fY~El~n~~~~~~~~~~~~~~~~~~~lysk~D~~~LErIV  424 (442)
T PF06862_consen  353 ILLYTERFHFFRRYRIRGIRHVIFYGPPENPQFYSELLNMLDESSGGEVDAADATVTVLYSKYDALRLERIV  424 (442)
T ss_pred             EEEEEhHHhhhhhceecCCcEEEEECCCCChhHHHHHHhhhcccccccccccCceEEEEecHhHHHHHHHHh
Confidence            99999843  34467889999999999999988877775554433      257899999998888777664

; GO: 0005634 nucleus

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

Probab=99.63  E-value=2.3e-15  Score=129.83  Aligned_cols=142  Identities=18%  Similarity=0.113  Sum_probs=90.2

Q ss_pred             cCCcEEEEcCCCChhhHHHHHHHHHhhhccCCC--ccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHH
Q 017573           32 KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQ--CQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQR  109 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~--~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~  109 (369)
                      ..+++++..++|+|||..++..+..........  .++|||||. ++..+|.+++.++......++....+.........
T Consensus        24 ~~~g~lL~de~GlGKT~~~i~~~~~l~~~~~~~~~~~~LIv~P~-~l~~~W~~E~~~~~~~~~~~v~~~~~~~~~~~~~~  102 (299)
T PF00176_consen   24 PPRGGLLADEMGLGKTITAIALISYLKNEFPQRGEKKTLIVVPS-SLLSQWKEEIEKWFDPDSLRVIIYDGDSERRRLSK  102 (299)
T ss_dssp             TT-EEEE---TTSSHHHHHHHHHHHHHHCCTTSS-S-EEEEE-T-TTHHHHHHHHHHHSGT-TS-EEEESSSCHHHHTTS
T ss_pred             CCCCEEEEECCCCCchhhhhhhhhhhhhccccccccceeEeecc-chhhhhhhhhccccccccccccccccccccccccc
Confidence            347899999999999988766655333332221  259999999 88899999999998655667777776662222222


Q ss_pred             HHccCCcEEEeccHHHH--------HHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEEeeCCh
Q 017573          110 ILQAGVHVVVGTPGRVF--------DMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMPP  181 (369)
Q Consensus       110 ~~~~~~~iiv~t~~~l~--------~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~saT~~~  181 (369)
                      ......+++++|++.+.        ..+..     .++++||+||+|.+.+..  ......+..+. ....+++||||-.
T Consensus       103 ~~~~~~~vvi~ty~~~~~~~~~~~~~~l~~-----~~~~~vIvDEaH~~k~~~--s~~~~~l~~l~-~~~~~lLSgTP~~  174 (299)
T PF00176_consen  103 NQLPKYDVVITTYETLRKARKKKDKEDLKQ-----IKWDRVIVDEAHRLKNKD--SKRYKALRKLR-ARYRWLLSGTPIQ  174 (299)
T ss_dssp             SSCCCSSEEEEEHHHHH--TSTHTTHHHHT-----SEEEEEEETTGGGGTTTT--SHHHHHHHCCC-ECEEEEE-SS-SS
T ss_pred             cccccceeeecccccccccccccccccccc-----ccceeEEEeccccccccc--ccccccccccc-cceEEeecccccc
Confidence            22356899999999998        22222     338999999999985433  33444444455 5567889999965


Q ss_pred             h
Q 017573          182 E  182 (369)
Q Consensus       182 ~  182 (369)
                      +
T Consensus       175 n  175 (299)
T PF00176_consen  175 N  175 (299)
T ss_dssp             S
T ss_pred             c
Confidence            4

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.

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

Probab=99.59  E-value=6e-15  Score=106.95  Aligned_cols=136  Identities=21%  Similarity=0.231  Sum_probs=81.3

Q ss_pred             cCCcEEEEcCCCChhhHHHHHHHHH-hhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHH
Q 017573           32 KGLDVIQQAQSGTGKTATFCSGILQ-QLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRI  110 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~~~~~~-~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~  110 (369)
                      +|+-.++-..+|+|||.-.+.-++. .+.++.   ++|++.|++.+++++.+.++..    ++.+  ...... .    .
T Consensus         3 kg~~~~~d~hpGaGKTr~vlp~~~~~~i~~~~---rvLvL~PTRvva~em~~aL~~~----~~~~--~t~~~~-~----~   68 (148)
T PF07652_consen    3 KGELTVLDLHPGAGKTRRVLPEIVREAIKRRL---RVLVLAPTRVVAEEMYEALKGL----PVRF--HTNARM-R----T   68 (148)
T ss_dssp             TTEEEEEE--TTSSTTTTHHHHHHHHHHHTT-----EEEEESSHHHHHHHHHHTTTS----SEEE--ESTTSS-------
T ss_pred             CCceeEEecCCCCCCcccccHHHHHHHHHccC---eEEEecccHHHHHHHHHHHhcC----Cccc--Cceeee-c----c
Confidence            4566789999999999866655444 344444   8999999999999888877643    3222  211111 1    1


Q ss_pred             HccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCC-ccCcEEEEEeeCChhH
Q 017573          111 LQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLP-AKVQVGVFSATMPPEA  183 (369)
Q Consensus       111 ~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~-~~~~~i~~saT~~~~~  183 (369)
                      ..++.-|-++|+..+.+.+.+ .....+++++|+||||.....+ ......+..... ....+++|||||+...
T Consensus        69 ~~g~~~i~vMc~at~~~~~~~-p~~~~~yd~II~DEcH~~Dp~s-IA~rg~l~~~~~~g~~~~i~mTATPPG~~  140 (148)
T PF07652_consen   69 HFGSSIIDVMCHATYGHFLLN-PCRLKNYDVIIMDECHFTDPTS-IAARGYLRELAESGEAKVIFMTATPPGSE  140 (148)
T ss_dssp             --SSSSEEEEEHHHHHHHHHT-SSCTTS-SEEEECTTT--SHHH-HHHHHHHHHHHHTTS-EEEEEESS-TT--
T ss_pred             ccCCCcccccccHHHHHHhcC-cccccCccEEEEeccccCCHHH-HhhheeHHHhhhccCeeEEEEeCCCCCCC
Confidence            235567899999998887766 5566789999999999743222 222222222221 2356999999998643

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 ....

>COG0653 SecA Preprotein translocase subunit SecA (ATPase, RNA helicase) [Intracellular trafficking and secretion]

Probab=99.53  E-value=3.2e-13  Score=124.71  Aligned_cols=316  Identities=21%  Similarity=0.246  Sum_probs=196.5

Q ss_pred             CCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEE
Q 017573           18 KPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHA   97 (369)
Q Consensus        18 ~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~   97 (369)
                      .++|+=.|.+-.+.-..+-+..+-||-|||+++.+++.-....+.   .+.+|+..--|+..-.+++.....++|+.+..
T Consensus        78 g~~~~dVQliG~i~lh~g~iaEM~TGEGKTL~atlp~ylnaL~gk---gVhvVTvNdYLA~RDae~m~~l~~~LGlsvG~  154 (822)
T COG0653          78 GMRHFDVQLLGGIVLHLGDIAEMRTGEGKTLVATLPAYLNALAGK---GVHVVTVNDYLARRDAEWMGPLYEFLGLSVGV  154 (822)
T ss_pred             CCChhhHHHhhhhhhcCCceeeeecCCchHHHHHHHHHHHhcCCC---CcEEeeehHHhhhhCHHHHHHHHHHcCCceee
Confidence            355555667767777888999999999999998877664444333   79999999999999999999999999999999


Q ss_pred             EECCcchHHHHHHHccCCcEEEeccHHH-HHHHHcCC------CCCCCccEEEEechhHhhc----------c------C
Q 017573           98 CVGGTSVREDQRILQAGVHVVVGTPGRV-FDMLRRQS------LRPDYIKMFVLDEADEMLS----------R------G  154 (369)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~iiv~t~~~l-~~~~~~~~------~~~~~~~~viiDE~H~~~~----------~------~  154 (369)
                      ...+....+.+...  .+||..+|...| +..++.+-      .....+.+.|+||++.+.=          .      .
T Consensus       155 ~~~~m~~~ek~~aY--~~DItY~TnnElGFDYLRDNm~~~~ee~vqr~~~faIvDEvDSILIDEARtPLiISG~~~~~~~  232 (822)
T COG0653         155 ILAGMSPEEKRAAY--ACDITYGTNNELGFDYLRDNMVTSQEEKVQRGLNFAIVDEVDSILIDEARTPLIISGPAEDSSE  232 (822)
T ss_pred             ccCCCChHHHHHHH--hcCceeccccccCcchhhhhhhccHHHhhhccCCeEEEcchhheeeeccccceeeecccccCch
Confidence            88888766665544  378999998877 23332221      1122367899999987541          1      0


Q ss_pred             cHHHHHHHHhhCCc--------c---------------------------------------------------------
Q 017573          155 FKDQIYDIFQLLPA--------K---------------------------------------------------------  169 (369)
Q Consensus       155 ~~~~~~~~~~~~~~--------~---------------------------------------------------------  169 (369)
                      .+..+..+...+..        .                                                         
T Consensus       233 ~Y~~~~~~v~~l~~~~d~~iDek~k~v~lte~G~~kae~~f~~~~Ly~~en~~~~h~~~~alrA~~l~~~D~dYIVrd~e  312 (822)
T COG0653         233 LYKKVDDLVRLLSEDEDFTIDEKSKNVSLTESGLEKAEELLGIENLYDLENVNLVHHLNQALRAHILFFRDVDYIVRDGE  312 (822)
T ss_pred             HHHHHHHHHHHhccccceeecchhcccccchhhHHHHHHHhCcccccchhhHHHHhhHHHHHHHHHHhhcCCeeEEecCe
Confidence            12222222211110        0                                                         


Q ss_pred             ----------------------------------------------------CcEEEEEeeCChhHHHHHHHhcCCCEEE
Q 017573          170 ----------------------------------------------------VQVGVFSATMPPEALEITRKFMNKPVRI  197 (369)
Q Consensus       170 ----------------------------------------------------~~~i~~saT~~~~~~~~~~~~~~~~~~~  197 (369)
                                                                          ....+||+|......++..-+...-+.+
T Consensus       313 v~IvD~ftGR~m~gRr~s~GLhQAiEAKEgv~i~~e~~tlatITfQn~fR~y~kl~gmTGTa~te~~EF~~iY~l~vv~i  392 (822)
T COG0653         313 VVIVDEFTGRMMEGRRWSDGLHQAIEAKEGVEIQEENQTLATITFQNLFRLYPKLAGMTGTADTEEEEFDVIYGLDVVVI  392 (822)
T ss_pred             EEEEecccCCcccCcCCCchhHHHHHHhcCCcccccceeehhhhHHHHHhhhhhhcCCCCcchhhhhhhhhccCCceeec
Confidence                                                                2233444444333222222222211111


Q ss_pred             EecCccccccceeEEEEEccchhhhHHHH-HHHHHhc-cCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHH
Q 017573          198 LVKRDELTLEGIKQFYVNVEKEEWKLETL-CDLYETL-AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRD  275 (369)
Q Consensus       198 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l-~~~~~~~-~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~  275 (369)
                      .........+.-...|   .....+...+ .++...+ .++++||-+.+++..+.+.+.|.+.+.+..++++.....+-+
T Consensus       393 PTnrp~~R~D~~D~vy---~t~~~K~~Aiv~~I~~~~~~gqPvLvgT~sie~SE~ls~~L~~~~i~h~VLNAk~h~~EA~  469 (822)
T COG0653         393 PTNRPIIRLDEPDLVY---KTEEEKFKAIVEDIKERHEKGQPVLVGTVSIEKSELLSKLLRKAGIPHNVLNAKNHAREAE  469 (822)
T ss_pred             cCCCcccCCCCccccc---cchHHHHHHHHHHHHHHHhcCCCEEEcCcceecchhHHHHHHhcCCCceeeccccHHHHHH
Confidence            1111111111111111   1222244333 3343333 457999999999999999999999999999999987655554


Q ss_pred             HHHHHHhcCCCcEEEEecCCcCCCCCCCCc-----------EEEEecCCCCccchhhhhcccccCCCceeEEEEecccc
Q 017573          276 IIMREFRSGSSRVLITTDLLARGIDVQQVS-----------LVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDD  343 (369)
Q Consensus       276 ~~~~~f~~~~~~vli~t~~~~~G~d~~~~~-----------~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~  343 (369)
                      .+-+.-..|  -|-|+|+++++|-|+.--.           +||-.....|-.-=.|.-||+||.|-+|.+-.|.+-.|
T Consensus       470 Iia~AG~~g--aVTiATNMAGRGTDIkLg~~~~~V~~lGGL~VIgTERhESRRIDnQLRGRsGRQGDpG~S~F~lSleD  546 (822)
T COG0653         470 IIAQAGQPG--AVTIATNMAGRGTDIKLGGNPEFVMELGGLHVIGTERHESRRIDNQLRGRAGRQGDPGSSRFYLSLED  546 (822)
T ss_pred             HHhhcCCCC--ccccccccccCCcccccCCCHHHHHHhCCcEEEecccchhhHHHHHhhcccccCCCcchhhhhhhhHH
Confidence            444333332  3889999999999985222           12222233333344699999999998898887777554

>KOG1016 consensus Predicted DNA helicase, DEAD-box superfamily [General function prediction only]

Probab=99.48  E-value=7.9e-13  Score=118.92  Aligned_cols=111  Identities=17%  Similarity=0.284  Sum_probs=91.6

Q ss_pred             CCeEEEeCCHhhHHHHHHHHhhC------------------CCeeEEecCCCCHHHHHHHHHHHhcCC---CcEEEEecC
Q 017573          236 TQSVIFVNTRRKVDWLTDKMRSR------------------DHTVSATHGDMDQNTRDIIMREFRSGS---SRVLITTDL  294 (369)
Q Consensus       236 ~k~lv~~~~~~~~~~~~~~l~~~------------------~~~~~~~~~~~~~~~r~~~~~~f~~~~---~~vli~t~~  294 (369)
                      .++|+|..+......+.+.|.++                  +.....+.|..+..+|++.+++|++..   +-++++|.+
T Consensus       720 ~kil~fSq~l~~Ld~ieeil~krq~pc~~gdnG~~aqkW~~n~sy~rldG~t~a~~rekLinqfN~e~~lsWlfllstra  799 (1387)
T KOG1016|consen  720 EKILIFSQNLTALDMIEEILKKRQIPCKDGDNGCPAQKWEKNRSYLRLDGTTSAADREKLINQFNSEPGLSWLFLLSTRA  799 (1387)
T ss_pred             ceEEEeecchhHHHHHHHHHhcccccCCCCCCCCchhhhhhccceecccCCcccchHHHHHHhccCCCCceeeeeehhcc
Confidence            36799999988888888888765                  123446677788999999999998743   347788999


Q ss_pred             CcCCCCCCCCcEEEEecCCCCccchhhhhcccccCCCceeEEEEeccccHHH
Q 017573          295 LARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERM  346 (369)
Q Consensus       295 ~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~  346 (369)
                      ..-|+|+-+.+.+++++..|++..-.|++.|+.|.|+...|++|----|...
T Consensus       800 g~lGinLIsanr~~ifda~wnpchdaqavcRvyrYGQ~KpcfvYRlVmD~~l  851 (1387)
T KOG1016|consen  800 GSLGINLISANRCIIFDACWNPCHDAQAVCRVYRYGQQKPCFVYRLVMDNSL  851 (1387)
T ss_pred             ccccceeeccceEEEEEeecCccccchhhhhhhhhcCcCceeEEeehhhhhh
Confidence            9999999999999999999999999999999999999999988866444433

>PRK15483 type III restriction-modification system StyLTI enzyme res; Provisional

Probab=99.43  E-value=1.5e-10  Score=109.75  Aligned_cols=73  Identities=18%  Similarity=0.193  Sum_probs=57.4

Q ss_pred             CCcEEEEecCCcCCCCCCCCcEEEEecCCCCccchhhhhcccccCC--Cce--------eEEEEeccccHHHHHHHHHHh
Q 017573          285 SSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFG--RKG--------VAINFVTRDDERMLFDIQKFY  354 (369)
Q Consensus       285 ~~~vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~--~~~--------~~~~~~~~~~~~~~~~~~~~~  354 (369)
                      ..+++++.+++.+|||.|.+-.++.+....|...-.|.+||+.|..  +.|        ..-++.+.+.......+++-+
T Consensus       501 ~~~fifs~~al~egwd~~~~~~~~~l~~~~s~~~~~q~~gr~lr~~vnq~G~R~~~~~~~LTvianesy~dFa~~LQ~EI  580 (986)
T PRK15483        501 TRRFLFSKWTLREGWDNPNVFQIAKLRSSGSETSKLQEVGRGLRLPVDENGHRVSQEEFRLNYLIDYDEKDFASKLVGEI  580 (986)
T ss_pred             CeEEEEEhHHhhhcCCCCCeEEEEEeccCCchHHHHHHhccceeccccccCccccCccEEEEEEeCccHHHHHHHHHHHH
Confidence            5679999999999999999999999998899999999999999952  222        234455566677777777666


Q ss_pred             ccc
Q 017573          355 NVV  357 (369)
Q Consensus       355 ~~~  357 (369)
                      ...
T Consensus       581 ~~~  583 (986)
T PRK15483        581 NSD  583 (986)
T ss_pred             Hhh
Confidence            543

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=99.39  E-value=7.3e-12  Score=105.89  Aligned_cols=73  Identities=23%  Similarity=0.210  Sum_probs=57.9

Q ss_pred             CCCCCCcHhhhhhhh----ccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCC---CccEEEEcCCHHHHHHHHHHHHH
Q 017573           14 YGFEKPSAIQQRGIV----PFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLV---QCQALVLAPTRELAQQIEKVMRA   86 (369)
Q Consensus        14 ~~~~~~~~~Q~~~~~----~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~---~~~~liv~P~~~l~~q~~~~~~~   86 (369)
                      |+|. |||.|.+...    .+.+++++++.+|||+|||++++.+++..+.....   +.+++|.+++.++.+|...++++
T Consensus         5 FPy~-~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~~~~~kvi~~t~T~~~~~q~i~~l~~   83 (289)
T smart00488        5 FPYE-PYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPERIQKIKLIYLSRTVSEIEKRLEELRK   83 (289)
T ss_pred             CCCC-CCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCcccccccceeEEeccHHHHHHHHHHHHh
Confidence            7884 6999999554    45568999999999999999999998866544322   23899999999998888777765


Q ss_pred             h
Q 017573           87 L   87 (369)
Q Consensus        87 ~   87 (369)
                      .
T Consensus        84 ~   84 (289)
T smart00488       84 L   84 (289)
T ss_pred             c
Confidence            4

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=99.39  E-value=7.3e-12  Score=105.89  Aligned_cols=73  Identities=23%  Similarity=0.210  Sum_probs=57.9

Q ss_pred             CCCCCCcHhhhhhhh----ccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCC---CccEEEEcCCHHHHHHHHHHHHH
Q 017573           14 YGFEKPSAIQQRGIV----PFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLV---QCQALVLAPTRELAQQIEKVMRA   86 (369)
Q Consensus        14 ~~~~~~~~~Q~~~~~----~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~---~~~~liv~P~~~l~~q~~~~~~~   86 (369)
                      |+|. |||.|.+...    .+.+++++++.+|||+|||++++.+++..+.....   +.+++|.+++.++.+|...++++
T Consensus         5 FPy~-~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~~~~~kvi~~t~T~~~~~q~i~~l~~   83 (289)
T smart00489        5 FPYE-PYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPERIQKIKLIYLSRTVSEIEKRLEELRK   83 (289)
T ss_pred             CCCC-CCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCcccccccceeEEeccHHHHHHHHHHHHh
Confidence            7884 6999999554    45568999999999999999999998866544322   23899999999998888777765


Q ss_pred             h
Q 017573           87 L   87 (369)
Q Consensus        87 ~   87 (369)
                      .
T Consensus        84 ~   84 (289)
T smart00489       84 L   84 (289)
T ss_pred             c
Confidence            4

>KOG2340 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.27  E-value=4.6e-10  Score=97.46  Aligned_cols=336  Identities=17%  Similarity=0.229  Sum_probs=206.9

Q ss_pred             CCCCCcHhhhhhhhccccCCcEEEEc-CCCChh--hHHHHHHHHHhh----------------------------hccCC
Q 017573           15 GFEKPSAIQQRGIVPFCKGLDVIQQA-QSGTGK--TATFCSGILQQL----------------------------DYGLV   63 (369)
Q Consensus        15 ~~~~~~~~Q~~~~~~~~~~~~~li~~-~tG~GK--T~~~~~~~~~~~----------------------------~~~~~   63 (369)
                      +-..+++.|.+++..+.+.++++.-. ..+.|+  +.++++.+++++                            .++..
T Consensus       213 ~s~pltalQ~~L~~~m~~YrDl~y~~~s~kn~~e~R~lYclH~lNHi~K~r~~IL~Nn~r~~Sqk~g~~~~~~frDQG~t  292 (698)
T KOG2340|consen  213 KSEPLTALQKELFKIMFNYRDLLYPTRSQKNGEEYRSLYCLHALNHILKTRDLILGNNRRLASQKEGENPDESFRDQGFT  292 (698)
T ss_pred             ccCcchHHHHHHHHHHHhhhhhccccccccccchhhhhHHHHHHHHHHHHHHHHhcchHhhhhhhcCCCCchhhhhcCCC
Confidence            44679999999999999988876433 333444  456667777665                            12233


Q ss_pred             CccEEEEcCCHHHHHHHHHHHHHhccccCc-EEEE--------EECC---------cchHHHHHHH--------------
Q 017573           64 QCQALVLAPTRELAQQIEKVMRALGDYLGV-KVHA--------CVGG---------TSVREDQRIL--------------  111 (369)
Q Consensus        64 ~~~~liv~P~~~l~~q~~~~~~~~~~~~~~-~v~~--------~~~~---------~~~~~~~~~~--------------  111 (369)
                      .+++|||||+++-|-...+.+..+.....- +..+        -.++         ..+......+              
T Consensus       293 RpkVLivvpfRe~A~riVn~lis~l~G~~q~k~~V~Nk~RF~~eys~~te~~~~~~~kP~D~~~lf~GNtDD~FriGl~f  372 (698)
T KOG2340|consen  293 RPKVLIVVPFRESAYRIVNLLISLLSGDDQGKSEVWNKKRFEGEYSGPTELPPPRAKKPEDFEELFSGNTDDAFRIGLAF  372 (698)
T ss_pred             CceEEEEecchHHHHHHHHHHHHHhcCccccchhhhhhhhhchhcCCCcccCCCCCCCchhHHHHhcCCCcchhhhhHHH
Confidence            458999999999999888888776322211 1000        0010         1111111111              


Q ss_pred             ----------ccCCcEEEeccHHHHHHHHcCCCC------CCCccEEEEechhHhhccCcHHHHHHHH---hhCCcc---
Q 017573          112 ----------QAGVHVVVGTPGRVFDMLRRQSLR------PDYIKMFVLDEADEMLSRGFKDQIYDIF---QLLPAK---  169 (369)
Q Consensus       112 ----------~~~~~iiv~t~~~l~~~~~~~~~~------~~~~~~viiDE~H~~~~~~~~~~~~~~~---~~~~~~---  169 (369)
                                ....||+||+|=.|...+...+-.      ++.+.++|+|.+|.+...+|.. +..++   ..+|..   
T Consensus       373 tkKtikLys~fy~SDIlVaSPLGLRmil~n~gdkkrd~dfLSSIEl~iIDQa~~~l~QNwEh-l~~ifdHLn~~P~k~h~  451 (698)
T KOG2340|consen  373 TKKTIKLYSKFYKSDILVASPLGLRMILGNTGDKKRDFDFLSSIELLIIDQADIMLMQNWEH-LLHIFDHLNLQPSKQHD  451 (698)
T ss_pred             HHHHHHHHhhhcccCeEEecchhhhhhhcCCCcccccchhhhhhhhhhhhhHHHHHHhhHHH-HHHHHHHhhcCcccccC
Confidence                      125799999999987777643322      3447799999999988666442 33333   333332   


Q ss_pred             ------------------CcEEEEEeeCChhHHHHHHHhcCCCE-EEEec---Cc-cc--cccceeEEEEEccc------
Q 017573          170 ------------------VQVGVFSATMPPEALEITRKFMNKPV-RILVK---RD-EL--TLEGIKQFYVNVEK------  218 (369)
Q Consensus       170 ------------------~~~i~~saT~~~~~~~~~~~~~~~~~-~~~~~---~~-~~--~~~~~~~~~~~~~~------  218 (369)
                                        .|.+++|+--.+....++...|.+.. .+...   .. ..  ....+.+.+.....      
T Consensus       452 ~DfSRVR~wyL~~qsr~~rQtl~Fs~y~~~~~nS~fn~~c~N~~Gkv~~~~~~~~gsi~~v~~~l~Qvf~ri~~~si~~~  531 (698)
T KOG2340|consen  452 VDFSRVRMWYLDGQSRYFRQTLLFSRYSHPLFNSLFNQYCQNMAGKVKARNLQSGGSISNVGIPLCQVFQRIEVKSIIET  531 (698)
T ss_pred             CChhheehheeccHHHHHHHHHHHHhhccHHHHHHHHHhhhhhcceeeeccccCCCchhhccchhhhhhhheeccCcccC
Confidence                              34555555555555555555554321 11110   00 00  01111122111111      


Q ss_pred             hhhhHH-HHHHHHHh---ccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecC
Q 017573          219 EEWKLE-TLCDLYET---LAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDL  294 (369)
Q Consensus       219 ~~~~~~-~l~~~~~~---~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~  294 (369)
                      .+.... .+..++-.   .....+|||.|+.-+--.+..++++.......++...+.+.-.++-+.|-.|...||+.|.-
T Consensus       532 ~D~RFkyFv~~ImPq~~k~t~s~~LiyIPSYfDFVRvRNy~K~e~i~F~~i~EYssk~~vsRAR~lF~qgr~~vlLyTER  611 (698)
T KOG2340|consen  532 PDARFKYFVDKIMPQLIKRTESGILIYIPSYFDFVRVRNYMKKEEISFVMINEYSSKSKVSRARELFFQGRKSVLLYTER  611 (698)
T ss_pred             chHHHHHHHHhhchhhcccccCceEEEecchhhHHHHHHHhhhhhcchHHHhhhhhHhhhhHHHHHHHhcCceEEEEehh
Confidence            111111 12222211   12347899999999999999999999888888888888888888999999999999999984


Q ss_pred             C--cCCCCCCCCcEEEEecCCCCccch---hhhhcccccCC----CceeEEEEeccccHHHHHHHH
Q 017573          295 L--ARGIDVQQVSLVINYDLPTQPENY---LHRIGRSGRFG----RKGVAINFVTRDDERMLFDIQ  351 (369)
Q Consensus       295 ~--~~G~d~~~~~~vi~~~~~~~~~~~---~Q~~GR~~R~~----~~~~~~~~~~~~~~~~~~~~~  351 (369)
                      +  -.-.++.+++.||++.+|.++.-|   +.+.+|..-.|    ..-.|.++++.-|.-.+..+.
T Consensus       612 ~hffrR~~ikGVk~vVfYqpP~~P~FYsEiinm~~k~~~~gn~d~d~~t~~ilytKyD~i~Le~iv  677 (698)
T KOG2340|consen  612 AHFFRRYHIKGVKNVVFYQPPNNPHFYSEIINMSDKTTSQGNTDLDIFTVRILYTKYDRIRLENIV  677 (698)
T ss_pred             hhhhhhheecceeeEEEecCCCCcHHHHHHHhhhhhhhccCCccccceEEEEEeechhhHHHHHhh
Confidence            3  345789999999999999987544   66666664443    336788888887776666554

>PF07517 SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011115 SecA protein binds to the plasma membrane where it interacts with proOmpA to support translocation of proOmpA through the membrane

Probab=99.24  E-value=2.2e-10  Score=94.20  Aligned_cols=130  Identities=23%  Similarity=0.301  Sum_probs=95.0

Q ss_pred             CCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCc
Q 017573           14 YGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGV   93 (369)
Q Consensus        14 ~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~   93 (369)
                      .|+ .|++.|.-+.-.+.+|+  +++..||-|||+++.++++-....+.   .+-|++.+.-|+..=.+++..++..+|+
T Consensus        74 ~g~-~p~~vQll~~l~L~~G~--laEm~TGEGKTli~~l~a~~~AL~G~---~V~vvT~NdyLA~RD~~~~~~~y~~LGl  147 (266)
T PF07517_consen   74 LGL-RPYDVQLLGALALHKGR--LAEMKTGEGKTLIAALPAALNALQGK---GVHVVTSNDYLAKRDAEEMRPFYEFLGL  147 (266)
T ss_dssp             TS-----HHHHHHHHHHHTTS--EEEESTTSHHHHHHHHHHHHHHTTSS----EEEEESSHHHHHHHHHHHHHHHHHTT-
T ss_pred             cCC-cccHHHHhhhhhcccce--eEEecCCCCcHHHHHHHHHHHHHhcC---CcEEEeccHHHhhccHHHHHHHHHHhhh
Confidence            444 78888888887665544  99999999999998777665555554   8999999999999999999999999999


Q ss_pred             EEEEEECCcchHHHHHHHccCCcEEEeccHHHHH-HHHcCCC------CCCCccEEEEechhHhh
Q 017573           94 KVHACVGGTSVREDQRILQAGVHVVVGTPGRVFD-MLRRQSL------RPDYIKMFVLDEADEML  151 (369)
Q Consensus        94 ~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~-~~~~~~~------~~~~~~~viiDE~H~~~  151 (369)
                      .+....++...........  ++|+++|...|.- .++....      ....++++|+||+|.+.
T Consensus       148 sv~~~~~~~~~~~r~~~Y~--~dI~Y~t~~~~~fD~Lrd~~~~~~~~~~~r~~~~~ivDEvDs~L  210 (266)
T PF07517_consen  148 SVGIITSDMSSEERREAYA--ADIVYGTNSEFGFDYLRDNLALSKNEQVQRGFDFAIVDEVDSIL  210 (266)
T ss_dssp             -EEEEETTTEHHHHHHHHH--SSEEEEEHHHHHHHHHHHTT-SSGGG--SSSSSEEEECTHHHHT
T ss_pred             ccccCccccCHHHHHHHHh--CcccccccchhhHHHHHHHHhhccchhccCCCCEEEEeccceEE
Confidence            9999999887655444333  5799999988853 4433211      13457899999999875

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 ....

>KOG1133 consensus Helicase of the DEAD superfamily [Replication, recombination and repair]

Probab=99.24  E-value=2.6e-08  Score=89.58  Aligned_cols=118  Identities=15%  Similarity=0.221  Sum_probs=78.2

Q ss_pred             hHHHHHHHHHhc---cCCCeEEEeCCHhhHHHHHHHHhhCCC-------eeEEecCCCCHHHHHHHHHHHhc----CCCc
Q 017573          222 KLETLCDLYETL---AITQSVIFVNTRRKVDWLTDKMRSRDH-------TVSATHGDMDQNTRDIIMREFRS----GSSR  287 (369)
Q Consensus       222 ~~~~l~~~~~~~---~~~k~lv~~~~~~~~~~~~~~l~~~~~-------~~~~~~~~~~~~~r~~~~~~f~~----~~~~  287 (369)
                      .++.+...+...   -++.+++|+||.+....+.+...+.|.       +-.++-..-+   -+.+++.|..    |.-.
T Consensus       613 ~l~~l~~~~~nL~~~VPgGvV~FfPSy~yL~~v~k~w~~~gil~ri~~kK~vF~E~k~~---~~dvl~~Ya~a~~~g~Ga  689 (821)
T KOG1133|consen  613 MIKDLGSSISNLSNAVPGGVVCFFPSYAYLGQVRKRWEQNGILARIVGKKKVFYEPKDT---VEDVLEGYAEAAERGRGA  689 (821)
T ss_pred             HHHHHHHHHHHHHhhCCCcEEEEeccHHHHHHHHHHHHhcchHHHhhccchhhccCccc---HHHHHHHHHHHhhcCCCe
Confidence            445555444432   227899999999999999988886532       3333333323   3446666643    4445


Q ss_pred             EEEEe--cCCcCCCCCCC--CcEEEEecCCCC--------------------c------------cchhhhhcccccCCC
Q 017573          288 VLITT--DLLARGIDVQQ--VSLVINYDLPTQ--------------------P------------ENYLHRIGRSGRFGR  331 (369)
Q Consensus       288 vli~t--~~~~~G~d~~~--~~~vi~~~~~~~--------------------~------------~~~~Q~~GR~~R~~~  331 (369)
                      +|+++  .-+++|+|+.+  ++.|+.++.|+.                    +            ....|.+|||.|-.+
T Consensus       690 iLlaVVGGKlSEGINF~D~LgRaVvvVGlPyPN~~s~EL~er~k~l~~k~~~~gagke~yEnlCMkAVNQsIGRAIRH~~  769 (821)
T KOG1133|consen  690 ILLAVVGGKLSEGINFSDDLGRAVVVVGLPYPNIQSVELQERMKHLDGKLPTPGAGKELYENLCMKAVNQSIGRAIRHRK  769 (821)
T ss_pred             EEEEEeccccccccccccccccEEEEeecCCCCCCCHHHHHHHHHhhhccCCCCchHHHHHHHHHHHHHHHHHHHHhhhc
Confidence            66664  48899999986  888888887742                    0            124799999999877


Q ss_pred             ceeEEEEeccc
Q 017573          332 KGVAINFVTRD  342 (369)
Q Consensus       332 ~~~~~~~~~~~  342 (369)
                      +-.++++++..
T Consensus       770 DYA~i~LlD~R  780 (821)
T KOG1133|consen  770 DYASIYLLDKR  780 (821)
T ss_pred             cceeEEEehhh
Confidence            76666666643

>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]

Probab=99.16  E-value=5.3e-11  Score=110.16  Aligned_cols=101  Identities=17%  Similarity=0.164  Sum_probs=87.8

Q ss_pred             CeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCC-CcEE-EEecCCcCCCCCCCCcEEEEecCCC
Q 017573          237 QSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGS-SRVL-ITTDLLARGIDVQQVSLVINYDLPT  314 (369)
Q Consensus       237 k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~-~~vl-i~t~~~~~G~d~~~~~~vi~~~~~~  314 (369)
                      ++++|+.....+.-+...|...+.....+.|.++...|.+.+..|..+. ..++ ++..+.+.|+|+..+++|+..++-|
T Consensus       541 kiiifsq~~~~l~l~~~~l~~~~~~~~~~~g~~~~~~r~~s~~~~~~~~~~~vll~Slkag~~glnlt~a~~v~~~d~~w  620 (674)
T KOG1001|consen  541 KIVIFSQLIWGLALVCLRLFFKGFVFLRYDGEMLMKIRTKSFTDFPCDPLVTALLMSLKAGKVGLNLTAASHVLLMDPWW  620 (674)
T ss_pred             ceeeehhHHHHHHHhhhhhhhcccccchhhhhhHHHHHHhhhcccccCccHHHHHHHHHHhhhhhchhhhhHHHhhchhc
Confidence            8888888888888888888888888999999999999999999998543 3444 5667999999999999999999999


Q ss_pred             CccchhhhhcccccCCCceeEEE
Q 017573          315 QPENYLHRIGRSGRFGRKGVAIN  337 (369)
Q Consensus       315 ~~~~~~Q~~GR~~R~~~~~~~~~  337 (369)
                      |+..-.|++-|+.|-|+...+.+
T Consensus       621 np~~eeQaidR~hrigq~k~v~v  643 (674)
T KOG1001|consen  621 NPAVEEQAIDRAHRIGQTKPVKV  643 (674)
T ss_pred             ChHHHHHHHHHHHHhcccceeee
Confidence            99999999999999998765554

>COG3587 Restriction endonuclease [Defense mechanisms]

Probab=99.15  E-value=2.8e-09  Score=97.87  Aligned_cols=71  Identities=18%  Similarity=0.222  Sum_probs=54.9

Q ss_pred             CCCcEEEEecCCcCCCCCCCCcEEEEecCCCCccchhhhhcccccC--CCce-----------eEEEEeccccHHHHHHH
Q 017573          284 GSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRF--GRKG-----------VAINFVTRDDERMLFDI  350 (369)
Q Consensus       284 ~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~--~~~~-----------~~~~~~~~~~~~~~~~~  350 (369)
                      ...+++++..++-+|||-|++=.++-+....|..+=.|.+||+.|.  ++.|           ...+++...+......+
T Consensus       482 ~plRFIFS~waLrEGWDNPNVFtIckL~~S~SeiSK~QeVGRGLRLaVNe~G~RV~~~~~~~n~L~vlv~~sek~Fv~~L  561 (985)
T COG3587         482 EPLRFIFSKWALREGWDNPNVFTICKLRSSGSEISKLQEVGRGLRLAVNENGERVTKDFDFPNELTVLVNESEKDFVKAL  561 (985)
T ss_pred             CcceeeeehhHHhhcCCCCCeeEEEEecCCCcchHHHHHhccceeeeeccccceecccccccceEEEEecccHHHHHHHH
Confidence            3578999999999999999999999999999999999999999994  2333           23345555666666555


Q ss_pred             HHHh
Q 017573          351 QKFY  354 (369)
Q Consensus       351 ~~~~  354 (369)
                      ++-.
T Consensus       562 qkEI  565 (985)
T COG3587         562 QKEI  565 (985)
T ss_pred             HHHH
Confidence            5433

>PF13872 AAA_34: P-loop containing NTP hydrolase pore-1

Probab=99.07  E-value=1.1e-09  Score=90.35  Aligned_cols=158  Identities=19%  Similarity=0.178  Sum_probs=107.5

Q ss_pred             CCcHhhhhhhhccc----------cCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHh
Q 017573           18 KPSAIQQRGIVPFC----------KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRAL   87 (369)
Q Consensus        18 ~~~~~Q~~~~~~~~----------~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~   87 (369)
                      .++..|.+++-...          ....+++-..||.||-......|++....+++  +.++++.+..|..+..++++..
T Consensus        37 ~LS~~QLEaV~yA~q~h~~~Lp~~~R~Gf~lGDGtGvGKGR~iAgiI~~n~l~Gr~--r~vwvS~s~dL~~Da~RDl~DI  114 (303)
T PF13872_consen   37 LLSALQLEAVIYACQRHEQILPGGSRAGFFLGDGTGVGKGRQIAGIILENWLRGRK--RAVWVSVSNDLKYDAERDLRDI  114 (303)
T ss_pred             cccHHHHHHHHHHHHHHHhhcccccCcEEEeccCCCcCccchhHHHHHHHHHcCCC--ceEEEECChhhhhHHHHHHHHh
Confidence            57888888885543          23678999999999998888888888877764  7999999999999999999987


Q ss_pred             ccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCC-----------C-ccEEEEechhHhhccCc
Q 017573           88 GDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPD-----------Y-IKMFVLDEADEMLSRGF  155 (369)
Q Consensus        88 ~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~-----------~-~~~viiDE~H~~~~~~~  155 (369)
                      ... .+.+..+..-...    ....-+..|+++||..|........-..+           . =.+||+||||...+...
T Consensus       115 G~~-~i~v~~l~~~~~~----~~~~~~~GvlF~TYs~L~~~~~~~~~~~sRl~ql~~W~g~dfdgvivfDEcH~akn~~~  189 (303)
T PF13872_consen  115 GAD-NIPVHPLNKFKYG----DIIRLKEGVLFSTYSTLISESQSGGKYRSRLDQLVDWCGEDFDGVIVFDECHKAKNLSS  189 (303)
T ss_pred             CCC-cccceechhhccC----cCCCCCCCccchhHHHHHhHHhccCCccchHHHHHHHHhcCCCceEEeccchhcCCCCc
Confidence            544 3333333321110    00122457999999998765432111111           1 25999999999875432


Q ss_pred             --------HHHHHHHHhhCCccCcEEEEEeeCChhH
Q 017573          156 --------KDQIYDIFQLLPAKVQVGVFSATMPPEA  183 (369)
Q Consensus       156 --------~~~~~~~~~~~~~~~~~i~~saT~~~~~  183 (369)
                              ......+.+.+| +.+++++|||...+.
T Consensus       190 ~~~~~sk~g~avl~LQ~~LP-~ARvvY~SATgasep  224 (303)
T PF13872_consen  190 GSKKPSKTGIAVLELQNRLP-NARVVYASATGASEP  224 (303)
T ss_pred             cCccccHHHHHHHHHHHhCC-CCcEEEecccccCCC
Confidence                    123444555565 566999999986544

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

Probab=98.95  E-value=1e-09  Score=102.66  Aligned_cols=259  Identities=18%  Similarity=0.159  Sum_probs=159.2

Q ss_pred             CCcHhhhhhhhcccc-CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEE
Q 017573           18 KPSAIQQRGIVPFCK-GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVH   96 (369)
Q Consensus        18 ~~~~~Q~~~~~~~~~-~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~   96 (369)
                      ...|.|.+.+..+.. ..++++-+|||+|||.++.+++...+..-+. .++++++|.++|+....+++.+.....|+++.
T Consensus       927 ~fn~~q~~if~~~y~td~~~~~g~ptgsgkt~~ae~a~~~~~~~~p~-~kvvyIap~kalvker~~Dw~~r~~~~g~k~i 1005 (1230)
T KOG0952|consen  927 YFNPIQTQIFHCLYHTDLNFLLGAPTGSGKTVVAELAIFRALSYYPG-SKVVYIAPDKALVKERSDDWSKRDELPGIKVI 1005 (1230)
T ss_pred             ccCCccceEEEEEeecchhhhhcCCccCcchhHHHHHHHHHhccCCC-ccEEEEcCCchhhcccccchhhhcccCCceeE
Confidence            455678888766665 4789999999999999999888877765544 59999999999999998888776555588898


Q ss_pred             EEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCC--CCCccEEEEechhHhhccCcHHHHH-------HHHhhCC
Q 017573           97 ACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLR--PDYIKMFVLDEADEMLSRGFKDQIY-------DIFQLLP  167 (369)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~--~~~~~~viiDE~H~~~~~~~~~~~~-------~~~~~~~  167 (369)
                      .++|+...+..   --.+++++|+||+++....+.|...  ...++.+++||.|.+... ....+.       .+-...+
T Consensus      1006 e~tgd~~pd~~---~v~~~~~~ittpek~dgi~Rsw~~r~~v~~v~~iv~de~hllg~~-rgPVle~ivsr~n~~s~~t~ 1081 (1230)
T KOG0952|consen 1006 ELTGDVTPDVK---AVREADIVITTPEKWDGISRSWQTRKYVQSVSLIVLDEIHLLGED-RGPVLEVIVSRMNYISSQTE 1081 (1230)
T ss_pred             eccCccCCChh---heecCceEEcccccccCccccccchhhhccccceeecccccccCC-CcceEEEEeeccccCccccC
Confidence            88888775522   1245799999999998877765543  455788999999976533 111111       1122233


Q ss_pred             ccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEE------EEccchh-hhHHHHHHHHHhccCCCeEE
Q 017573          168 AKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFY------VNVEKEE-WKLETLCDLYETLAITQSVI  240 (369)
Q Consensus       168 ~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~-~~~~~l~~~~~~~~~~k~lv  240 (369)
                      +..+.+++|-- ..+..++..++--++. +.. +....+......+      ..++... ........+-...+.++++|
T Consensus      1082 ~~vr~~glsta-~~na~dla~wl~~~~~-~nf-~~svrpvp~~~~i~gfp~~~~cprm~smnkpa~qaik~~sp~~p~li 1158 (1230)
T KOG0952|consen 1082 EPVRYLGLSTA-LANANDLADWLNIKDM-YNF-RPSVRPVPLEVHIDGFPGQHYCPRMMSMNKPAFQAIKTHSPIKPVLI 1158 (1230)
T ss_pred             cchhhhhHhhh-hhccHHHHHHhCCCCc-CCC-CcccccCCceEeecCCCchhcchhhhhcccHHHHHHhcCCCCCceEE
Confidence            34555554433 3344455544443332 111 1111111111111      1122222 23344455555567789999


Q ss_pred             EeCCHhh----HHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCC
Q 017573          241 FVNTRRK----VDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSS  286 (369)
Q Consensus       241 ~~~~~~~----~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~  286 (369)
                      |+.++..    +..+...+........+++.+  ..+-+.++..-.+...
T Consensus      1159 fv~srrqtrlta~~li~~~~~~~~p~~fl~~d--e~e~e~~~~~~~d~~L 1206 (1230)
T KOG0952|consen 1159 FVSSRRQTRLTALDLIASCATEDNPKQFLNMD--ELELEIIMSKVRDTNL 1206 (1230)
T ss_pred             EeecccccccchHhHHhhccCCCCchhccCCC--HHHHHHHHHHhcccch
Confidence            9998765    444444444444455555544  5666666666665443

>COG3421 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=98.95  E-value=3.4e-08  Score=87.53  Aligned_cols=107  Identities=15%  Similarity=0.188  Sum_probs=71.4

Q ss_pred             EEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHH-----hcc-------ccCcEEEEEECCcch
Q 017573           37 IQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRA-----LGD-------YLGVKVHACVGGTSV  104 (369)
Q Consensus        37 li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~-----~~~-------~~~~~v~~~~~~~~~  104 (369)
                      ++.++||||||+++...|++...++.+  +.|+.|.....++.....+..     +.-       ...+.+..+..-.. 
T Consensus         1 lf~matgsgkt~~ma~lil~~y~kgyr--~flffvnq~nilekt~~nftd~~s~kylf~e~i~~~d~~i~ikkvn~fse-   77 (812)
T COG3421           1 LFEMATGSGKTLVMAGLILECYKKGYR--NFLFFVNQANILEKTKLNFTDSVSSKYLFSENININDENIEIKKVNNFSE-   77 (812)
T ss_pred             CcccccCCChhhHHHHHHHHHHHhchh--hEEEEecchhHHHHHHhhcccchhhhHhhhhhhhcCCceeeeeeecccCc-
Confidence            356899999999999999999888876  688999988888877776632     110       00112211111111 


Q ss_pred             HHHHHHHccCCcEEEeccHHHHHHHHcCCCCC---CC---cc-EEEEechhHhhc
Q 017573          105 REDQRILQAGVHVVVGTPGRVFDMLRRQSLRP---DY---IK-MFVLDEADEMLS  152 (369)
Q Consensus       105 ~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~---~~---~~-~viiDE~H~~~~  152 (369)
                            ......|+++|.+.|+..+.+...+.   ..   .. +++-||+|++-.
T Consensus        78 ------hnd~iei~fttiq~l~~d~~~~ken~itledl~~~klvfl~deahhln~  126 (812)
T COG3421          78 ------HNDAIEIYFTTIQGLFSDFTRAKENAITLEDLKDQKLVFLADEAHHLNT  126 (812)
T ss_pred             ------cCCceEEEEeehHHHHHHHHhhccccccHhhHhhCceEEEechhhhhhh
Confidence                  24467899999999988776544332   21   12 678899999864

>PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A

Probab=98.89  E-value=8.9e-09  Score=85.50  Aligned_cols=69  Identities=26%  Similarity=0.261  Sum_probs=50.8

Q ss_pred             CCcHhhhhhhhccccCCc-EEEEcCCCChhhHHHHHHHHHhh-----hccCCCccEEEEcCCHHHHHHHHHHHHH
Q 017573           18 KPSAIQQRGIVPFCKGLD-VIQQAQSGTGKTATFCSGILQQL-----DYGLVQCQALVLAPTRELAQQIEKVMRA   86 (369)
Q Consensus        18 ~~~~~Q~~~~~~~~~~~~-~li~~~tG~GKT~~~~~~~~~~~-----~~~~~~~~~liv~P~~~l~~q~~~~~~~   86 (369)
                      ++++.|.+|+..++.... .+|+||+|+|||.+....+....     .....+.++|+++|+..-+.+..+.+.+
T Consensus         1 ~ln~~Q~~Ai~~~~~~~~~~~i~GpPGTGKT~~l~~~i~~~~~~~~~~~~~~~~~il~~~~sN~avd~~~~~l~~   75 (236)
T PF13086_consen    1 KLNESQREAIQSALSSNGITLIQGPPGTGKTTTLASIIAQLLQRFKSRSADRGKKILVVSPSNAAVDNILERLKK   75 (236)
T ss_dssp             ---HHHHHHHHHHCTSSE-EEEE-STTSSHHHHHHHHHHHH-------HCCCSS-EEEEESSHHHHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHHcCCCCEEEECCCCCChHHHHHHHHHHhccchhhhhhhccccceeecCCchhHHHHHHHHHh
Confidence            468899999999999988 99999999999976554444431     1233444899999999999999888877

>PF13307 Helicase_C_2: Helicase C-terminal domain; PDB: 4A15_A 2VSF_A 3CRV_A 3CRW_1 2VL7_A

Probab=98.86  E-value=1.2e-08  Score=79.15  Aligned_cols=111  Identities=21%  Similarity=0.354  Sum_probs=76.5

Q ss_pred             HHHhccCCCeEEEeCCHhhHHHHHHHHhhCCC--eeEEecCCCCHHHHHHHHHHHhcCCCcEEEEec--CCcCCCCCCC-
Q 017573          229 LYETLAITQSVIFVNTRRKVDWLTDKMRSRDH--TVSATHGDMDQNTRDIIMREFRSGSSRVLITTD--LLARGIDVQQ-  303 (369)
Q Consensus       229 ~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~~~--~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~--~~~~G~d~~~-  303 (369)
                      +++.. +++++||++|.+..+.+.+.++....  ...++..  +..++.++++.|..++-.||+++.  .+.+|+|+|+ 
T Consensus         4 l~~~~-~g~~lv~f~Sy~~l~~~~~~~~~~~~~~~~~v~~q--~~~~~~~~l~~~~~~~~~il~~v~~g~~~EGiD~~~~   80 (167)
T PF13307_consen    4 LISAV-PGGVLVFFPSYRRLEKVYERLKERLEEKGIPVFVQ--GSKSRDELLEEFKRGEGAILLAVAGGSFSEGIDFPGD   80 (167)
T ss_dssp             HHHCC-SSEEEEEESSHHHHHHHHTT-TSS-E-ETSCEEES--TCCHHHHHHHHHCCSSSEEEEEETTSCCGSSS--ECE
T ss_pred             HHhcC-CCCEEEEeCCHHHHHHHHHHHHhhcccccceeeec--CcchHHHHHHHHHhccCeEEEEEecccEEEeecCCCc
Confidence            34433 48999999999999999999987642  1222222  356788899999999889999998  9999999996 


Q ss_pred             -CcEEEEecCCCCc------------------------------cchhhhhcccccCCCceeEEEEeccc
Q 017573          304 -VSLVINYDLPTQP------------------------------ENYLHRIGRSGRFGRKGVAINFVTRD  342 (369)
Q Consensus       304 -~~~vi~~~~~~~~------------------------------~~~~Q~~GR~~R~~~~~~~~~~~~~~  342 (369)
                       ++.||+.+.|...                              ....|++||+.|..++--++++.++.
T Consensus        81 ~~r~vii~glPfp~~~d~~~~~~~~~~~~~~~~~~~~~~~~~a~~~l~Qa~GR~iR~~~D~g~i~llD~R  150 (167)
T PF13307_consen   81 LLRAVIIVGLPFPPPSDPLVQAKREYLDKQGKNPFRDWYLPPAIRKLKQAIGRLIRSEDDYGVIILLDSR  150 (167)
T ss_dssp             SEEEEEEES-----TTCHHHHHHHHHHHHCCTTCHHHHTHHHHHHHHHHHHHCC--STT-EEEEEEESGG
T ss_pred             hhheeeecCCCCCCCCCHHHHHHHHHHHHHhccchhhHhhHHHHHHHhhhcCcceeccCCcEEEEEEcCc
Confidence             7789998887421                              12489999999998776666666654

>KOG1802 consensus RNA helicase nonsense mRNA reducing factor (pNORF1) [RNA processing and modification]

Probab=98.85  E-value=7.5e-08  Score=86.32  Aligned_cols=85  Identities=22%  Similarity=0.200  Sum_probs=68.5

Q ss_pred             HHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhc
Q 017573            9 RGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALG   88 (369)
Q Consensus         9 ~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~   88 (369)
                      +.+..+++..++.-|..|+.++++..-.+|++|+|+|||.+....+++.... .. .++|+++|+..-+.|+++.+.+. 
T Consensus       401 ~~~s~~~lpkLN~SQ~~AV~~VL~rplsLIQGPPGTGKTvtsa~IVyhl~~~-~~-~~VLvcApSNiAVDqLaeKIh~t-  477 (935)
T KOG1802|consen  401 RRFSVPNLPKLNASQSNAVKHVLQRPLSLIQGPPGTGKTVTSATIVYHLARQ-HA-GPVLVCAPSNIAVDQLAEKIHKT-  477 (935)
T ss_pred             hhhcCCCchhhchHHHHHHHHHHcCCceeeecCCCCCceehhHHHHHHHHHh-cC-CceEEEcccchhHHHHHHHHHhc-
Confidence            3566778899999999999999999999999999999998876666655544 22 38999999999999999988764 


Q ss_pred             cccCcEEEEEE
Q 017573           89 DYLGVKVHACV   99 (369)
Q Consensus        89 ~~~~~~v~~~~   99 (369)
                         +++|..+.
T Consensus       478 ---gLKVvRl~  485 (935)
T KOG1802|consen  478 ---GLKVVRLC  485 (935)
T ss_pred             ---CceEeeee
Confidence               45554443

>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]

Probab=98.82  E-value=4.3e-08  Score=90.59  Aligned_cols=307  Identities=15%  Similarity=0.186  Sum_probs=173.4

Q ss_pred             hhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCc--cEEEEcCCHHHHHHHHHHHHH-----hccccCcEE
Q 017573           23 QQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQC--QALVLAPTRELAQQIEKVMRA-----LGDYLGVKV   95 (369)
Q Consensus        23 Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~--~~liv~P~~~l~~q~~~~~~~-----~~~~~~~~v   95 (369)
                      -..+++.+.+++-+++.+.||.|||......+++.+.....+.  .+.+--|++..+.-..+++..     .+...+.++
T Consensus       383 ~~~i~q~v~dn~v~~I~getgcgk~tq~aq~iLe~~~~ns~g~~~na~v~qprrisaisiaerva~er~e~~g~tvgy~v  462 (1282)
T KOG0921|consen  383 RSEILQAVAENRVVIIKGETGCGKSTQVAQFLLESFLENSNGASFNAVVSQPRRISAISLAERVANERGEEVGETCGYNV  462 (1282)
T ss_pred             HHHHHHHHhcCceeeEeecccccchhHHHHHHHHHHhhccccccccceeccccccchHHHHHHHHHhhHHhhcccccccc
Confidence            3455566667888999999999999998888888876554332  355556777666666665532     222223333


Q ss_pred             EEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccC-cHHHHHHHHhhCCccCcEEE
Q 017573           96 HACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRG-FKDQIYDIFQLLPAKVQVGV  174 (369)
Q Consensus        96 ~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~-~~~~~~~~~~~~~~~~~~i~  174 (369)
                      .....-..         .--.|.++|.+-+.+.+.....   .+..+|+||.|+....+ +...+.+=+.......+.++
T Consensus       463 Rf~Sa~pr---------pyg~i~fctvgvllr~~e~glr---g~sh~i~deiherdv~~dfll~~lr~m~~ty~dl~v~l  530 (1282)
T KOG0921|consen  463 RFDSATPR---------PYGSIMFCTVGVLLRMMENGLR---GISHVIIDEIHERDVDTDFVLIVLREMISTYRDLRVVL  530 (1282)
T ss_pred             cccccccc---------cccceeeeccchhhhhhhhccc---ccccccchhhhhhccchHHHHHHHHhhhccchhhhhhh
Confidence            22221111         1125888999888887776433   35789999999864222 22211111111112333445


Q ss_pred             EEeeCChhHH--------------------HHHHHhcCCCE-EEE----------ecCccccccc-eeE-EEEEc-----
Q 017573          175 FSATMPPEAL--------------------EITRKFMNKPV-RIL----------VKRDELTLEG-IKQ-FYVNV-----  216 (369)
Q Consensus       175 ~saT~~~~~~--------------------~~~~~~~~~~~-~~~----------~~~~~~~~~~-~~~-~~~~~-----  216 (369)
                      ||||...+..                    .+....+..+. .+.          ...+...+.. ... .-...     
T Consensus       531 msatIdTd~f~~~f~~~p~~~~~grt~pvq~F~led~~~~~~~vp~~~~~~k~k~~~~~~~~~~ddK~~n~n~~~dd~~~  610 (1282)
T KOG0921|consen  531 MSATIDTDLFTNFFSSIPDVTVHGRTFPVQSFFLEDIIQMTQFVPSEPSQKKRKKDDDEEDEEVDDKGRNMNILCDPSYN  610 (1282)
T ss_pred             hhcccchhhhhhhhccccceeeccccccHHHHHHHHhhhhhhccCCCcCccchhhcccccCchhhhcccccccccChhhc
Confidence            5555432211                    11111111110 000          0000000000 000 00000     


Q ss_pred             ----------cchhhhHHHHHHHHH----hccCCCeEEEeCCHhhHHHHHHHHhhC-------CCeeEEecCCCCHHHHH
Q 017573          217 ----------EKEEWKLETLCDLYE----TLAITQSVIFVNTRRKVDWLTDKMRSR-------DHTVSATHGDMDQNTRD  275 (369)
Q Consensus       217 ----------~~~~~~~~~l~~~~~----~~~~~k~lv~~~~~~~~~~~~~~l~~~-------~~~~~~~~~~~~~~~r~  275 (369)
                                .........+..++.    ..-.+-+++|.+.....-.+...+...       ...+...|+.....+..
T Consensus       611 ~~~~~am~~~se~d~~f~l~Eal~~~i~s~~i~gailvflpgwa~i~~L~~~ll~~~~fg~~~~y~ilp~Hsq~~~~eqr  690 (1282)
T KOG0921|consen  611 ESTRTAMSRLSEKDIPFGLIEALLNDIASRNIDGAVLVFLPGWAEIMTLCNRLLEHQEFGQANKYEILPLHSQLTSQEQR  690 (1282)
T ss_pred             chhhhhhhcchhhcchhHHHHHHHhhhcccCCccceeeecCchHHhhhhhhhhhhhhhhccchhcccccchhhcccHhhh
Confidence                      000001222222222    223357889999998888888777644       34677788888877888


Q ss_pred             HHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecC------------------CCCccchhhhhcccccCCCceeEEE
Q 017573          276 IIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDL------------------PTQPENYLHRIGRSGRFGRKGVAIN  337 (369)
Q Consensus       276 ~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~------------------~~~~~~~~Q~~GR~~R~~~~~~~~~  337 (369)
                      ++.+....|..+++++|.+.+..+.+.++..|++.+.                  -.+....+|+-||++|. ++|.|..
T Consensus       691 kvf~~~p~gv~kii~stniaetsiTidd~v~vid~cka~~~~~~s~nn~~~~Atvw~sktn~eqr~gr~grv-R~G~~f~  769 (1282)
T KOG0921|consen  691 KVFEPVPEGVTKIILSTNIAETSITIDDVVYVIDSCKAKEKLFTSHNNMTHYATVWASKTNLEQRKGRAGRV-RPGFCFH  769 (1282)
T ss_pred             hccCcccccccccccccceeeEeeeecceeEEEeeeeeeeeeeccccceeeeeeecccccchHhhcccCcee-ccccccc
Confidence            8888778888899999998888887766666654331                  12556789999999997 7788887


Q ss_pred             Eeccc
Q 017573          338 FVTRD  342 (369)
Q Consensus       338 ~~~~~  342 (369)
                      +++..
T Consensus       770 lcs~a  774 (1282)
T KOG0921|consen  770 LCSRA  774 (1282)
T ss_pred             ccHHH
Confidence            77654

>PF02562 PhoH: PhoH-like protein; InterPro: IPR003714 PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation and belongings to the phosphate regulon (pho) in Escherichia coli []

Probab=98.80  E-value=3.5e-09  Score=83.60  Aligned_cols=143  Identities=15%  Similarity=0.170  Sum_probs=74.2

Q ss_pred             CCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEE
Q 017573           16 FEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKV   95 (369)
Q Consensus        16 ~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v   95 (369)
                      +...+..|..+++++.+.+.+++.+|.|+|||+.++..+++.+..+... +++++-|..+..    +++..+.....-+.
T Consensus         2 I~p~~~~Q~~~~~al~~~~~v~~~G~AGTGKT~LA~a~Al~~v~~g~~~-kiii~Rp~v~~~----~~lGflpG~~~eK~   76 (205)
T PF02562_consen    2 IKPKNEEQKFALDALLNNDLVIVNGPAGTGKTFLALAAALELVKEGEYD-KIIITRPPVEAG----EDLGFLPGDLEEKM   76 (205)
T ss_dssp             ----SHHHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-S-EEEEEE-S--TT--------SS--------
T ss_pred             ccCCCHHHHHHHHHHHhCCeEEEECCCCCcHHHHHHHHHHHHHHhCCCc-EEEEEecCCCCc----cccccCCCCHHHHH
Confidence            3456789999999999889999999999999999999999888775544 788888876431    12211100000000


Q ss_pred             E-----------EEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHh
Q 017573           96 H-----------ACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQ  164 (369)
Q Consensus        96 ~-----------~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~  164 (369)
                      .           .+.+...   ..... ....|-+.+...+..    .  .+. -.+||+|||+.+.    ...+..++.
T Consensus        77 ~p~~~p~~d~l~~~~~~~~---~~~~~-~~~~Ie~~~~~~iRG----r--t~~-~~~iIvDEaQN~t----~~~~k~ilT  141 (205)
T PF02562_consen   77 EPYLRPIYDALEELFGKEK---LEELI-QNGKIEIEPLAFIRG----R--TFD-NAFIIVDEAQNLT----PEELKMILT  141 (205)
T ss_dssp             -TTTHHHHHHHTTTS-TTC---HHHHH-HTTSEEEEEGGGGTT--------B--SEEEEE-SGGG------HHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHhChHh---HHHHh-hcCeEEEEehhhhcC----c--ccc-ceEEEEecccCCC----HHHHHHHHc
Confidence            0           0001111   01111 223455555333221    1  111 2799999999863    567788889


Q ss_pred             hCCccCcEEEEEee
Q 017573          165 LLPAKVQVGVFSAT  178 (369)
Q Consensus       165 ~~~~~~~~i~~saT  178 (369)
                      ++..+++++++.-.
T Consensus       142 R~g~~skii~~GD~  155 (205)
T PF02562_consen  142 RIGEGSKIIITGDP  155 (205)
T ss_dssp             TB-TT-EEEEEE--
T ss_pred             ccCCCcEEEEecCc
Confidence            99888887775444

; GO: 0005524 ATP binding; PDB: 3B85_A.

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A

Probab=98.76  E-value=4.4e-08  Score=78.21  Aligned_cols=123  Identities=16%  Similarity=0.209  Sum_probs=71.3

Q ss_pred             CCcHhhhhhhhccccCC--cEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEE
Q 017573           18 KPSAIQQRGIVPFCKGL--DVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKV   95 (369)
Q Consensus        18 ~~~~~Q~~~~~~~~~~~--~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v   95 (369)
                      +|++-|++++..+..++  -.+++++.|+|||.+. ..+...+...  +.++++++|+...+..+.+..       +.+.
T Consensus         1 ~L~~~Q~~a~~~~l~~~~~~~~l~G~aGtGKT~~l-~~~~~~~~~~--g~~v~~~apT~~Aa~~L~~~~-------~~~a   70 (196)
T PF13604_consen    1 TLNEEQREAVRAILTSGDRVSVLQGPAGTGKTTLL-KALAEALEAA--GKRVIGLAPTNKAAKELREKT-------GIEA   70 (196)
T ss_dssp             -S-HHHHHHHHHHHHCTCSEEEEEESTTSTHHHHH-HHHHHHHHHT--T--EEEEESSHHHHHHHHHHH-------TS-E
T ss_pred             CCCHHHHHHHHHHHhcCCeEEEEEECCCCCHHHHH-HHHHHHHHhC--CCeEEEECCcHHHHHHHHHhh-------Ccch
Confidence            47899999999997543  4788899999999764 4455555443  238999999988777655542       1111


Q ss_pred             EEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCC----CCCCccEEEEechhHhhccCcHHHHHHHHhhCCc-cC
Q 017573           96 HACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSL----RPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPA-KV  170 (369)
Q Consensus        96 ~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~----~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~-~~  170 (369)
                                              .|..+++........    .....+++|+||+-++.    ...+..++...+. ..
T Consensus        71 ------------------------~Ti~~~l~~~~~~~~~~~~~~~~~~vliVDEasmv~----~~~~~~ll~~~~~~~~  122 (196)
T PF13604_consen   71 ------------------------QTIHSFLYRIPNGDDEGRPELPKKDVLIVDEASMVD----SRQLARLLRLAKKSGA  122 (196)
T ss_dssp             ------------------------EEHHHHTTEECCEECCSSCC-TSTSEEEESSGGG-B----HHHHHHHHHHS-T-T-
T ss_pred             ------------------------hhHHHHHhcCCcccccccccCCcccEEEEecccccC----HHHHHHHHHHHHhcCC
Confidence                                    121121111111000    03345899999999874    4556677777766 55


Q ss_pred             cEEEEEee
Q 017573          171 QVGVFSAT  178 (369)
Q Consensus       171 ~~i~~saT  178 (369)
                      +++++.-+
T Consensus       123 klilvGD~  130 (196)
T PF13604_consen  123 KLILVGDP  130 (196)
T ss_dssp             EEEEEE-T
T ss_pred             EEEEECCc
Confidence            56654444

>KOG1131 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, 5'-3' helicase subunit RAD3 [Transcription; Replication, recombination and repair]

Probab=98.68  E-value=7.3e-06  Score=71.95  Aligned_cols=75  Identities=13%  Similarity=0.020  Sum_probs=49.9

Q ss_pred             HhCCCCCCcHhhhhhhhccc----cCCcEEEEcCCCChhhHHHHHHHHHhhhccCCC-ccEEEEcCCHHHHHHHHHHHHH
Q 017573           12 YAYGFEKPSAIQQRGIVPFC----KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQ-CQALVLAPTRELAQQIEKVMRA   86 (369)
Q Consensus        12 ~~~~~~~~~~~Q~~~~~~~~----~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~-~~~liv~P~~~l~~q~~~~~~~   86 (369)
                      .-|++...+|-|-+-...+.    .+.++++.+|+|+|||.+.+..+......-+.. .|.++-.-+..-++....+++.
T Consensus        10 v~FPY~~iYPEQ~~YM~elKrsLDakGh~llEMPSGTGKTvsLLSli~aYq~~~p~~~~KliYCSRTvpEieK~l~El~~   89 (755)
T KOG1131|consen   10 VYFPYDYIYPEQYEYMRELKRSLDAKGHCLLEMPSGTGKTVSLLSLIIAYQLHYPDEHRKLIYCSRTVPEIEKALEELKR   89 (755)
T ss_pred             EecCCcccCHHHHHHHHHHHHhhccCCcEEEECCCCCCcchHHHHHHHHHHHhCCcccceEEEecCcchHHHHHHHHHHH
Confidence            34788899999987665544    368899999999999988776666554433322 2566655555444444444443

>TIGR00596 rad1 DNA repair protein (rad1)

Probab=98.66  E-value=1.7e-06  Score=82.58  Aligned_cols=68  Identities=13%  Similarity=0.102  Sum_probs=58.8

Q ss_pred             CCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEEeeCCh
Q 017573          114 GVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMPP  181 (369)
Q Consensus       114 ~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~saT~~~  181 (369)
                      ...|+++||+.+..-+..+.+..+.+..+|+||||++........+.+++..-++..-+.++|+.|..
T Consensus         7 ~ggi~~~T~rIl~~DlL~~ri~~~~itgiiv~~Ahr~~~~~~eaFI~rlyr~~n~~gfIkafSdsP~~   74 (814)
T TIGR00596         7 EGGIFSITSRILVVDLLTGIIPPELITGILVLRADRIIESSQEAFILRLYRQKNKTGFIKAFSDNPEA   74 (814)
T ss_pred             cCCEEEEechhhHhHHhcCCCCHHHccEEEEeecccccccccHHHHHHHHHHhCCCcceEEecCCCcc
Confidence            35799999999999888888999999999999999998776667777777777777889999999974

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

>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function

Probab=98.56  E-value=5.5e-07  Score=79.13  Aligned_cols=108  Identities=14%  Similarity=0.159  Sum_probs=66.8

Q ss_pred             cEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHccC
Q 017573           35 DVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAG  114 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~  114 (369)
                      -++|.|.+|||||++++..+... .....+.++++++++.++...+.+.+.+...                      ...
T Consensus         3 v~~I~G~aGTGKTvla~~l~~~l-~~~~~~~~~~~l~~n~~l~~~l~~~l~~~~~----------------------~~~   59 (352)
T PF09848_consen    3 VILITGGAGTGKTVLALNLAKEL-QNSEEGKKVLYLCGNHPLRNKLREQLAKKYN----------------------PKL   59 (352)
T ss_pred             EEEEEecCCcCHHHHHHHHHHHh-hccccCCceEEEEecchHHHHHHHHHhhhcc----------------------cch
Confidence            47999999999998876555544 2222333899999999999888777765320                      001


Q ss_pred             CcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccC-------cHHHHHHHHhh
Q 017573          115 VHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRG-------FKDQIYDIFQL  165 (369)
Q Consensus       115 ~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~-------~~~~~~~~~~~  165 (369)
                      ....+..+..+.............+++||+||||++....       ....+..+++.
T Consensus        60 ~~~~~~~~~~~i~~~~~~~~~~~~~DviivDEAqrl~~~~~~~~~~~~~~~L~~i~~~  117 (352)
T PF09848_consen   60 KKSDFRKPTSFINNYSESDKEKNKYDVIIVDEAQRLRTKGDQYNNFSEPNQLDEIIKR  117 (352)
T ss_pred             hhhhhhhhHHHHhhcccccccCCcCCEEEEehhHhhhhccccccccccHHHHHHHHhc
Confidence            1233334444433333222344558999999999997631       23455555555

It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].

>PRK10536 hypothetical protein; Provisional

Probab=98.51  E-value=1.2e-06  Score=71.39  Aligned_cols=143  Identities=18%  Similarity=0.135  Sum_probs=80.5

Q ss_pred             CCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHH-----------HHHHHHH
Q 017573           16 FEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELA-----------QQIEKVM   84 (369)
Q Consensus        16 ~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~-----------~q~~~~~   84 (369)
                      +.-.+..|..++..+.++..+++.||+|+|||+.+...+++.+..+.. .++++.-|..+..           +.+.-++
T Consensus        57 i~p~n~~Q~~~l~al~~~~lV~i~G~aGTGKT~La~a~a~~~l~~~~~-~kIiI~RP~v~~ge~LGfLPG~~~eK~~p~~  135 (262)
T PRK10536         57 ILARNEAQAHYLKAIESKQLIFATGEAGCGKTWISAAKAAEALIHKDV-DRIIVTRPVLQADEDLGFLPGDIAEKFAPYF  135 (262)
T ss_pred             ccCCCHHHHHHHHHHhcCCeEEEECCCCCCHHHHHHHHHHHHHhcCCe-eEEEEeCCCCCchhhhCcCCCCHHHHHHHHH
Confidence            344677899999988888899999999999999988888876644332 2556655554321           1111111


Q ss_pred             HHhccccCcEEEEEECCcchHHHHHHHc-cCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHH
Q 017573           85 RALGDYLGVKVHACVGGTSVREDQRILQ-AGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIF  163 (369)
Q Consensus        85 ~~~~~~~~~~v~~~~~~~~~~~~~~~~~-~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~  163 (369)
                      .-+...+..    +.+.   ......+. ....|-+....    +++-..  +. -++||+||++++.    ...+..++
T Consensus       136 ~pi~D~L~~----~~~~---~~~~~~~~~~~~~Iei~~l~----ymRGrt--l~-~~~vIvDEaqn~~----~~~~k~~l  197 (262)
T PRK10536        136 RPVYDVLVR----RLGA---SFMQYCLRPEIGKVEIAPFA----YMRGRT--FE-NAVVILDEAQNVT----AAQMKMFL  197 (262)
T ss_pred             HHHHHHHHH----HhCh---HHHHHHHHhccCcEEEecHH----HhcCCc--cc-CCEEEEechhcCC----HHHHHHHH
Confidence            111111100    0011   11111111 12234444422    222222  22 2799999999873    46777888


Q ss_pred             hhCCccCcEEEEEee
Q 017573          164 QLLPAKVQVGVFSAT  178 (369)
Q Consensus       164 ~~~~~~~~~i~~saT  178 (369)
                      ..++.+.++++ ++-
T Consensus       198 tR~g~~sk~v~-~GD  211 (262)
T PRK10536        198 TRLGENVTVIV-NGD  211 (262)
T ss_pred             hhcCCCCEEEE-eCC
Confidence            88888887665 444

>KOG1132 consensus Helicase of the DEAD superfamily [Replication, recombination and repair]

Probab=98.50  E-value=6.4e-07  Score=83.15  Aligned_cols=103  Identities=17%  Similarity=0.192  Sum_probs=65.2

Q ss_pred             CCeEEEeCCHhhHHHHHHHHhhC-------CCeeEEecCCCCHHHHHHHHHHHhcC--------CCcEEEEecCCcCCCC
Q 017573          236 TQSVIFVNTRRKVDWLTDKMRSR-------DHTVSATHGDMDQNTRDIIMREFRSG--------SSRVLITTDLLARGID  300 (369)
Q Consensus       236 ~k~lv~~~~~~~~~~~~~~l~~~-------~~~~~~~~~~~~~~~r~~~~~~f~~~--------~~~vli~t~~~~~G~d  300 (369)
                      ...|+|+++....+++....+..       +.+-.++-.. +..+-.+++..|.+.        ..-+.|+-...++|+|
T Consensus       562 ~G~L~FfPSY~vmdk~~tfw~~~~~we~~~~vk~l~vEPr-~k~~f~e~m~~y~~~i~~pes~ga~~~aVcRGKVSEGlD  640 (945)
T KOG1132|consen  562 YGLLIFFPSYPVMDKLITFWQNRGLWERMEKVKKLVVEPR-SKSEFTEVMSRYYNAIADPESSGAVFFAVCRGKVSEGLD  640 (945)
T ss_pred             cceEEeccchHHHHHHHHHHHcchHHHHhhcccCceeccC-CccchHHHHHHHHHHhhCccccceEEEEEecccccCCCC
Confidence            35899999998777775555432       2222233222 455556667777542        1223455568899999


Q ss_pred             CCC--CcEEEEecCCCC--------------------------------------ccchhhhhcccccCCCc-eeEEEEe
Q 017573          301 VQQ--VSLVINYDLPTQ--------------------------------------PENYLHRIGRSGRFGRK-GVAINFV  339 (369)
Q Consensus       301 ~~~--~~~vi~~~~~~~--------------------------------------~~~~~Q~~GR~~R~~~~-~~~~~~~  339 (369)
                      +.+  .+.||..+.|.-                                      ...+.|++||+.|-.++ |.++ ++
T Consensus       641 FsD~~~RaVI~tGlPyP~~~D~~V~lK~~y~D~~~~~~g~~s~~lsg~eWY~~qA~RAvNQAiGRviRHR~D~Gav~-l~  719 (945)
T KOG1132|consen  641 FSDDNGRAVIITGLPYPPVMDPRVKLKKQYLDENSSLKGAKSQLLSGQEWYSQQAYRAVNQAIGRVIRHRNDYGAVI-LC  719 (945)
T ss_pred             ccccCCceeEEecCCCCCCCCHHHHHHHHhhhhhccccccccccccchHHHHhhHHHHHHHHHHHHHhhhcccceee-Ee
Confidence            974  777888887631                                      12358999999998666 5555 54


Q ss_pred             c
Q 017573          340 T  340 (369)
Q Consensus       340 ~  340 (369)
                      +
T Consensus       720 D  720 (945)
T KOG1132|consen  720 D  720 (945)
T ss_pred             e
Confidence            4

>PF13245 AAA_19: Part of AAA domain

Probab=98.48  E-value=6.4e-07  Score=59.02  Aligned_cols=52  Identities=33%  Similarity=0.391  Sum_probs=39.8

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhc-cCCCccEEEEcCCHHHHHHHHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDY-GLVQCQALVLAPTRELAQQIEKVM   84 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~-~~~~~~~liv~P~~~l~~q~~~~~   84 (369)
                      +.-++|.+|+|+|||..++-.+.+.+.. ...+.++++++|++..+.++.+.+
T Consensus        10 ~~~~vv~g~pGtGKT~~~~~~i~~l~~~~~~~~~~vlv~a~t~~aa~~l~~rl   62 (76)
T PF13245_consen   10 SPLFVVQGPPGTGKTTTLAARIAELLAARADPGKRVLVLAPTRAAADELRERL   62 (76)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHHhcCCCCeEEEECCCHHHHHHHHHHH
Confidence            4556679999999998777676666642 112448999999999999888877

>KOG1803 consensus DNA helicase [Replication, recombination and repair]

Probab=98.45  E-value=6e-07  Score=80.08  Aligned_cols=66  Identities=23%  Similarity=0.209  Sum_probs=55.9

Q ss_pred             CCCcHhhhhhhhccccC-CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHH
Q 017573           17 EKPSAIQQRGIVPFCKG-LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMR   85 (369)
Q Consensus        17 ~~~~~~Q~~~~~~~~~~-~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~   85 (369)
                      ..+.+-|++|+...... .-.+++||+|+|||.+....+...+.++.   ++|+..|+..-+.+..+.+.
T Consensus       184 ~~ln~SQk~Av~~~~~~k~l~~I~GPPGTGKT~TlvEiI~qlvk~~k---~VLVcaPSn~AVdNiverl~  250 (649)
T KOG1803|consen  184 KNLNSSQKAAVSFAINNKDLLIIHGPPGTGKTRTLVEIISQLVKQKK---RVLVCAPSNVAVDNIVERLT  250 (649)
T ss_pred             ccccHHHHHHHHHHhccCCceEeeCCCCCCceeeHHHHHHHHHHcCC---eEEEEcCchHHHHHHHHHhc
Confidence            46888899999888877 45799999999999998888887777765   89999999998888888643

>TIGR00376 DNA helicase, putative

Probab=98.43  E-value=2.3e-06  Score=80.48  Aligned_cols=67  Identities=22%  Similarity=0.224  Sum_probs=55.7

Q ss_pred             CCCcHhhhhhhhccccC-CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHH
Q 017573           17 EKPSAIQQRGIVPFCKG-LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRA   86 (369)
Q Consensus        17 ~~~~~~Q~~~~~~~~~~-~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~   86 (369)
                      ..+.+.|.+++..+... ...+|+||+|+|||.++...+.+.+..+.   ++++++|+..-+.++.+.+.+
T Consensus       156 ~~ln~~Q~~Av~~~l~~~~~~lI~GpPGTGKT~t~~~ii~~~~~~g~---~VLv~a~sn~Avd~l~e~l~~  223 (637)
T TIGR00376       156 PNLNESQKEAVSFALSSKDLFLIHGPPGTGKTRTLVELIRQLVKRGL---RVLVTAPSNIAVDNLLERLAL  223 (637)
T ss_pred             CCCCHHHHHHHHHHhcCCCeEEEEcCCCCCHHHHHHHHHHHHHHcCC---CEEEEcCcHHHHHHHHHHHHh
Confidence            46799999999998876 67899999999999887666665555444   899999999988888888876

The gene product may represent a DNA helicase. Eukaryotic members of this family have been characterized as binding certain single-stranded G-rich DNA sequences (GGGGT and GGGCT). A number of related proteins are characterized as helicases.

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=98.41  E-value=3.1e-06  Score=80.94  Aligned_cols=126  Identities=20%  Similarity=0.179  Sum_probs=78.9

Q ss_pred             CCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEE
Q 017573           17 EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVH   96 (369)
Q Consensus        17 ~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~   96 (369)
                      ..+++-|++|+..+..++-+++.+++|+|||.++ ..++..+........+++++||-.-+..+.+..       +... 
T Consensus       322 ~~l~~~Q~~Ai~~~~~~~~~iitGgpGTGKTt~l-~~i~~~~~~~~~~~~v~l~ApTg~AA~~L~e~~-------g~~a-  392 (720)
T TIGR01448       322 KGLSEEQKQALDTAIQHKVVILTGGPGTGKTTIT-RAIIELAEELGGLLPVGLAAPTGRAAKRLGEVT-------GLTA-  392 (720)
T ss_pred             CCCCHHHHHHHHHHHhCCeEEEECCCCCCHHHHH-HHHHHHHHHcCCCceEEEEeCchHHHHHHHHhc-------CCcc-
Confidence            5899999999999998899999999999999764 444444443321136888899976665433321       1111 


Q ss_pred             EEECCcchHHHHHHHccCCcEEEeccHHHHHHHHc-----CCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCccCc
Q 017573           97 ACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRR-----QSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQ  171 (369)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~-----~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~  171 (369)
                                             .|.++++.....     ........+++|+||++++..    ..+..+++.++...+
T Consensus       393 -----------------------~Tih~lL~~~~~~~~~~~~~~~~~~~llIvDEaSMvd~----~~~~~Ll~~~~~~~r  445 (720)
T TIGR01448       393 -----------------------STIHRLLGYGPDTFRHNHLEDPIDCDLLIVDESSMMDT----WLALSLLAALPDHAR  445 (720)
T ss_pred             -----------------------ccHHHHhhccCCccchhhhhccccCCEEEEeccccCCH----HHHHHHHHhCCCCCE
Confidence                                   111111110000     000112368999999998743    345666677787888


Q ss_pred             EEEEEee
Q 017573          172 VGVFSAT  178 (369)
Q Consensus       172 ~i~~saT  178 (369)
                      ++++.-+
T Consensus       446 lilvGD~  452 (720)
T TIGR01448       446 LLLVGDT  452 (720)
T ss_pred             EEEECcc
Confidence            8876555

This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=98.38  E-value=2.6e-06  Score=79.32  Aligned_cols=142  Identities=17%  Similarity=0.177  Sum_probs=86.8

Q ss_pred             CcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhcc-CCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEE
Q 017573           19 PSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYG-LVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHA   97 (369)
Q Consensus        19 ~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~-~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~   97 (369)
                      ..++|+.|+.....++-++|.+++|+|||.+....+....... ....++.+++||..-+..+.+.+.......+..   
T Consensus       153 ~~d~Qk~Av~~a~~~~~~vItGgpGTGKTt~v~~ll~~l~~~~~~~~~~i~l~APTgkAA~rL~e~~~~~~~~~~~~---  229 (615)
T PRK10875        153 EVDWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQLADGERCRIRLAAPTGKAAARLTESLGKALRQLPLT---  229 (615)
T ss_pred             CCHHHHHHHHHHhcCCeEEEEeCCCCCHHHHHHHHHHHHHHhcCCCCcEEEEECCcHHHHHHHHHHHHhhhhccccc---
Confidence            3589999999999999999999999999977533332222211 122368889999888887777665533222110   


Q ss_pred             EECCcchHHHHHHHccCCcEEEeccHHHHHHHH------cCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCccCc
Q 017573           98 CVGGTSVREDQRILQAGVHVVVGTPGRVFDMLR------RQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQ  171 (369)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~------~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~  171 (369)
                             +....    ....-..|.++|+....      ....+.-.++++|+||+-++.    ...+..+++.+++..+
T Consensus       230 -------~~~~~----~~~~~a~TiHrlLg~~~~~~~~~~~~~~~l~~dvlIvDEaSMvd----~~lm~~ll~al~~~~r  294 (615)
T PRK10875        230 -------DEQKK----RIPEEASTLHRLLGAQPGSQRLRYHAGNPLHLDVLVVDEASMVD----LPMMARLIDALPPHAR  294 (615)
T ss_pred             -------hhhhh----cCCCchHHHHHHhCcCCCccchhhccccCCCCCeEEEChHhccc----HHHHHHHHHhcccCCE
Confidence                   00000    00112234444432211      111122336899999999763    4566677888888888


Q ss_pred             EEEEEee
Q 017573          172 VGVFSAT  178 (369)
Q Consensus       172 ~i~~saT  178 (369)
                      +|++.-.
T Consensus       295 lIlvGD~  301 (615)
T PRK10875        295 VIFLGDR  301 (615)
T ss_pred             EEEecch
Confidence            8887655

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit

Probab=98.38  E-value=5e-06  Score=77.24  Aligned_cols=141  Identities=18%  Similarity=0.177  Sum_probs=85.1

Q ss_pred             cHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccC--CCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEE
Q 017573           20 SAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGL--VQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHA   97 (369)
Q Consensus        20 ~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~--~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~   97 (369)
                      .+.|+.++.....++-++|.|++|+|||.+....+........  ...++++.+||-.-+..+.+........++..   
T Consensus       147 ~~~Qk~A~~~al~~~~~vitGgpGTGKTt~v~~ll~~l~~~~~~~~~~~I~l~APTGkAA~rL~e~~~~~~~~l~~~---  223 (586)
T TIGR01447       147 QNWQKVAVALALKSNFSLITGGPGTGKTTTVARLLLALVKQSPKQGKLRIALAAPTGKAAARLAESLRKAVKNLAAA---  223 (586)
T ss_pred             cHHHHHHHHHHhhCCeEEEEcCCCCCHHHHHHHHHHHHHHhccccCCCcEEEECCcHHHHHHHHHHHHhhhcccccc---
Confidence            3799999999999999999999999999775332222211111  12379999999877777666665532221110   


Q ss_pred             EECCcchHHHHHHHccCCcEEEeccHHHHHHHH------cCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCccCc
Q 017573           98 CVGGTSVREDQRILQAGVHVVVGTPGRVFDMLR------RQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQ  171 (369)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~------~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~  171 (369)
                             ...    .....+-..|.++|+....      ....+...++++|+||+-++.    ...+..+++.+++..+
T Consensus       224 -------~~~----~~~~~~~a~TiHrlLg~~~~~~~~~~~~~~~l~~dvlIiDEaSMvd----~~l~~~ll~al~~~~r  288 (586)
T TIGR01447       224 -------EAL----IAALPSEAVTIHRLLGIKPDTKRFRHHERNPLPLDVLVVDEASMVD----LPLMAKLLKALPPNTK  288 (586)
T ss_pred             -------hhh----hhccccccchhhhhhcccCCcchhhhcccCCCcccEEEEcccccCC----HHHHHHHHHhcCCCCE
Confidence                   000    0011122344444433211      111122347999999999763    3456677788888888


Q ss_pred             EEEEEee
Q 017573          172 VGVFSAT  178 (369)
Q Consensus       172 ~i~~saT  178 (369)
                      +|++.-.
T Consensus       289 lIlvGD~  295 (586)
T TIGR01447       289 LILLGDK  295 (586)
T ss_pred             EEEECCh
Confidence            8875544

This family describes the exodeoxyribonuclease V alpha subunit, RecD. RecD is part of a RecBCD complex. A related family in the Gram-positive bacteria separates in a phylogenetic tree, has an additional N-terminal extension of about 200 residues, and is not supported as a member of a RecBCD complex by neighboring genes. The related family is consequently described by a different model.

>PF00580 UvrD-helicase: UvrD/REP helicase N-terminal domain; InterPro: IPR000212 Members of this family are helicases that catalyse ATP dependent unwinding of double stranded DNA to single stranded DNA

Probab=98.30  E-value=4.2e-06  Score=72.73  Aligned_cols=122  Identities=23%  Similarity=0.143  Sum_probs=79.3

Q ss_pred             CcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhcc-CCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEE
Q 017573           19 PSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYG-LVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHA   97 (369)
Q Consensus        19 ~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~-~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~   97 (369)
                      +++-|.+++..  ..+.++|.|+.|||||.+++.-+...+..+ ....+++++++|+..+.++.+.+...........  
T Consensus         1 l~~eQ~~~i~~--~~~~~lV~a~AGSGKT~~l~~ri~~ll~~~~~~~~~Il~lTft~~aa~e~~~ri~~~l~~~~~~~--   76 (315)
T PF00580_consen    1 LTDEQRRIIRS--TEGPLLVNAGAGSGKTTTLLERIAYLLYEGGVPPERILVLTFTNAAAQEMRERIRELLEEEQQES--   76 (315)
T ss_dssp             S-HHHHHHHHS---SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHHHHHHCCHCC--
T ss_pred             CCHHHHHHHhC--CCCCEEEEeCCCCCchHHHHHHHHHhhccccCChHHheecccCHHHHHHHHHHHHHhcCcccccc--
Confidence            57889999988  889999999999999999887777777655 3444899999999999999998887543321100  


Q ss_pred             EECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCC--CccEEEEechh
Q 017573           98 CVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPD--YIKMFVLDEAD  148 (369)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~--~~~~viiDE~H  148 (369)
                          ...............+.|+|.+.|...+.+......  .-+.-++|+..
T Consensus        77 ----~~~~~~~~~~~~~~~~~i~T~hsf~~~ll~~~~~~~~~~~~~~i~~~~~  125 (315)
T PF00580_consen   77 ----SDNERLRRQLSNIDRIYISTFHSFCYRLLREYGYEIGIDPNFEILDEEE  125 (315)
T ss_dssp             ----TT-HHHHHHHHHCTTSEEEEHHHHHHHHHHHHHGGTTSHTTTEEECHHH
T ss_pred             ----cccccccccccccchheeehhhhhhhhhhhhhhhhhhccccceeecchh
Confidence                000011222223457899999988654433221111  12567777776

THe family includes both Rep and UvrD helcases. The Rep family helicases are composed of four structural domains []. The Rep proteins function as dimers.; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding; PDB: 1UAA_B 1W36_B 3K70_B 2IS6_B 3LFU_A 2IS2_B 2IS1_B 2IS4_A 1QHG_A 1PJR_A ....

>smart00492 HELICc3 helicase superfamily c-terminal domain

Probab=98.24  E-value=1.4e-05  Score=59.81  Aligned_cols=73  Identities=16%  Similarity=0.243  Sum_probs=53.5

Q ss_pred             CCHHHHHHHHHHHhcCC-CcEEEEecCCcCCCCCCC--CcEEEEecCCCC------------------------------
Q 017573          269 MDQNTRDIIMREFRSGS-SRVLITTDLLARGIDVQQ--VSLVINYDLPTQ------------------------------  315 (369)
Q Consensus       269 ~~~~~r~~~~~~f~~~~-~~vli~t~~~~~G~d~~~--~~~vi~~~~~~~------------------------------  315 (369)
                      .+..+...+++.|.... ..||+++..+.+|+|+|+  ++.||+.+.|..                              
T Consensus        31 ~~~~~~~~~l~~f~~~~~~~iL~~~~~~~EGiD~~g~~~r~vii~glPfp~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~  110 (141)
T smart00492       31 EDGKETGKLLEKYVEACENAILLATARFSEGVDFPGDYLRAVIIDGLPFPYPDSPILKARLELLRDKGQIRPFDFVSLPD  110 (141)
T ss_pred             CChhHHHHHHHHHHHcCCCEEEEEccceecceecCCCCeeEEEEEecCCCCCCCHHHHHHHHHHHHhCCCCchhHHHHHH
Confidence            44556788999998654 379999988999999996  678888886631                              


Q ss_pred             -ccchhhhhcccccCCCceeEEEEecc
Q 017573          316 -PENYLHRIGRSGRFGRKGVAINFVTR  341 (369)
Q Consensus       316 -~~~~~Q~~GR~~R~~~~~~~~~~~~~  341 (369)
                       ...+.|.+||+.|..++--++++.++
T Consensus       111 a~~~l~Qa~GR~iR~~~D~g~i~l~D~  137 (141)
T smart00492      111 AMRTLAQCVGRLIRGANDYGVVVIADK  137 (141)
T ss_pred             HHHHHHHHhCccccCcCceEEEEEEec
Confidence             12348999999998766445555554

>PF12340 DUF3638: Protein of unknown function (DUF3638); InterPro: IPR022099 This domain family is found in eukaryotes, and is approximately 230 amino acids in length

Probab=98.20  E-value=1.7e-05  Score=63.41  Aligned_cols=120  Identities=18%  Similarity=0.191  Sum_probs=74.7

Q ss_pred             CHHHHHHHHhCCCCCCcHhhhhhhhcccc---CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHH
Q 017573            4 QENLLRGIYAYGFEKPSAIQQRGIVPFCK---GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQI   80 (369)
Q Consensus         4 ~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~---~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~   80 (369)
                      |+++.=.++  +-..+|+.|.+....+.+   +++.+.+.-+|.|||.+.+..+...+..+..  -+.+++|. +|.+|.
T Consensus        11 P~wLl~E~e--~~iliR~~Q~~ia~~mi~~~~~~n~v~QlnMGeGKTsVI~Pmla~~LAdg~~--LvrviVpk-~Ll~q~   85 (229)
T PF12340_consen   11 PDWLLFEIE--SNILIRPVQVEIAREMISPPSGKNSVMQLNMGEGKTSVIVPMLALALADGSR--LVRVIVPK-ALLEQM   85 (229)
T ss_pred             hHHHHHHHH--cCceeeHHHHHHHHHHhCCCCCCCeEeeecccCCccchHHHHHHHHHcCCCc--EEEEEcCH-HHHHHH
Confidence            444444443  335899999999999886   4789999999999998865444444444431  45666664 799999


Q ss_pred             HHHHHHhcccc-CcEEEEE--ECCcchHH-----HHHH---HccCCcEEEeccHHHHHH
Q 017573           81 EKVMRALGDYL-GVKVHAC--VGGTSVRE-----DQRI---LQAGVHVVVGTPGRVFDM  128 (369)
Q Consensus        81 ~~~~~~~~~~~-~~~v~~~--~~~~~~~~-----~~~~---~~~~~~iiv~t~~~l~~~  128 (369)
                      ...+....... +-.+..+  ..+.....     ....   ....-.|+++||+.+.+.
T Consensus        86 ~~~L~~~lg~l~~r~i~~lpFsR~~~~~~~~~~~~~~l~~~~~~~~gill~~PEhilSf  144 (229)
T PF12340_consen   86 RQMLRSRLGGLLNRRIYHLPFSRSTPLTPETLEKIRQLLEECMRSGGILLATPEHILSF  144 (229)
T ss_pred             HHHHHHHHHHHhCCeeEEecccCCCCCCHHHHHHHHHHHHHHHHcCCEEEeChHHHHHH
Confidence            88887644322 3333222  22222111     1111   123457999999998554

There are two conserved sequence motifs: LLE and NMG.

>smart00491 HELICc2 helicase superfamily c-terminal domain

Probab=98.19  E-value=1.5e-05  Score=59.75  Aligned_cols=70  Identities=16%  Similarity=0.287  Sum_probs=51.4

Q ss_pred             HHHHHHHHHHhcCCC---cEEEEecC--CcCCCCCCC--CcEEEEecCCCC-----------------------------
Q 017573          272 NTRDIIMREFRSGSS---RVLITTDL--LARGIDVQQ--VSLVINYDLPTQ-----------------------------  315 (369)
Q Consensus       272 ~~r~~~~~~f~~~~~---~vli~t~~--~~~G~d~~~--~~~vi~~~~~~~-----------------------------  315 (369)
                      .+..++++.|.+...   .||+++..  +.+|+|+|+  ++.||+.+.|..                             
T Consensus        31 ~~~~~~l~~f~~~~~~~g~iL~~v~~G~~~EGiD~~g~~~r~vii~glPfp~~~d~~~~~~~~~~~~~~~~~~~~~~~~~  110 (142)
T smart00491       31 GETEELLEKYSAACEARGALLLAVARGKVSEGIDFPDDLGRAVIIVGIPFPNPDSPILRARLEYLDEKGGIRPFDEVYLF  110 (142)
T ss_pred             chHHHHHHHHHHhcCCCCEEEEEEeCCeeecceecCCCccEEEEEEecCCCCCCCHHHHHHHHHHHHhcCCCcHHHHHHH
Confidence            344678888876443   58998886  999999996  678988887631                             


Q ss_pred             --ccchhhhhcccccCCCceeEEEEecc
Q 017573          316 --PENYLHRIGRSGRFGRKGVAINFVTR  341 (369)
Q Consensus       316 --~~~~~Q~~GR~~R~~~~~~~~~~~~~  341 (369)
                        ...+.|.+||+.|..++--++++.++
T Consensus       111 ~a~~~~~Qa~GR~iR~~~D~g~i~l~D~  138 (142)
T smart00491      111 DAMRALAQAIGRAIRHKNDYGVVVLLDK  138 (142)
T ss_pred             HHHHHHHHHhCccccCccceEEEEEEec
Confidence              02348999999999776556666554

>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]

Probab=98.19  E-value=7.3e-06  Score=79.18  Aligned_cols=148  Identities=17%  Similarity=0.003  Sum_probs=94.9

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhcc---------------CCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEE
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDYG---------------LVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHA   97 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~~---------------~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~   97 (369)
                      |+.+++...+|.|||...+...+....+.               ...+.+|||||. ++..||.+++.+..... +.+..
T Consensus       374 g~~~~~ade~~~qk~~~~l~~~l~~~~k~~~~~cS~~~~e~~n~~~tgaTLII~P~-aIl~QW~~EI~kH~~~~-lKv~~  451 (1394)
T KOG0298|consen  374 GKRVQCADEMGWQKTSEKLILELSDLPKLCPSCCSELVKEGENLVETGATLIICPN-AILMQWFEEIHKHISSL-LKVLL  451 (1394)
T ss_pred             CcceeehhhhhccchHHHHHHHHhcccccchhhhhHHHhcccceeecCceEEECcH-HHHHHHHHHHHHhcccc-ceEEE
Confidence            57789999999999988766555443111               011258999997 88899999999887664 55555


Q ss_pred             EECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCC--------------------ccEEEEechhHhhccCcHH
Q 017573           98 CVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDY--------------------IKMFVLDEADEMLSRGFKD  157 (369)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~--------------------~~~viiDE~H~~~~~~~~~  157 (369)
                      ..|=.+.........-++||++|||+.+...+.....+.+.                    |=-|++||++++..  ...
T Consensus       452 Y~Girk~~~~~~~el~~yDIVlTtYdiLr~El~hte~~~~~R~lR~qsr~~~~~SPL~~v~wWRIclDEaQMves--ssS  529 (1394)
T KOG0298|consen  452 YFGIRKTFWLSPFELLQYDIVLTTYDILRNELYHTEDFGSDRQLRHQSRYMRPNSPLLMVNWWRICLDEAQMVES--SSS  529 (1394)
T ss_pred             EechhhhcccCchhhhccCEEEeehHHHHhHhhcccccCChhhhhcccCCCCCCCchHHHHHHHHhhhHHHhhcc--hHH
Confidence            44422211111122246999999999997655443211110                    22689999998754  355


Q ss_pred             HHHHHHhhCCccCcEEEEEeeCChhHHH
Q 017573          158 QIYDIFQLLPAKVQVGVFSATMPPEALE  185 (369)
Q Consensus       158 ~~~~~~~~~~~~~~~i~~saT~~~~~~~  185 (369)
                      ...++...++.. ..-++|+||-..+.+
T Consensus       530 ~~a~M~~rL~~i-n~W~VTGTPiq~Idd  556 (1394)
T KOG0298|consen  530 AAAEMVRRLHAI-NRWCVTGTPIQKIDD  556 (1394)
T ss_pred             HHHHHHHHhhhh-ceeeecCCchhhhhh
Confidence            666666676643 356789998766444

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=98.16  E-value=9.5e-06  Score=60.48  Aligned_cols=116  Identities=16%  Similarity=0.119  Sum_probs=55.8

Q ss_pred             cCCcEEEEcCCCChhhHHHHHHHHHhhhcc--CCCccEEE-EcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHH
Q 017573           32 KGLDVIQQAQSGTGKTATFCSGILQQLDYG--LVQCQALV-LAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQ  108 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~~~~~~~~~~~--~~~~~~li-v~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~  108 (369)
                      +++.++|.||+|+|||..+-..+.......  .....+++ -+|...-...+...+..........              
T Consensus         3 ~~~~~~i~G~~G~GKT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~--------------   68 (131)
T PF13401_consen    3 SQRILVISGPPGSGKTTLIKRLARQLNAEAEIKNHPDVIYVNCPSSRTPRDFAQEILEALGLPLKS--------------   68 (131)
T ss_dssp             ----EEEEE-TTSSHHHHHHHHHHHHHHHHHHCCCEEEEEEEHHHHSSHHHHHHHHHHHHT-SSSS--------------
T ss_pred             CCcccEEEcCCCCCHHHHHHHHHHHhHHhhhccCCCcEEEEEeCCCCCHHHHHHHHHHHhCccccc--------------
Confidence            356789999999999987644444332210  00113444 3443332344444443322111100              


Q ss_pred             HHHccCCcEEEecc----HHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEEeeC
Q 017573          109 RILQAGVHVVVGTP----GRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATM  179 (369)
Q Consensus       109 ~~~~~~~~iiv~t~----~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~saT~  179 (369)
                                -.+.    +.+...+.+...     .++|+||+|++.  . ...+..+........-.+.+++++
T Consensus        69 ----------~~~~~~l~~~~~~~l~~~~~-----~~lviDe~~~l~--~-~~~l~~l~~l~~~~~~~vvl~G~~  125 (131)
T PF13401_consen   69 ----------RQTSDELRSLLIDALDRRRV-----VLLVIDEADHLF--S-DEFLEFLRSLLNESNIKVVLVGTP  125 (131)
T ss_dssp             ----------TS-HHHHHHHHHHHHHHCTE-----EEEEEETTHHHH--T-HHHHHHHHHHTCSCBEEEEEEESS
T ss_pred             ----------cCCHHHHHHHHHHHHHhcCC-----eEEEEeChHhcC--C-HHHHHHHHHHHhCCCCeEEEEECh
Confidence                      1112    233344444332     689999999974  1 445555555555544456678876

>PRK06526 transposase; Provisional

Probab=98.12  E-value=2.9e-05  Score=64.44  Aligned_cols=40  Identities=20%  Similarity=0.094  Sum_probs=27.6

Q ss_pred             hccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEE
Q 017573           28 VPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVL   70 (369)
Q Consensus        28 ~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv   70 (369)
                      +.+..++++++.||+|+|||..+..........+.   +++++
T Consensus        93 ~fi~~~~nlll~Gp~GtGKThLa~al~~~a~~~g~---~v~f~  132 (254)
T PRK06526         93 DFVTGKENVVFLGPPGTGKTHLAIGLGIRACQAGH---RVLFA  132 (254)
T ss_pred             chhhcCceEEEEeCCCCchHHHHHHHHHHHHHCCC---chhhh
Confidence            33445689999999999999877655555544433   55553

>PRK04296 thymidine kinase; Provisional

Probab=98.09  E-value=1.8e-05  Score=62.99  Aligned_cols=112  Identities=13%  Similarity=0.177  Sum_probs=57.7

Q ss_pred             cEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHccC
Q 017573           35 DVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAG  114 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~  114 (369)
                      -.++.+|+|+|||..++..+......+.   +++++-|...-.    ..........++.+.                  
T Consensus         4 i~litG~~GsGKTT~~l~~~~~~~~~g~---~v~i~k~~~d~~----~~~~~i~~~lg~~~~------------------   58 (190)
T PRK04296          4 LEFIYGAMNSGKSTELLQRAYNYEERGM---KVLVFKPAIDDR----YGEGKVVSRIGLSRE------------------   58 (190)
T ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHcCC---eEEEEecccccc----ccCCcEecCCCCccc------------------
Confidence            4688999999999877666555544433   788876631100    000011111111110                  


Q ss_pred             CcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEEeeC
Q 017573          115 VHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATM  179 (369)
Q Consensus       115 ~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~saT~  179 (369)
                       .+.+...+.+...+..   ....+++||+||+|.+..    +.+..+.+.+.+....+.+|+-.
T Consensus        59 -~~~~~~~~~~~~~~~~---~~~~~dvviIDEaq~l~~----~~v~~l~~~l~~~g~~vi~tgl~  115 (190)
T PRK04296         59 -AIPVSSDTDIFELIEE---EGEKIDCVLIDEAQFLDK----EQVVQLAEVLDDLGIPVICYGLD  115 (190)
T ss_pred             -ceEeCChHHHHHHHHh---hCCCCCEEEEEccccCCH----HHHHHHHHHHHHcCCeEEEEecC
Confidence             1223444555555444   234579999999986522    33444555533333344455543

>PRK08181 transposase; Validated

Probab=98.08  E-value=6.2e-05  Score=62.89  Aligned_cols=131  Identities=16%  Similarity=0.198  Sum_probs=71.0

Q ss_pred             HHHHhCCCCC---CcHhhhhhhh----ccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHH
Q 017573            9 RGIYAYGFEK---PSAIQQRGIV----PFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIE   81 (369)
Q Consensus         9 ~~l~~~~~~~---~~~~Q~~~~~----~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~   81 (369)
                      +.++.|.+..   +...|..++.    .+.+++++++.||+|+|||..+.....+....+.   +++++. ...|..+..
T Consensus        75 ~tle~fd~~~~~~~~~~~~~~L~~~~~~~~~~~nlll~Gp~GtGKTHLa~Aia~~a~~~g~---~v~f~~-~~~L~~~l~  150 (269)
T PRK08181         75 KTLDSFDFEAVPMVSKAQVMAIAAGDSWLAKGANLLLFGPPGGGKSHLAAAIGLALIENGW---RVLFTR-TTDLVQKLQ  150 (269)
T ss_pred             CCHhhCCccCCCCCCHHHHHHHHHHHHHHhcCceEEEEecCCCcHHHHHHHHHHHHHHcCC---ceeeee-HHHHHHHHH
Confidence            4455555433   3456666663    3346789999999999999776555544444432   565543 334444332


Q ss_pred             HHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccC-cHHHHH
Q 017573           82 KVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRG-FKDQIY  160 (369)
Q Consensus        82 ~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~-~~~~~~  160 (369)
                      ....                              +   .+.+.+...+.       ..+++|+||.+...... ....+.
T Consensus       151 ~a~~------------------------------~---~~~~~~l~~l~-------~~dLLIIDDlg~~~~~~~~~~~Lf  190 (269)
T PRK08181        151 VARR------------------------------E---LQLESAIAKLD-------KFDLLILDDLAYVTKDQAETSVLF  190 (269)
T ss_pred             HHHh------------------------------C---CcHHHHHHHHh-------cCCEEEEeccccccCCHHHHHHHH
Confidence            1100                              0   12222223222       26899999999764322 234556


Q ss_pred             HHHhhCCccCcEEEEEeeCChhH
Q 017573          161 DIFQLLPAKVQVGVFSATMPPEA  183 (369)
Q Consensus       161 ~~~~~~~~~~~~i~~saT~~~~~  183 (369)
                      .+++.......+++.|-.++..+
T Consensus       191 ~lin~R~~~~s~IiTSN~~~~~w  213 (269)
T PRK08181        191 ELISARYERRSILITANQPFGEW  213 (269)
T ss_pred             HHHHHHHhCCCEEEEcCCCHHHH
Confidence            66655433445665555444333

>KOG0383 consensus Predicted helicase [General function prediction only]

Probab=98.06  E-value=4.4e-07  Score=83.75  Aligned_cols=63  Identities=17%  Similarity=0.220  Sum_probs=52.1

Q ss_pred             CCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcC---CCcEEEEecCCcCC
Q 017573          235 ITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSG---SSRVLITTDLLARG  298 (369)
Q Consensus       235 ~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~---~~~vli~t~~~~~G  298 (369)
                      +.++++|..-.+..+-+...+.-.+ ....+.|......|...++.|+..   ...+|++|.+.+.|
T Consensus       631 ghrvl~~~q~~~~ldlled~~~~~~-~~~r~dG~~~~~~rq~ai~~~n~~~~~~~cfllstra~g~g  696 (696)
T KOG0383|consen  631 GHRVLIFSQMIHMLDLLEDYLTYEG-KYERIDGPITGPERQAAIDRFNAPGSNQFCFLLSTRAGGLG  696 (696)
T ss_pred             chhhHHHHHHHHHHHHhHHHHhccC-cceeccCCccchhhhhhccccCCCCccceEEEeecccccCC
Confidence            3488888888888888888887777 888999999999999999999842   45688899887655

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=98.01  E-value=0.00011  Score=70.68  Aligned_cols=61  Identities=13%  Similarity=0.113  Sum_probs=45.3

Q ss_pred             CCCcHhhhhhhhccccC-CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHH
Q 017573           17 EKPSAIQQRGIVPFCKG-LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQI   80 (369)
Q Consensus        17 ~~~~~~Q~~~~~~~~~~-~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~   80 (369)
                      ..+++-|++++..+..+ +-+++.+++|+|||.++ -.+...+...  +.+++.++|+..-+..+
T Consensus       351 ~~Ls~~Q~~Av~~i~~s~~~~il~G~aGTGKTtll-~~i~~~~~~~--g~~V~~~ApTg~Aa~~L  412 (744)
T TIGR02768       351 YRLSEEQYEAVRHVTGSGDIAVVVGRAGTGKSTML-KAAREAWEAA--GYRVIGAALSGKAAEGL  412 (744)
T ss_pred             CCCCHHHHHHHHHHhcCCCEEEEEecCCCCHHHHH-HHHHHHHHhC--CCeEEEEeCcHHHHHHH
Confidence            47899999999998874 66899999999999764 3444444432  23789999986655444

This protein contains domains distinctive of a single strand exonuclease (N-terminus, MobA/MobL, pfam03389) as well as a helicase domain (central region, homologous to the corresponding region of the F-type relaxase TraI, TIGR02760). This protein likely fills the same role as TraI(F), nicking (at the oriT site) and unwinding the coiled plasmid prior to conjugative transfer.

>COG1875 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]

Probab=97.98  E-value=4.8e-05  Score=64.33  Aligned_cols=141  Identities=16%  Similarity=0.146  Sum_probs=85.4

Q ss_pred             hCCCCCCcHhhhhhhhccccC--CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccc
Q 017573           13 AYGFEKPSAIQQRGIVPFCKG--LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDY   90 (369)
Q Consensus        13 ~~~~~~~~~~Q~~~~~~~~~~--~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~   90 (369)
                      .+|+..-...|.-|++.++..  +-+.+.++.|||||+.++.+.+++....+.-.++++-=|+..+.+            
T Consensus       223 vwGi~prn~eQ~~ALdlLld~dI~lV~L~G~AGtGKTlLALaAgleqv~e~~~y~KiiVtRp~vpvG~------------  290 (436)
T COG1875         223 VWGIRPRNAEQRVALDLLLDDDIDLVSLGGKAGTGKTLLALAAGLEQVLERKRYRKIIVTRPTVPVGE------------  290 (436)
T ss_pred             hhccCcccHHHHHHHHHhcCCCCCeEEeeccCCccHhHHHHHHHHHHHHHHhhhceEEEecCCcCccc------------
Confidence            467777778899999998876  568899999999999999988888765554447777667654432            


Q ss_pred             cCcEEEEEECCcchHHH--H-------HHHccCCcEEEeccHHHHHHHHcCCCCCCC----------ccEEEEechhHhh
Q 017573           91 LGVKVHACVGGTSVRED--Q-------RILQAGVHVVVGTPGRVFDMLRRQSLRPDY----------IKMFVLDEADEML  151 (369)
Q Consensus        91 ~~~~v~~~~~~~~~~~~--~-------~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~----------~~~viiDE~H~~~  151 (369)
                         .+..+-|....+..  -       ..+....+   ++.+.+...+.+..+....          =.++|+|||+++.
T Consensus       291 ---dIGfLPG~eEeKm~PWmq~i~DnLE~L~~~~~---~~~~~l~~~l~~~~iev~alt~IRGRSl~~~FiIIDEaQNLT  364 (436)
T COG1875         291 ---DIGFLPGTEEEKMGPWMQAIFDNLEVLFSPNE---PGDRALEEILSRGRIEVEALTYIRGRSLPDSFIIIDEAQNLT  364 (436)
T ss_pred             ---ccCcCCCchhhhccchHHHHHhHHHHHhcccc---cchHHHHHHHhccceeeeeeeeecccccccceEEEehhhccC
Confidence               11111111111100  0       00000000   1133344443333322111          1489999999873


Q ss_pred             ccCcHHHHHHHHhhCCccCcEEEE
Q 017573          152 SRGFKDQIYDIFQLLPAKVQVGVF  175 (369)
Q Consensus       152 ~~~~~~~~~~~~~~~~~~~~~i~~  175 (369)
                          ...+..++.+..+..+++++
T Consensus       365 ----pheikTiltR~G~GsKIVl~  384 (436)
T COG1875         365 ----PHELKTILTRAGEGSKIVLT  384 (436)
T ss_pred             ----HHHHHHHHHhccCCCEEEEc
Confidence                56778888899888887763

>KOG0989 consensus Replication factor C, subunit RFC4 [Replication, recombination and repair]

Probab=97.93  E-value=1.8e-05  Score=65.15  Aligned_cols=43  Identities=16%  Similarity=0.233  Sum_probs=30.8

Q ss_pred             CCCccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEEeeC
Q 017573          136 PDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATM  179 (369)
Q Consensus       136 ~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~saT~  179 (369)
                      ...+.++|+||||.+.... ...+.+.+...+...++++++.-+
T Consensus       127 ~~~fKiiIlDEcdsmtsda-q~aLrr~mE~~s~~trFiLIcnyl  169 (346)
T KOG0989|consen  127 CPPFKIIILDECDSMTSDA-QAALRRTMEDFSRTTRFILICNYL  169 (346)
T ss_pred             CCcceEEEEechhhhhHHH-HHHHHHHHhccccceEEEEEcCCh
Confidence            3447999999999987655 455666666666677777766554

>cd00009 AAA The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold

Probab=97.85  E-value=0.00022  Score=54.12  Aligned_cols=38  Identities=24%  Similarity=0.210  Sum_probs=23.6

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCC
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPT   73 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~   73 (369)
                      ++.+++.||+|+|||..+. .+...+..  .+..++++.+.
T Consensus        19 ~~~v~i~G~~G~GKT~l~~-~i~~~~~~--~~~~v~~~~~~   56 (151)
T cd00009          19 PKNLLLYGPPGTGKTTLAR-AIANELFR--PGAPFLYLNAS   56 (151)
T ss_pred             CCeEEEECCCCCCHHHHHH-HHHHHhhc--CCCCeEEEehh
Confidence            5789999999999997643 33333321  12255555443

The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.84  E-value=0.00069  Score=59.70  Aligned_cols=123  Identities=12%  Similarity=0.076  Sum_probs=67.5

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHhhhcc-CCCccEEEEcCCH--HHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHH
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQLDYG-LVQCQALVLAPTR--ELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRI  110 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~~~~~-~~~~~~liv~P~~--~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~  110 (369)
                      +.+++.+|||+|||.++.-.+....... ..+.++.+++-..  .-+..   ++..+....++.+..             
T Consensus       175 ~vi~lvGptGvGKTTT~aKLA~~~~~~~~~~g~~V~lit~Dt~R~aa~e---QL~~~a~~lgvpv~~-------------  238 (388)
T PRK12723        175 RVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIGAKK---QIQTYGDIMGIPVKA-------------  238 (388)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHhhhccCCCeEEEEeccCccHHHHH---HHHHHhhcCCcceEe-------------
Confidence            5689999999999988755444332221 2233566665432  32222   244444444544422             


Q ss_pred             HccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccC-cHHHHHHHHhhCCcc-CcEEEEEeeCChhHH
Q 017573          111 LQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRG-FKDQIYDIFQLLPAK-VQVGVFSATMPPEAL  184 (369)
Q Consensus       111 ~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~-~~~~~~~~~~~~~~~-~~~i~~saT~~~~~~  184 (369)
                              +-+++.+...+..    ..++++|++|++.+..... ....+..++....+. ..++.+|||...+..
T Consensus       239 --------~~~~~~l~~~L~~----~~~~DlVLIDTaGr~~~~~~~l~el~~~l~~~~~~~e~~LVlsat~~~~~~  302 (388)
T PRK12723        239 --------IESFKDLKEEITQ----SKDFDLVLVDTIGKSPKDFMKLAEMKELLNACGRDAEFHLAVSSTTKTSDV  302 (388)
T ss_pred             --------eCcHHHHHHHHHH----hCCCCEEEEcCCCCCccCHHHHHHHHHHHHhcCCCCeEEEEEcCCCCHHHH
Confidence                    1133444443333    1347999999999865221 224455555554433 456779999875433

>PRK13889 conjugal transfer relaxase TraA; Provisional

Probab=97.78  E-value=0.00026  Score=69.45  Aligned_cols=124  Identities=17%  Similarity=0.073  Sum_probs=74.7

Q ss_pred             CCCcHhhhhhhhccccCC-cEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEE
Q 017573           17 EKPSAIQQRGIVPFCKGL-DVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKV   95 (369)
Q Consensus        17 ~~~~~~Q~~~~~~~~~~~-~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v   95 (369)
                      ..+++-|++++..+..++ -+++.++.|+|||++ +..+...+...  +.+++.++|+-.-+..+.+.       .++..
T Consensus       345 ~~Ls~eQr~Av~~il~s~~v~vv~G~AGTGKTT~-l~~~~~~~e~~--G~~V~~~ApTGkAA~~L~e~-------tGi~a  414 (988)
T PRK13889        345 LVLSGEQADALAHVTDGRDLGVVVGYAGTGKSAM-LGVAREAWEAA--GYEVRGAALSGIAAENLEGG-------SGIAS  414 (988)
T ss_pred             CCCCHHHHHHHHHHhcCCCeEEEEeCCCCCHHHH-HHHHHHHHHHc--CCeEEEecCcHHHHHHHhhc-------cCcch
Confidence            479999999999999864 579999999999986 44455444432  33788999986555433221       12111


Q ss_pred             EEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhC-CccCcEEE
Q 017573           96 HACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLL-PAKVQVGV  174 (369)
Q Consensus        96 ~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~-~~~~~~i~  174 (369)
                                              .|..+|..-...........+++|+||+-++...    .+..++... +...++|+
T Consensus       415 ------------------------~TI~sll~~~~~~~~~l~~~~vlIVDEASMv~~~----~m~~LL~~a~~~garvVL  466 (988)
T PRK13889        415 ------------------------RTIASLEHGWGQGRDLLTSRDVLVIDEAGMVGTR----QLERVLSHAADAGAKVVL  466 (988)
T ss_pred             ------------------------hhHHHHHhhhcccccccccCcEEEEECcccCCHH----HHHHHHHhhhhCCCEEEE
Confidence                                    1222222111122222344589999999987544    344455433 44666776


Q ss_pred             EEee
Q 017573          175 FSAT  178 (369)
Q Consensus       175 ~saT  178 (369)
                      +.-+
T Consensus       467 VGD~  470 (988)
T PRK13889        467 VGDP  470 (988)
T ss_pred             ECCH
Confidence            5544

>PF13871 Helicase_C_4: Helicase_C-like

Probab=97.77  E-value=7.4e-05  Score=61.91  Aligned_cols=68  Identities=22%  Similarity=0.357  Sum_probs=55.4

Q ss_pred             HHHHHHHhcCCCcEEEEecCCcCCCCCCC--------CcEEEEecCCCCccchhhhhcccccCCCc-eeEEEEeccc
Q 017573          275 DIIMREFRSGSSRVLITTDLLARGIDVQQ--------VSLVINYDLPTQPENYLHRIGRSGRFGRK-GVAINFVTRD  342 (369)
Q Consensus       275 ~~~~~~f~~~~~~vli~t~~~~~G~d~~~--------~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~-~~~~~~~~~~  342 (369)
                      ....+.|.+|+..|+|.+.+.++|+.+..        -++.|.+.+||+....+|.+||+.|.|+. ...|.+...+
T Consensus        51 ~~e~~~F~~g~k~v~iis~AgstGiSlHAd~~~~nqr~Rv~i~le~pwsad~aiQ~~GR~hRsnQ~~~P~y~~l~t~  127 (278)
T PF13871_consen   51 IAEKQAFMDGEKDVAIISDAGSTGISLHADRRVKNQRRRVHITLELPWSADKAIQQFGRTHRSNQVSAPEYRFLVTD  127 (278)
T ss_pred             HHHHHHHhCCCceEEEEecccccccchhccccCCCCCceEEEEeeCCCCHHHHHHHhccccccccccCCEEEEeecC
Confidence            35677899999999999999999998752        34567899999999999999999999876 4555555543

>KOG1805 consensus DNA replication helicase [Replication, recombination and repair]

Probab=97.76  E-value=0.00012  Score=69.37  Aligned_cols=125  Identities=17%  Similarity=0.161  Sum_probs=77.4

Q ss_pred             CCCCcHhhhhhhhccccC-CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcE
Q 017573           16 FEKPSAIQQRGIVPFCKG-LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVK   94 (369)
Q Consensus        16 ~~~~~~~Q~~~~~~~~~~-~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~   94 (369)
                      ...++.-|++|+..++.. ...+|.|=+|+|||.+....+--.+..++   ++|+.+=|-+-+.+..-.++.+    ++.
T Consensus       667 ~~~LN~dQr~A~~k~L~aedy~LI~GMPGTGKTTtI~~LIkiL~~~gk---kVLLtsyThsAVDNILiKL~~~----~i~  739 (1100)
T KOG1805|consen  667 LLRLNNDQRQALLKALAAEDYALILGMPGTGKTTTISLLIKILVALGK---KVLLTSYTHSAVDNILIKLKGF----GIY  739 (1100)
T ss_pred             HhhcCHHHHHHHHHHHhccchheeecCCCCCchhhHHHHHHHHHHcCC---eEEEEehhhHHHHHHHHHHhcc----Ccc
Confidence            357889999999888766 45799999999999775544443344433   7887777766666666666554    222


Q ss_pred             EEEEECCcchH-----------------HHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhh
Q 017573           95 VHACVGGTSVR-----------------EDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEML  151 (369)
Q Consensus        95 v~~~~~~~~~~-----------------~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~  151 (369)
                      ...+..+...-                 .....+-++..|+.+|--.+.+.+.    ....||+.|+|||-.+.
T Consensus       740 ~lRLG~~~kih~~v~e~~~~~~~s~ks~~~l~~~~~~~~IVa~TClgi~~plf----~~R~FD~cIiDEASQI~  809 (1100)
T KOG1805|consen  740 ILRLGSEEKIHPDVEEFTLTNETSEKSYADLKKFLDQTSIVACTCLGINHPLF----VNRQFDYCIIDEASQIL  809 (1100)
T ss_pred             eeecCCccccchHHHHHhcccccchhhHHHHHHHhCCCcEEEEEccCCCchhh----hccccCEEEEccccccc
Confidence            22222221111                 1112233456788887544443332    23448999999999865

>PRK13826 Dtr system oriT relaxase; Provisional

Probab=97.73  E-value=0.00068  Score=67.11  Aligned_cols=124  Identities=19%  Similarity=0.141  Sum_probs=74.1

Q ss_pred             CCCcHhhhhhhhcccc-CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEE
Q 017573           17 EKPSAIQQRGIVPFCK-GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKV   95 (369)
Q Consensus        17 ~~~~~~Q~~~~~~~~~-~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v   95 (369)
                      ..+++-|.+++..+.. ++-.++.|+.|+|||.+. -.+...+...  +.+++.++|+-.-+..+.+..       |+..
T Consensus       380 ~~Ls~eQ~~Av~~i~~~~r~~~v~G~AGTGKTt~l-~~~~~~~e~~--G~~V~g~ApTgkAA~~L~e~~-------Gi~a  449 (1102)
T PRK13826        380 ARLSDEQKTAIEHVAGPARIAAVVGRAGAGKTTMM-KAAREAWEAA--GYRVVGGALAGKAAEGLEKEA-------GIQS  449 (1102)
T ss_pred             CCCCHHHHHHHHHHhccCCeEEEEeCCCCCHHHHH-HHHHHHHHHc--CCeEEEEcCcHHHHHHHHHhh-------CCCe
Confidence            4799999999998864 456899999999999764 4455444432  237889999866554443211       2222


Q ss_pred             EEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCC-ccCcEEE
Q 017573           96 HACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLP-AKVQVGV  174 (369)
Q Consensus        96 ~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~-~~~~~i~  174 (369)
                      .                        |..+|..........+..-+++|+||+.++..    ..+..++...+ ...++++
T Consensus       450 ~------------------------TIas~ll~~~~~~~~l~~~~vlVIDEAsMv~~----~~m~~Ll~~~~~~garvVL  501 (1102)
T PRK13826        450 R------------------------TLSSWELRWNQGRDQLDNKTVFVLDEAGMVAS----RQMALFVEAVTRAGAKLVL  501 (1102)
T ss_pred             e------------------------eHHHHHhhhccCccCCCCCcEEEEECcccCCH----HHHHHHHHHHHhcCCEEEE
Confidence            1                        11122111111112233347999999998743    34445555554 4566776


Q ss_pred             EEee
Q 017573          175 FSAT  178 (369)
Q Consensus       175 ~saT  178 (369)
                      +.-+
T Consensus       502 VGD~  505 (1102)
T PRK13826        502 VGDP  505 (1102)
T ss_pred             ECCH
Confidence            5544

>PF00448 SRP54: SRP54-type protein, GTPase domain; InterPro: IPR000897 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]

Probab=97.73  E-value=0.00034  Score=55.77  Aligned_cols=133  Identities=17%  Similarity=0.168  Sum_probs=70.3

Q ss_pred             cEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHccC
Q 017573           35 DVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAG  114 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~  114 (369)
                      -+++.||||+|||.++.-.+.....+   +.++.+++.-.--+ --.++++.+....++.+..........         
T Consensus         3 vi~lvGptGvGKTTt~aKLAa~~~~~---~~~v~lis~D~~R~-ga~eQL~~~a~~l~vp~~~~~~~~~~~---------   69 (196)
T PF00448_consen    3 VIALVGPTGVGKTTTIAKLAARLKLK---GKKVALISADTYRI-GAVEQLKTYAEILGVPFYVARTESDPA---------   69 (196)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHHT---T--EEEEEESTSST-HHHHHHHHHHHHHTEEEEESSTTSCHH---------
T ss_pred             EEEEECCCCCchHhHHHHHHHHHhhc---cccceeecCCCCCc-cHHHHHHHHHHHhccccchhhcchhhH---------
Confidence            36899999999998876666555444   22676666432111 123344444444455553322111100         


Q ss_pred             CcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhh-ccCcHHHHHHHHhhCCccCcEEEEEeeCChhHHHHHHHh
Q 017573          115 VHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEML-SRGFKDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKF  190 (369)
Q Consensus       115 ~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~-~~~~~~~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~  190 (369)
                              +.+.+.+..  ...+++++|++|-+.+.. +......+..+.....+....+.++||...+.......+
T Consensus        70 --------~~~~~~l~~--~~~~~~D~vlIDT~Gr~~~d~~~~~el~~~~~~~~~~~~~LVlsa~~~~~~~~~~~~~  136 (196)
T PF00448_consen   70 --------EIAREALEK--FRKKGYDLVLIDTAGRSPRDEELLEELKKLLEALNPDEVHLVLSATMGQEDLEQALAF  136 (196)
T ss_dssp             --------HHHHHHHHH--HHHTTSSEEEEEE-SSSSTHHHHHHHHHHHHHHHSSSEEEEEEEGGGGGHHHHHHHHH
T ss_pred             --------HHHHHHHHH--HhhcCCCEEEEecCCcchhhHHHHHHHHHHhhhcCCccceEEEecccChHHHHHHHHH
Confidence                    111122221  111236899999886543 223345666666666666667779999876655444433

SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the GTPase domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species. The GTPase domain is evolutionary related to P-loop NTPase domains found in a variety of other proteins []. These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homologue of ftsY; and bacterial flagellar biosynthesis protein flhF.; GO: 0005525 GTP binding, 0006614 SRP-dependent cotranslational protein targeting to membrane; PDB: 2OG2_A 3B9Q_A 3DM9_B 3DMD_B 3E70_C 3DM5_B 2XXA_C 2J28_9 1ZU5_B 1ZU4_A ....

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=97.73  E-value=0.00089  Score=58.21  Aligned_cols=133  Identities=16%  Similarity=0.190  Sum_probs=74.1

Q ss_pred             cCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHH
Q 017573           32 KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL  111 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~  111 (369)
                      +++-+.+.||||.|||.+..-.+.......... ++-+|+--.= -.--.++++.++..+++++                
T Consensus       202 ~~~vi~LVGPTGVGKTTTlAKLAar~~~~~~~~-kVaiITtDtY-RIGA~EQLk~Ya~im~vp~----------------  263 (407)
T COG1419         202 QKRVIALVGPTGVGKTTTLAKLAARYVMLKKKK-KVAIITTDTY-RIGAVEQLKTYADIMGVPL----------------  263 (407)
T ss_pred             cCcEEEEECCCCCcHHHHHHHHHHHHHhhccCc-ceEEEEeccc-hhhHHHHHHHHHHHhCCce----------------
Confidence            367889999999999988765555554222222 4555443211 1112345555555445544                


Q ss_pred             ccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHh-hccCcHHHHHHHHhhCCccCcEEEEEeeCChh-HHHHHHH
Q 017573          112 QAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEM-LSRGFKDQIYDIFQLLPAKVQVGVFSATMPPE-ALEITRK  189 (369)
Q Consensus       112 ~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~-~~~~~~~~~~~~~~~~~~~~~~i~~saT~~~~-~~~~~~~  189 (369)
                           .++-++..|...+..    +.++|+|.+|=+-+- .+......+..+.+...+....+.+|||.... ..+....
T Consensus       264 -----~vv~~~~el~~ai~~----l~~~d~ILVDTaGrs~~D~~~i~el~~~~~~~~~i~~~Lvlsat~K~~dlkei~~~  334 (407)
T COG1419         264 -----EVVYSPKELAEAIEA----LRDCDVILVDTAGRSQYDKEKIEELKELIDVSHSIEVYLVLSATTKYEDLKEIIKQ  334 (407)
T ss_pred             -----EEecCHHHHHHHHHH----hhcCCEEEEeCCCCCccCHHHHHHHHHHHhccccceEEEEEecCcchHHHHHHHHH
Confidence                 344455555544433    223588999965543 34444455556665554555567789998653 3334444


Q ss_pred             hc
Q 017573          190 FM  191 (369)
Q Consensus       190 ~~  191 (369)
                      +.
T Consensus       335 f~  336 (407)
T COG1419         335 FS  336 (407)
T ss_pred             hc
Confidence            33

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=97.70  E-value=0.00015  Score=54.74  Aligned_cols=41  Identities=17%  Similarity=0.086  Sum_probs=26.8

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHH
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTREL   76 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l   76 (369)
                      +..+++.+|+|+|||..+...+. .+....  ..++++.+....
T Consensus         2 ~~~~~l~G~~G~GKTtl~~~l~~-~~~~~~--~~~~~~~~~~~~   42 (148)
T smart00382        2 GEVILIVGPPGSGKTTLARALAR-ELGPPG--GGVIYIDGEDIL   42 (148)
T ss_pred             CCEEEEECCCCCcHHHHHHHHHh-ccCCCC--CCEEEECCEEcc
Confidence            46789999999999987644433 332221  247777776543

AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.

>PRK14974 cell division protein FtsY; Provisional

Probab=97.68  E-value=0.001  Score=57.46  Aligned_cols=131  Identities=22%  Similarity=0.282  Sum_probs=71.1

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCC---HHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHH
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPT---RELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRI  110 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~---~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~  110 (369)
                      .-+++.+++|+|||.+....+. .+...  +.+++++...   .+-..|+......    .++.+.....+....     
T Consensus       141 ~vi~~~G~~GvGKTTtiakLA~-~l~~~--g~~V~li~~Dt~R~~a~eqL~~~a~~----lgv~v~~~~~g~dp~-----  208 (336)
T PRK14974        141 VVIVFVGVNGTGKTTTIAKLAY-YLKKN--GFSVVIAAGDTFRAGAIEQLEEHAER----LGVKVIKHKYGADPA-----  208 (336)
T ss_pred             eEEEEEcCCCCCHHHHHHHHHH-HHHHc--CCeEEEecCCcCcHHHHHHHHHHHHH----cCCceecccCCCCHH-----
Confidence            4578999999999987544443 33322  2266666543   3344454443333    344442211111100     


Q ss_pred             HccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhh-ccCcHHHHHHHHhhCCccCcEEEEEeeCChhHHHHHHH
Q 017573          111 LQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEML-SRGFKDQIYDIFQLLPAKVQVGVFSATMPPEALEITRK  189 (369)
Q Consensus       111 ~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~-~~~~~~~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~  189 (369)
                                  ..+...+...  ...+.++|++|.++++. +......+..+.....+...++.++||...+.......
T Consensus       209 ------------~v~~~ai~~~--~~~~~DvVLIDTaGr~~~~~~lm~eL~~i~~~~~pd~~iLVl~a~~g~d~~~~a~~  274 (336)
T PRK14974        209 ------------AVAYDAIEHA--KARGIDVVLIDTAGRMHTDANLMDELKKIVRVTKPDLVIFVGDALAGNDAVEQARE  274 (336)
T ss_pred             ------------HHHHHHHHHH--HhCCCCEEEEECCCccCCcHHHHHHHHHHHHhhCCceEEEeeccccchhHHHHHHH
Confidence                        0011211111  11236899999999875 33345666666666666676788899887665555544


Q ss_pred             h
Q 017573          190 F  190 (369)
Q Consensus       190 ~  190 (369)
                      +
T Consensus       275 f  275 (336)
T PRK14974        275 F  275 (336)
T ss_pred             H
Confidence            4

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.66  E-value=0.001  Score=58.07  Aligned_cols=128  Identities=16%  Similarity=0.175  Sum_probs=67.2

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCC--H-HHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHH
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPT--R-ELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRI  110 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~--~-~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~  110 (369)
                      +.+.+.||+|+|||..+...+......+   .++.++..-  + +-+.|+.    .+....++.+.              
T Consensus       242 ~vI~LVGptGvGKTTTiaKLA~~L~~~G---kkVglI~aDt~RiaAvEQLk----~yae~lgipv~--------------  300 (436)
T PRK11889        242 QTIALIGPTGVGKTTTLAKMAWQFHGKK---KTVGFITTDHSRIGTVQQLQ----DYVKTIGFEVI--------------  300 (436)
T ss_pred             cEEEEECCCCCcHHHHHHHHHHHHHHcC---CcEEEEecCCcchHHHHHHH----HHhhhcCCcEE--------------
Confidence            5689999999999987765555443332   256665542  2 2333333    33222233221              


Q ss_pred             HccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhc-cCcHHHHHHHHhhCCccCcEEEEEeeCChhH-HHHHH
Q 017573          111 LQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLS-RGFKDQIYDIFQLLPAKVQVGVFSATMPPEA-LEITR  188 (369)
Q Consensus       111 ~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~-~~~~~~~~~~~~~~~~~~~~i~~saT~~~~~-~~~~~  188 (369)
                             ...++..+...+..-.. ..++++|++|-+-+... ......+..++....+...++.+|||..... .+...
T Consensus       301 -------v~~d~~~L~~aL~~lk~-~~~~DvVLIDTaGRs~kd~~lm~EL~~~lk~~~PdevlLVLsATtk~~d~~~i~~  372 (436)
T PRK11889        301 -------AVRDEAAMTRALTYFKE-EARVDYILIDTAGKNYRASETVEEMIETMGQVEPDYICLTLSASMKSKDMIEIIT  372 (436)
T ss_pred             -------ecCCHHHHHHHHHHHHh-ccCCCEEEEeCccccCcCHHHHHHHHHHHhhcCCCeEEEEECCccChHHHHHHHH
Confidence                   12345555544433111 12369999998866432 2223444555544444444566888866543 44444


Q ss_pred             Hh
Q 017573          189 KF  190 (369)
Q Consensus       189 ~~  190 (369)
                      .+
T Consensus       373 ~F  374 (436)
T PRK11889        373 NF  374 (436)
T ss_pred             Hh
Confidence            43

>PRK06835 DNA replication protein DnaC; Validated

Probab=97.60  E-value=0.0012  Score=56.94  Aligned_cols=43  Identities=23%  Similarity=0.215  Sum_probs=27.9

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQ   79 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q   79 (369)
                      +.++++.||+|+|||..+...+...+..+.   .++++. ...+..+
T Consensus       183 ~~~Lll~G~~GtGKThLa~aIa~~l~~~g~---~V~y~t-~~~l~~~  225 (329)
T PRK06835        183 NENLLFYGNTGTGKTFLSNCIAKELLDRGK---SVIYRT-ADELIEI  225 (329)
T ss_pred             CCcEEEECCCCCcHHHHHHHHHHHHHHCCC---eEEEEE-HHHHHHH
Confidence            588999999999999876544444444332   565544 3444443

>PRK11054 helD DNA helicase IV; Provisional

Probab=97.58  E-value=0.00035  Score=66.48  Aligned_cols=76  Identities=22%  Similarity=0.174  Sum_probs=58.2

Q ss_pred             HhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccC-CCccEEEEcCCHHHHHHHHHHHHHhcc
Q 017573           12 YAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGL-VQCQALVLAPTRELAQQIEKVMRALGD   89 (369)
Q Consensus        12 ~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~-~~~~~liv~P~~~l~~q~~~~~~~~~~   89 (369)
                      ....-..+++-|++++..-  ..+++|.|+.|||||.++..-+...+..+. ...++++++.++..+..+.+.+.+...
T Consensus       190 ~~~e~~~L~~~Q~~av~~~--~~~~lV~agaGSGKT~vl~~r~ayLl~~~~~~~~~IL~ltft~~AA~em~eRL~~~lg  266 (684)
T PRK11054        190 SQVESSPLNPSQARAVVNG--EDSLLVLAGAGSGKTSVLVARAGWLLARGQAQPEQILLLAFGRQAAEEMDERIRERLG  266 (684)
T ss_pred             HhccCCCCCHHHHHHHhCC--CCCeEEEEeCCCCHHHHHHHHHHHHHHhCCCCHHHeEEEeccHHHHHHHHHHHHHhcC
Confidence            3344457999999999643  367899999999999988776665554432 233899999999999999998876543

>PRK10919 ATP-dependent DNA helicase Rep; Provisional

Probab=97.56  E-value=0.00018  Score=68.72  Aligned_cols=69  Identities=16%  Similarity=0.119  Sum_probs=56.9

Q ss_pred             CCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhc-cCCCccEEEEcCCHHHHHHHHHHHHHhc
Q 017573           18 KPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY-GLVQCQALVLAPTRELAQQIEKVMRALG   88 (369)
Q Consensus        18 ~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~-~~~~~~~liv~P~~~l~~q~~~~~~~~~   88 (369)
                      .+++-|++++.+  ..+.++|.|++|||||.+...-+...+.. +-...++|+++.|+.-+.++.+.+.+..
T Consensus         2 ~Ln~~Q~~av~~--~~g~~lV~AgpGSGKT~vL~~Ria~Li~~~~v~p~~IL~lTFT~kAA~em~~Rl~~~l   71 (672)
T PRK10919          2 RLNPGQQQAVEF--VTGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVAQTL   71 (672)
T ss_pred             CCCHHHHHHHhC--CCCCEEEEecCCCCHHHHHHHHHHHHHHhcCCCHHHeeeEechHHHHHHHHHHHHHHh
Confidence            478999999976  35789999999999999988888777754 3334489999999999999999887754

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=97.55  E-value=0.0031  Score=48.77  Aligned_cols=38  Identities=16%  Similarity=0.168  Sum_probs=25.0

Q ss_pred             EEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHH
Q 017573           36 VIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTREL   76 (369)
Q Consensus        36 ~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l   76 (369)
                      +++.|++|+|||..+...+......   +..++++......
T Consensus         2 ~~i~G~~G~GKT~l~~~i~~~~~~~---~~~v~~~~~e~~~   39 (165)
T cd01120           2 ILVFGPTGSGKTTLALQLALNIATK---GGKVVYVDIEEEI   39 (165)
T ss_pred             eeEeCCCCCCHHHHHHHHHHHHHhc---CCEEEEEECCcch
Confidence            6899999999998765544444332   2267777665443

This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.

>PRK05642 DNA replication initiation factor; Validated

Probab=97.52  E-value=0.00084  Score=55.36  Aligned_cols=43  Identities=16%  Similarity=0.427  Sum_probs=28.7

Q ss_pred             ccEEEEechhHhhcc-CcHHHHHHHHhhCCccCcEEEEEeeCCh
Q 017573          139 IKMFVLDEADEMLSR-GFKDQIYDIFQLLPAKVQVGVFSATMPP  181 (369)
Q Consensus       139 ~~~viiDE~H~~~~~-~~~~~~~~~~~~~~~~~~~i~~saT~~~  181 (369)
                      .+++++|++|.+... .+...+..+++.+......+++|++.++
T Consensus        98 ~d~LiiDDi~~~~~~~~~~~~Lf~l~n~~~~~g~~ilits~~~p  141 (234)
T PRK05642         98 YELVCLDDLDVIAGKADWEEALFHLFNRLRDSGRRLLLAASKSP  141 (234)
T ss_pred             CCEEEEechhhhcCChHHHHHHHHHHHHHHhcCCEEEEeCCCCH
Confidence            589999999987543 3456677777766554445566666543

>PRK06921 hypothetical protein; Provisional

Probab=97.51  E-value=0.0023  Score=53.73  Aligned_cols=38  Identities=18%  Similarity=0.160  Sum_probs=24.5

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcC
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAP   72 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P   72 (369)
                      +.++++.|++|+|||..+... +..+.... +..++++..
T Consensus       117 ~~~l~l~G~~G~GKThLa~ai-a~~l~~~~-g~~v~y~~~  154 (266)
T PRK06921        117 KNSIALLGQPGSGKTHLLTAA-ANELMRKK-GVPVLYFPF  154 (266)
T ss_pred             CCeEEEECCCCCcHHHHHHHH-HHHHhhhc-CceEEEEEH
Confidence            578999999999999775433 43433221 225666553

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=97.51  E-value=0.00049  Score=59.56  Aligned_cols=41  Identities=17%  Similarity=-0.014  Sum_probs=32.2

Q ss_pred             CCcHhhhhhhhccccCC----cEEEEcCCCChhhHHHHHHHHHhh
Q 017573           18 KPSAIQQRGIVPFCKGL----DVIQQAQSGTGKTATFCSGILQQL   58 (369)
Q Consensus        18 ~~~~~Q~~~~~~~~~~~----~~li~~~tG~GKT~~~~~~~~~~~   58 (369)
                      .++|+|...+..+.+.+    ..++.||.|.|||..+...+...+
T Consensus         3 ~~yPWl~~~~~~~~~~~r~~ha~Lf~G~~G~GK~~~A~~~A~~ll   47 (328)
T PRK05707          3 EIYPWQQSLWQQLAGRGRHPHAYLLHGPAGIGKRALAERLAAALL   47 (328)
T ss_pred             cCCCCcHHHHHHHHHCCCcceeeeeECCCCCCHHHHHHHHHHHHc
Confidence            35899999999988653    478999999999988765555444

>cd01124 KaiC KaiC is a circadian clock protein primarily found in cyanobacteria KaiC is a RecA-like ATPase, having both Walker A and Walker B motifs

Probab=97.48  E-value=0.0035  Score=49.83  Aligned_cols=48  Identities=21%  Similarity=0.223  Sum_probs=34.6

Q ss_pred             EEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHh
Q 017573           36 VIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRAL   87 (369)
Q Consensus        36 ~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~   87 (369)
                      +++.||+|+|||..++..+...+..+.   +++|++.. ....+..+.+..+
T Consensus         2 ~li~G~~G~GKT~l~~~~~~~~~~~g~---~v~~~s~e-~~~~~~~~~~~~~   49 (187)
T cd01124           2 TLLSGGPGTGKTTFALQFLYAGLARGE---PGLYVTLE-ESPEELIENAESL   49 (187)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHCCC---cEEEEECC-CCHHHHHHHHHHc
Confidence            689999999999888777776665543   78888754 4455666666554

A related protein is found in archaea.

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=97.47  E-value=0.028  Score=60.25  Aligned_cols=236  Identities=12%  Similarity=0.142  Sum_probs=121.5

Q ss_pred             CCcHhhhhhhhccccC--CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEE
Q 017573           18 KPSAIQQRGIVPFCKG--LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKV   95 (369)
Q Consensus        18 ~~~~~Q~~~~~~~~~~--~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v   95 (369)
                      .+++-|++++..++.+  +-.++.++.|+|||.+. -.+...+...  +.+++.++|+..-+..+.+.....       .
T Consensus       429 ~Ls~~Q~~Av~~il~s~~~v~ii~G~aGTGKTt~l-~~l~~~~~~~--G~~V~~lAPTgrAA~~L~e~~g~~-------A  498 (1960)
T TIGR02760       429 ALSPSNKDAVSTLFTSTKRFIIINGFGGTGSTEIA-QLLLHLASEQ--GYEIQIITAGSLSAQELRQKIPRL-------A  498 (1960)
T ss_pred             CCCHHHHHHHHHHHhCCCCeEEEEECCCCCHHHHH-HHHHHHHHhc--CCeEEEEeCCHHHHHHHHHHhcch-------h
Confidence            6889999999998875  56899999999999764 4444444432  338999999987666655543211       0


Q ss_pred             EEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhC-CccCcEEE
Q 017573           96 HACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLL-PAKVQVGV  174 (369)
Q Consensus        96 ~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~-~~~~~~i~  174 (369)
                            .+...+...+..  ..-..|.+.|.    .....+..-+++|+||+.++.    ...+..++... +.+.++++
T Consensus       499 ------~Ti~~~l~~l~~--~~~~~tv~~fl----~~~~~l~~~~vlIVDEAsMl~----~~~~~~Ll~~a~~~garvVl  562 (1960)
T TIGR02760       499 ------STFITWVKNLFN--DDQDHTVQGLL----DKSSPFSNKDIFVVDEANKLS----NNELLKLIDKAEQHNSKLIL  562 (1960)
T ss_pred             ------hhHHHHHHhhcc--cccchhHHHhh----cccCCCCCCCEEEEECCCCCC----HHHHHHHHHHHhhcCCEEEE
Confidence                  011111111111  11122333333    122222345899999999874    34455566555 35677887


Q ss_pred             EEeeCC------hhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHH-HHHHHhcc-CCCeEEEeCCHh
Q 017573          175 FSATMP------PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETL-CDLYETLA-ITQSVIFVNTRR  246 (369)
Q Consensus       175 ~saT~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l-~~~~~~~~-~~k~lv~~~~~~  246 (369)
                      +.-+-.      .+....+.........+......  ...+  .+.. .........+ ..++...+ ..+++|+..+..
T Consensus       563 vGD~~QL~sV~aG~~f~~L~~~gv~t~~l~~i~rq--~~~v--~i~~-~~~~~r~~~ia~~y~~L~~~r~~tliv~~t~~  637 (1960)
T TIGR02760       563 LNDSAQRQGMSAGSAIDLLKEGGVTTYAWVDTKQQ--KASV--EISE-AVDKLRVDYIASAWLDLTPDRQNSQVLATTHR  637 (1960)
T ss_pred             EcChhhcCccccchHHHHHHHCCCcEEEeeccccc--Ccce--eeec-cCchHHHHHHHHHHHhcccccCceEEEcCCcH
Confidence            766531      22333333322121222111111  1111  1111 1122222233 33333332 236899999988


Q ss_pred             hHHHHHHHHhhC----C------CeeEEecC-CCCHHHHHHHHHHHhcCC
Q 017573          247 KVDWLTDKMRSR----D------HTVSATHG-DMDQNTRDIIMREFRSGS  285 (369)
Q Consensus       247 ~~~~~~~~l~~~----~------~~~~~~~~-~~~~~~r~~~~~~f~~~~  285 (369)
                      +.+.+....+..    |      .....+.. +++..++. ....|+.|+
T Consensus       638 dr~~Ln~~iR~~L~~~G~L~~~~~~~~~L~p~~lt~~e~r-~~~~Yr~Gd  686 (1960)
T TIGR02760       638 EQQDLTQIIRNALKQEGQLSRQEVTVPTLKPVNLTGIQRR-NAAHYKQGM  686 (1960)
T ss_pred             HHHHHHHHHHHHHHHcCCcCCCceEEEEeccCCCCHHHHh-hHhhcCCCC
Confidence            887776665432    2      23333333 45666655 336666554

This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.

>PHA02533 17 large terminase protein; Provisional

Probab=97.45  E-value=0.001  Score=61.39  Aligned_cols=122  Identities=13%  Similarity=0.063  Sum_probs=74.1

Q ss_pred             CCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCc--EE
Q 017573           18 KPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGV--KV   95 (369)
Q Consensus        18 ~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~--~v   95 (369)
                      .|+|+|++.+..+..++-.++..+-..|||.++...++....... +..+++++|+..-+....+.++.+....+.  ..
T Consensus        59 ~L~p~Q~~i~~~~~~~R~~ii~~aRq~GKStl~a~~al~~a~~~~-~~~v~i~A~~~~QA~~vF~~ik~~ie~~P~l~~~  137 (534)
T PHA02533         59 QMRDYQKDMLKIMHKNRFNACNLSRQLGKTTVVAIFLLHYVCFNK-DKNVGILAHKASMAAEVLDRTKQAIELLPDFLQP  137 (534)
T ss_pred             CCcHHHHHHHHHHhcCeEEEEEEcCcCChHHHHHHHHHHHHHhCC-CCEEEEEeCCHHHHHHHHHHHHHHHHhCHHHhhc
Confidence            689999999988766777789999999999887654443333222 338999999998888887777655433211  10


Q ss_pred             EEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhh
Q 017573           96 HACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEML  151 (369)
Q Consensus        96 ~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~  151 (369)
                      .... ...   ..-.+.++..|.+.|.+.       ......+.+++++||+|...
T Consensus       138 ~i~~-~~~---~~I~l~NGS~I~~lss~~-------~t~rG~~~~~liiDE~a~~~  182 (534)
T PHA02533        138 GIVE-WNK---GSIELENGSKIGAYASSP-------DAVRGNSFAMIYIDECAFIP  182 (534)
T ss_pred             ceee-cCc---cEEEeCCCCEEEEEeCCC-------CccCCCCCceEEEeccccCC
Confidence            0000 000   000012344554444321       11233346789999999764

>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=97.44  E-value=0.00093  Score=54.43  Aligned_cols=106  Identities=19%  Similarity=0.296  Sum_probs=60.2

Q ss_pred             cEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHccC
Q 017573           35 DVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAG  114 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~  114 (369)
                      .++++||+|+|||-. +.++.+.+....++.+++++... .........+..                            
T Consensus        36 ~l~l~G~~G~GKTHL-L~Ai~~~~~~~~~~~~v~y~~~~-~f~~~~~~~~~~----------------------------   85 (219)
T PF00308_consen   36 PLFLYGPSGLGKTHL-LQAIANEAQKQHPGKRVVYLSAE-EFIREFADALRD----------------------------   85 (219)
T ss_dssp             EEEEEESTTSSHHHH-HHHHHHHHHHHCTTS-EEEEEHH-HHHHHHHHHHHT----------------------------
T ss_pred             ceEEECCCCCCHHHH-HHHHHHHHHhccccccceeecHH-HHHHHHHHHHHc----------------------------
Confidence            489999999999974 45555555544344477776543 332222222211                            


Q ss_pred             CcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccC-cHHHHHHHHhhCCc-cCcEEEEEeeCChh
Q 017573          115 VHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRG-FKDQIYDIFQLLPA-KVQVGVFSATMPPE  182 (369)
Q Consensus       115 ~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~-~~~~~~~~~~~~~~-~~~~i~~saT~~~~  182 (369)
                           ...+.+...+..       .+++++|++|.+.+.. +...+..+++.+.. +.++++.|..++..
T Consensus        86 -----~~~~~~~~~~~~-------~DlL~iDDi~~l~~~~~~q~~lf~l~n~~~~~~k~li~ts~~~P~~  143 (219)
T PF00308_consen   86 -----GEIEEFKDRLRS-------ADLLIIDDIQFLAGKQRTQEELFHLFNRLIESGKQLILTSDRPPSE  143 (219)
T ss_dssp             -----TSHHHHHHHHCT-------SSEEEEETGGGGTTHHHHHHHHHHHHHHHHHTTSEEEEEESS-TTT
T ss_pred             -----ccchhhhhhhhc-------CCEEEEecchhhcCchHHHHHHHHHHHHHHhhCCeEEEEeCCCCcc
Confidence                 122334333332       6999999999986542 45666666666544 45566555455433

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.

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.42  E-value=0.0016  Score=56.97  Aligned_cols=127  Identities=20%  Similarity=0.148  Sum_probs=63.1

Q ss_pred             cCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHH
Q 017573           32 KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL  111 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~  111 (369)
                      +++.+++.+|||+|||..+...+......... .++.+++... .-.--.++++.+....++.+...             
T Consensus       136 ~g~ii~lvGptGvGKTTtiakLA~~~~~~~G~-~~V~lit~D~-~R~ga~EqL~~~a~~~gv~~~~~-------------  200 (374)
T PRK14722        136 RGGVFALMGPTGVGKTTTTAKLAARCVMRFGA-SKVALLTTDS-YRIGGHEQLRIFGKILGVPVHAV-------------  200 (374)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHhcCC-CeEEEEeccc-ccccHHHHHHHHHHHcCCceEec-------------
Confidence            35788999999999998876555443322111 1455554322 11111233444433334443322             


Q ss_pred             ccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccC-cHHHHHHHHhhCCccCcEEEEEeeCChhHHH
Q 017573          112 QAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRG-FKDQIYDIFQLLPAKVQVGVFSATMPPEALE  185 (369)
Q Consensus       112 ~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~-~~~~~~~~~~~~~~~~~~i~~saT~~~~~~~  185 (369)
                              -+...+...+.+    ..+.++++||++-...... ..+.+..+.....+...++.++||...+...
T Consensus       201 --------~~~~~l~~~l~~----l~~~DlVLIDTaG~~~~d~~l~e~La~L~~~~~~~~~lLVLsAts~~~~l~  263 (374)
T PRK14722        201 --------KDGGDLQLALAE----LRNKHMVLIDTIGMSQRDRTVSDQIAMLHGADTPVQRLLLLNATSHGDTLN  263 (374)
T ss_pred             --------CCcccHHHHHHH----hcCCCEEEEcCCCCCcccHHHHHHHHHHhccCCCCeEEEEecCccChHHHH
Confidence                    222223222322    1235899999997542211 2222332222222234477789998765543

>PRK06893 DNA replication initiation factor; Validated

Probab=97.41  E-value=0.00053  Score=56.40  Aligned_cols=45  Identities=18%  Similarity=0.369  Sum_probs=28.4

Q ss_pred             CccEEEEechhHhhc-cCcHHHHHHHHhhCCc-cCcEEEEEeeCChh
Q 017573          138 YIKMFVLDEADEMLS-RGFKDQIYDIFQLLPA-KVQVGVFSATMPPE  182 (369)
Q Consensus       138 ~~~~viiDE~H~~~~-~~~~~~~~~~~~~~~~-~~~~i~~saT~~~~  182 (369)
                      ..+++++||+|.+.. ..+...+..+++.... +.+++.+|++.++.
T Consensus        91 ~~dlLilDDi~~~~~~~~~~~~l~~l~n~~~~~~~~illits~~~p~  137 (229)
T PRK06893         91 QQDLVCLDDLQAVIGNEEWELAIFDLFNRIKEQGKTLLLISADCSPH  137 (229)
T ss_pred             cCCEEEEeChhhhcCChHHHHHHHHHHHHHHHcCCcEEEEeCCCChH
Confidence            368999999998753 3334456666655543 34566677775443

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=97.40  E-value=0.0016  Score=55.87  Aligned_cols=144  Identities=14%  Similarity=0.079  Sum_probs=75.7

Q ss_pred             CCCCcHhhhhhhhcccc----C---CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhc
Q 017573           16 FEKPSAIQQRGIVPFCK----G---LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALG   88 (369)
Q Consensus        16 ~~~~~~~Q~~~~~~~~~----~---~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~   88 (369)
                      +..++|+|..++..+..    +   ...++.||.|.||+..+...+...+-.+.....   -|+.          ++.+.
T Consensus         2 ~~~~yPW~~~~~~~l~~~~~~~rl~HA~Lf~Gp~G~GK~~lA~~lA~~LlC~~~~~~~---~c~~----------c~~~~   68 (319)
T PRK08769          2 TSAFSPWQQRAYDQTVAALDAGRLGHGLLICGPEGLGKRAVALALAEHVLASGPDPAA---AQRT----------RQLIA   68 (319)
T ss_pred             CccccccHHHHHHHHHHHHHcCCcceeEeeECCCCCCHHHHHHHHHHHHhCCCCCCCC---cchH----------HHHHh
Confidence            35789999999988764    2   358999999999998876555544433221111   1111          11111


Q ss_pred             cccCcEEEEEE--CCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhC
Q 017573           89 DYLGVKVHACV--GGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLL  166 (369)
Q Consensus        89 ~~~~~~v~~~~--~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~  166 (369)
                      ....-++..+.  .+..  ..    .....|.|-....+.+.+...... ...+++|||++|.+.... ...+.+++..-
T Consensus        69 ~g~HPD~~~i~~~p~~~--~~----k~~~~I~idqIR~l~~~~~~~p~~-g~~kV~iI~~ae~m~~~A-aNaLLKtLEEP  140 (319)
T PRK08769         69 AGTHPDLQLVSFIPNRT--GD----KLRTEIVIEQVREISQKLALTPQY-GIAQVVIVDPADAINRAA-CNALLKTLEEP  140 (319)
T ss_pred             cCCCCCEEEEecCCCcc--cc----cccccccHHHHHHHHHHHhhCccc-CCcEEEEeccHhhhCHHH-HHHHHHHhhCC
Confidence            11122233221  1110  00    001123333333333333333222 246899999999985333 55666667776


Q ss_pred             CccCcEEEEEeeCC
Q 017573          167 PAKVQVGVFSATMP  180 (369)
Q Consensus       167 ~~~~~~i~~saT~~  180 (369)
                      ++...++++|..+.
T Consensus       141 p~~~~fiL~~~~~~  154 (319)
T PRK08769        141 SPGRYLWLISAQPA  154 (319)
T ss_pred             CCCCeEEEEECChh
Confidence            66666666655443

>TIGR02785 addA_Gpos recombination helicase AddA, Firmicutes type

Probab=97.40  E-value=0.0013  Score=67.47  Aligned_cols=124  Identities=16%  Similarity=0.162  Sum_probs=81.6

Q ss_pred             CCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEE
Q 017573           18 KPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHA   97 (369)
Q Consensus        18 ~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~   97 (369)
                      ++++-|++++..  .+++++|.|+.|||||.+..--++..+..+....++++||=|+.-+.++.+++.+.....- .   
T Consensus         1 ~~t~~Q~~ai~~--~~~~~lv~A~AGsGKT~~lv~r~~~~~~~~~~~~~il~~tFt~~aa~e~~~ri~~~l~~~~-~---   74 (1232)
T TIGR02785         1 QWTDEQWQAIYT--RGQNILVSASAGSGKTAVLVERIIKKILRGVDIDRLLVVTFTNAAAREMKERIEEALQKAL-Q---   74 (1232)
T ss_pred             CCCHHHHHHHhC--CCCCEEEEecCCCcHHHHHHHHHHHHHhcCCCHhhEEEEeccHHHHHHHHHHHHHHHHHHH-h---
Confidence            357899999973  6889999999999999998887777776553334799999999999999888877543210 0   


Q ss_pred             EECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCc--cEEEEechhH
Q 017573           98 CVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYI--KMFVLDEADE  149 (369)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~--~~viiDE~H~  149 (369)
                        .........+.+..-...-|+|.++|...+-+.....-++  ++=|.||...
T Consensus        75 --~~p~~~~L~~q~~~~~~~~i~Tihsf~~~~~~~~~~~l~ldP~F~i~de~e~  126 (1232)
T TIGR02785        75 --QEPNSKHLRRQLALLNTANISTLHSFCLKVIRKHYYLLDLDPSFRILTDTEQ  126 (1232)
T ss_pred             --cCchhHHHHHHHhhccCCeEeeHHHHHHHHHHHhhhhcCCCCCceeCCHHHH
Confidence              0111111222223334678999999965544433322222  3455887765

AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination. The term AddAB is used broadly, with AddA homologous between the Firmicutes (as modeled here) and the alphaproteobacteria, while the partner AddB proteins show no strong homology across the two groups of species.

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=97.40  E-value=0.0015  Score=58.83  Aligned_cols=37  Identities=14%  Similarity=0.130  Sum_probs=24.4

Q ss_pred             cEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcC
Q 017573           35 DVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAP   72 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P   72 (369)
                      .+++.||+|+|||..+. ++.+.+.....+.+++++..
T Consensus       138 ~l~l~G~~G~GKThL~~-ai~~~l~~~~~~~~v~yi~~  174 (405)
T TIGR00362       138 PLFIYGGVGLGKTHLLH-AIGNEILENNPNAKVVYVSS  174 (405)
T ss_pred             eEEEECCCCCcHHHHHH-HHHHHHHHhCCCCcEEEEEH
Confidence            57999999999997753 44444443333336777643

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).

>KOG1513 consensus Nuclear helicase MOP-3/SNO (DEAD-box superfamily) [Transcription; Signal transduction mechanisms]

Probab=97.39  E-value=0.00017  Score=66.77  Aligned_cols=158  Identities=22%  Similarity=0.249  Sum_probs=99.1

Q ss_pred             CCCCcHhhhhhhhcccc--------C--CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHH
Q 017573           16 FEKPSAIQQRGIVPFCK--------G--LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMR   85 (369)
Q Consensus        16 ~~~~~~~Q~~~~~~~~~--------~--~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~   85 (369)
                      ..++...|.+++-...+        |  -.++|-...|.||-.+..-.|++...++.+  ++|++.-+..|.-+..+.++
T Consensus       262 sg~lSALQLEav~YAcQ~He~llPsG~RaGfLiGDGAGVGKGRTvAgiIfeNyLkGRK--rAlW~SVSsDLKfDAERDL~  339 (1300)
T KOG1513|consen  262 SGHLSALQLEAVTYACQAHEVLLPSGQRAGFLIGDGAGVGKGRTVAGIIFENYLKGRK--RALWFSVSSDLKFDAERDLR  339 (1300)
T ss_pred             ccchhHHHHHHHHHHHhhhhhcCCCCccceeeeccCcccCCCceeEEEEehhhhcccc--eeEEEEeccccccchhhchh
Confidence            35688889988855432        3  357888888888876655555555555543  89999999999988888888


Q ss_pred             HhccccCcEEEEEECCc----chHHHHHHHccCCcEEEeccHHHHHHHHcCCCC------------CCC-ccEEEEechh
Q 017573           86 ALGDYLGVKVHACVGGT----SVREDQRILQAGVHVVVGTPGRVFDMLRRQSLR------------PDY-IKMFVLDEAD  148 (369)
Q Consensus        86 ~~~~~~~~~v~~~~~~~----~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~------------~~~-~~~viiDE~H  148 (369)
                      ..... ++.|..+..-.    ..++. .  ..+-.|+++||..|........-.            ... =++||+||||
T Consensus       340 DigA~-~I~V~alnK~KYakIss~en-~--n~krGViFaTYtaLIGEs~~~~~kyrtR~rQllqW~Ge~feGvIvfDECH  415 (1300)
T KOG1513|consen  340 DIGAT-GIAVHALNKFKYAKISSKEN-T--NTKRGVIFATYTALIGESQGKGGKYRTRFRQLLQWCGEDFEGVIVFDECH  415 (1300)
T ss_pred             hcCCC-Cccceehhhccccccccccc-C--CccceeEEEeeHhhhhhccccCchHHHHHHHHHHHhhhccceeEEehhhh
Confidence            76433 45554433211    00011 0  112469999997774322211000            011 1699999999


Q ss_pred             Hhhcc---------CcHHHHHHHHhhCCccCcEEEEEeeCC
Q 017573          149 EMLSR---------GFKDQIYDIFQLLPAKVQVGVFSATMP  180 (369)
Q Consensus       149 ~~~~~---------~~~~~~~~~~~~~~~~~~~i~~saT~~  180 (369)
                      ...+.         ...+.+..+-+.+| +.+++.-|||-.
T Consensus       416 kAKNL~p~~~~k~TKtG~tVLdLQk~LP-~ARVVYASATGA  455 (1300)
T KOG1513|consen  416 KAKNLVPTAGAKSTKTGKTVLDLQKKLP-NARVVYASATGA  455 (1300)
T ss_pred             hhcccccccCCCcCcccHhHHHHHHhCC-CceEEEeeccCC
Confidence            87541         13466667777776 566888899954

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=97.38  E-value=0.0037  Score=56.20  Aligned_cols=126  Identities=17%  Similarity=0.167  Sum_probs=64.1

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhh-hccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQL-DYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL  111 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~-~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~  111 (369)
                      ++.+++.+|+|+|||.++...+.... ..+.  .++.++.--..-. ...+++..+....++.+..              
T Consensus       221 ~~~i~~vGptGvGKTTt~~kLA~~~~~~~~g--~~V~li~~D~~r~-~a~eqL~~~a~~~~vp~~~--------------  283 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLAKLAARYALLYGK--KKVALITLDTYRI-GAVEQLKTYAKIMGIPVEV--------------  283 (424)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCC--CeEEEEECCccHH-HHHHHHHHHHHHhCCceEc--------------
Confidence            56789999999999987765544433 2221  2566665322110 0113333333222333211              


Q ss_pred             ccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhc-cCcHHHHHHHHh-hCCccCcEEEEEeeCChhHHHH
Q 017573          112 QAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLS-RGFKDQIYDIFQ-LLPAKVQVGVFSATMPPEALEI  186 (369)
Q Consensus       112 ~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~-~~~~~~~~~~~~-~~~~~~~~i~~saT~~~~~~~~  186 (369)
                             +.+++.+...+...    ..+++|++|.+-+... ......+..++. ...+....+.++||........
T Consensus       284 -------~~~~~~l~~~l~~~----~~~DlVlIDt~G~~~~d~~~~~~L~~ll~~~~~~~~~~LVl~a~~~~~~l~~  349 (424)
T PRK05703        284 -------VYDPKELAKALEQL----RDCDVILIDTAGRSQRDKRLIEELKALIEFSGEPIDVYLVLSATTKYEDLKD  349 (424)
T ss_pred             -------cCCHHhHHHHHHHh----CCCCEEEEeCCCCCCCCHHHHHHHHHHHhccCCCCeEEEEEECCCCHHHHHH
Confidence                   12333444444331    2369999998865321 112234445544 2223344677899987644443

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=97.38  E-value=0.0015  Score=53.83  Aligned_cols=41  Identities=10%  Similarity=0.299  Sum_probs=24.5

Q ss_pred             ccEEEEechhHhhccCcHHHHHHHHhhCCccCc-EEEEEeeCC
Q 017573          139 IKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQ-VGVFSATMP  180 (369)
Q Consensus       139 ~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~-~i~~saT~~  180 (369)
                      .+++++||+|.+.... ...+..+++....... ++.++++.+
T Consensus        91 ~~~liiDdi~~l~~~~-~~~L~~~~~~~~~~~~~~vl~~~~~~  132 (227)
T PRK08903         91 AELYAVDDVERLDDAQ-QIALFNLFNRVRAHGQGALLVAGPAA  132 (227)
T ss_pred             CCEEEEeChhhcCchH-HHHHHHHHHHHHHcCCcEEEEeCCCC
Confidence            5799999999875332 4445555554433333 455666644

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=97.38  E-value=0.0013  Score=59.59  Aligned_cols=107  Identities=14%  Similarity=0.231  Sum_probs=58.8

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHcc
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQA  113 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~  113 (369)
                      ..+++.|++|+|||..+ .++.+.+.....+.+++++.+ ..+.......+..-                          
T Consensus       142 npl~i~G~~G~GKTHLl-~Ai~~~l~~~~~~~~v~yv~~-~~f~~~~~~~l~~~--------------------------  193 (450)
T PRK14087        142 NPLFIYGESGMGKTHLL-KAAKNYIESNFSDLKVSYMSG-DEFARKAVDILQKT--------------------------  193 (450)
T ss_pred             CceEEECCCCCcHHHHH-HHHHHHHHHhCCCCeEEEEEH-HHHHHHHHHHHHHh--------------------------
Confidence            35899999999999654 455555544333446777665 44544444333220                          


Q ss_pred             CCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhcc-CcHHHHHHHHhhCCc-cCcEEEEEeeCCh
Q 017573          114 GVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSR-GFKDQIYDIFQLLPA-KVQVGVFSATMPP  181 (369)
Q Consensus       114 ~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~-~~~~~~~~~~~~~~~-~~~~i~~saT~~~  181 (369)
                        .   ...+.+...+.       ..+++++||+|.+... .....+..+++.+.. +.+++ +|+..++
T Consensus       194 --~---~~~~~~~~~~~-------~~dvLiIDDiq~l~~k~~~~e~lf~l~N~~~~~~k~iI-ltsd~~P  250 (450)
T PRK14087        194 --H---KEIEQFKNEIC-------QNDVLIIDDVQFLSYKEKTNEIFFTIFNNFIENDKQLF-FSSDKSP  250 (450)
T ss_pred             --h---hHHHHHHHHhc-------cCCEEEEeccccccCCHHHHHHHHHHHHHHHHcCCcEE-EECCCCH
Confidence              0   01122222222       3689999999987643 234556666655543 34555 4544433

>PRK08084 DNA replication initiation factor; Provisional

Probab=97.37  E-value=0.0009  Score=55.26  Aligned_cols=36  Identities=6%  Similarity=-0.019  Sum_probs=23.0

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcC
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAP   72 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P   72 (369)
                      ..++++||+|+|||..+.....+....   +.++.++..
T Consensus        46 ~~l~l~Gp~G~GKThLl~a~~~~~~~~---~~~v~y~~~   81 (235)
T PRK08084         46 GYIYLWSREGAGRSHLLHAACAELSQR---GRAVGYVPL   81 (235)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHhC---CCeEEEEEH
Confidence            678999999999997654333333222   225666543

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.37  E-value=0.00077  Score=60.58  Aligned_cols=21  Identities=24%  Similarity=0.047  Sum_probs=16.8

Q ss_pred             cEEEEcCCCChhhHHHHHHHH
Q 017573           35 DVIQQAQSGTGKTATFCSGIL   55 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~~~~~   55 (369)
                      ..+++||.|+|||.++...+.
T Consensus        42 a~Lf~GP~GtGKTTlAriLAk   62 (484)
T PRK14956         42 AYIFFGPRGVGKTTIARILAK   62 (484)
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            369999999999988754444

>PRK12377 putative replication protein; Provisional

Probab=97.37  E-value=0.0018  Score=53.52  Aligned_cols=43  Identities=16%  Similarity=0.224  Sum_probs=26.6

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHH
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQI   80 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~   80 (369)
                      .++++.||+|+|||..+...+......+.   .+++ ++...+..++
T Consensus       102 ~~l~l~G~~GtGKThLa~AIa~~l~~~g~---~v~~-i~~~~l~~~l  144 (248)
T PRK12377        102 TNFVFSGKPGTGKNHLAAAIGNRLLAKGR---SVIV-VTVPDVMSRL  144 (248)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHcCC---CeEE-EEHHHHHHHH
Confidence            67999999999999776544443333322   4544 3444555544

>PF03354 Terminase_1: Phage Terminase ; InterPro: IPR005021 This entry is represented by Lactococcus phage bIL285, Orf41 (terminase)

Probab=97.37  E-value=0.00045  Score=63.45  Aligned_cols=145  Identities=15%  Similarity=0.084  Sum_probs=80.8

Q ss_pred             Hhhhhhhhccc-----cC----CcEEEEcCCCChhhHHHHHHHHHhh-hccCCCccEEEEcCCHHHHHHHHHHHHHhccc
Q 017573           21 AIQQRGIVPFC-----KG----LDVIQQAQSGTGKTATFCSGILQQL-DYGLVQCQALVLAPTRELAQQIEKVMRALGDY   90 (369)
Q Consensus        21 ~~Q~~~~~~~~-----~~----~~~li~~~tG~GKT~~~~~~~~~~~-~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~   90 (369)
                      |+|+.++..+.     .+    +.+++..|-|-|||..+...++..+ ..+..+..++++++++.-+....+.+.++...
T Consensus         1 PwQ~fi~~~i~G~~~~~g~rrf~~~~l~v~RkNGKS~l~a~i~ly~l~~~g~~~~~i~~~A~~~~QA~~~f~~~~~~i~~   80 (477)
T PF03354_consen    1 PWQKFILRSIFGWRKDDGRRRFREVYLEVPRKNGKSTLAAAIALYMLFLDGEPGAEIYCAANTRDQAKIVFDEAKKMIEA   80 (477)
T ss_pred             CcHHHHHHHHhceEcCCCCEEEEEEEEEEcCccCccHHHHHHHHHHHhcCCccCceEEEEeCCHHHHHHHHHHHHHHHHh
Confidence            57777776655     12    4579999999999976655444333 44555568999999999999998888877544


Q ss_pred             cCcEEEEEECCcchHHHHHH-HccCCcEEEeccHHHHHHHHc--CCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCC
Q 017573           91 LGVKVHACVGGTSVREDQRI-LQAGVHVVVGTPGRVFDMLRR--QSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLP  167 (369)
Q Consensus        91 ~~~~v~~~~~~~~~~~~~~~-~~~~~~iiv~t~~~l~~~~~~--~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~  167 (369)
                      .+.......        .+. ......|.....+.+...+..  ......+.+++|+||+|...+......+..-....+
T Consensus        81 ~~~l~~~~~--------~~~~~~~~~~i~~~~~~s~~~~~s~~~~~~dG~~~~~~i~DE~h~~~~~~~~~~l~~g~~~r~  152 (477)
T PF03354_consen   81 SPELRKRKK--------PKIIKSNKKEIEFPKTGSFFKALSSDADSLDGLNPSLAIFDELHAHKDDELYDALESGMGARP  152 (477)
T ss_pred             Chhhccchh--------hhhhhhhceEEEEcCCCcEEEEEecCCCCccCCCCceEEEeCCCCCCCHHHHHHHHhhhccCC
Confidence            211110000        000 011123333322333222222  223334468999999999865433333333333322


Q ss_pred             ccCcEEE
Q 017573          168 AKVQVGV  174 (369)
Q Consensus       168 ~~~~~i~  174 (369)
                       +++++.
T Consensus       153 -~pl~~~  158 (477)
T PF03354_consen  153 -NPLIII  158 (477)
T ss_pred             -CceEEE
Confidence             444444

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=97.36  E-value=0.0015  Score=53.77  Aligned_cols=23  Identities=17%  Similarity=0.159  Sum_probs=18.2

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFCSGIL   55 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~   55 (369)
                      +..+++.||+|+|||..+...+.
T Consensus        38 ~~~lll~G~~G~GKT~la~~~~~   60 (226)
T TIGR03420        38 DRFLYLWGESGSGKSHLLQAACA   60 (226)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHH
Confidence            47899999999999987654433

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.

>TIGR01075 uvrD DNA helicase II

Probab=97.36  E-value=0.00067  Score=65.71  Aligned_cols=71  Identities=17%  Similarity=0.163  Sum_probs=58.1

Q ss_pred             CCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhc-cCCCccEEEEcCCHHHHHHHHHHHHHhcc
Q 017573           17 EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY-GLVQCQALVLAPTRELAQQIEKVMRALGD   89 (369)
Q Consensus        17 ~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~-~~~~~~~liv~P~~~l~~q~~~~~~~~~~   89 (369)
                      ..|++-|++++.+-  ...++|.|++|||||.+...-+...+.. +-...++|+++.|+.-+.++.+.+.+...
T Consensus         3 ~~Ln~~Q~~av~~~--~g~~lV~AgaGSGKT~~L~~Ria~Li~~~~v~p~~IL~lTFTnkAA~em~~Rl~~~~~   74 (715)
T TIGR01075         3 DGLNDKQREAVAAP--PGNLLVLAGAGSGKTRVLTHRIAWLLSVENASPHSIMAVTFTNKAAAEMRHRIGALLG   74 (715)
T ss_pred             cccCHHHHHHHcCC--CCCEEEEecCCCCHHHHHHHHHHHHHHcCCCCHHHeEeeeccHHHHHHHHHHHHHHhc
Confidence            46899999999763  5789999999999999987777776654 33344899999999999999999887653

Designed to identify uvrD members of the uvrD/rep subfamily.

>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins

Probab=97.34  E-value=0.00045  Score=61.06  Aligned_cols=55  Identities=29%  Similarity=0.322  Sum_probs=39.8

Q ss_pred             CCcHhhhhhhhcc------ccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHH
Q 017573           18 KPSAIQQRGIVPF------CKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRE   75 (369)
Q Consensus        18 ~~~~~Q~~~~~~~------~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~   75 (369)
                      +|++-|+++++.+      .++.++++.|+-|+|||..+ -.+.+.+...  +..+++++|+-.
T Consensus         1 ~Ln~eQ~~~~~~v~~~~~~~~~~~~fv~G~~GtGKs~l~-~~i~~~~~~~--~~~~~~~a~tg~   61 (364)
T PF05970_consen    1 KLNEEQRRVFDTVIEAIENEEGLNFFVTGPAGTGKSFLI-KAIIDYLRSR--GKKVLVTAPTGI   61 (364)
T ss_pred             CCCHHHHHHHHHHHHHHHccCCcEEEEEcCCCCChhHHH-HHHHHHhccc--cceEEEecchHH
Confidence            4678899999888      67889999999999999764 4444444432  225777777643

The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].

>PRK08727 hypothetical protein; Validated

Probab=97.34  E-value=0.0016  Score=53.67  Aligned_cols=35  Identities=20%  Similarity=0.050  Sum_probs=22.5

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEc
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLA   71 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~   71 (369)
                      ..+++.||+|+|||..+.....+....+   .+++++.
T Consensus        42 ~~l~l~G~~G~GKThL~~a~~~~~~~~~---~~~~y~~   76 (233)
T PRK08727         42 DWLYLSGPAGTGKTHLALALCAAAEQAG---RSSAYLP   76 (233)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHcC---CcEEEEe
Confidence            4589999999999976544333333332   2666654

>PF13177 DNA_pol3_delta2: DNA polymerase III, delta subunit; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G 1IQP_E 2GNO_A 1SXJ_E 1A5T_A

Probab=97.32  E-value=0.00082  Score=51.89  Aligned_cols=124  Identities=10%  Similarity=0.093  Sum_probs=61.7

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHcc
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQA  113 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~  113 (369)
                      ...++.||.|+||+..+...+...+...... .   .|..-..       ++.......-++..+......         
T Consensus        20 ha~L~~G~~g~gk~~~a~~~a~~ll~~~~~~-~---~c~~c~~-------c~~~~~~~~~d~~~~~~~~~~---------   79 (162)
T PF13177_consen   20 HALLFHGPSGSGKKTLALAFARALLCSNPNE-D---PCGECRS-------CRRIEEGNHPDFIIIKPDKKK---------   79 (162)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHHC-TT-CT-T-----SSSHH-------HHHHHTT-CTTEEEEETTTSS---------
T ss_pred             eeEEEECCCCCCHHHHHHHHHHHHcCCCCCC-C---CCCCCHH-------HHHHHhccCcceEEEeccccc---------
Confidence            4579999999999988766666555443322 1   2222111       222211112233333322210         


Q ss_pred             CCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEEeeCC
Q 017573          114 GVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMP  180 (369)
Q Consensus       114 ~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~saT~~  180 (369)
                       ..|-+-....+...+...... ...+++|+||+|.+.... ...+.+++..-+....++++|..+.
T Consensus        80 -~~i~i~~ir~i~~~~~~~~~~-~~~KviiI~~ad~l~~~a-~NaLLK~LEepp~~~~fiL~t~~~~  143 (162)
T PF13177_consen   80 -KSIKIDQIREIIEFLSLSPSE-GKYKVIIIDEADKLTEEA-QNALLKTLEEPPENTYFILITNNPS  143 (162)
T ss_dssp             -SSBSHHHHHHHHHHCTSS-TT-SSSEEEEEETGGGS-HHH-HHHHHHHHHSTTTTEEEEEEES-GG
T ss_pred             -chhhHHHHHHHHHHHHHHHhc-CCceEEEeehHhhhhHHH-HHHHHHHhcCCCCCEEEEEEECChH
Confidence             012121112222222222222 347899999999876443 5667777777777777666665554

...

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=97.31  E-value=0.0021  Score=58.75  Aligned_cols=105  Identities=13%  Similarity=0.243  Sum_probs=56.0

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHcc
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQA  113 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~  113 (369)
                      ..+++.||+|+|||..+. ++.+.+.....+.+++++.. ..+..+....++.                           
T Consensus       149 ~~l~l~G~~G~GKThL~~-ai~~~~~~~~~~~~v~yi~~-~~~~~~~~~~~~~---------------------------  199 (450)
T PRK00149        149 NPLFIYGGVGLGKTHLLH-AIGNYILEKNPNAKVVYVTS-EKFTNDFVNALRN---------------------------  199 (450)
T ss_pred             CeEEEECCCCCCHHHHHH-HHHHHHHHhCCCCeEEEEEH-HHHHHHHHHHHHc---------------------------
Confidence            458999999999997654 34444443322335666644 3444433332211                           


Q ss_pred             CCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccC-cHHHHHHHHhhCCc-cCcEEEEEeeCCh
Q 017573          114 GVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRG-FKDQIYDIFQLLPA-KVQVGVFSATMPP  181 (369)
Q Consensus       114 ~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~-~~~~~~~~~~~~~~-~~~~i~~saT~~~  181 (369)
                            .+.+.+...+.       ..+++++||+|.+.... ....+..+++.+.. ..+++ +|++.++
T Consensus       200 ------~~~~~~~~~~~-------~~dlLiiDDi~~l~~~~~~~~~l~~~~n~l~~~~~~ii-its~~~p  255 (450)
T PRK00149        200 ------NTMEEFKEKYR-------SVDVLLIDDIQFLAGKERTQEEFFHTFNALHEAGKQIV-LTSDRPP  255 (450)
T ss_pred             ------CcHHHHHHHHh-------cCCEEEEehhhhhcCCHHHHHHHHHHHHHHHHCCCcEE-EECCCCH
Confidence                  01123333222       26899999999885432 23445555544432 34444 5555443

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=97.30  E-value=0.004  Score=52.83  Aligned_cols=78  Identities=14%  Similarity=0.089  Sum_probs=47.9

Q ss_pred             HHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHH
Q 017573            5 ENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVM   84 (369)
Q Consensus         5 ~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~   84 (369)
                      +++.++|..-+..+-.+.-.+++.-+..+.-+++.|++|+|||..++..+.+.+...  +.+++|++--. -..++.+.+
T Consensus         2 ~~~~~~~~~~~~~tg~~~Ld~~~gG~~~g~~~~i~g~~G~GKT~l~~~~~~~~~~~~--g~~vl~iS~E~-~~~~~~~r~   78 (271)
T cd01122           2 EEIREALSNEEVWWPFPVLNKLTKGLRKGELIILTAGTGVGKTTFLREYALDLITQH--GVRVGTISLEE-PVVRTARRL   78 (271)
T ss_pred             chhhccccccCCCCCcceeeeeeEEEcCCcEEEEEcCCCCCHHHHHHHHHHHHHHhc--CceEEEEEccc-CHHHHHHHH
Confidence            355666665455554444444555566678899999999999987766666554441  22788876432 234444444


Q ss_pred             H
Q 017573           85 R   85 (369)
Q Consensus        85 ~   85 (369)
                      .
T Consensus        79 ~   79 (271)
T cd01122          79 L   79 (271)
T ss_pred             H
Confidence            3

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

>TIGR01074 rep ATP-dependent DNA helicase Rep

Probab=97.30  E-value=0.00065  Score=65.45  Aligned_cols=69  Identities=17%  Similarity=0.132  Sum_probs=56.3

Q ss_pred             CCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhc-cCCCccEEEEcCCHHHHHHHHHHHHHhc
Q 017573           18 KPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY-GLVQCQALVLAPTRELAQQIEKVMRALG   88 (369)
Q Consensus        18 ~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~-~~~~~~~liv~P~~~l~~q~~~~~~~~~   88 (369)
                      .+++-|++++.+  ..++++|.|++|||||.+.+.-+...+.. +....++++|+.++.-+.++.+.+.+..
T Consensus         1 ~Ln~~Q~~av~~--~~~~~~V~Ag~GSGKT~~L~~ri~~ll~~~~~~p~~IL~vTFt~~Aa~em~~Rl~~~l   70 (664)
T TIGR01074         1 KLNPQQQEAVEY--VTGPCLVLAGAGSGKTRVITNKIAYLIQNCGYKARNIAAVTFTNKAAREMKERVAKTL   70 (664)
T ss_pred             CCCHHHHHHHhC--CCCCEEEEecCCCCHHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHHh
Confidence            378899999875  35789999999999999988888877754 3334489999999999999999887754

Designed to identify rep members of the uvrD/rep subfamily.

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.30  E-value=0.0013  Score=60.52  Aligned_cols=38  Identities=13%  Similarity=0.294  Sum_probs=25.8

Q ss_pred             CccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEE
Q 017573          138 YIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFS  176 (369)
Q Consensus       138 ~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~s  176 (369)
                      +++++|+||+|++.... ...+.+.+...|+...+++.|
T Consensus       119 ~~kV~iIDE~~~ls~~a-~naLLk~LEepp~~~~fIlat  156 (509)
T PRK14958        119 RFKVYLIDEVHMLSGHS-FNALLKTLEEPPSHVKFILAT  156 (509)
T ss_pred             CcEEEEEEChHhcCHHH-HHHHHHHHhccCCCeEEEEEE
Confidence            46899999999986544 344555666666666666544

>PRK11773 uvrD DNA-dependent helicase II; Provisional

Probab=97.28  E-value=0.00068  Score=65.65  Aligned_cols=71  Identities=14%  Similarity=0.151  Sum_probs=57.7

Q ss_pred             CCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhc-cCCCccEEEEcCCHHHHHHHHHHHHHhcc
Q 017573           17 EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY-GLVQCQALVLAPTRELAQQIEKVMRALGD   89 (369)
Q Consensus        17 ~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~-~~~~~~~liv~P~~~l~~q~~~~~~~~~~   89 (369)
                      ..|++-|++++.+.  .+.++|.|++|||||.+...-+...+.. +-...++|+++-|+..+.++.+.+.+...
T Consensus         8 ~~Ln~~Q~~av~~~--~g~~lV~AgaGSGKT~vl~~Ria~Li~~~~v~p~~IL~lTFT~kAA~Em~~Rl~~~~~   79 (721)
T PRK11773          8 DSLNDKQREAVAAP--LGNMLVLAGAGSGKTRVLVHRIAWLMQVENASPYSIMAVTFTNKAAAEMRHRIEQLLG   79 (721)
T ss_pred             HhcCHHHHHHHhCC--CCCEEEEecCCCCHHHHHHHHHHHHHHcCCCChhHeEeeeccHHHHHHHHHHHHHHhc
Confidence            46999999999753  5789999999999999987777766653 33334899999999999999999887643

>PRK07952 DNA replication protein DnaC; Validated

Probab=97.26  E-value=0.0035  Score=51.69  Aligned_cols=48  Identities=19%  Similarity=0.115  Sum_probs=29.3

Q ss_pred             cHhhhhhhhcccc--------CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEE
Q 017573           20 SAIQQRGIVPFCK--------GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVL   70 (369)
Q Consensus        20 ~~~Q~~~~~~~~~--------~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv   70 (369)
                      .+.|+.++..+.+        ...+++.+++|+|||..+...+.+....+.   +++++
T Consensus        78 ~~~q~~al~~a~~~~~~~~~~~~~~~l~G~~GtGKThLa~aia~~l~~~g~---~v~~i  133 (244)
T PRK07952         78 CEGQMNALSKARQYVEEFDGNIASFIFSGKPGTGKNHLAAAICNELLLRGK---SVLII  133 (244)
T ss_pred             CchHHHHHHHHHHHHHhhccCCceEEEECCCCCCHHHHHHHHHHHHHhcCC---eEEEE
Confidence            3456556544432        147899999999999776544444333322   56555

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=97.24  E-value=0.0016  Score=61.54  Aligned_cols=38  Identities=13%  Similarity=0.295  Sum_probs=24.2

Q ss_pred             CccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEE
Q 017573          138 YIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFS  176 (369)
Q Consensus       138 ~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~s  176 (369)
                      +++++||||+|++.... ...+.+++..-++...+|+.|
T Consensus       119 r~KVIIIDEah~LT~~A-~NALLKtLEEPP~~v~FILaT  156 (830)
T PRK07003        119 RFKVYMIDEVHMLTNHA-FNAMLKTLEEPPPHVKFILAT  156 (830)
T ss_pred             CceEEEEeChhhCCHHH-HHHHHHHHHhcCCCeEEEEEE
Confidence            47899999999986544 344455555555555455433

>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=97.24  E-value=0.00025  Score=54.81  Aligned_cols=124  Identities=19%  Similarity=0.228  Sum_probs=53.6

Q ss_pred             EEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHccCCc
Q 017573           37 IQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVH  116 (369)
Q Consensus        37 li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~  116 (369)
                      ++.|+-|-|||.+.-+++...+..+.  .++++-+|+.+-++...+.+.+-....+.+....   ...........++..
T Consensus         1 VltA~RGRGKSa~lGl~~a~l~~~~~--~~I~vtAP~~~~~~~lf~~~~~~l~~~~~~~~~~---~~~~~~~~~~~~~~~   75 (177)
T PF05127_consen    1 VLTADRGRGKSAALGLAAAALIQKGK--IRILVTAPSPENVQTLFEFAEKGLKALGYKEEKK---KRIGQIIKLRFNKQR   75 (177)
T ss_dssp             -EEE-TTSSHHHHHHHCCCCSSS-------EEEE-SS--S-HHHHHCC-----------------------------CCC
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHhcC--ceEEEecCCHHHHHHHHHHHHhhccccccccccc---cccccccccccccce
Confidence            47899999999765444444443333  3799999999887777766655433333332000   000000111123456


Q ss_pred             EEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEEeeCC
Q 017573          117 VVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMP  180 (369)
Q Consensus       117 iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~saT~~  180 (369)
                      |-+..|+.+....       ...|++|+|||=.+    ....+..++...+    .+.+|.|..
T Consensus        76 i~f~~Pd~l~~~~-------~~~DlliVDEAAaI----p~p~L~~ll~~~~----~vv~stTi~  124 (177)
T PF05127_consen   76 IEFVAPDELLAEK-------PQADLLIVDEAAAI----PLPLLKQLLRRFP----RVVFSTTIH  124 (177)
T ss_dssp             --B--HHHHCCT-----------SCEEECTGGGS-----HHHHHHHHCCSS----EEEEEEEBS
T ss_pred             EEEECCHHHHhCc-------CCCCEEEEechhcC----CHHHHHHHHhhCC----EEEEEeecc
Confidence            7777777664321       12489999999876    3445555554443    566677764

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.

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=97.23  E-value=0.002  Score=54.22  Aligned_cols=21  Identities=33%  Similarity=0.295  Sum_probs=17.0

Q ss_pred             CCcEEEEcCCCChhhHHHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFCSG   53 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~   53 (369)
                      ..++++.||+|+|||..+-..
T Consensus        42 ~~~vll~GppGtGKTtlA~~i   62 (261)
T TIGR02881        42 VLHMIFKGNPGTGKTTVARIL   62 (261)
T ss_pred             cceEEEEcCCCCCHHHHHHHH
Confidence            367899999999999876433

Members of this protein family are the stage V sporulation protein K (SpoVK), a close homolog of the Rubisco expression protein CbbX (TIGR02880) and a members of the ATPase family associated with various cellular activities (pfam00004). Members are strictly limited to bacterial endospore-forming species, but are not universal in this group and are missing from the Clostridium group.

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.23  E-value=0.0021  Score=58.44  Aligned_cols=22  Identities=27%  Similarity=0.223  Sum_probs=17.8

Q ss_pred             CcEEEEcCCCChhhHHHHHHHH
Q 017573           34 LDVIQQAQSGTGKTATFCSGIL   55 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~   55 (369)
                      +..+++||.|+|||.++.+.+.
T Consensus        36 ha~Lf~Gp~G~GKTT~ArilAk   57 (491)
T PRK14964         36 QSILLVGASGVGKTTCARIISL   57 (491)
T ss_pred             ceEEEECCCCccHHHHHHHHHH
Confidence            5689999999999988754443

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=97.21  E-value=0.002  Score=55.40  Aligned_cols=138  Identities=8%  Similarity=-0.033  Sum_probs=68.1

Q ss_pred             CcHhhhhhhhcccc----C---CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhcccc
Q 017573           19 PSAIQQRGIVPFCK----G---LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYL   91 (369)
Q Consensus        19 ~~~~Q~~~~~~~~~----~---~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~   91 (369)
                      ++|+|+..++.+.+    +   ...++.||.|.||+..+...+...+-....+...   |-.       ...++.+....
T Consensus         3 ~yPW~~~~~~~l~~~~~~~rl~HA~Lf~G~~G~GK~~lA~~~A~~llC~~~~~~~~---Cg~-------C~sC~~~~~g~   72 (325)
T PRK06871          3 LYPWLQPTYQQITQAFQQGLGHHALLFKADSGLGTEQLIRALAQWLMCQTPQGDQP---CGQ-------CHSCHLFQAGN   72 (325)
T ss_pred             CCcchHHHHHHHHHHHHcCCcceeEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCC---CCC-------CHHHHHHhcCC
Confidence            47888888877663    2   4578999999999988765555444322111010   100       11233332222


Q ss_pred             CcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCccCc
Q 017573           92 GVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQ  171 (369)
Q Consensus        92 ~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~  171 (369)
                      .-++..+.+...           ..|-|-....+.+.+..... ....+++|+|++|.+.... ...+.+++..-|+...
T Consensus        73 HPD~~~i~p~~~-----------~~I~id~iR~l~~~~~~~~~-~g~~KV~iI~~a~~m~~~A-aNaLLKtLEEPp~~~~  139 (325)
T PRK06871         73 HPDFHILEPIDN-----------KDIGVDQVREINEKVSQHAQ-QGGNKVVYIQGAERLTEAA-ANALLKTLEEPRPNTY  139 (325)
T ss_pred             CCCEEEEccccC-----------CCCCHHHHHHHHHHHhhccc-cCCceEEEEechhhhCHHH-HHHHHHHhcCCCCCeE
Confidence            222332222100           01211122222222222222 2346899999999986433 4555566666555555


Q ss_pred             EEEEEeeC
Q 017573          172 VGVFSATM  179 (369)
Q Consensus       172 ~i~~saT~  179 (369)
                      +++.|..+
T Consensus       140 fiL~t~~~  147 (325)
T PRK06871        140 FLLQADLS  147 (325)
T ss_pred             EEEEECCh
Confidence            55544443

>COG2256 MGS1 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]

Probab=97.19  E-value=0.002  Score=55.68  Aligned_cols=17  Identities=35%  Similarity=0.374  Sum_probs=15.2

Q ss_pred             CcEEEEcCCCChhhHHH
Q 017573           34 LDVIQQAQSGTGKTATF   50 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~   50 (369)
                      .+.|+++|+|+|||..+
T Consensus        49 ~SmIl~GPPG~GKTTlA   65 (436)
T COG2256          49 HSMILWGPPGTGKTTLA   65 (436)
T ss_pred             ceeEEECCCCCCHHHHH
Confidence            56899999999999876

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.17  E-value=0.0023  Score=59.64  Aligned_cols=39  Identities=15%  Similarity=0.316  Sum_probs=24.8

Q ss_pred             CccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEEee
Q 017573          138 YIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSAT  178 (369)
Q Consensus       138 ~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~saT  178 (369)
                      +++++|+||+|++.... ...+.+.+...+....+|+ ++|
T Consensus       118 k~KV~IIDEVh~LS~~A-~NALLKtLEEPP~~v~FIL-aTt  156 (702)
T PRK14960        118 RFKVYLIDEVHMLSTHS-FNALLKTLEEPPEHVKFLF-ATT  156 (702)
T ss_pred             CcEEEEEechHhcCHHH-HHHHHHHHhcCCCCcEEEE-EEC
Confidence            46899999999886443 3445555555555554554 444

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical

Probab=97.17  E-value=0.002  Score=53.01  Aligned_cols=132  Identities=15%  Similarity=0.155  Sum_probs=69.1

Q ss_pred             cCCcEEEEcCCCChhhHHHHHHHHHhhhc-cCCCccEEEEcCCHHHHHHHHHHHHHhcccc-----CcEEEEEECCcchH
Q 017573           32 KGLDVIQQAQSGTGKTATFCSGILQQLDY-GLVQCQALVLAPTRELAQQIEKVMRALGDYL-----GVKVHACVGGTSVR  105 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~~~~~~~~~~-~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~-----~~~v~~~~~~~~~~  105 (369)
                      .|..+++.+|+|+|||..++..+.+.+.+ +.   ++++++-. +-.+++.+++..+....     ..............
T Consensus        18 ~gs~~li~G~~GsGKT~l~~q~l~~~~~~~ge---~vlyvs~e-e~~~~l~~~~~s~g~d~~~~~~~g~l~~~d~~~~~~   93 (226)
T PF06745_consen   18 KGSVVLISGPPGSGKTTLALQFLYNGLKNFGE---KVLYVSFE-EPPEELIENMKSFGWDLEEYEDSGKLKIIDAFPERI   93 (226)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHHHT-----EEEEESS-S-HHHHHHHHHTTTS-HHHHHHTTSEEEEESSGGGS
T ss_pred             CCcEEEEEeCCCCCcHHHHHHHHHHhhhhcCC---cEEEEEec-CCHHHHHHHHHHcCCcHHHHhhcCCEEEEecccccc
Confidence            45778999999999999888888877776 55   78888854 33455666666542111     00111221111100


Q ss_pred             HHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhc----cCcHHHHHHHHhhCCccCcEEEEEee
Q 017573          106 EDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLS----RGFKDQIYDIFQLLPAKVQVGVFSAT  178 (369)
Q Consensus       106 ~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~----~~~~~~~~~~~~~~~~~~~~i~~saT  178 (369)
                      ..        .  -...+.+...+.+.. ...+.+.+|+|-...+..    ......+..+...+.......++++.
T Consensus        94 ~~--------~--~~~~~~l~~~i~~~i-~~~~~~~vVIDsls~l~~~~~~~~~r~~l~~l~~~l~~~~~t~llt~~  159 (226)
T PF06745_consen   94 GW--------S--PNDLEELLSKIREAI-EELKPDRVVIDSLSALLLYDDPEELRRFLRALIKFLKSRGVTTLLTSE  159 (226)
T ss_dssp             T---------T--SCCHHHHHHHHHHHH-HHHTSSEEEEETHHHHTTSSSGGGHHHHHHHHHHHHHHTTEEEEEEEE
T ss_pred             cc--------c--ccCHHHHHHHHHHHH-HhcCCCEEEEECHHHHhhcCCHHHHHHHHHHHHHHHHHCCCEEEEEEc
Confidence            00        0  122333333322210 111138999999988821    22334455555555555555566666

More than one copy is sometimes found in each protein in this entry. These include KaiC, which is one of the Kai proteins among which direct protein-protein association may be a critical process in the generation of circadian rhythms in cyanobacteria []. The circadian clock protein KaiC, is encoded in the kaiABC operon that controls circadian rhythms and may be universal in Cyanobacteria. Each member contains two copies of this domain, which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor. RadA/Sms is a highly conserved eubacterial protein that shares sequence similarity with both RecA strand transferase and lon protease. The RadA/Sms family are probable ATP-dependent proteases involved in both DNA repair and degradation of proteins, peptides, glycopeptides. They are classified in as non-peptidase homologues and unassigned peptidases in MEROPS peptidase family S16 (lon protease family, clan SJ). RadA/Sms is involved in recombination and recombinational repair, most likely involving the stabilisation or processing of branched DNA molecules or blocked replication forks because of its genetic redundancy with RecG and RuvABC [].; PDB: 2W0M_A 2ZTS_C 4DUG_B 3K0E_B 3K09_B 3S1A_E 3JZM_E 2GBL_B 3DVL_A 1TF7_C ....

>PRK09183 transposase/IS protein; Provisional

Probab=97.16  E-value=0.011  Score=49.49  Aligned_cols=39  Identities=15%  Similarity=0.178  Sum_probs=26.7

Q ss_pred             cccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEc
Q 017573           30 FCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLA   71 (369)
Q Consensus        30 ~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~   71 (369)
                      +..+.++++.||+|+|||..+..........+.   +++++.
T Consensus        99 i~~~~~v~l~Gp~GtGKThLa~al~~~a~~~G~---~v~~~~  137 (259)
T PRK09183         99 IERNENIVLLGPSGVGKTHLAIALGYEAVRAGI---KVRFTT  137 (259)
T ss_pred             hhcCCeEEEEeCCCCCHHHHHHHHHHHHHHcCC---eEEEEe
Confidence            456789999999999999776555443333332   566653

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.14  E-value=0.0027  Score=59.13  Aligned_cols=39  Identities=15%  Similarity=0.378  Sum_probs=24.2

Q ss_pred             CccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEEe
Q 017573          138 YIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSA  177 (369)
Q Consensus       138 ~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~sa  177 (369)
                      +++++||||+|++....+ +.+.++++.-+....+|+.|-
T Consensus       124 r~KViIIDEah~Ls~~Aa-NALLKTLEEPP~~v~FILaTt  162 (700)
T PRK12323        124 RFKVYMIDEVHMLTNHAF-NAMLKTLEEPPEHVKFILATT  162 (700)
T ss_pred             CceEEEEEChHhcCHHHH-HHHHHhhccCCCCceEEEEeC
Confidence            478999999999864432 334444444445555555443

>COG1435 Tdk Thymidine kinase [Nucleotide transport and metabolism]

Probab=97.14  E-value=0.011  Score=46.08  Aligned_cols=104  Identities=18%  Similarity=0.202  Sum_probs=60.5

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHcc
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQA  113 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~  113 (369)
                      .-.++.+|+.||||...+..+.+....+.   ++++..|...-          .   .+........+..          
T Consensus         5 ~l~~i~gpM~SGKT~eLl~r~~~~~~~g~---~v~vfkp~iD~----------R---~~~~~V~Sr~G~~----------   58 (201)
T COG1435           5 WLEFIYGPMFSGKTEELLRRARRYKEAGM---KVLVFKPAIDT----------R---YGVGKVSSRIGLS----------   58 (201)
T ss_pred             EEEEEEccCcCcchHHHHHHHHHHHHcCC---eEEEEeccccc----------c---cccceeeeccCCc----------
Confidence            34589999999999876666555554544   88998886321          0   0111111122221          


Q ss_pred             CCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhh
Q 017573          114 GVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQL  165 (369)
Q Consensus       114 ~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~  165 (369)
                      ..-+.|-+...+...+........ +++|.+||++.+... .-..+..+.+.
T Consensus        59 ~~A~~i~~~~~i~~~i~~~~~~~~-~~~v~IDEaQF~~~~-~v~~l~~lad~  108 (201)
T COG1435          59 SEAVVIPSDTDIFDEIAALHEKPP-VDCVLIDEAQFFDEE-LVYVLNELADR  108 (201)
T ss_pred             ccceecCChHHHHHHHHhcccCCC-cCEEEEehhHhCCHH-HHHHHHHHHhh
Confidence            123556666777777666443333 689999999976432 23444444444

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=97.12  E-value=0.0025  Score=61.89  Aligned_cols=39  Identities=21%  Similarity=0.374  Sum_probs=26.5

Q ss_pred             CCccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEE
Q 017573          137 DYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFS  176 (369)
Q Consensus       137 ~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~s  176 (369)
                      .+++++||||+|++.... ...+.++++..+....+|+.|
T Consensus       119 ~~~KV~IIDEad~lt~~a-~NaLLK~LEEpP~~~~fIl~t  157 (824)
T PRK07764        119 SRYKIFIIDEAHMVTPQG-FNALLKIVEEPPEHLKFIFAT  157 (824)
T ss_pred             CCceEEEEechhhcCHHH-HHHHHHHHhCCCCCeEEEEEe
Confidence            347899999999986443 445556666666666566544

>PRK08116 hypothetical protein; Validated

Probab=97.10  E-value=0.0091  Score=50.29  Aligned_cols=41  Identities=20%  Similarity=0.174  Sum_probs=25.1

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHH
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQ   78 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~   78 (369)
                      ..++++|++|+|||..+.. +++.+....  ..++++ +...+..
T Consensus       115 ~gl~l~G~~GtGKThLa~a-ia~~l~~~~--~~v~~~-~~~~ll~  155 (268)
T PRK08116        115 VGLLLWGSVGTGKTYLAAC-IANELIEKG--VPVIFV-NFPQLLN  155 (268)
T ss_pred             ceEEEECCCCCCHHHHHHH-HHHHHHHcC--CeEEEE-EHHHHHH
Confidence            3499999999999987654 444443322  245554 4344444

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.08  E-value=0.0024  Score=61.51  Aligned_cols=37  Identities=14%  Similarity=0.267  Sum_probs=23.2

Q ss_pred             CccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEE
Q 017573          138 YIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVF  175 (369)
Q Consensus       138 ~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~  175 (369)
                      +++++||||+|++.... ...+.+++..-+....+|+.
T Consensus       119 k~KViIIDEAh~LT~eA-qNALLKtLEEPP~~vrFILa  155 (944)
T PRK14949        119 RFKVYLIDEVHMLSRSS-FNALLKTLEEPPEHVKFLLA  155 (944)
T ss_pred             CcEEEEEechHhcCHHH-HHHHHHHHhccCCCeEEEEE
Confidence            46899999999985332 34445555554545544443

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=97.06  E-value=0.0056  Score=53.78  Aligned_cols=38  Identities=13%  Similarity=0.201  Sum_probs=23.9

Q ss_pred             CccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEE
Q 017573          138 YIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFS  176 (369)
Q Consensus       138 ~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~s  176 (369)
                      ..+++|+||+|.+... ....+..++...+....+++.+
T Consensus       125 ~~~vlilDe~~~l~~~-~~~~L~~~le~~~~~~~~Il~~  162 (337)
T PRK12402        125 DYKTILLDNAEALRED-AQQALRRIMEQYSRTCRFIIAT  162 (337)
T ss_pred             CCcEEEEeCcccCCHH-HHHHHHHHHHhccCCCeEEEEe
Confidence            3579999999987532 2344555555555556555533

>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif

Probab=97.06  E-value=0.00093  Score=52.43  Aligned_cols=66  Identities=20%  Similarity=0.311  Sum_probs=30.4

Q ss_pred             HHHHhCCCCCCcHhhhhhhhcc------ccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHH
Q 017573            9 RGIYAYGFEKPSAIQQRGIVPF------CKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQ   78 (369)
Q Consensus         9 ~~l~~~~~~~~~~~Q~~~~~~~------~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~   78 (369)
                      ..++.+.+...+..++..+..+      .+++++++.||+|+|||..+...+.+.+..+.   +++++ +...|..
T Consensus        17 ~~~~~~d~~~~~~~~~~~~~~l~~~~~~~~~~~l~l~G~~G~GKThLa~ai~~~~~~~g~---~v~f~-~~~~L~~   88 (178)
T PF01695_consen   17 ATLENFDFSNERGIDKAQIAQLAALEFIENGENLILYGPPGTGKTHLAVAIANEAIRKGY---SVLFI-TASDLLD   88 (178)
T ss_dssp             -----------------HHHHHHHH-S-SC--EEEEEESTTSSHHHHHHHHHHHHHHTT-----EEEE-EHHHHHH
T ss_pred             cccccccccchhhHHHHHHHHHhcCCCcccCeEEEEEhhHhHHHHHHHHHHHHHhccCCc---ceeEe-ecCceec
Confidence            3445555555555555555443      35689999999999999887666666655443   56664 4444544

They are found associated with IS21 family insertion sequences []. Functionally they have not been characterised, but they may be involved in transposition [].; GO: 0005524 ATP binding; PDB: 3EC2_A 3ECC_A 2W58_A 2QGZ_A.

>PTZ00293 thymidine kinase; Provisional

Probab=97.04  E-value=0.0085  Score=47.84  Aligned_cols=39  Identities=13%  Similarity=0.054  Sum_probs=27.9

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCH
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTR   74 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~   74 (369)
                      |.=-++.||+++|||.-.+..+.+....+.   +++++-|..
T Consensus         4 G~i~vi~GpMfSGKTteLLr~i~~y~~ag~---kv~~~kp~~   42 (211)
T PTZ00293          4 GTISVIIGPMFSGKTTELMRLVKRFTYSEK---KCVVIKYSK   42 (211)
T ss_pred             eEEEEEECCCCChHHHHHHHHHHHHHHcCC---ceEEEEecc
Confidence            344588999999999766655555444443   799988864

>PLN03025 replication factor C subunit; Provisional

Probab=97.03  E-value=0.008  Score=52.25  Aligned_cols=40  Identities=20%  Similarity=0.361  Sum_probs=25.6

Q ss_pred             CccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEEeeC
Q 017573          138 YIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATM  179 (369)
Q Consensus       138 ~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~saT~  179 (369)
                      ..+++|+||+|.+.... ...+.+.+...++...+++ +++.
T Consensus        99 ~~kviiiDE~d~lt~~a-q~aL~~~lE~~~~~t~~il-~~n~  138 (319)
T PLN03025         99 RHKIVILDEADSMTSGA-QQALRRTMEIYSNTTRFAL-ACNT  138 (319)
T ss_pred             CeEEEEEechhhcCHHH-HHHHHHHHhcccCCceEEE-EeCC
Confidence            36899999999986433 4555566666555555554 4443

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=97.03  E-value=0.0077  Score=54.58  Aligned_cols=36  Identities=17%  Similarity=0.174  Sum_probs=23.6

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcC
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAP   72 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P   72 (369)
                      ..+++.||+|+|||..+. ++.+.+...  +.+++++..
T Consensus       142 npl~L~G~~G~GKTHLl~-Ai~~~l~~~--~~~v~yi~~  177 (445)
T PRK12422        142 NPIYLFGPEGSGKTHLMQ-AAVHALRES--GGKILYVRS  177 (445)
T ss_pred             ceEEEEcCCCCCHHHHHH-HHHHHHHHc--CCCEEEeeH
Confidence            358999999999997654 444444322  236777654

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=97.03  E-value=0.0032  Score=54.70  Aligned_cols=140  Identities=10%  Similarity=-0.036  Sum_probs=71.5

Q ss_pred             CCcHhhhhhhhcccc----C---CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccc
Q 017573           18 KPSAIQQRGIVPFCK----G---LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDY   90 (369)
Q Consensus        18 ~~~~~Q~~~~~~~~~----~---~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~   90 (369)
                      .++|+|+..++.+.+    +   ...++.||.|.||+..+...+...+-..+.+...-=.|++          ++.+...
T Consensus         2 ~~yPWl~~~~~~l~~~~~~~rl~HA~Lf~G~~G~Gk~~lA~~~A~~LlC~~~~~~~~Cg~C~s----------C~~~~~g   71 (334)
T PRK07993          2 KWYPWLRPDYEQLVGSYQAGRGHHALLIQALPGMGDDALIYALSRWLMCQQPQGHKSCGHCRG----------CQLMQAG   71 (334)
T ss_pred             CCCCCChHHHHHHHHHHHcCCcceEEeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHH----------HHHHHcC
Confidence            468899999888763    2   3578999999999988765555444322111011001222          3333222


Q ss_pred             cCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCccC
Q 017573           91 LGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKV  170 (369)
Q Consensus        91 ~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~  170 (369)
                      ..-++..+.+...          +..|-|-....+.+.+...... ...+++|+|++|.+.... ...+.+++..=|+..
T Consensus        72 ~HPD~~~i~p~~~----------~~~I~idqiR~l~~~~~~~~~~-g~~kV~iI~~ae~m~~~A-aNaLLKtLEEPp~~t  139 (334)
T PRK07993         72 THPDYYTLTPEKG----------KSSLGVDAVREVTEKLYEHARL-GGAKVVWLPDAALLTDAA-ANALLKTLEEPPENT  139 (334)
T ss_pred             CCCCEEEEecccc----------cccCCHHHHHHHHHHHhhcccc-CCceEEEEcchHhhCHHH-HHHHHHHhcCCCCCe
Confidence            2223333322111          0112222222333333333322 346899999999985332 445555555545555


Q ss_pred             cEEEEEeeC
Q 017573          171 QVGVFSATM  179 (369)
Q Consensus       171 ~~i~~saT~  179 (369)
                      .++++|..+
T Consensus       140 ~fiL~t~~~  148 (334)
T PRK07993        140 WFFLACREP  148 (334)
T ss_pred             EEEEEECCh
Confidence            555555444

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=97.02  E-value=0.014  Score=47.92  Aligned_cols=53  Identities=17%  Similarity=0.117  Sum_probs=35.6

Q ss_pred             ccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHh
Q 017573           31 CKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRAL   87 (369)
Q Consensus        31 ~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~   87 (369)
                      ..+.-+++.+++|+|||..++..+...+..+.   ++++++.. .-..+..+.+..+
T Consensus        22 ~~g~~~~i~G~~G~GKTtl~~~~~~~~~~~g~---~~~yi~~e-~~~~~~~~~~~~~   74 (230)
T PRK08533         22 PAGSLILIEGDESTGKSILSQRLAYGFLQNGY---SVSYVSTQ-LTTTEFIKQMMSL   74 (230)
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHHHhCCC---cEEEEeCC-CCHHHHHHHHHHh
Confidence            44678899999999999886666665544443   78888854 3334555555443

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.00  E-value=0.003  Score=55.90  Aligned_cols=37  Identities=11%  Similarity=0.269  Sum_probs=22.2

Q ss_pred             CccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEE
Q 017573          138 YIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVF  175 (369)
Q Consensus       138 ~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~  175 (369)
                      ..+++|+||+|.+.... ...+.+.+...+....+++.
T Consensus       119 ~~kviIIDEa~~l~~~a-~naLLk~lEe~~~~~~fIl~  155 (363)
T PRK14961        119 RFKVYLIDEVHMLSRHS-FNALLKTLEEPPQHIKFILA  155 (363)
T ss_pred             CceEEEEEChhhcCHHH-HHHHHHHHhcCCCCeEEEEE
Confidence            35899999999986433 23344444444445545543

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=96.99  E-value=0.006  Score=54.89  Aligned_cols=36  Identities=28%  Similarity=0.387  Sum_probs=22.6

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEE
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVL   70 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv   70 (369)
                      .+++|.||+|+|||..+- .++..+........++++
T Consensus        56 ~~~lI~G~~GtGKT~l~~-~v~~~l~~~~~~~~~v~i   91 (394)
T PRK00411         56 LNVLIYGPPGTGKTTTVK-KVFEELEEIAVKVVYVYI   91 (394)
T ss_pred             CeEEEECCCCCCHHHHHH-HHHHHHHHhcCCcEEEEE
Confidence            679999999999997754 344444332222245555

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=96.99  E-value=0.008  Score=49.79  Aligned_cols=52  Identities=21%  Similarity=0.213  Sum_probs=38.2

Q ss_pred             cCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHh
Q 017573           32 KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRAL   87 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~   87 (369)
                      .|..++|.||+|+|||..++..+.+.+..+.   +++|++-. .-..+..+++..+
T Consensus        20 ~gs~~lI~G~pGsGKT~la~~~l~~~~~~ge---~~lyvs~e-e~~~~i~~~~~~~   71 (237)
T TIGR03877        20 ERNVVLLSGGPGTGKSIFSQQFLWNGLQMGE---PGIYVALE-EHPVQVRRNMAQF   71 (237)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHHHcCC---cEEEEEee-CCHHHHHHHHHHh
Confidence            3577899999999999988777777665544   78888843 4555666666654

Members of this family contain a single copy of the KaiC domain (pfam06745) that occurs in two copies of the circadian clock protein kinase KaiC itself. Members occur primarily in thermophilic archaea and in Thermotoga.

>TIGR01547 phage_term_2 phage terminase, large subunit, PBSX family

Probab=96.98  E-value=0.0029  Score=56.92  Aligned_cols=148  Identities=16%  Similarity=0.220  Sum_probs=78.5

Q ss_pred             cEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHH-HHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHcc
Q 017573           35 DVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRE-LAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQA  113 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~-l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~  113 (369)
                      -.++.++.|||||.++...++..+.....+.+++++-|+.. +.......+.......++....-....+.  .......
T Consensus         3 ~~i~~GgrgSGKS~~~~~~~~~~~~~~~~~~~~~~~r~~~~sl~~sv~~~l~~~i~~~g~~~~~~~~~~~~--~i~~~~~   80 (396)
T TIGR01547         3 EIIAKGGRRSGKTFAIALKLVEKLAINKKQQNILAARKVQNSIRDSVFKDIENLLSIEGINYEFKKSKSSM--EIKILNT   80 (396)
T ss_pred             eEEEeCCCCcccHHHHHHHHHHHHHhcCCCcEEEEEehhhhHHHHHHHHHHHHHHHHcCChhheeecCCcc--EEEecCC
Confidence            35789999999998887766666555322347888888876 55666777766555445432221111110  0001111


Q ss_pred             CCcEEEecc-HHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEEeeCChhHHHHHHHhc
Q 017573          114 GVHVVVGTP-GRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFM  191 (369)
Q Consensus       114 ~~~iiv~t~-~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~  191 (369)
                      +..|++..- +.... +..    ...++.+.+||+..+....+.....+ ++. +.....+++|.+|....--....+.
T Consensus        81 g~~i~f~g~~d~~~~-ik~----~~~~~~~~idEa~~~~~~~~~~l~~r-lr~-~~~~~~i~~t~NP~~~~~w~~~~f~  152 (396)
T TIGR01547        81 GKKFIFKGLNDKPNK-LKS----GAGIAIIWFEEASQLTFEDIKELIPR-LRE-TGGKKFIIFSSNPESPLHWVKKRFI  152 (396)
T ss_pred             CeEEEeecccCChhH-hhC----cceeeeehhhhhhhcCHHHHHHHHHH-hhc-cCCccEEEEEcCcCCCccHHHHHHH
Confidence            334555443 22211 111    12268999999998854433333322 222 1222247789998653333333433

This model detects members of a highly divergent family of the large subunit of phage terminase. All members are encoded by phage genomes or within prophage regions of bacterial genomes. This is a distinct family from pfam03354.

>PHA03368 DNA packaging terminase subunit 1; Provisional

Probab=96.95  E-value=0.004  Score=57.71  Aligned_cols=134  Identities=12%  Similarity=0.111  Sum_probs=79.9

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhcccc--CcEEEEEECCcchHHHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYL--GVKVHACVGGTSVREDQRI  110 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~--~~~v~~~~~~~~~~~~~~~  110 (369)
                      .+-.++..|--.|||.+.. +++..+.....+-++++.+|....++...+++.......  +..+....| ...   ...
T Consensus       254 qk~tVflVPRR~GKTwivv-~iI~~ll~s~~Gi~IgytAH~~~ts~~vF~eI~~~le~~f~~~~v~~vkG-e~I---~i~  328 (738)
T PHA03368        254 QRATVFLVPRRHGKTWFLV-PLIALALATFRGIKIGYTAHIRKATEPVFEEIGARLRQWFGASRVDHVKG-ETI---SFS  328 (738)
T ss_pred             ccceEEEecccCCchhhHH-HHHHHHHHhCCCCEEEEEcCcHHHHHHHHHHHHHHHhhhcchhheeeecC-cEE---EEE
Confidence            4678999999999998765 333333323234489999999999999998887754421  111222222 111   000


Q ss_pred             HccC--CcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEEeeCC
Q 017573          111 LQAG--VHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMP  180 (369)
Q Consensus       111 ~~~~--~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~saT~~  180 (369)
                      +.++  ..|.+.|      ....+......++++|+|||+.+....+...+ .++..  .+++++++|.|-.
T Consensus       329 f~nG~kstI~FaS------arntNsiRGqtfDLLIVDEAqFIk~~al~~il-p~l~~--~n~k~I~ISS~Ns  391 (738)
T PHA03368        329 FPDGSRSTIVFAS------SHNTNGIRGQDFNLLFVDEANFIRPDAVQTIM-GFLNQ--TNCKIIFVSSTNT  391 (738)
T ss_pred             ecCCCccEEEEEe------ccCCCCccCCcccEEEEechhhCCHHHHHHHH-HHHhc--cCccEEEEecCCC
Confidence            1111  2344432      12334456667999999999988655433333 22222  2778899998854

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.95  E-value=0.035  Score=50.74  Aligned_cols=40  Identities=15%  Similarity=0.114  Sum_probs=25.0

Q ss_pred             ccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEc
Q 017573           31 CKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLA   71 (369)
Q Consensus        31 ~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~   71 (369)
                      ..++.+.+.+|+|+|||..+...+....... .+.++.++.
T Consensus       348 ~~G~vIaLVGPtGvGKTTtaakLAa~la~~~-~gkkVaLId  387 (559)
T PRK12727        348 ERGGVIALVGPTGAGKTTTIAKLAQRFAAQH-APRDVALVT  387 (559)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHHHHHHHhc-CCCceEEEe
Confidence            3467889999999999987654444333322 122555554

>KOG0739 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=96.93  E-value=0.03  Score=46.58  Aligned_cols=120  Identities=18%  Similarity=0.156  Sum_probs=67.2

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHcc
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQA  113 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~  113 (369)
                      +.+++.+|+|+||+..+=..+      ...+ .+++-+.+..|+..|.-+-.++.                         
T Consensus       167 rgiLLyGPPGTGKSYLAKAVA------TEAn-STFFSvSSSDLvSKWmGESEkLV-------------------------  214 (439)
T KOG0739|consen  167 RGILLYGPPGTGKSYLAKAVA------TEAN-STFFSVSSSDLVSKWMGESEKLV-------------------------  214 (439)
T ss_pred             eeEEEeCCCCCcHHHHHHHHH------hhcC-CceEEeehHHHHHHHhccHHHHH-------------------------
Confidence            458999999999996542111      1122 57777777788765544333321                         


Q ss_pred             CCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccC---cHHHHHHHHhh----C---C-ccCcEEEEEeeCCh-
Q 017573          114 GVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRG---FKDQIYDIFQL----L---P-AKVQVGVFSATMPP-  181 (369)
Q Consensus       114 ~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~---~~~~~~~~~~~----~---~-~~~~~i~~saT~~~-  181 (369)
                               ..|+.+-++..     .++|.+||++.++...   -.+...++...    +   . ..--++.+.||..+ 
T Consensus       215 ---------knLFemARe~k-----PSIIFiDEiDslcg~r~enEseasRRIKTEfLVQMqGVG~d~~gvLVLgATNiPw  280 (439)
T KOG0739|consen  215 ---------KNLFEMARENK-----PSIIFIDEIDSLCGSRSENESEASRRIKTEFLVQMQGVGNDNDGVLVLGATNIPW  280 (439)
T ss_pred             ---------HHHHHHHHhcC-----CcEEEeehhhhhccCCCCCchHHHHHHHHHHHHhhhccccCCCceEEEecCCCch
Confidence                     12334444433     4889999999877422   22222333222    1   1 23446777888654 


Q ss_pred             hHHHHHHHhcCCCEEEEe
Q 017573          182 EALEITRKFMNKPVRILV  199 (369)
Q Consensus       182 ~~~~~~~~~~~~~~~~~~  199 (369)
                      .+...+++-+.+.+.+..
T Consensus       281 ~LDsAIRRRFekRIYIPL  298 (439)
T KOG0739|consen  281 VLDSAIRRRFEKRIYIPL  298 (439)
T ss_pred             hHHHHHHHHhhcceeccC
Confidence            444555666665554443

>PRK14712 conjugal transfer nickase/helicase TraI; Provisional

Probab=96.93  E-value=0.0061  Score=62.79  Aligned_cols=63  Identities=19%  Similarity=0.249  Sum_probs=44.5

Q ss_pred             CCCcHhhhhhhhccccC--CcEEEEcCCCChhhHHHHHHHHHhhhc--cCCCccEEEEcCCHHHHHHH
Q 017573           17 EKPSAIQQRGIVPFCKG--LDVIQQAQSGTGKTATFCSGILQQLDY--GLVQCQALVLAPTRELAQQI   80 (369)
Q Consensus        17 ~~~~~~Q~~~~~~~~~~--~~~li~~~tG~GKT~~~~~~~~~~~~~--~~~~~~~liv~P~~~l~~q~   80 (369)
                      ..+++-|++++..++.+  +-++|.+..|+|||.+. ..++..+..  ...+.+++.++|+-.-+..+
T Consensus       834 ~~Lt~~Qr~Av~~iLts~dr~~~IqG~AGTGKTT~l-~~i~~~~~~l~e~~g~~V~glAPTgkAa~~L  900 (1623)
T PRK14712        834 EKLTSGQRAATRMILETSDRFTVVQGYAGVGKTTQF-RAVMSAVNMLPESERPRVVGLGPTHRAVGEM  900 (1623)
T ss_pred             cccCHHHHHHHHHHHhCCCceEEEEeCCCCCHHHHH-HHHHHHHHHHhhccCceEEEEechHHHHHHH
Confidence            37999999999999865  67899999999999773 222322221  11233688899987665544

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=96.92  E-value=0.02  Score=51.50  Aligned_cols=130  Identities=15%  Similarity=0.168  Sum_probs=64.0

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCC--HHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHH
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPT--RELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL  111 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~--~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~  111 (369)
                      ..+++.+++|+|||.++...+.. +...  +.+++++...  +.-+   .+++..+....++.+........        
T Consensus        96 ~vI~lvG~~GsGKTTtaakLA~~-L~~~--g~kV~lV~~D~~R~aa---~eQL~~la~~~gvp~~~~~~~~d--------  161 (437)
T PRK00771         96 QTIMLVGLQGSGKTTTAAKLARY-FKKK--GLKVGLVAADTYRPAA---YDQLKQLAEKIGVPFYGDPDNKD--------  161 (437)
T ss_pred             eEEEEECCCCCcHHHHHHHHHHH-HHHc--CCeEEEecCCCCCHHH---HHHHHHHHHHcCCcEEecCCccC--------
Confidence            45789999999999887655543 3332  2256666542  2211   22333333333433321110000        


Q ss_pred             ccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhh-ccCcHHHHHHHHhhCCccCcEEEEEeeCChhHHHHHHHh
Q 017573          112 QAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEML-SRGFKDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKF  190 (369)
Q Consensus       112 ~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~-~~~~~~~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~  190 (369)
                               ..+.+...+....    ..++||+|.+-+.. +....+++..+.....+...++.++|+...+..+....+
T Consensus       162 ---------~~~i~~~al~~~~----~~DvVIIDTAGr~~~d~~lm~El~~l~~~~~pdevlLVvda~~gq~av~~a~~F  228 (437)
T PRK00771        162 ---------AVEIAKEGLEKFK----KADVIIVDTAGRHALEEDLIEEMKEIKEAVKPDEVLLVIDATIGQQAKNQAKAF  228 (437)
T ss_pred             ---------HHHHHHHHHHHhh----cCCEEEEECCCcccchHHHHHHHHHHHHHhcccceeEEEeccccHHHHHHHHHH
Confidence                     0011122222211    13889999885432 222334555555555555556777887765555555443

>CHL00181 cbbX CbbX; Provisional

Probab=96.92  E-value=0.008  Score=51.15  Aligned_cols=23  Identities=30%  Similarity=0.281  Sum_probs=18.0

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFCSGIL   55 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~   55 (369)
                      +.++++.||+|+|||.++-..+-
T Consensus        59 ~~~ill~G~pGtGKT~lAr~la~   81 (287)
T CHL00181         59 GLHMSFTGSPGTGKTTVALKMAD   81 (287)
T ss_pred             CceEEEECCCCCCHHHHHHHHHH
Confidence            45689999999999988754433

>TIGR01073 pcrA ATP-dependent DNA helicase PcrA

Probab=96.91  E-value=0.0033  Score=61.14  Aligned_cols=71  Identities=15%  Similarity=0.178  Sum_probs=57.3

Q ss_pred             CCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhcc-CCCccEEEEcCCHHHHHHHHHHHHHhcc
Q 017573           17 EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYG-LVQCQALVLAPTRELAQQIEKVMRALGD   89 (369)
Q Consensus        17 ~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~-~~~~~~liv~P~~~l~~q~~~~~~~~~~   89 (369)
                      ..|++-|++++.+.  .+.++|.|+.|||||.+...-+...+... -...++|.++-|+.-+..+.+.+.+...
T Consensus         3 ~~Ln~~Q~~av~~~--~g~~lV~AgaGSGKT~~l~~ria~Li~~~~i~P~~IL~lTFT~kAA~em~~Rl~~~~~   74 (726)
T TIGR01073         3 AHLNPEQREAVKTT--EGPLLIMAGAGSGKTRVLTHRIAHLIAEKNVAPWNILAITFTNKAAREMKERVEKLLG   74 (726)
T ss_pred             cccCHHHHHHHhCC--CCCEEEEeCCCCCHHHHHHHHHHHHHHcCCCCHHHeeeeeccHHHHHHHHHHHHHHhc
Confidence            46899999999763  57899999999999999887777777543 2334899999999999999888876643

Designed to identify pcrA members of the uvrD/rep subfamily.

>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA

Probab=96.90  E-value=0.0024  Score=59.56  Aligned_cols=126  Identities=15%  Similarity=0.097  Sum_probs=77.6

Q ss_pred             CCCcHhhhhhhhccccC--CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHH-HHHHHhccccCc
Q 017573           17 EKPSAIQQRGIVPFCKG--LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIE-KVMRALGDYLGV   93 (369)
Q Consensus        17 ~~~~~~Q~~~~~~~~~~--~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~-~~~~~~~~~~~~   93 (369)
                      ...+|||.+..+.+-..  +.+.+..+.-+|||.+++.++...+...+.  .+|++.|+...++++. +.+..+......
T Consensus        15 ~~~~Py~~eimd~~~~~~v~~Vv~~k~aQ~GkT~~~~n~~g~~i~~~P~--~~l~v~Pt~~~a~~~~~~rl~Pmi~~sp~   92 (557)
T PF05876_consen   15 TDRTPYLREIMDALSDPSVREVVVMKSAQVGKTELLLNWIGYSIDQDPG--PMLYVQPTDDAAKDFSKERLDPMIRASPV   92 (557)
T ss_pred             CCCChhHHHHHHhcCCcCccEEEEEEcchhhHhHHHHhhceEEEEeCCC--CEEEEEEcHHHHHHHHHHHHHHHHHhCHH
Confidence            46789999999998876  689999999999999776666665555443  7999999999999886 455544332211


Q ss_pred             EEEEEEC---Ccc-hHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhh
Q 017573           94 KVHACVG---GTS-VREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEML  151 (369)
Q Consensus        94 ~v~~~~~---~~~-~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~  151 (369)
                      --..+..   ... .......+. +..+.+....+-.      .+....++++++||++.+.
T Consensus        93 l~~~~~~~~~~~~~~t~~~k~f~-gg~l~~~ga~S~~------~l~s~~~r~~~~DEvD~~p  147 (557)
T PF05876_consen   93 LRRKLSPSKSRDSGNTILYKRFP-GGFLYLVGANSPS------NLRSRPARYLLLDEVDRYP  147 (557)
T ss_pred             HHHHhCchhhcccCCchhheecC-CCEEEEEeCCCCc------ccccCCcCEEEEechhhcc
Confidence            0011111   000 001111112 3345544432221      1233347899999999984

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].

>PRK13709 conjugal transfer nickase/helicase TraI; Provisional

Probab=96.89  E-value=0.0083  Score=62.60  Aligned_cols=63  Identities=17%  Similarity=0.225  Sum_probs=45.1

Q ss_pred             CCCcHhhhhhhhccccC--CcEEEEcCCCChhhHHHHHHHHHhhhc--cCCCccEEEEcCCHHHHHHH
Q 017573           17 EKPSAIQQRGIVPFCKG--LDVIQQAQSGTGKTATFCSGILQQLDY--GLVQCQALVLAPTRELAQQI   80 (369)
Q Consensus        17 ~~~~~~Q~~~~~~~~~~--~~~li~~~tG~GKT~~~~~~~~~~~~~--~~~~~~~liv~P~~~l~~q~   80 (369)
                      ..+++.|++++..++.+  +-++|.+..|+|||.+. -.+...+..  ...+.+++.++|+-.-+..+
T Consensus       966 ~~Lt~~Q~~Av~~il~s~dr~~~I~G~AGTGKTT~l-~~v~~~~~~l~~~~~~~V~glAPTgrAAk~L 1032 (1747)
T PRK13709        966 EGLTSGQRAATRMILESTDRFTVVQGYAGVGKTTQF-RAVMSAVNTLPESERPRVVGLGPTHRAVGEM 1032 (1747)
T ss_pred             CCCCHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHHH-HHHHHHHHHhhcccCceEEEECCcHHHHHHH
Confidence            47899999999999975  56899999999999763 344433321  11233688899997665543

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.89  E-value=0.005  Score=57.43  Aligned_cols=24  Identities=17%  Similarity=-0.002  Sum_probs=18.6

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHh
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQ   57 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~   57 (369)
                      ...|+.+|.|+|||.++...+...
T Consensus        39 ha~Lf~GPpG~GKTtiArilAk~L   62 (624)
T PRK14959         39 PAYLFSGTRGVGKTTIARIFAKAL   62 (624)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHhc
Confidence            457899999999999876555443

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.89  E-value=0.008  Score=54.81  Aligned_cols=21  Identities=29%  Similarity=0.134  Sum_probs=16.5

Q ss_pred             cEEEEcCCCChhhHHHHHHHH
Q 017573           35 DVIQQAQSGTGKTATFCSGIL   55 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~~~~~   55 (369)
                      ..+++||+|+|||..+-..+.
T Consensus        38 ~~Lf~GPpGtGKTTlA~~lA~   58 (472)
T PRK14962         38 AYIFAGPRGTGKTTVARILAK   58 (472)
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            369999999999988754433

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=96.88  E-value=0.0061  Score=56.60  Aligned_cols=24  Identities=21%  Similarity=0.004  Sum_probs=18.4

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHh
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQ   57 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~   57 (369)
                      +..++.||.|+|||..|...+...
T Consensus        39 hA~Lf~GP~GvGKTTlA~~lAk~L   62 (605)
T PRK05896         39 HAYIFSGPRGIGKTSIAKIFAKAI   62 (605)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHh
Confidence            457899999999998876554433

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=96.87  E-value=0.01  Score=50.43  Aligned_cols=20  Identities=30%  Similarity=0.336  Sum_probs=16.8

Q ss_pred             CCcEEEEcCCCChhhHHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFCS   52 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~   52 (369)
                      +.++++.||+|+|||.++..
T Consensus        58 ~~~vll~G~pGTGKT~lA~~   77 (284)
T TIGR02880        58 TLHMSFTGNPGTGKTTVALR   77 (284)
T ss_pred             CceEEEEcCCCCCHHHHHHH
Confidence            45899999999999987743

Proteins in this family are now designated CbbX. Some previously were CfxQ (carbon fixation Q). Its gene is often found immmediately downstream of the Rubisco large and small chain genes, and it is suggested to be necessary for Rubisco expression. CbbX has been shown to be necessary for photoautotrophic growth. This protein belongs to the larger family of pfam00004, ATPase family Associated with various cellular Activities. Within that larger family, members of this family are most closely related to the stage V sporulation protein K, or SpoVK, in endospore-forming bacteria such as Bacillus subtilis.

>COG4626 Phage terminase-like protein, large subunit [General function prediction only]

Probab=96.86  E-value=0.008  Score=54.39  Aligned_cols=149  Identities=12%  Similarity=0.011  Sum_probs=85.4

Q ss_pred             CCCcHhhhhhhhcccc------C----CcEEEEcCCCChhhHHHHHHH-HHhhhccCCCccEEEEcCCHHHHHHHHHHHH
Q 017573           17 EKPSAIQQRGIVPFCK------G----LDVIQQAQSGTGKTATFCSGI-LQQLDYGLVQCQALVLAPTRELAQQIEKVMR   85 (369)
Q Consensus        17 ~~~~~~Q~~~~~~~~~------~----~~~li~~~tG~GKT~~~~~~~-~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~   85 (369)
                      ..+-|+|..++-.+.-      +    +.++|..|-+-|||..+...+ ...+.....+..+.|++|+..-+.+.....+
T Consensus        60 ~~l~PwQkFiia~l~G~~~k~T~~rrf~e~fI~v~RkngKt~l~A~i~~~~~l~~~~~~~~~~i~A~s~~qa~~~F~~ar  139 (546)
T COG4626          60 ESLEPWQKFIVAALFGFYDKQTGIRRFKEAFIFIPRKNGKSTLAAGIMMTALLLNWRSGAGIYILAPSVEQAANSFNPAR  139 (546)
T ss_pred             cccchHHHHHHHHHhceeecCCCceEEEEEEEEEecCCchHHHHHHHHHHHHHhhhhcCCcEEEEeccHHHHHHhhHHHH
Confidence            3688999999988762      1    347999999999996654322 3333333445589999999988888888777


Q ss_pred             HhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHc--CCCCCCCccEEEEechhHhhccCcHHHHHHHH
Q 017573           86 ALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRR--QSLRPDYIKMFVLDEADEMLSRGFKDQIYDIF  163 (369)
Q Consensus        86 ~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~--~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~  163 (369)
                      ......+          ......+.......|...-.......+..  ...+..+..+.|+||.|.+....  ..+..+.
T Consensus       140 ~mv~~~~----------~l~~~~~~q~~s~~i~~~~~~s~ik~~aa~~~~~Dg~~~~~~I~DEih~f~~~~--~~~~~~~  207 (546)
T COG4626         140 DMVKRDD----------DLRDLCNVQTHSRTITHRKTDSTIKAVAADPNTVDGLNSVGAIIDELHLFGKQE--DMYSEAK  207 (546)
T ss_pred             HHHHhCc----------chhhhhccccceeEEEecccceeeeeeccCCCcccCCCcceEEEehhhhhcCHH--HHHHHHH
Confidence            7654322          10111111111111222211122222222  22334446799999999875542  4555555


Q ss_pred             hhCC--ccCcEEEEEe
Q 017573          164 QLLP--AKVQVGVFSA  177 (369)
Q Consensus       164 ~~~~--~~~~~i~~sa  177 (369)
                      ..+.  +..++++.|.
T Consensus       208 ~g~~ar~~~l~~~ITT  223 (546)
T COG4626         208 GGLGARPEGLVVYITT  223 (546)
T ss_pred             hhhccCcCceEEEEec
Confidence            4443  3556666555

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=96.86  E-value=0.024  Score=50.67  Aligned_cols=131  Identities=10%  Similarity=0.138  Sum_probs=63.3

Q ss_pred             cEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcC--CHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHc
Q 017573           35 DVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAP--TRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQ  112 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P--~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~  112 (369)
                      -+.+.+++|+|||+++.-.+......+   .++++++.  .+.-+.   ++++.+....++.+........+...     
T Consensus       102 vi~lvG~~GvGKTTtaaKLA~~l~~~G---~kV~lV~~D~~R~aA~---eQLk~~a~~~~vp~~~~~~~~dp~~i-----  170 (429)
T TIGR01425       102 VIMFVGLQGSGKTTTCTKLAYYYQRKG---FKPCLVCADTFRAGAF---DQLKQNATKARIPFYGSYTESDPVKI-----  170 (429)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCC---CCEEEEcCcccchhHH---HHHHHHhhccCCeEEeecCCCCHHHH-----
Confidence            478999999999987655544332222   26777664  233332   23333333334444332222111000     


Q ss_pred             cCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhc-cCcHHHHHHHHhhCCccCcEEEEEeeCChhHHHHHHHh
Q 017573          113 AGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLS-RGFKDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKF  190 (369)
Q Consensus       113 ~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~-~~~~~~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~  190 (369)
                              ..+.+ .....     ..+++||+|=+-+... ......+..+.....+...++.++||...+..+....+
T Consensus       171 --------~~~~l-~~~~~-----~~~DvViIDTaGr~~~d~~lm~El~~i~~~~~p~e~lLVlda~~Gq~a~~~a~~F  235 (429)
T TIGR01425       171 --------ASEGV-EKFKK-----ENFDIIIVDTSGRHKQEDSLFEEMLQVAEAIQPDNIIFVMDGSIGQAAEAQAKAF  235 (429)
T ss_pred             --------HHHHH-HHHHh-----CCCCEEEEECCCCCcchHHHHHHHHHHhhhcCCcEEEEEeccccChhHHHHHHHH
Confidence                    00011 11111     2257778877654321 22334555555555555556667777665544444443

This model represents examples from the eukaryotic cytosol of the signal recognition particle protein component, SRP54. This GTP-binding protein is a component of the eukaryotic signal recognition particle, along with several other protein subunits and a 7S RNA. Some species, including Arabidopsis, have several closely related forms. The extreme C-terminal region is glycine-rich and lower in complexity, poorly conserved between species, and excluded from this model.

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=96.85  E-value=0.018  Score=52.29  Aligned_cols=38  Identities=13%  Similarity=0.069  Sum_probs=25.1

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcC
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAP   72 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P   72 (369)
                      ..+++.||+|+|||..+. ++.+.+.....+.+++++..
T Consensus       131 n~l~lyG~~G~GKTHLl~-ai~~~l~~~~~~~~v~yi~~  168 (440)
T PRK14088        131 NPLFIYGGVGLGKTHLLQ-SIGNYVVQNEPDLRVMYITS  168 (440)
T ss_pred             CeEEEEcCCCCcHHHHHH-HHHHHHHHhCCCCeEEEEEH
Confidence            358999999999997654 44444443333336777754

>PRK05986 cob(I)alamin adenolsyltransferase/cobinamide ATP-dependent adenolsyltransferase; Validated

Probab=96.84  E-value=0.0071  Score=47.39  Aligned_cols=142  Identities=17%  Similarity=0.190  Sum_probs=74.2

Q ss_pred             ccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHH-HHHHHHhccccCcEEEEEECCcchHHHHH
Q 017573           31 CKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQI-EKVMRALGDYLGVKVHACVGGTSVREDQR  109 (369)
Q Consensus        31 ~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~-~~~~~~~~~~~~~~v~~~~~~~~~~~~~~  109 (369)
                      .+...+.+..++|.|||.+++..++.++..+.   +++++-=.+.-...= ...+.+.   .++.......+.....   
T Consensus        20 ~~~g~v~v~~g~GkGKtt~a~g~a~ra~g~G~---~V~ivQFlKg~~~~GE~~~l~~l---~~v~~~~~g~~~~~~~---   90 (191)
T PRK05986         20 EEKGLLIVHTGNGKGKSTAAFGMALRAVGHGK---KVGVVQFIKGAWSTGERNLLEFG---GGVEFHVMGTGFTWET---   90 (191)
T ss_pred             ccCCeEEEECCCCCChHHHHHHHHHHHHHCCC---eEEEEEEecCCCccCHHHHHhcC---CCcEEEECCCCCcccC---
Confidence            35688999999999999999988888887776   677765433221000 1112221   1233222111111000   


Q ss_pred             HHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCc--HHHHHHHHhhCCccCcEEEEEeeCChhHHH
Q 017573          110 ILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGF--KDQIYDIFQLLPAKVQVGVFSATMPPEALE  185 (369)
Q Consensus       110 ~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~--~~~~~~~~~~~~~~~~~i~~saT~~~~~~~  185 (369)
                         .+..--............. .+....+++||+||+-...+.++  .+.+..++...|+...+|+..-.+++.+.+
T Consensus        91 ---~~~~e~~~~~~~~~~~a~~-~l~~~~ydlvVLDEi~~Al~~gli~~eevi~~L~~rp~~~evVlTGR~~p~~Lie  164 (191)
T PRK05986         91 ---QDRERDIAAAREGWEEAKR-MLADESYDLVVLDELTYALKYGYLDVEEVLEALNARPGMQHVVITGRGAPRELIE  164 (191)
T ss_pred             ---CCcHHHHHHHHHHHHHHHH-HHhCCCCCEEEEehhhHHHHCCCccHHHHHHHHHcCCCCCEEEEECCCCCHHHHH
Confidence               0000000011111111111 12233479999999998876664  466777777777676666544444444433

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=96.84  E-value=0.0098  Score=55.34  Aligned_cols=104  Identities=15%  Similarity=0.221  Sum_probs=57.1

Q ss_pred             cEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHccC
Q 017573           35 DVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAG  114 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~  114 (369)
                      .++++|++|+|||..+. ++.+.+.....+.+++|+.. ..+..++...+..                            
T Consensus       316 pL~LyG~sGsGKTHLL~-AIa~~a~~~~~g~~V~Yita-eef~~el~~al~~----------------------------  365 (617)
T PRK14086        316 PLFIYGESGLGKTHLLH-AIGHYARRLYPGTRVRYVSS-EEFTNEFINSIRD----------------------------  365 (617)
T ss_pred             cEEEECCCCCCHHHHHH-HHHHHHHHhCCCCeEEEeeH-HHHHHHHHHHHHh----------------------------
Confidence            38999999999997643 44444433223336666554 3444433332211                            


Q ss_pred             CcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccC-cHHHHHHHHhhCCc-cCcEEEEEeeCC
Q 017573          115 VHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRG-FKDQIYDIFQLLPA-KVQVGVFSATMP  180 (369)
Q Consensus       115 ~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~-~~~~~~~~~~~~~~-~~~~i~~saT~~  180 (369)
                           ...+.|.+.+.       .+++++|||+|.+.... +...+..+++.+.. +.++++.|-.++
T Consensus       366 -----~~~~~f~~~y~-------~~DLLlIDDIq~l~gke~tqeeLF~l~N~l~e~gk~IIITSd~~P  421 (617)
T PRK14086        366 -----GKGDSFRRRYR-------EMDILLVDDIQFLEDKESTQEEFFHTFNTLHNANKQIVLSSDRPP  421 (617)
T ss_pred             -----ccHHHHHHHhh-------cCCEEEEehhccccCCHHHHHHHHHHHHHHHhcCCCEEEecCCCh
Confidence                 01122222222       26899999999886433 34556666666544 455665444333

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=96.84  E-value=0.0057  Score=57.58  Aligned_cols=38  Identities=13%  Similarity=0.267  Sum_probs=24.1

Q ss_pred             CccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEE
Q 017573          138 YIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFS  176 (369)
Q Consensus       138 ~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~s  176 (369)
                      ..+++||||+|.+.... ...+.+.+...+....+|+.|
T Consensus       119 k~KVIIIDEad~Ls~~A-~NALLKtLEEPp~~v~fILaT  156 (709)
T PRK08691        119 KYKVYIIDEVHMLSKSA-FNAMLKTLEEPPEHVKFILAT  156 (709)
T ss_pred             CcEEEEEECccccCHHH-HHHHHHHHHhCCCCcEEEEEe
Confidence            46899999999875433 334455555555566565544

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=96.83  E-value=0.011  Score=51.74  Aligned_cols=121  Identities=11%  Similarity=0.032  Sum_probs=58.5

Q ss_pred             CCc-EEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHH
Q 017573           33 GLD-VIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL  111 (369)
Q Consensus        33 ~~~-~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~  111 (369)
                      ..+ .++.||+|+|||..+...+-........+...-..+          ..+.........++..+..+...       
T Consensus        23 ~~halL~~Gp~G~Gktt~a~~lA~~l~~~~~~~~~~~~~~----------~~~~~~~~~~~~d~lel~~s~~~-------   85 (325)
T COG0470          23 LPHALLFYGPPGVGKTTAALALAKELLCENPTGLLPCGHC----------RSCKLIPAGNHPDFLELNPSDLR-------   85 (325)
T ss_pred             CCceeeeeCCCCCCHHHHHHHHHHHHhCCCcccCCcccch----------hhhhHHhhcCCCceEEecccccC-------
Confidence            344 999999999999887655544443322211111111          11222212222233333332221       


Q ss_pred             ccCCcEEEeccHHHHHHHHcCCCC--CCCccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEE
Q 017573          112 QAGVHVVVGTPGRVFDMLRRQSLR--PDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFS  176 (369)
Q Consensus       112 ~~~~~iiv~t~~~l~~~~~~~~~~--~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~s  176 (369)
                        ..++   ..+............  ...+.++|+||++.+... ....+.+.+..-+.+..+++.+
T Consensus        86 --~~~i---~~~~vr~~~~~~~~~~~~~~~kviiidead~mt~~-A~nallk~lEep~~~~~~il~~  146 (325)
T COG0470          86 --KIDI---IVEQVRELAEFLSESPLEGGYKVVIIDEADKLTED-AANALLKTLEEPPKNTRFILIT  146 (325)
T ss_pred             --CCcc---hHHHHHHHHHHhccCCCCCCceEEEeCcHHHHhHH-HHHHHHHHhccCCCCeEEEEEc
Confidence              1111   222222222222222  245799999999998642 2455555555555556555544

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.82  E-value=0.0061  Score=56.88  Aligned_cols=38  Identities=18%  Similarity=0.328  Sum_probs=24.6

Q ss_pred             CccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEE
Q 017573          138 YIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFS  176 (369)
Q Consensus       138 ~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~s  176 (369)
                      ..+++|+||+|.+.... ...+.+.+...+....+|+.|
T Consensus       118 ~~KVvIIDEah~Lt~~A-~NALLK~LEEpp~~~~fIL~t  155 (584)
T PRK14952        118 RYRIFIVDEAHMVTTAG-FNALLKIVEEPPEHLIFIFAT  155 (584)
T ss_pred             CceEEEEECCCcCCHHH-HHHHHHHHhcCCCCeEEEEEe
Confidence            46899999999986443 344455555555555555544

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=96.81  E-value=0.0094  Score=51.84  Aligned_cols=38  Identities=11%  Similarity=0.155  Sum_probs=25.6

Q ss_pred             ccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEE
Q 017573          139 IKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFS  176 (369)
Q Consensus       139 ~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~s  176 (369)
                      .+++|+||+|.+........+..++...+...++++.|
T Consensus       101 ~~vliiDe~d~l~~~~~~~~L~~~le~~~~~~~~Ilt~  138 (316)
T PHA02544        101 GKVIIIDEFDRLGLADAQRHLRSFMEAYSKNCSFIITA  138 (316)
T ss_pred             CeEEEEECcccccCHHHHHHHHHHHHhcCCCceEEEEc
Confidence            58999999998843334455666667666666666533

>PF13173 AAA_14: AAA domain

Probab=96.80  E-value=0.026  Score=41.66  Aligned_cols=41  Identities=10%  Similarity=0.161  Sum_probs=26.9

Q ss_pred             ccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEEeeCChhH
Q 017573          139 IKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMPPEA  183 (369)
Q Consensus       139 ~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~saT~~~~~  183 (369)
                      -.++++||+|.+  .++...+..+.+.. ++.+++ +|++.....
T Consensus        62 ~~~i~iDEiq~~--~~~~~~lk~l~d~~-~~~~ii-~tgS~~~~l  102 (128)
T PF13173_consen   62 KKYIFIDEIQYL--PDWEDALKFLVDNG-PNIKII-LTGSSSSLL  102 (128)
T ss_pred             CcEEEEehhhhh--ccHHHHHHHHHHhc-cCceEE-EEccchHHH
Confidence            478999999998  45667777777755 344444 466554333

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.79  E-value=0.011  Score=54.63  Aligned_cols=38  Identities=13%  Similarity=0.252  Sum_probs=24.6

Q ss_pred             CccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEE
Q 017573          138 YIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFS  176 (369)
Q Consensus       138 ~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~s  176 (369)
                      ..+++|+||+|++.... ...+.+.+...+....+++.|
T Consensus       119 ~~kViIIDEa~~ls~~a-~naLLK~LEepp~~v~fIL~T  156 (546)
T PRK14957        119 RYKVYLIDEVHMLSKQS-FNALLKTLEEPPEYVKFILAT  156 (546)
T ss_pred             CcEEEEEechhhccHHH-HHHHHHHHhcCCCCceEEEEE
Confidence            35899999999986433 345555556555555555544

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=96.79  E-value=0.0044  Score=58.30  Aligned_cols=37  Identities=14%  Similarity=0.275  Sum_probs=23.8

Q ss_pred             CccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEE
Q 017573          138 YIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVF  175 (369)
Q Consensus       138 ~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~  175 (369)
                      +++++||||+|++.... ...+.+++..-+....+|+.
T Consensus       119 ~~KV~IIDEah~Ls~~a-~NALLKtLEEPp~~v~FIL~  155 (647)
T PRK07994        119 RFKVYLIDEVHMLSRHS-FNALLKTLEEPPEHVKFLLA  155 (647)
T ss_pred             CCEEEEEechHhCCHHH-HHHHHHHHHcCCCCeEEEEe
Confidence            46899999999986443 44455555555555544443

>COG3973 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=96.78  E-value=0.0051  Score=55.92  Aligned_cols=82  Identities=29%  Similarity=0.255  Sum_probs=55.1

Q ss_pred             HHHHHHHHhCCCCCCcHh-------hhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhcc---CCCccEEEEcCCH
Q 017573            5 ENLLRGIYAYGFEKPSAI-------QQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYG---LVQCQALVLAPTR   74 (369)
Q Consensus         5 ~~i~~~l~~~~~~~~~~~-------Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~---~~~~~~liv~P~~   74 (369)
                      +-++..|++..-.+++++       |.+++. -..++-.+|+|..|||||.+++--++..+...   ..++.+|++.|++
T Consensus       192 EvL~~~Lek~ss~~mrdIV~TIQkEQneIIR-~ek~~ilVVQGaAGSGKTtiALHRvAyLlY~~R~~l~~k~vlvl~PN~  270 (747)
T COG3973         192 EVLQRVLEKNSSAKMRDIVETIQKEQNEIIR-FEKNKILVVQGAAGSGKTTIALHRVAYLLYGYRGPLQAKPVLVLGPNR  270 (747)
T ss_pred             HHHHHHHHhccchhHHHHHHHhhHhHHHHHh-ccCCCeEEEecCCCCCchhHHHHHHHHHHhccccccccCceEEEcCcH
Confidence            345667777665565543       555552 24567789999999999999875554444321   1222599999999


Q ss_pred             HHHHHHHHHHHHh
Q 017573           75 ELAQQIEKVMRAL   87 (369)
Q Consensus        75 ~l~~q~~~~~~~~   87 (369)
                      ....-..+.+-++
T Consensus       271 vFleYis~VLPeL  283 (747)
T COG3973         271 VFLEYISRVLPEL  283 (747)
T ss_pred             HHHHHHHHhchhh
Confidence            9888777766554

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP

Probab=96.77  E-value=0.019  Score=43.73  Aligned_cols=131  Identities=18%  Similarity=0.246  Sum_probs=70.8

Q ss_pred             cEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHH---HHHHHHHHHHHhccccCcEEEEEECCcc-----hHH
Q 017573           35 DVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRE---LAQQIEKVMRALGDYLGVKVHACVGGTS-----VRE  106 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~---l~~q~~~~~~~~~~~~~~~v~~~~~~~~-----~~~  106 (369)
                      -+.|..++|.|||.+++..++..+..+.   +++++-=.+.   -.+  ...+.++.   +++......+..     ...
T Consensus         4 ~i~vy~g~G~Gkt~~a~g~~~ra~~~g~---~v~~vQFlKg~~~~gE--~~~l~~l~---~v~~~~~g~~~~~~~~~~~~   75 (159)
T cd00561           4 LIQVYTGNGKGKTTAALGLALRALGHGY---RVGVVQFLKGGWKYGE--LKALERLP---NIEIHRMGRGFFWTTENDEE   75 (159)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCC---eEEEEEEeCCCCccCH--HHHHHhCC---CcEEEECCCCCccCCCChHH
Confidence            4677888999999999888888877765   7777432222   111  11233331   333332222111     001


Q ss_pred             HHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccC--cHHHHHHHHhhCCccCcEEEEEeeCChhHH
Q 017573          107 DQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRG--FKDQIYDIFQLLPAKVQVGVFSATMPPEAL  184 (369)
Q Consensus       107 ~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~--~~~~~~~~~~~~~~~~~~i~~saT~~~~~~  184 (369)
                      .....          -+.+ ..... ......+|++|+||+-.....+  ..+.+..+++..|....+|+.+-.+++.+.
T Consensus        76 ~~~~a----------~~~~-~~a~~-~~~~~~~dLlVLDEi~~a~~~gli~~~~v~~ll~~rp~~~evIlTGr~~p~~l~  143 (159)
T cd00561          76 DIAAA----------AEGW-AFAKE-AIASGEYDLVILDEINYALGYGLLDVEEVVDLLKAKPEDLELVLTGRNAPKELI  143 (159)
T ss_pred             HHHHH----------HHHH-HHHHH-HHhcCCCCEEEEechHhHhhCCCCCHHHHHHHHHcCCCCCEEEEECCCCCHHHH
Confidence            00000          0111 11111 1123347999999999876544  346777788887777777765555555544


Q ss_pred             H
Q 017573          185 E  185 (369)
Q Consensus       185 ~  185 (369)
                      +
T Consensus       144 e  144 (159)
T cd00561         144 E  144 (159)
T ss_pred             H
Confidence            3

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.

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.76  E-value=0.0079  Score=56.53  Aligned_cols=39  Identities=15%  Similarity=0.298  Sum_probs=24.7

Q ss_pred             CCccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEE
Q 017573          137 DYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFS  176 (369)
Q Consensus       137 ~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~s  176 (369)
                      ..++++|+||+|++.... ...+.+.+..-++...+|+.|
T Consensus       118 ~~~KVvIIdev~~Lt~~a-~naLLk~LEepp~~~~fIl~t  156 (576)
T PRK14965        118 SRYKIFIIDEVHMLSTNA-FNALLKTLEEPPPHVKFIFAT  156 (576)
T ss_pred             CCceEEEEEChhhCCHHH-HHHHHHHHHcCCCCeEEEEEe
Confidence            346899999999886433 345555555555555555444

>PF00004 AAA: ATPase family associated with various cellular activities (AAA); InterPro: IPR003959 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport

Probab=96.76  E-value=0.0053  Score=45.52  Aligned_cols=16  Identities=31%  Similarity=0.468  Sum_probs=13.6

Q ss_pred             EEEEcCCCChhhHHHH
Q 017573           36 VIQQAQSGTGKTATFC   51 (369)
Q Consensus        36 ~li~~~tG~GKT~~~~   51 (369)
                      +++.||+|+|||..+-
T Consensus         1 ill~G~~G~GKT~l~~   16 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLAR   16 (132)
T ss_dssp             EEEESSTTSSHHHHHH
T ss_pred             CEEECcCCCCeeHHHH
Confidence            5899999999997653

Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. The functional variety seen between AAA ATPases is in part due to their extensive number of accessory domains and factors, and to their variable organisation within oligomeric assemblies, in addition to changes in key functional residues within the ATPase domain itself. More information about these proteins can be found at Protein of the Month: AAA ATPases [].; GO: 0005524 ATP binding; PDB: 3H4M_A 1NSF_A 1D2N_A 1HQY_E 1DO0_E 1DO2_C 1G4B_E 1HT1_F 1G4A_F 1HT2_G ....

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.75  E-value=0.0063  Score=57.08  Aligned_cols=22  Identities=18%  Similarity=0.074  Sum_probs=17.1

Q ss_pred             cEEEEcCCCChhhHHHHHHHHH
Q 017573           35 DVIQQAQSGTGKTATFCSGILQ   56 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~~~~~~   56 (369)
                      -.+++||.|+|||.++...+-.
T Consensus        40 a~Lf~Gp~GvGKTtlAr~lAk~   61 (618)
T PRK14951         40 AYLFTGTRGVGKTTVSRILAKS   61 (618)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            3599999999999887554443

>PHA00729 NTP-binding motif containing protein

Probab=96.75  E-value=0.012  Score=47.51  Aligned_cols=18  Identities=22%  Similarity=0.344  Sum_probs=15.5

Q ss_pred             CcEEEEcCCCChhhHHHH
Q 017573           34 LDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~   51 (369)
                      .++++.|++|+|||..+.
T Consensus        18 ~nIlItG~pGvGKT~LA~   35 (226)
T PHA00729         18 VSAVIFGKQGSGKTTYAL   35 (226)
T ss_pred             EEEEEECCCCCCHHHHHH
Confidence            379999999999997764

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=96.74  E-value=0.0052  Score=53.33  Aligned_cols=40  Identities=15%  Similarity=-0.041  Sum_probs=30.3

Q ss_pred             CcHhhhhhhhccccC-----CcEEEEcCCCChhhHHHHHHHHHhh
Q 017573           19 PSAIQQRGIVPFCKG-----LDVIQQAQSGTGKTATFCSGILQQL   58 (369)
Q Consensus        19 ~~~~Q~~~~~~~~~~-----~~~li~~~tG~GKT~~~~~~~~~~~   58 (369)
                      ++|+|+..++.+...     ...++.||.|.||+..+...+...+
T Consensus         2 ~yPW~~~~~~~l~~~~~rl~ha~Lf~Gp~G~GK~~lA~~~A~~Ll   46 (342)
T PRK06964          2 LYPWQTDDWNRLQALRARLPHALLLHGQAGIGKLDFAQHLAQGLL   46 (342)
T ss_pred             CCcccHHHHHHHHHhcCCcceEEEEECCCCCCHHHHHHHHHHHHc
Confidence            478888888887752     4578999999999988765554444

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=96.74  E-value=0.019  Score=50.64  Aligned_cols=51  Identities=20%  Similarity=0.236  Sum_probs=32.9

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHh
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRAL   87 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~   87 (369)
                      +.-+++.+++|+|||..++..+......+   .+++|+... +...|......++
T Consensus        82 GslvLI~G~pG~GKStLllq~a~~~a~~g---~~VlYvs~E-Es~~qi~~Ra~rl  132 (372)
T cd01121          82 GSVILIGGDPGIGKSTLLLQVAARLAKRG---GKVLYVSGE-ESPEQIKLRADRL  132 (372)
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHhcC---CeEEEEECC-cCHHHHHHHHHHc
Confidence            35579999999999987765555444332   278888754 3344555444443

This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional

Probab=96.74  E-value=0.012  Score=52.53  Aligned_cols=33  Identities=21%  Similarity=0.229  Sum_probs=26.5

Q ss_pred             CcHhhhhhhhccccCCcEEEEcCCCChhhHHHH
Q 017573           19 PSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        19 ~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~   51 (369)
                      +......++..+..++++++.+|+|+|||..+-
T Consensus       180 ~e~~le~l~~~L~~~~~iil~GppGtGKT~lA~  212 (459)
T PRK11331        180 PETTIETILKRLTIKKNIILQGPPGVGKTFVAR  212 (459)
T ss_pred             CHHHHHHHHHHHhcCCCEEEECCCCCCHHHHHH
Confidence            444556667777789999999999999998764

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=96.73  E-value=0.0077  Score=55.24  Aligned_cols=22  Identities=18%  Similarity=0.025  Sum_probs=17.6

Q ss_pred             CcEEEEcCCCChhhHHHHHHHH
Q 017573           34 LDVIQQAQSGTGKTATFCSGIL   55 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~   55 (369)
                      +..+++||.|+|||.++-..+.
T Consensus        44 ~a~Lf~Gp~G~GKTT~ArilAk   65 (507)
T PRK06645         44 GGYLLTGIRGVGKTTSARIIAK   65 (507)
T ss_pred             ceEEEECCCCCCHHHHHHHHHH
Confidence            4689999999999988754443

>PRK11823 DNA repair protein RadA; Provisional

Probab=96.73  E-value=0.013  Score=53.21  Aligned_cols=51  Identities=24%  Similarity=0.238  Sum_probs=33.9

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHh
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRAL   87 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~   87 (369)
                      +.-+++.+++|+|||..++..+......+   .+++|+.-. +...|......++
T Consensus        80 Gs~~lI~G~pG~GKTtL~lq~a~~~a~~g---~~vlYvs~E-es~~qi~~ra~rl  130 (446)
T PRK11823         80 GSVVLIGGDPGIGKSTLLLQVAARLAAAG---GKVLYVSGE-ESASQIKLRAERL  130 (446)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHhcC---CeEEEEEcc-ccHHHHHHHHHHc
Confidence            35679999999999987766655544332   378998754 3445665555544

>PHA03333 putative ATPase subunit of terminase; Provisional

Probab=96.72  E-value=0.026  Score=52.83  Aligned_cols=71  Identities=14%  Similarity=0.133  Sum_probs=49.4

Q ss_pred             CCCcHhhhhhhhccc---cCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhcc
Q 017573           17 EKPSAIQQRGIVPFC---KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGD   89 (369)
Q Consensus        17 ~~~~~~Q~~~~~~~~---~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~   89 (369)
                      .-|.|.=.+-++++.   +.+-.++.+|-|-|||.+..+.+...+...  +.+++|.+|...-+.+..+.+.+...
T Consensus       168 ~~~~~~~~~~id~~~~~fkq~~tV~taPRqrGKS~iVgi~l~~La~f~--Gi~IlvTAH~~~ts~evF~rv~~~le  241 (752)
T PHA03333        168 EAPSPRTLREIDRIFDEYGKCYTAATVPRRCGKTTIMAIILAAMISFL--EIDIVVQAQRKTMCLTLYNRVETVVH  241 (752)
T ss_pred             CCCChhhHHHHHHHHHHHhhcceEEEeccCCCcHHHHHHHHHHHHHhc--CCeEEEECCChhhHHHHHHHHHHHHH
Confidence            344555555555554   346778999999999987765555444312  23899999999888888887776654

>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.71  E-value=0.057  Score=45.32  Aligned_cols=128  Identities=16%  Similarity=0.195  Sum_probs=65.9

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCC---HHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHH
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPT---RELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRI  110 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~---~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~  110 (369)
                      ..+.+.+++|+|||..+...+......+   .++.++..-   .+...||.....    ..++++..             
T Consensus        76 ~~i~~~G~~g~GKTtl~~~l~~~l~~~~---~~v~~i~~D~~ri~~~~ql~~~~~----~~~~~~~~-------------  135 (270)
T PRK06731         76 QTIALIGPTGVGKTTTLAKMAWQFHGKK---KTVGFITTDHSRIGTVQQLQDYVK----TIGFEVIA-------------  135 (270)
T ss_pred             CEEEEECCCCCcHHHHHHHHHHHHHHcC---CeEEEEecCCCCHHHHHHHHHHhh----hcCceEEe-------------
Confidence            5789999999999987654443332222   245555542   244555543322    22333321             


Q ss_pred             HccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhh-ccCcHHHHHHHHhhCCccCcEEEEEeeCCh-hHHHHHH
Q 017573          111 LQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEML-SRGFKDQIYDIFQLLPAKVQVGVFSATMPP-EALEITR  188 (369)
Q Consensus       111 ~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~-~~~~~~~~~~~~~~~~~~~~~i~~saT~~~-~~~~~~~  188 (369)
                              ..+++.+...+..-. ...+++++++|.+=+.. +......+..+.....+...++.++||... +..+...
T Consensus       136 --------~~~~~~l~~~l~~l~-~~~~~D~ViIDt~Gr~~~~~~~l~el~~~~~~~~~~~~~LVl~a~~~~~d~~~~~~  206 (270)
T PRK06731        136 --------VRDEAAMTRALTYFK-EEARVDYILIDTAGKNYRASETVEEMIETMGQVEPDYICLTLSASMKSKDMIEIIT  206 (270)
T ss_pred             --------cCCHHHHHHHHHHHH-hcCCCCEEEEECCCCCcCCHHHHHHHHHHHhhhCCCeEEEEEcCccCHHHHHHHHH
Confidence                    123334433332210 11246999999886543 222334455555555444446678998765 4444444


Q ss_pred             Hh
Q 017573          189 KF  190 (369)
Q Consensus       189 ~~  190 (369)
                      .+
T Consensus       207 ~f  208 (270)
T PRK06731        207 NF  208 (270)
T ss_pred             Hh
Confidence            43

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=96.71  E-value=0.01  Score=52.30  Aligned_cols=44  Identities=16%  Similarity=0.360  Sum_probs=30.6

Q ss_pred             ccEEEEechhHhhcc-CcHHHHHHHHhhCCccC-cEEEEEeeCChh
Q 017573          139 IKMFVLDEADEMLSR-GFKDQIYDIFQLLPAKV-QVGVFSATMPPE  182 (369)
Q Consensus       139 ~~~viiDE~H~~~~~-~~~~~~~~~~~~~~~~~-~~i~~saT~~~~  182 (369)
                      ++++++|.++.+... .+...+..+++.+.... |+++.|..+|..
T Consensus       176 ~dlllIDDiq~l~gk~~~qeefFh~FN~l~~~~kqIvltsdr~P~~  221 (408)
T COG0593         176 LDLLLIDDIQFLAGKERTQEEFFHTFNALLENGKQIVLTSDRPPKE  221 (408)
T ss_pred             cCeeeechHhHhcCChhHHHHHHHHHHHHHhcCCEEEEEcCCCchh
Confidence            699999999998754 45677777777776544 666555555444

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=96.69  E-value=0.048  Score=45.07  Aligned_cols=51  Identities=18%  Similarity=0.228  Sum_probs=36.4

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHh
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRAL   87 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~   87 (369)
                      +.-+++.+++|+|||..+...+...+..+.   +++|+.-... ..+..+++..+
T Consensus        25 g~~~~i~G~~GsGKt~l~~~~~~~~~~~g~---~~~y~~~e~~-~~~~~~~~~~~   75 (234)
T PRK06067         25 PSLILIEGDHGTGKSVLSQQFVYGALKQGK---KVYVITTENT-SKSYLKQMESV   75 (234)
T ss_pred             CcEEEEECCCCCChHHHHHHHHHHHHhCCC---EEEEEEcCCC-HHHHHHHHHHC
Confidence            466899999999999887777666655443   7888876533 35566666655

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=96.68  E-value=0.037  Score=53.45  Aligned_cols=40  Identities=10%  Similarity=0.419  Sum_probs=23.0

Q ss_pred             CccEEEEechhHhhccCcHHHHHHHHhhCC-ccCcEEEEEee
Q 017573          138 YIKMFVLDEADEMLSRGFKDQIYDIFQLLP-AKVQVGVFSAT  178 (369)
Q Consensus       138 ~~~~viiDE~H~~~~~~~~~~~~~~~~~~~-~~~~~i~~saT  178 (369)
                      ...+||+||+|.+.... ...+..+++... ...+++++..+
T Consensus       869 ~v~IIILDEID~L~kK~-QDVLYnLFR~~~~s~SKLiLIGIS  909 (1164)
T PTZ00112        869 NVSILIIDEIDYLITKT-QKVLFTLFDWPTKINSKLVLIAIS  909 (1164)
T ss_pred             cceEEEeehHhhhCccH-HHHHHHHHHHhhccCCeEEEEEec
Confidence            35789999999987542 344555554322 23344443443

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=96.68  E-value=0.01  Score=51.02  Aligned_cols=140  Identities=10%  Similarity=0.027  Sum_probs=70.8

Q ss_pred             CCcHhhhhhhhcccc----C---CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccc
Q 017573           18 KPSAIQQRGIVPFCK----G---LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDY   90 (369)
Q Consensus        18 ~~~~~Q~~~~~~~~~----~---~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~   90 (369)
                      .++|+|+..+..+.+    +   ...++.||.|.||+..+...+...+-..... .   -|..       ...++.+...
T Consensus         3 ~~yPWl~~~~~~l~~~~~~~rl~hA~L~~G~~G~Gk~~lA~~~a~~llC~~~~~-~---~Cg~-------C~sC~~~~~g   71 (319)
T PRK06090          3 NDYPWLVPVWQNWKAGLDAGRIPGALLLQSDEGLGVESLVELFSRALLCQNYQS-E---ACGF-------CHSCELMQSG   71 (319)
T ss_pred             cCcccHHHHHHHHHHHHHcCCcceeEeeECCCCCCHHHHHHHHHHHHcCCCCCC-C---CCCC-------CHHHHHHHcC
Confidence            568888888877763    2   3589999999999987765555444332211 1   0111       0112222222


Q ss_pred             cCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCccC
Q 017573           91 LGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKV  170 (369)
Q Consensus        91 ~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~  170 (369)
                      ..-++..+.....          +..|-|-....+.+.+.... .....+++|||++|.+... ....+.+++..-|++.
T Consensus        72 ~HPD~~~i~p~~~----------~~~I~vdqiR~l~~~~~~~~-~~~~~kV~iI~~ae~m~~~-AaNaLLKtLEEPp~~t  139 (319)
T PRK06090         72 NHPDLHVIKPEKE----------GKSITVEQIRQCNRLAQESS-QLNGYRLFVIEPADAMNES-ASNALLKTLEEPAPNC  139 (319)
T ss_pred             CCCCEEEEecCcC----------CCcCCHHHHHHHHHHHhhCc-ccCCceEEEecchhhhCHH-HHHHHHHHhcCCCCCe
Confidence            2223333322110          00121112122222222222 2234689999999998533 2455556666655566


Q ss_pred             cEEEEEeeCC
Q 017573          171 QVGVFSATMP  180 (369)
Q Consensus       171 ~~i~~saT~~  180 (369)
                      .++++|..+.
T Consensus       140 ~fiL~t~~~~  149 (319)
T PRK06090        140 LFLLVTHNQK  149 (319)
T ss_pred             EEEEEECChh
Confidence            5555555543

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=96.66  E-value=0.013  Score=53.94  Aligned_cols=39  Identities=15%  Similarity=0.300  Sum_probs=26.0

Q ss_pred             CCccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEE
Q 017573          137 DYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFS  176 (369)
Q Consensus       137 ~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~s  176 (369)
                      ..++++|+||+|.+.... ...+.+.+...++...+++.+
T Consensus       116 ~~~KVvIIDEad~Lt~~A-~NALLK~LEEpp~~t~FIL~t  154 (535)
T PRK08451        116 ARFKIFIIDEVHMLTKEA-FNALLKTLEEPPSYVKFILAT  154 (535)
T ss_pred             CCeEEEEEECcccCCHHH-HHHHHHHHhhcCCceEEEEEE
Confidence            346899999999986433 345555666656666666544

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=96.66  E-value=0.0082  Score=56.16  Aligned_cols=22  Identities=23%  Similarity=0.083  Sum_probs=17.1

Q ss_pred             CcEEEEcCCCChhhHHHHHHHH
Q 017573           34 LDVIQQAQSGTGKTATFCSGIL   55 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~   55 (369)
                      +..+++||.|+|||.++-..+.
T Consensus        39 hayLf~Gp~GtGKTt~Ak~lAk   60 (559)
T PRK05563         39 HAYLFSGPRGTGKTSAAKIFAK   60 (559)
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            3478999999999988755443

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=96.65  E-value=0.0024  Score=53.21  Aligned_cols=72  Identities=14%  Similarity=0.265  Sum_probs=47.9

Q ss_pred             HHHHhCCCCCCcHhhhhhhhccc-------cCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHH
Q 017573            9 RGIYAYGFEKPSAIQQRGIVPFC-------KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIE   81 (369)
Q Consensus         9 ~~l~~~~~~~~~~~Q~~~~~~~~-------~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~   81 (369)
                      +.++.+.|......++.++..+.       ++.++++.||+|+|||..+.....+.+ ..  + ..++.++...++.++.
T Consensus        74 k~~~~~d~~~~~~~~~~~l~~~~~~~~~~~~~~nl~l~G~~G~GKThLa~Ai~~~l~-~~--g-~sv~f~~~~el~~~Lk  149 (254)
T COG1484          74 KTFEEFDFEFQPGIDKKALEDLASLVEFFERGENLVLLGPPGVGKTHLAIAIGNELL-KA--G-ISVLFITAPDLLSKLK  149 (254)
T ss_pred             CCcccccccCCcchhHHHHHHHHHHHHHhccCCcEEEECCCCCcHHHHHHHHHHHHH-Hc--C-CeEEEEEHHHHHHHHH
Confidence            34455666666667777665543       567999999999999988765555555 32  2 4555566667776655


Q ss_pred             HHH
Q 017573           82 KVM   84 (369)
Q Consensus        82 ~~~   84 (369)
                      ..+
T Consensus       150 ~~~  152 (254)
T COG1484         150 AAF  152 (254)
T ss_pred             HHH
Confidence            544

>PF02572 CobA_CobO_BtuR: ATP:corrinoid adenosyltransferase BtuR/CobO/CobP; InterPro: IPR003724 ATP:cob(I)alamin (or ATP:corrinoid) adenosyltransferases (2

Probab=96.64  E-value=0.046  Score=42.24  Aligned_cols=139  Identities=15%  Similarity=0.221  Sum_probs=63.8

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHcc
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQA  113 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~  113 (369)
                      .-+.|....|-|||.+++-.++.++-.+.   +++++-=.+.-.  ...+...+....++.......+........    
T Consensus         4 G~i~vytG~GKGKTTAAlGlalRA~G~G~---rV~ivQFlKg~~--~~GE~~~l~~l~~~~~~~~g~~f~~~~~~~----   74 (172)
T PF02572_consen    4 GLIQVYTGDGKGKTTAALGLALRAAGHGM---RVLIVQFLKGGR--YSGELKALKKLPNVEIERFGKGFVWRMNEE----   74 (172)
T ss_dssp             --EEEEESSSS-HHHHHHHHHHHHHCTT-----EEEEESS--SS----HHHHHHGGGT--EEEE--TT----GGGH----
T ss_pred             cEEEEEeCCCCCchHHHHHHHHHHHhCCC---EEEEEEEecCCC--CcCHHHHHHhCCeEEEEEcCCcccccCCCc----
Confidence            34678888999999999999888887766   888887655511  112222221111233322221111000000    


Q ss_pred             CCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCc--HHHHHHHHhhCCccCcEEEEEeeCChhHH
Q 017573          114 GVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGF--KDQIYDIFQLLPAKVQVGVFSATMPPEAL  184 (369)
Q Consensus       114 ~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~--~~~~~~~~~~~~~~~~~i~~saT~~~~~~  184 (369)
                      ..+  ....+..++..... .....+++||+||+-...+.++  ...+..++..-|....+|+....+++.+.
T Consensus        75 ~~~--~~~~~~~~~~a~~~-i~~~~~dlvILDEi~~a~~~gll~~~~v~~~l~~rp~~~evVlTGR~~~~~l~  144 (172)
T PF02572_consen   75 EED--RAAAREGLEEAKEA-ISSGEYDLVILDEINYAVDYGLLSEEEVLDLLENRPESLEVVLTGRNAPEELI  144 (172)
T ss_dssp             HHH--HHHHHHHHHHHHHH-TT-TT-SEEEEETHHHHHHTTSS-HHHHHHHHHTS-TT-EEEEE-SS--HHHH
T ss_pred             HHH--HHHHHHHHHHHHHH-HhCCCCCEEEEcchHHHhHCCCccHHHHHHHHHcCCCCeEEEEECCCCCHHHH
Confidence            001  11111112222221 2234589999999998876653  35667777777777766654444444443

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.

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=96.63  E-value=0.01  Score=47.15  Aligned_cols=25  Identities=16%  Similarity=0.045  Sum_probs=18.6

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHhh
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQL   58 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~~   58 (369)
                      ...++.||+|+|||..+...+...+
T Consensus        15 ~~~L~~G~~G~gkt~~a~~~~~~l~   39 (188)
T TIGR00678        15 HAYLFAGPEGVGKELLALALAKALL   39 (188)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHc
Confidence            4589999999999987655444433

At position 126-127 of the seed alignment, this family lacks the HM motif of gamma/tau; at 132 it has a near-invariant A vs. an invariant F in gamma/tau.

>PRK08939 primosomal protein DnaI; Reviewed

Probab=96.63  E-value=0.024  Score=48.71  Aligned_cols=36  Identities=14%  Similarity=0.109  Sum_probs=24.2

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEc
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLA   71 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~   71 (369)
                      ++++++.||+|+|||..+...+......+.   ++.++.
T Consensus       156 ~~gl~L~G~~G~GKThLa~Aia~~l~~~g~---~v~~~~  191 (306)
T PRK08939        156 VKGLYLYGDFGVGKSYLLAAIANELAKKGV---SSTLLH  191 (306)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHcCC---CEEEEE
Confidence            468999999999999876544444443332   555543

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=96.61  E-value=0.019  Score=47.73  Aligned_cols=40  Identities=23%  Similarity=0.115  Sum_probs=30.3

Q ss_pred             cccCCcEEEEcCCCChhhHHHHHHHHHhhhc-cCCCccEEEEcC
Q 017573           30 FCKGLDVIQQAQSGTGKTATFCSGILQQLDY-GLVQCQALVLAP   72 (369)
Q Consensus        30 ~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~-~~~~~~~liv~P   72 (369)
                      +..|.-++|.|++|+|||..++..+.+.+.. +.   +++|++.
T Consensus        10 l~~G~l~lI~G~~G~GKT~~~~~~~~~~~~~~g~---~vly~s~   50 (242)
T cd00984          10 LQPGDLIIIAARPSMGKTAFALNIAENIAKKQGK---PVLFFSL   50 (242)
T ss_pred             CCCCeEEEEEeCCCCCHHHHHHHHHHHHHHhCCC---ceEEEeC
Confidence            3456778999999999998877666666554 33   7888884

The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.

>KOG0991 consensus Replication factor C, subunit RFC2 [Replication, recombination and repair]

Probab=96.59  E-value=0.0066  Score=48.49  Aligned_cols=39  Identities=18%  Similarity=0.314  Sum_probs=26.1

Q ss_pred             CCccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEE
Q 017573          137 DYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFS  176 (369)
Q Consensus       137 ~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~s  176 (369)
                      .+.+.+|+||++.+.+. ..+.+.+.+....+..++.+..
T Consensus       112 grhKIiILDEADSMT~g-AQQAlRRtMEiyS~ttRFalaC  150 (333)
T KOG0991|consen  112 GRHKIIILDEADSMTAG-AQQALRRTMEIYSNTTRFALAC  150 (333)
T ss_pred             CceeEEEeeccchhhhH-HHHHHHHHHHHHcccchhhhhh
Confidence            44689999999998643 3566666666666555554433

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=96.57  E-value=0.034  Score=48.45  Aligned_cols=37  Identities=19%  Similarity=0.340  Sum_probs=24.1

Q ss_pred             ccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEE
Q 017573          139 IKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFS  176 (369)
Q Consensus       139 ~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~s  176 (369)
                      .+++++||+|.+.... ...+..++...++...+++.+
T Consensus       103 ~~vviiDe~~~l~~~~-~~~L~~~le~~~~~~~lIl~~  139 (319)
T PRK00440        103 FKIIFLDEADNLTSDA-QQALRRTMEMYSQNTRFILSC  139 (319)
T ss_pred             ceEEEEeCcccCCHHH-HHHHHHHHhcCCCCCeEEEEe
Confidence            5799999999875432 345555666656666566544

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.56  E-value=0.009  Score=53.60  Aligned_cols=23  Identities=22%  Similarity=0.062  Sum_probs=17.9

Q ss_pred             cEEEEcCCCChhhHHHHHHHHHh
Q 017573           35 DVIQQAQSGTGKTATFCSGILQQ   57 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~~~~~~~   57 (369)
                      ..+++||+|+|||.++...+...
T Consensus        40 a~lf~Gp~G~GKtt~A~~~a~~l   62 (397)
T PRK14955         40 GYIFSGLRGVGKTTAARVFAKAV   62 (397)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999998876554433

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.54  E-value=0.052  Score=48.26  Aligned_cols=124  Identities=16%  Similarity=0.165  Sum_probs=62.3

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHhh-hccCCCccEEEEcCC--HHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHH
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQL-DYGLVQCQALVLAPT--RELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRI  110 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~~-~~~~~~~~~liv~P~--~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~  110 (369)
                      .-+++.+|+|+|||..+...+.... ..+.   ++.++.--  +..+.+   ++..+....++.+..             
T Consensus       224 ~vi~lvGptGvGKTTtaaKLA~~~~~~~G~---~V~Lit~Dt~R~aA~e---QLk~yAe~lgvp~~~-------------  284 (432)
T PRK12724        224 KVVFFVGPTGSGKTTSIAKLAAKYFLHMGK---SVSLYTTDNYRIAAIE---QLKRYADTMGMPFYP-------------  284 (432)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHhcCC---eEEEecccchhhhHHH---HHHHHHHhcCCCeee-------------
Confidence            3478999999999988766655432 2222   55555522  222222   233332222332211             


Q ss_pred             HccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhh-ccCcHHHHHHHHhhCC---ccCcEEEEEeeCChhHHHH
Q 017573          111 LQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEML-SRGFKDQIYDIFQLLP---AKVQVGVFSATMPPEALEI  186 (369)
Q Consensus       111 ~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~-~~~~~~~~~~~~~~~~---~~~~~i~~saT~~~~~~~~  186 (369)
                              +.....+...+..     ..+++|++|=+-+.. +......+..+.....   +...++.++||...+....
T Consensus       285 --------~~~~~~l~~~l~~-----~~~D~VLIDTaGr~~rd~~~l~eL~~~~~~~~~~~~~e~~LVLsAt~~~~~~~~  351 (432)
T PRK12724        285 --------VKDIKKFKETLAR-----DGSELILIDTAGYSHRNLEQLERMQSFYSCFGEKDSVENLLVLSSTSSYHHTLT  351 (432)
T ss_pred             --------hHHHHHHHHHHHh-----CCCCEEEEeCCCCCccCHHHHHHHHHHHHhhcCCCCCeEEEEEeCCCCHHHHHH
Confidence                    0112233333332     346999999665432 2223344455554432   2235677899988744443


Q ss_pred             HHH
Q 017573          187 TRK  189 (369)
Q Consensus       187 ~~~  189 (369)
                      ...
T Consensus       352 ~~~  354 (432)
T PRK12724        352 VLK  354 (432)
T ss_pred             HHH
Confidence            333

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.53  E-value=0.011  Score=54.44  Aligned_cols=20  Identities=25%  Similarity=0.207  Sum_probs=16.1

Q ss_pred             EEEEcCCCChhhHHHHHHHH
Q 017573           36 VIQQAQSGTGKTATFCSGIL   55 (369)
Q Consensus        36 ~li~~~tG~GKT~~~~~~~~   55 (369)
                      +++.||+|+|||.++...+.
T Consensus        39 ~Lf~GppGtGKTTlA~~lA~   58 (504)
T PRK14963         39 YLFSGPRGVGKTTTARLIAM   58 (504)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            59999999999988754443

>PRK10867 signal recognition particle protein; Provisional

Probab=96.52  E-value=0.076  Score=47.81  Aligned_cols=36  Identities=19%  Similarity=0.116  Sum_probs=24.0

Q ss_pred             cEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcC
Q 017573           35 DVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAP   72 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P   72 (369)
                      -+++++++|+|||.++.-.+......  .+.+++++.-
T Consensus       102 vI~~vG~~GsGKTTtaakLA~~l~~~--~G~kV~lV~~  137 (433)
T PRK10867        102 VIMMVGLQGAGKTTTAGKLAKYLKKK--KKKKVLLVAA  137 (433)
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHh--cCCcEEEEEc
Confidence            47899999999998876665544333  1226666653

>PRK05973 replicative DNA helicase; Provisional

Probab=96.50  E-value=0.0078  Score=49.27  Aligned_cols=58  Identities=21%  Similarity=0.186  Sum_probs=40.8

Q ss_pred             hhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHh
Q 017573           26 GIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRAL   87 (369)
Q Consensus        26 ~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~   87 (369)
                      ..--+..|.-++|.|++|+|||..++..+.+.+..+.   +++|++-- .-..|..+++..+
T Consensus        57 l~GGl~~Gsl~LIaG~PG~GKT~lalqfa~~~a~~Ge---~vlyfSlE-es~~~i~~R~~s~  114 (237)
T PRK05973         57 LFSQLKPGDLVLLGARPGHGKTLLGLELAVEAMKSGR---TGVFFTLE-YTEQDVRDRLRAL  114 (237)
T ss_pred             hcCCCCCCCEEEEEeCCCCCHHHHHHHHHHHHHhcCC---eEEEEEEe-CCHHHHHHHHHHc
Confidence            4445556778999999999999988877776665543   78887643 3345666666655

>TIGR00708 cobA cob(I)alamin adenosyltransferase

Probab=96.50  E-value=0.0061  Score=47.02  Aligned_cols=133  Identities=19%  Similarity=0.235  Sum_probs=69.6

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHH-HHHHHHHhccccCcEEEEEECCc-----chHHH
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQ-IEKVMRALGDYLGVKVHACVGGT-----SVRED  107 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q-~~~~~~~~~~~~~~~v~~~~~~~-----~~~~~  107 (369)
                      .-+.+..++|.|||.+++..++.+...+.   +++++-=.+.-... -...+.++    ++.+.....+.     .....
T Consensus         6 Gli~v~~g~GkGKtt~a~g~a~ra~~~g~---~v~ivQFlKg~~~~GE~~~l~~~----~~~~~~~g~g~~~~~~~~~~~   78 (173)
T TIGR00708         6 GIIIVHTGNGKGKTTAAFGMALRALGHGK---KVGVIQFIKGAWPNGERAAFEPH----GVEFQVMGTGFTWETQNREAD   78 (173)
T ss_pred             cEEEEECCCCCChHHHHHHHHHHHHHCCC---eEEEEEEecCCcccChHHHHHhc----CcEEEECCCCCeecCCCcHHH
Confidence            45788899999999999888888877765   67766322211000 00112221    22222211111     00010


Q ss_pred             HHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCc--HHHHHHHHhhCCccCcEEEEEeeCChhHHH
Q 017573          108 QRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGF--KDQIYDIFQLLPAKVQVGVFSATMPPEALE  185 (369)
Q Consensus       108 ~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~--~~~~~~~~~~~~~~~~~i~~saT~~~~~~~  185 (369)
                      ..           ........... .+....+|+||+||+-...+.++  .+.+..+++..|+...+|+..-.+++.+.+
T Consensus        79 ~~-----------~~~~~~~~a~~-~l~~~~~DlvVLDEi~~A~~~gli~~~~v~~lL~~rp~~~evVlTGR~~p~~l~e  146 (173)
T TIGR00708        79 TA-----------IAKAAWQHAKE-MLADPELDLVLLDELTYALKYGYLDVEEVVEALQERPGHQHVIITGRGCPQDLLE  146 (173)
T ss_pred             HH-----------HHHHHHHHHHH-HHhcCCCCEEEehhhHHHHHCCCcCHHHHHHHHHhCCCCCEEEEECCCCCHHHHH
Confidence            00           01111111111 11223479999999998776653  356677777777777777644445444433

Alternate name: corrinoid adenosyltransferase.

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

Probab=96.48  E-value=0.0095  Score=48.99  Aligned_cols=85  Identities=26%  Similarity=0.385  Sum_probs=64.0

Q ss_pred             CccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCc-chHHHHHHHc-cCCcEEEeccHHHHHHHHcCCCCCCCccE
Q 017573           64 QCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGT-SVREDQRILQ-AGVHVVVGTPGRVFDMLRRQSLRPDYIKM  141 (369)
Q Consensus        64 ~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~-~~~~~~~~~~-~~~~iiv~t~~~l~~~~~~~~~~~~~~~~  141 (369)
                      .|.+||||.+---+.++.+.++.+... +..+.-+.... ..+++...+. ...+|.|+||.++..+++.+.+..+.+..
T Consensus       126 sP~~lvvs~SalRa~dl~R~l~~~~~k-~~~v~KLFaKH~Kl~eqv~~L~~~~~~i~vGTP~Rl~kLle~~~L~l~~l~~  204 (252)
T PF14617_consen  126 SPHVLVVSSSALRAADLIRALRSFKGK-DCKVAKLFAKHIKLEEQVKLLKKTRVHIAVGTPGRLSKLLENGALSLSNLKR  204 (252)
T ss_pred             CCEEEEEcchHHHHHHHHHHHHhhccC-CchHHHHHHhhccHHHHHHHHHhCCceEEEeChHHHHHHHHcCCCCcccCeE
Confidence            457899999888888888888877421 22333333333 4555555555 47899999999999999999999999999


Q ss_pred             EEEechhH
Q 017573          142 FVLDEADE  149 (369)
Q Consensus       142 viiDE~H~  149 (369)
                      ||+|--|.
T Consensus       205 ivlD~s~~  212 (252)
T PF14617_consen  205 IVLDWSYL  212 (252)
T ss_pred             EEEcCCcc
Confidence            99998774

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.47  E-value=0.04  Score=48.18  Aligned_cols=37  Identities=22%  Similarity=0.101  Sum_probs=25.0

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcC
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAP   72 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P   72 (369)
                      ++.+.+.+|+|+|||..+...+......+.   ++.+++.
T Consensus       206 ~~ii~lvGptGvGKTTt~akLA~~l~~~g~---~V~lIta  242 (407)
T PRK12726        206 HRIISLIGQTGVGKTTTLVKLGWQLLKQNR---TVGFITT  242 (407)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHcCC---eEEEEeC
Confidence            566899999999999876655544433332   5666554

>COG2805 PilT Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=96.47  E-value=0.025  Score=47.19  Aligned_cols=116  Identities=15%  Similarity=0.201  Sum_probs=58.5

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHH---HHhccccCcEEEEEECCcchHHHHHH
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVM---RALGDYLGVKVHACVGGTSVREDQRI  110 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~---~~~~~~~~~~v~~~~~~~~~~~~~~~  110 (369)
                      .-++|.+|||||||.+ +.++++++++.... .+|=+=.-.+-+.+..+.+   ++.    |...     ..-....+..
T Consensus       126 GLILVTGpTGSGKSTT-lAamId~iN~~~~~-HIlTIEDPIE~vh~skkslI~QREv----G~dT-----~sF~~aLraA  194 (353)
T COG2805         126 GLILVTGPTGSGKSTT-LAAMIDYINKHKAK-HILTIEDPIEYVHESKKSLINQREV----GRDT-----LSFANALRAA  194 (353)
T ss_pred             ceEEEeCCCCCcHHHH-HHHHHHHHhccCCc-ceEEecCchHhhhcchHhhhhHHHh----cccH-----HHHHHHHHHH
Confidence            4589999999999976 56778888776543 3433322222221111111   111    1111     1111233344


Q ss_pred             HccCCcEEEec----cHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCc
Q 017573          111 LQAGVHVVVGT----PGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPA  168 (369)
Q Consensus       111 ~~~~~~iiv~t----~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~  168 (369)
                      +..++|||+.-    .++..-.+....     -+.+|+--.|.   .+..+.+.++...+|.
T Consensus       195 LReDPDVIlvGEmRD~ETi~~ALtAAE-----TGHLV~~TLHT---~sA~~ti~RiidvFp~  248 (353)
T COG2805         195 LREDPDVILVGEMRDLETIRLALTAAE-----TGHLVFGTLHT---NSAAKTIDRIIDVFPA  248 (353)
T ss_pred             hhcCCCEEEEeccccHHHHHHHHHHHh-----cCCEEEEeccc---ccHHHHHHHHHHhCCh
Confidence            55667777652    233333333222     25677777775   3344566666666664

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=96.46  E-value=0.11  Score=43.93  Aligned_cols=133  Identities=21%  Similarity=0.252  Sum_probs=64.6

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcC--CHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHH
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAP--TRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL  111 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P--~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~  111 (369)
                      +-+.+.+|+|+|||.++...+......+   .+++++.-  .+.-+.+   ++..+....+..+.  ......+..    
T Consensus        73 ~vi~l~G~~G~GKTTt~akLA~~l~~~g---~~V~li~~D~~r~~a~~---ql~~~~~~~~i~~~--~~~~~~dp~----  140 (272)
T TIGR00064        73 NVILFVGVNGVGKTTTIAKLANKLKKQG---KSVLLAAGDTFRAAAIE---QLEEWAKRLGVDVI--KQKEGADPA----  140 (272)
T ss_pred             eEEEEECCCCCcHHHHHHHHHHHHHhcC---CEEEEEeCCCCCHHHHH---HHHHHHHhCCeEEE--eCCCCCCHH----
Confidence            4577889999999988765554443332   26776663  2332222   22222222243332  211110000    


Q ss_pred             ccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhh-ccCcHHHHHHHHhhCC------ccCcEEEEEeeCChhHH
Q 017573          112 QAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEML-SRGFKDQIYDIFQLLP------AKVQVGVFSATMPPEAL  184 (369)
Q Consensus       112 ~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~-~~~~~~~~~~~~~~~~------~~~~~i~~saT~~~~~~  184 (369)
                                 ......+..  ....++++|++|=+-+.. +.....++..+.+..+      +...++.++||...+..
T Consensus       141 -----------~~~~~~l~~--~~~~~~D~ViIDT~G~~~~d~~~~~el~~~~~~~~~~~~~~~~~~~LVl~a~~~~~~~  207 (272)
T TIGR00064       141 -----------AVAFDAIQK--AKARNIDVVLIDTAGRLQNKVNLMDELKKIKRVIKKVDKDAPDEVLLVLDATTGQNAL  207 (272)
T ss_pred             -----------HHHHHHHHH--HHHCCCCEEEEeCCCCCcchHHHHHHHHHHHHHHhcccCCCCceEEEEEECCCCHHHH
Confidence                       111111111  012336899999776543 2223344555554443      44556778888765544


Q ss_pred             HHHHHhc
Q 017573          185 EITRKFM  191 (369)
Q Consensus       185 ~~~~~~~  191 (369)
                      .....+.
T Consensus       208 ~~~~~f~  214 (272)
T TIGR00064       208 EQAKVFN  214 (272)
T ss_pred             HHHHHHH
Confidence            4444433

There is a weak division between FtsY and SRP54; both are GTPases. In E.coli, ftsY is an essential gene located in an operon with cell division genes ftsE and ftsX, but its apparent function is as the signal recognition particle docking protein.

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=96.46  E-value=0.028  Score=49.26  Aligned_cols=42  Identities=19%  Similarity=0.313  Sum_probs=28.1

Q ss_pred             CCccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEEeeC
Q 017573          137 DYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATM  179 (369)
Q Consensus       137 ~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~saT~  179 (369)
                      ..+.++||||+|.+.... ...+.+++..-+....++++|..+
T Consensus       140 g~~rVviIDeAd~l~~~a-anaLLk~LEEpp~~~~fiLit~~~  181 (351)
T PRK09112        140 GNWRIVIIDPADDMNRNA-ANAILKTLEEPPARALFILISHSS  181 (351)
T ss_pred             CCceEEEEEchhhcCHHH-HHHHHHHHhcCCCCceEEEEECCh
Confidence            346899999999985433 455666666655566666665443

>cd03115 SRP The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes

Probab=96.46  E-value=0.14  Score=39.98  Aligned_cols=33  Identities=27%  Similarity=0.306  Sum_probs=21.7

Q ss_pred             EEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEc
Q 017573           36 VIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLA   71 (369)
Q Consensus        36 ~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~   71 (369)
                      +++.+++|+|||..+...+......+.   +++++.
T Consensus         3 ~~~~G~~G~GKTt~~~~la~~~~~~g~---~v~~i~   35 (173)
T cd03115           3 ILLVGLQGVGKTTTAAKLALYLKKKGK---KVLLVA   35 (173)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCC---cEEEEE
Confidence            578999999999887555544333322   555544

SRP recognizes N-terminal sighnal sequences of newly synthesized polypeptides at the ribosome. The SRP-polypeptide complex is then targeted to the membrane by an interaction between SRP and its cognated receptor (SR). In mammals, SRP consists of six protein subunits and a 7SL RNA. One of these subunits is a 54 kd protein (SRP54), which is a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 is a multidomain protein that consists of an N-terminal domain, followed by a central G (GTPase) domain and a C-terminal M domain.

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=96.43  E-value=0.04  Score=45.36  Aligned_cols=51  Identities=22%  Similarity=0.212  Sum_probs=33.0

Q ss_pred             cCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHH
Q 017573           32 KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRA   86 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~   86 (369)
                      .|..+++.+++|+|||..+...+.+.+..+.   ++++++.- ....+..+....
T Consensus        19 ~G~~~~i~G~~G~GKT~l~~~~~~~~~~~g~---~~~~is~e-~~~~~i~~~~~~   69 (229)
T TIGR03881        19 RGFFVAVTGEPGTGKTIFCLHFAYKGLRDGD---PVIYVTTE-ESRESIIRQAAQ   69 (229)
T ss_pred             CCeEEEEECCCCCChHHHHHHHHHHHHhcCC---eEEEEEcc-CCHHHHHHHHHH
Confidence            4678899999999999877665555554433   67777642 333444444433

Members of this protein family are archaeal single-domain KaiC_related proteins, homologous to the Cyanobacterial circadian clock cycle protein KaiC, an autokinase/autophosphorylase that has two copies of the domain.

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=96.41  E-value=0.017  Score=51.37  Aligned_cols=41  Identities=15%  Similarity=0.277  Sum_probs=24.7

Q ss_pred             CCccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEEeeC
Q 017573          137 DYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATM  179 (369)
Q Consensus       137 ~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~saT~  179 (369)
                      .+.+++|+||+|.+.... ...+.+++..-++...++ +++|-
T Consensus       116 ~~~kViiIDead~m~~~a-anaLLk~LEep~~~~~fI-L~a~~  156 (394)
T PRK07940        116 GRWRIVVIEDADRLTERA-ANALLKAVEEPPPRTVWL-LCAPS  156 (394)
T ss_pred             CCcEEEEEechhhcCHHH-HHHHHHHhhcCCCCCeEE-EEECC
Confidence            346899999999985433 344555555544455444 44443

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=96.41  E-value=0.012  Score=51.94  Aligned_cols=145  Identities=12%  Similarity=0.084  Sum_probs=68.5

Q ss_pred             hhhhhhhccc----cC---CcEEEEcCCCChhhHHHHHHHHHhhhccCCC-------ccEEEEcCCHHHHHHHHHHHHHh
Q 017573           22 IQQRGIVPFC----KG---LDVIQQAQSGTGKTATFCSGILQQLDYGLVQ-------CQALVLAPTRELAQQIEKVMRAL   87 (369)
Q Consensus        22 ~Q~~~~~~~~----~~---~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~-------~~~liv~P~~~l~~q~~~~~~~~   87 (369)
                      .|.++...+.    .+   ...++.||.|+||+..+...+...+-....+       +..+-+|+.-.       .++.+
T Consensus        23 Gq~~~~~~L~~~~~~~rl~HA~Lf~Gp~G~GK~~lA~~~A~~Llc~~~~~~~~~~~~~~~l~~~~~c~-------~c~~i   95 (365)
T PRK07471         23 GHAAAEAALLDAYRSGRLHHAWLIGGPQGIGKATLAYRMARFLLATPPPGGDGAVPPPTSLAIDPDHP-------VARRI   95 (365)
T ss_pred             ChHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHHhCCCCCCCCccccccccccCCCCCh-------HHHHH
Confidence            3555555443    22   3589999999999988766555554332211       11222333211       12222


Q ss_pred             ccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCC
Q 017573           88 GDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLP  167 (369)
Q Consensus        88 ~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~  167 (369)
                      .....-++..+.........    .....|.|-....+.+.+... .......++|+||+|.+... ....+.+.+..-+
T Consensus        96 ~~~~HPDl~~i~~~~~~~~~----~~~~~I~VdqiR~l~~~~~~~-~~~~~~kVviIDead~m~~~-aanaLLK~LEepp  169 (365)
T PRK07471         96 AAGAHGGLLTLERSWNEKGK----RLRTVITVDEVRELISFFGLT-AAEGGWRVVIVDTADEMNAN-AANALLKVLEEPP  169 (365)
T ss_pred             HccCCCCeEEEecccccccc----cccccccHHHHHHHHHHhCcC-cccCCCEEEEEechHhcCHH-HHHHHHHHHhcCC
Confidence            11111222222221100000    001234333333333333322 22344689999999987533 2445556666655


Q ss_pred             ccCcEEEEEeeC
Q 017573          168 AKVQVGVFSATM  179 (369)
Q Consensus       168 ~~~~~i~~saT~  179 (369)
                      ....++++|..+
T Consensus       170 ~~~~~IL~t~~~  181 (365)
T PRK07471        170 ARSLFLLVSHAP  181 (365)
T ss_pred             CCeEEEEEECCc
Confidence            556566555554

>KOG2028 consensus ATPase related to the helicase subunit of the Holliday junction resolvase [Replication, recombination and repair]

Probab=96.41  E-value=0.023  Score=48.66  Aligned_cols=18  Identities=33%  Similarity=0.305  Sum_probs=15.3

Q ss_pred             CcEEEEcCCCChhhHHHH
Q 017573           34 LDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~   51 (369)
                      ...++|+|+|+|||..+=
T Consensus       163 pSmIlWGppG~GKTtlAr  180 (554)
T KOG2028|consen  163 PSMILWGPPGTGKTTLAR  180 (554)
T ss_pred             CceEEecCCCCchHHHHH
Confidence            468999999999997763

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.40  E-value=0.011  Score=55.63  Aligned_cols=24  Identities=21%  Similarity=0.033  Sum_probs=18.4

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHh
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQ   57 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~   57 (369)
                      ...|++||.|+|||.++...+...
T Consensus        39 ha~Lf~Gp~GvGKttlA~~lAk~L   62 (620)
T PRK14954         39 HGYIFSGLRGVGKTTAARVFAKAV   62 (620)
T ss_pred             eeEEEECCCCCCHHHHHHHHHHHh
Confidence            347899999999998876554433

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.39  E-value=0.015  Score=54.01  Aligned_cols=39  Identities=13%  Similarity=0.278  Sum_probs=24.4

Q ss_pred             CCccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEE
Q 017573          137 DYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFS  176 (369)
Q Consensus       137 ~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~s  176 (369)
                      .+++++|+||+|.+.... ...+.+.+...+....+|+.|
T Consensus       118 ~~~kVvIIDEad~ls~~a-~naLLK~LEepp~~~~fIL~t  156 (527)
T PRK14969        118 GRFKVYIIDEVHMLSKSA-FNAMLKTLEEPPEHVKFILAT  156 (527)
T ss_pred             CCceEEEEcCcccCCHHH-HHHHHHHHhCCCCCEEEEEEe
Confidence            346899999999886433 334445555555555555544

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=96.39  E-value=0.024  Score=53.33  Aligned_cols=39  Identities=13%  Similarity=0.260  Sum_probs=25.2

Q ss_pred             CCccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEE
Q 017573          137 DYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFS  176 (369)
Q Consensus       137 ~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~s  176 (369)
                      ...+++|+||+|.+.... ...+.+.+...++...+|+.|
T Consensus       131 a~~KVvIIDEad~Ls~~a-~naLLKtLEePp~~~~fIl~t  169 (598)
T PRK09111        131 ARYKVYIIDEVHMLSTAA-FNALLKTLEEPPPHVKFIFAT  169 (598)
T ss_pred             CCcEEEEEEChHhCCHHH-HHHHHHHHHhCCCCeEEEEEe
Confidence            346899999999986433 344455555555566566544

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=96.38  E-value=0.012  Score=55.83  Aligned_cols=136  Identities=15%  Similarity=0.119  Sum_probs=72.9

Q ss_pred             cCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHH
Q 017573           32 KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL  111 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~  111 (369)
                      ..+-+++++|.|+|||+.+..+.. ....   +..+.++.-.. -..+-.+.++.+....+--+... ++.   .. .+.
T Consensus        36 ~~RL~li~APAGfGKttl~aq~~~-~~~~---~~~v~Wlslde-~dndp~rF~~yLi~al~~~~p~~-~~~---a~-~l~  105 (894)
T COG2909          36 DYRLILISAPAGFGKTTLLAQWRE-LAAD---GAAVAWLSLDE-SDNDPARFLSYLIAALQQATPTL-GDE---AQ-TLL  105 (894)
T ss_pred             CceEEEEeCCCCCcHHHHHHHHHH-hcCc---ccceeEeecCC-ccCCHHHHHHHHHHHHHHhCccc-cHH---HH-HHH
Confidence            346689999999999987655543 2222   22566665332 12222222222222111111111 111   11 111


Q ss_pred             ccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEEeeCC
Q 017573          112 QAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMP  180 (369)
Q Consensus       112 ~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~saT~~  180 (369)
                      .+  +..+ ..+.+.+.+...--...+.=++|+|+.|.+.+......+..+++..|++...++.|-+-+
T Consensus       106 q~--~~~~-~l~~l~~~L~~Ela~~~~pl~LVlDDyHli~~~~l~~~l~fLl~~~P~~l~lvv~SR~rP  171 (894)
T COG2909         106 QK--HQYV-SLESLLSSLLNELASYEGPLYLVLDDYHLISDPALHEALRFLLKHAPENLTLVVTSRSRP  171 (894)
T ss_pred             Hh--cccc-cHHHHHHHHHHHHHhhcCceEEEeccccccCcccHHHHHHHHHHhCCCCeEEEEEeccCC
Confidence            11  1111 122222222221111122348999999999988888999999999999999888887754

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.34  E-value=0.038  Score=52.97  Aligned_cols=124  Identities=18%  Similarity=0.117  Sum_probs=62.2

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHc
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQ  112 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~  112 (369)
                      ++-+.+.+|+|+|||+++...+........ +.++.+++.-..-+ -..++++.+....++.+.                
T Consensus       185 g~Vi~lVGpnGvGKTTTiaKLA~~~~~~~G-~kkV~lit~Dt~Ri-gA~eQL~~~a~~~gvpv~----------------  246 (767)
T PRK14723        185 GGVLALVGPTGVGKTTTTAKLAARCVAREG-ADQLALLTTDSFRI-GALEQLRIYGRILGVPVH----------------  246 (767)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHhhHHHHcC-CCeEEEecCcccch-HHHHHHHHHHHhCCCCcc----------------
Confidence            345789999999999776544433322211 11555555432211 012334444333333221                


Q ss_pred             cCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhc-cCcHHHHHHHHhhCCccCcEEEEEeeCChhH
Q 017573          113 AGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLS-RGFKDQIYDIFQLLPAKVQVGVFSATMPPEA  183 (369)
Q Consensus       113 ~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~-~~~~~~~~~~~~~~~~~~~~i~~saT~~~~~  183 (369)
                           .+.+++.+...+...    ...++|+||=+-+... ....+.+..+.....+...++.++||...+.
T Consensus       247 -----~~~~~~~l~~al~~~----~~~D~VLIDTAGRs~~d~~l~eel~~l~~~~~p~e~~LVLsAt~~~~~  309 (767)
T PRK14723        247 -----AVKDAADLRFALAAL----GDKHLVLIDTVGMSQRDRNVSEQIAMLCGVGRPVRRLLLLNAASHGDT  309 (767)
T ss_pred             -----ccCCHHHHHHHHHHh----cCCCEEEEeCCCCCccCHHHHHHHHHHhccCCCCeEEEEECCCCcHHH
Confidence                 122455555555432    2357888887765431 2223333344434444455667888875443

>COG1223 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=96.33  E-value=0.044  Score=44.77  Aligned_cols=47  Identities=21%  Similarity=0.339  Sum_probs=28.8

Q ss_pred             ccEEEEechhHhh-ccCc-------HHHHHHHHhh---CCccCcEEEEEeeCChhHHH
Q 017573          139 IKMFVLDEADEML-SRGF-------KDQIYDIFQL---LPAKVQVGVFSATMPPEALE  185 (369)
Q Consensus       139 ~~~viiDE~H~~~-~~~~-------~~~~~~~~~~---~~~~~~~i~~saT~~~~~~~  185 (369)
                      ..++.+||.+.+. +..|       .+.++.++..   +..+.-++...||..++..+
T Consensus       211 PcivFiDE~DAiaLdRryQelRGDVsEiVNALLTelDgi~eneGVvtIaaTN~p~~LD  268 (368)
T COG1223         211 PCIVFIDELDAIALDRRYQELRGDVSEIVNALLTELDGIKENEGVVTIAATNRPELLD  268 (368)
T ss_pred             CeEEEehhhhhhhhhhhHHHhcccHHHHHHHHHHhccCcccCCceEEEeecCChhhcC
Confidence            4788899999764 2222       2333344333   34566688889998776544

>PF02456 Adeno_IVa2: Adenovirus IVa2 protein; InterPro: IPR003389 Va2 protein can interact with the adenoviral packaging signal and this interaction involves DNA sequences that have previously been demonstrated to be required for packaging []

Probab=96.33  E-value=0.014  Score=48.62  Aligned_cols=41  Identities=10%  Similarity=0.200  Sum_probs=25.4

Q ss_pred             EEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHH
Q 017573           36 VIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELA   77 (369)
Q Consensus        36 ~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~   77 (369)
                      .+|.||||+||+-. +-.++..-.-.+....+++|+|.+..+
T Consensus        90 ~~VYGPTG~GKSqL-lRNLis~~lI~P~PETVfFItP~~~mI  130 (369)
T PF02456_consen   90 GVVYGPTGSGKSQL-LRNLISCQLIQPPPETVFFITPQKDMI  130 (369)
T ss_pred             EEEECCCCCCHHHH-HHHhhhcCcccCCCCceEEECCCCCCC
Confidence            58999999999943 222222211122333799999987543

During the course of lytic infection, the adenovirus major late promoter (MLP) is induced to high levels after replication of viral DNA has started. IVa2 is a transcriptional activator of the major late promoter [].; GO: 0019083 viral transcription

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=96.32  E-value=0.017  Score=53.99  Aligned_cols=21  Identities=24%  Similarity=0.164  Sum_probs=16.6

Q ss_pred             cEEEEcCCCChhhHHHHHHHH
Q 017573           35 DVIQQAQSGTGKTATFCSGIL   55 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~~~~~   55 (369)
                      ..++.||.|+|||.++...+.
T Consensus        40 ayLf~Gp~G~GKTt~Ar~lAk   60 (563)
T PRK06647         40 AYIFSGPRGVGKTSSARAFAR   60 (563)
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            479999999999988754433

>TIGR00959 ffh signal recognition particle protein

Probab=96.32  E-value=0.061  Score=48.39  Aligned_cols=35  Identities=23%  Similarity=0.207  Sum_probs=23.6

Q ss_pred             cEEEEcCCCChhhHHHHHHHHHhh-hccCCCccEEEEcC
Q 017573           35 DVIQQAQSGTGKTATFCSGILQQL-DYGLVQCQALVLAP   72 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~~~~~~~~-~~~~~~~~~liv~P   72 (369)
                      -+++.+++|+|||.++.-.+.... ..+.   +++++.-
T Consensus       101 vi~~vG~~GsGKTTtaakLA~~l~~~~g~---kV~lV~~  136 (428)
T TIGR00959       101 VILMVGLQGSGKTTTCGKLAYYLKKKQGK---KVLLVAC  136 (428)
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHhCCC---eEEEEec
Confidence            478999999999988766555433 2222   5666553

This model represents Ffh (Fifty-Four Homolog), the protein component that forms the bacterial (and organellar) signal recognition particle together with a 4.5S RNA. Ffh is a GTPase homologous to eukaryotic SRP54 and also to the GTPase FtsY (TIGR00064) that is the receptor for the signal recognition particle.

>COG2109 BtuR ATP:corrinoid adenosyltransferase [Coenzyme metabolism]

Probab=96.32  E-value=0.036  Score=42.87  Aligned_cols=141  Identities=18%  Similarity=0.244  Sum_probs=71.6

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHH-HHHHHHhccccCcEEEEEECCcchHHHHHHHc
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQI-EKVMRALGDYLGVKVHACVGGTSVREDQRILQ  112 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~-~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~  112 (369)
                      .-++|.-..|-|||.+++-.++.++-.+.   ++.|+-=-+.-...= ...+.++    +..+....-+........  .
T Consensus        29 Gli~V~TG~GKGKTTAAlG~alRa~GhG~---rv~vvQFiKg~~~~GE~~~~~~~----~~~v~~~~~~~g~tw~~~--~   99 (198)
T COG2109          29 GLIIVFTGNGKGKTTAALGLALRALGHGL---RVGVVQFIKGGWKYGEEAALEKF----GLGVEFHGMGEGFTWETQ--D   99 (198)
T ss_pred             CeEEEEecCCCChhHHHHHHHHHHhcCCC---EEEEEEEeecCcchhHHHHHHhh----ccceeEEecCCceeCCCc--C
Confidence            34789999999999999999998888776   676664322211111 1112222    222222111111000000  0


Q ss_pred             cCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCc--HHHHHHHHhhCCccCcEEEEEeeCChhHHHH
Q 017573          113 AGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGF--KDQIYDIFQLLPAKVQVGVFSATMPPEALEI  186 (369)
Q Consensus       113 ~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~--~~~~~~~~~~~~~~~~~i~~saT~~~~~~~~  186 (369)
                      ++.++  ............ .+....+++||+||.-.....++  .+.+..++..-|....+|+..-..++.+.+.
T Consensus       100 ~~~d~--~aa~~~w~~a~~-~l~~~~ydlviLDEl~~al~~g~l~~eeV~~~l~~kP~~~~vIiTGr~ap~~lie~  172 (198)
T COG2109         100 READI--AAAKAGWEHAKE-ALADGKYDLVILDELNYALRYGLLPLEEVVALLKARPEHTHVIITGRGAPPELIEL  172 (198)
T ss_pred             cHHHH--HHHHHHHHHHHH-HHhCCCCCEEEEehhhHHHHcCCCCHHHHHHHHhcCCCCcEEEEECCCCCHHHHHH
Confidence            01122  111111111111 12223479999999998775553  4667777777776776666444444454443

>PRK07414 cob(I)yrinic acid a,c-diamide adenosyltransferase; Validated

Probab=96.31  E-value=0.22  Score=38.65  Aligned_cols=138  Identities=15%  Similarity=0.145  Sum_probs=74.5

Q ss_pred             ccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCc-----chH
Q 017573           31 CKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGT-----SVR  105 (369)
Q Consensus        31 ~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~-----~~~  105 (369)
                      ....-+.|.-..|-|||.+++-.++.++-++.   +++|+-=.+.-...=...+-+...  ++.......+.     ...
T Consensus        19 ~~~Gli~VYtGdGKGKTTAAlGlalRAaG~G~---rV~iiQFlKg~~~~GE~~~l~~~~--~v~~~~~g~~~~~~~~~~~   93 (178)
T PRK07414         19 TIEGLVQVFTSSQRNFFTSVMAQALRIAGQGT---PVLIVQFLKGGIQQGPDRPIQLGQ--NLDWVRCDLPRCLDTPHLD   93 (178)
T ss_pred             CCCCEEEEEeCCCCCchHHHHHHHHHHhcCCC---EEEEEEEecCCCcchHHHHHHhCC--CcEEEECCCCCeeeCCCcC
Confidence            34456788899999999999999998887766   787776444321111111111111  23332211110     000


Q ss_pred             -HHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCc--HHHHHHHHhhCCccCcEEEEEeeCChh
Q 017573          106 -EDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGF--KDQIYDIFQLLPAKVQVGVFSATMPPE  182 (369)
Q Consensus       106 -~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~--~~~~~~~~~~~~~~~~~i~~saT~~~~  182 (369)
                       ...           ...+........ .+....++++|+||+-...+.++  .+.+..+++..|+...+|+..-.+++.
T Consensus        94 ~~~~-----------~~~~~~~~~a~~-~l~~~~~dlvVLDEi~~Al~~gli~~eeVl~~L~~rp~~~evILTGR~~p~~  161 (178)
T PRK07414         94 ESEK-----------KALQELWQYTQA-VVDEGRYSLVVLDELSLAIQFGLIPETEVLEFLEKRPSHVDVILTGPEMPES  161 (178)
T ss_pred             HHHH-----------HHHHHHHHHHHH-HHhCCCCCEEEEehhHHHHHCCCccHHHHHHHHHhCCCCCEEEEECCCCCHH
Confidence             010           011111111111 12233479999999998876664  366777778777777777644445544


Q ss_pred             HHH
Q 017573          183 ALE  185 (369)
Q Consensus       183 ~~~  185 (369)
                      +.+
T Consensus       162 Lie  164 (178)
T PRK07414        162 LLA  164 (178)
T ss_pred             HHH
Confidence            443

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=96.30  E-value=0.024  Score=60.75  Aligned_cols=62  Identities=29%  Similarity=0.306  Sum_probs=44.1

Q ss_pred             CCCcHhhhhhhhccccC--CcEEEEcCCCChhhHHHH---HHHHHhhhccCCCccEEEEcCCHHHHHHH
Q 017573           17 EKPSAIQQRGIVPFCKG--LDVIQQAQSGTGKTATFC---SGILQQLDYGLVQCQALVLAPTRELAQQI   80 (369)
Q Consensus        17 ~~~~~~Q~~~~~~~~~~--~~~li~~~tG~GKT~~~~---~~~~~~~~~~~~~~~~liv~P~~~l~~q~   80 (369)
                      ..+++.|++++..++.+  +-++|.++.|+|||.+.-   .++...+...  +.+++.++|+..-+..+
T Consensus      1018 ~~Lt~~Q~~Ai~~il~~~~~~~~i~G~AGtGKTt~l~~~~~~i~~~~~~~--g~~v~glApT~~Aa~~L 1084 (1960)
T TIGR02760      1018 ERLTHGQKQAIHLIISTKDRFVAVQGLAGVGKTTMLESRYKPVLQAFESE--QLQVIGLAPTHEAVGEL 1084 (1960)
T ss_pred             CCCCHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHhHHHHHHHHHHHHHhc--CCeEEEEeChHHHHHHH
Confidence            47999999999998865  556889999999997652   2333333322  23788889996655544

This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.

>KOG0733 consensus Nuclear AAA ATPase (VCP subfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=96.29  E-value=0.044  Score=50.28  Aligned_cols=80  Identities=19%  Similarity=0.244  Sum_probs=48.1

Q ss_pred             CccEEEEechhHhhc-------cCcHHHHHHHHhhC---CccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCcccccc
Q 017573          138 YIKMFVLDEADEMLS-------RGFKDQIYDIFQLL---PAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLE  207 (369)
Q Consensus       138 ~~~~viiDE~H~~~~-------~~~~~~~~~~~~~~---~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  207 (369)
                      ...+|.+||++.+..       +...+.++.++..+   .....++.+.||-.|+.-+-.-               ..+.
T Consensus       604 aPCVIFFDEiDaL~p~R~~~~s~~s~RvvNqLLtElDGl~~R~gV~viaATNRPDiIDpAi---------------LRPG  668 (802)
T KOG0733|consen  604 APCVIFFDEIDALVPRRSDEGSSVSSRVVNQLLTELDGLEERRGVYVIAATNRPDIIDPAI---------------LRPG  668 (802)
T ss_pred             CCeEEEecchhhcCcccCCCCchhHHHHHHHHHHHhcccccccceEEEeecCCCcccchhh---------------cCCC
Confidence            358999999998862       11234444444443   4466788899998876543221               1122


Q ss_pred             ce-eEEEEEccchhhhHHHHHHHHHh
Q 017573          208 GI-KQFYVNVEKEEWKLETLCDLYET  232 (369)
Q Consensus       208 ~~-~~~~~~~~~~~~~~~~l~~~~~~  232 (369)
                      .. ...|+..+..+...+.|..+.+.
T Consensus       669 RlDk~LyV~lPn~~eR~~ILK~~tkn  694 (802)
T KOG0733|consen  669 RLDKLLYVGLPNAEERVAILKTITKN  694 (802)
T ss_pred             ccCceeeecCCCHHHHHHHHHHHhcc
Confidence            22 34556667777777777776664

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=96.26  E-value=0.038  Score=46.57  Aligned_cols=120  Identities=15%  Similarity=0.185  Sum_probs=59.1

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHhhhccC----CCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHH
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQLDYGL----VQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQR  109 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~~~~~~----~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~  109 (369)
                      .+.++.|++|-|||.++--..-.+-....    .-+-+.+-+|...-...++..+-...   +.....   .......  
T Consensus        62 p~lLivG~snnGKT~Ii~rF~~~hp~~~d~~~~~~PVv~vq~P~~p~~~~~Y~~IL~~l---gaP~~~---~~~~~~~--  133 (302)
T PF05621_consen   62 PNLLIVGDSNNGKTMIIERFRRLHPPQSDEDAERIPVVYVQMPPEPDERRFYSAILEAL---GAPYRP---RDRVAKL--  133 (302)
T ss_pred             CceEEecCCCCcHHHHHHHHHHHCCCCCCCCCccccEEEEecCCCCChHHHHHHHHHHh---CcccCC---CCCHHHH--
Confidence            57999999999999765322221111100    11234555666655555544443321   111100   0000000  


Q ss_pred             HHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcH--HHHHHHHhhCCcc--CcEEEEEeeC
Q 017573          110 ILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFK--DQIYDIFQLLPAK--VQVGVFSATM  179 (369)
Q Consensus       110 ~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~--~~~~~~~~~~~~~--~~~i~~saT~  179 (369)
                                  -....+.+...+     .+++||||+|++...+..  +...+.++.+.+.  ..+++ -+|.
T Consensus       134 ------------~~~~~~llr~~~-----vrmLIIDE~H~lLaGs~~~qr~~Ln~LK~L~NeL~ipiV~-vGt~  189 (302)
T PF05621_consen  134 ------------EQQVLRLLRRLG-----VRMLIIDEFHNLLAGSYRKQREFLNALKFLGNELQIPIVG-VGTR  189 (302)
T ss_pred             ------------HHHHHHHHHHcC-----CcEEEeechHHHhcccHHHHHHHHHHHHHHhhccCCCeEE-eccH
Confidence                        011224444433     689999999998755433  3444555555543  33454 3564

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>PF00265 TK: Thymidine kinase; InterPro: IPR001267 Thymidine kinase (TK) (2

Probab=96.19  E-value=0.011  Score=46.08  Aligned_cols=36  Identities=19%  Similarity=0.168  Sum_probs=24.8

Q ss_pred             EEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCH
Q 017573           36 VIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTR   74 (369)
Q Consensus        36 ~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~   74 (369)
                      .++.+|++||||.-.+..+......+.   +++++-|..
T Consensus         4 ~~i~GpM~sGKS~eLi~~~~~~~~~~~---~v~~~kp~~   39 (176)
T PF00265_consen    4 EFITGPMFSGKSTELIRRIHRYEIAGK---KVLVFKPAI   39 (176)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHHHTT----EEEEEEEST
T ss_pred             EEEECCcCChhHHHHHHHHHHHHhCCC---eEEEEEecc
Confidence            478999999999775544443333332   889988864

7.1.21 from EC) is an ubiquitous enzyme that catalyzes the ATP-dependent phosphorylation of thymidine. Two different families of Thymidine kinase have been identified [, ] and are represented in this entry; one groups together Thymidine kinase from herpesviruses, as well as cytosolic thymidylate kinases and the second family groups Thymidine kinase from various sources that include, vertebrates, bacteria, the Bacteriophage T4, poxviruses, African swine fever virus (ASFV) and Fish lymphocystis disease virus (FLDV). The major capsid protein of insect iridescent viruses also belongs to this family.; GO: 0004797 thymidine kinase activity, 0005524 ATP binding; PDB: 1XX6_B 2J9R_A 2J87_B 3E2I_A 2JA1_A 2UZ3_B 2B8T_B 2WVJ_A 1W4R_F 1XBT_F ....

>COG1444 Predicted P-loop ATPase fused to an acetyltransferase [General function prediction only]

Probab=96.17  E-value=0.05  Score=51.74  Aligned_cols=152  Identities=18%  Similarity=0.224  Sum_probs=89.0

Q ss_pred             HHHHHhCCCCCCcHhhhhhhhccccC--CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHH
Q 017573            8 LRGIYAYGFEKPSAIQQRGIVPFCKG--LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMR   85 (369)
Q Consensus         8 ~~~l~~~~~~~~~~~Q~~~~~~~~~~--~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~   85 (369)
                      -+.+.....+.+..-|.+.+..+.+.  +-+++.|+-|=|||.++=+++........ ...+++.+|+.+-++...+...
T Consensus       204 ~~~l~~l~~T~dQ~~~l~~~~~l~~~~~~~~vlTAdRGRGKSA~lGi~~~~~~~~~~-~~~iiVTAP~~~nv~~Lf~fa~  282 (758)
T COG1444         204 PRELYELCLTEDQAEALEILERLLDAPKRALVLTADRGRGKSAALGIALAAAARLAG-SVRIIVTAPTPANVQTLFEFAG  282 (758)
T ss_pred             CHHHhhhhcChhHHHHHHHHHHHHcCCCceEEEEcCCCCcHhHHHhHHHHHHHHhcC-CceEEEeCCCHHHHHHHHHHHH
Confidence            34454455566666677777777765  35899999999999765544432222221 2379999999999988888777


Q ss_pred             HhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhh
Q 017573           86 ALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQL  165 (369)
Q Consensus        86 ~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~  165 (369)
                      +-....|.+-.+......  .......+...|=+.+|+...          ..-+++|+|||=.+    ....+..+...
T Consensus       283 ~~l~~lg~~~~v~~d~~g--~~~~~~~~~~~i~y~~P~~a~----------~~~DllvVDEAAaI----plplL~~l~~~  346 (758)
T COG1444         283 KGLEFLGYKRKVAPDALG--EIREVSGDGFRIEYVPPDDAQ----------EEADLLVVDEAAAI----PLPLLHKLLRR  346 (758)
T ss_pred             HhHHHhCCcccccccccc--ceeeecCCceeEEeeCcchhc----------ccCCEEEEehhhcC----ChHHHHHHHhh
Confidence            755555544222111110  000000111224445554432          01489999999865    34455555555


Q ss_pred             CCccCcEEEEEeeCC
Q 017573          166 LPAKVQVGVFSATMP  180 (369)
Q Consensus       166 ~~~~~~~i~~saT~~  180 (369)
                      .+    .++||.|.+
T Consensus       347 ~~----rv~~sTTIh  357 (758)
T COG1444         347 FP----RVLFSTTIH  357 (758)
T ss_pred             cC----ceEEEeeec
Confidence            43    677788864

>TIGR00767 rho transcription termination factor Rho

Probab=96.16  E-value=0.019  Score=50.52  Aligned_cols=31  Identities=26%  Similarity=0.260  Sum_probs=22.5

Q ss_pred             cccCCcEEEEcCCCChhhHHHHHHHHHhhhcc
Q 017573           30 FCKGLDVIQQAQSGTGKTATFCSGILQQLDYG   61 (369)
Q Consensus        30 ~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~   61 (369)
                      +-.|+.+++.+|+|+|||..+ ..+.+.+..+
T Consensus       165 ig~Gq~~~IvG~~g~GKTtL~-~~i~~~I~~n  195 (415)
T TIGR00767       165 IGKGQRGLIVAPPKAGKTVLL-QKIAQAITRN  195 (415)
T ss_pred             eCCCCEEEEECCCCCChhHHH-HHHHHhhccc
Confidence            346899999999999999764 3455555443

Members of this family differ in the specificity of RNA binding.

>COG2874 FlaH Predicted ATPases involved in biogenesis of archaeal flagella [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=96.16  E-value=0.14  Score=40.61  Aligned_cols=128  Identities=14%  Similarity=0.165  Sum_probs=67.7

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHc
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQ  112 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~  112 (369)
                      |.-+++.++.|+|||...+..++-.+..+.   ++.+++.- .-......++...    +..+.           ...+.
T Consensus        28 GsL~lIEGd~~tGKSvLsqr~~YG~L~~g~---~v~yvsTe-~T~refi~qm~sl----~ydv~-----------~~~l~   88 (235)
T COG2874          28 GSLILIEGDNGTGKSVLSQRFAYGFLMNGY---RVTYVSTE-LTVREFIKQMESL----SYDVS-----------DFLLS   88 (235)
T ss_pred             CeEEEEECCCCccHHHHHHHHHHHHHhCCc---eEEEEEec-hhHHHHHHHHHhc----CCCch-----------HHHhc
Confidence            345799999999999888777777777665   56666532 2222233333322    11110           00011


Q ss_pred             cCCcEEEe-----------ccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHH---hhCCccCcEEEEEee
Q 017573          113 AGVHVVVG-----------TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIF---QLLPAKVQVGVFSAT  178 (369)
Q Consensus       113 ~~~~iiv~-----------t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~---~~~~~~~~~i~~saT  178 (369)
                      +. -.++.           +...+++.+.+..- ..+-+++|+|-...+........+.+++   +.+....+++.+|+.
T Consensus        89 G~-l~~~~~~~~~~~~~~~~~~~~L~~l~~~~k-~~~~dViIIDSls~~~~~~~~~~vl~fm~~~r~l~d~gKvIilTvh  166 (235)
T COG2874          89 GR-LLFFPVNLEPVNWGRRSARKLLDLLLEFIK-RWEKDVIIIDSLSAFATYDSEDAVLNFMTFLRKLSDLGKVIILTVH  166 (235)
T ss_pred             ce-eEEEEecccccccChHHHHHHHHHHHhhHH-hhcCCEEEEecccHHhhcccHHHHHHHHHHHHHHHhCCCEEEEEeC
Confidence            10 01111           11223333322111 1223899999998876444343444444   334456778999999


Q ss_pred             CCh
Q 017573          179 MPP  181 (369)
Q Consensus       179 ~~~  181 (369)
                      |..
T Consensus       167 p~~  169 (235)
T COG2874         167 PSA  169 (235)
T ss_pred             hhh
Confidence            864

>PRK04195 replication factor C large subunit; Provisional

Probab=96.15  E-value=0.038  Score=51.02  Aligned_cols=19  Identities=21%  Similarity=0.240  Sum_probs=16.3

Q ss_pred             CCcEEEEcCCCChhhHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~   51 (369)
                      .+.+++.||+|+|||..+-
T Consensus        39 ~~~lLL~GppG~GKTtla~   57 (482)
T PRK04195         39 KKALLLYGPPGVGKTSLAH   57 (482)
T ss_pred             CCeEEEECCCCCCHHHHHH
Confidence            4679999999999997764

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=96.11  E-value=0.019  Score=50.24  Aligned_cols=29  Identities=24%  Similarity=0.287  Sum_probs=21.6

Q ss_pred             cCCcEEEEcCCCChhhHHHHHHHHHhhhcc
Q 017573           32 KGLDVIQQAQSGTGKTATFCSGILQQLDYG   61 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~~~~~~~~~~~   61 (369)
                      .|++.+|.||.|+|||..+ ..+++.+...
T Consensus       168 kGQR~lIvgppGvGKTTLa-K~Ian~I~~n  196 (416)
T PRK09376        168 KGQRGLIVAPPKAGKTVLL-QNIANSITTN  196 (416)
T ss_pred             cCceEEEeCCCCCChhHHH-HHHHHHHHhh
Confidence            5799999999999999654 3455555443

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=96.10  E-value=0.031  Score=48.45  Aligned_cols=145  Identities=12%  Similarity=0.053  Sum_probs=70.1

Q ss_pred             CcHhhhhhhhccccC-----CcEEEEcCCCChhhHHHHHHHHHhhhccCC-CccEEEEcCCHHHHHHHHHHHHHhccccC
Q 017573           19 PSAIQQRGIVPFCKG-----LDVIQQAQSGTGKTATFCSGILQQLDYGLV-QCQALVLAPTRELAQQIEKVMRALGDYLG   92 (369)
Q Consensus        19 ~~~~Q~~~~~~~~~~-----~~~li~~~tG~GKT~~~~~~~~~~~~~~~~-~~~~liv~P~~~l~~q~~~~~~~~~~~~~   92 (369)
                      +||+|+..+..+...     ...++.||.|.|||..+...+...+-..+. +...-=-|+          .++.+.....
T Consensus         2 ~yPW~~~~w~~l~~~~~r~~hA~Lf~G~~G~GK~~la~~~a~~llC~~~~~~~~~Cg~C~----------~C~~~~~~~H   71 (325)
T PRK08699          2 IYPWHQEQWRQIAEHWERRPNAWLFAGKKGIGKTAFARFAAQALLCETPAPGHKPCGECM----------SCHLFGQGSH   71 (325)
T ss_pred             CCCccHHHHHHHHHhcCCcceEEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCcCH----------HHHHHhcCCC
Confidence            478888888887742     357999999999998876554443322211 000000111          2233322222


Q ss_pred             cEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCccCcE
Q 017573           93 VKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQV  172 (369)
Q Consensus        93 ~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~  172 (369)
                      -++..+......+...   +....|-|-....+.+.+...... ...+++|+|++|.+... ....+.+++...+....+
T Consensus        72 pD~~~~~p~~~~~~~g---~~~~~I~id~iR~l~~~~~~~p~~-~~~kV~iiEp~~~Ld~~-a~naLLk~LEep~~~~~~  146 (325)
T PRK08699         72 PDFYEITPLSDEPENG---RKLLQIKIDAVREIIDNVYLTSVR-GGLRVILIHPAESMNLQ-AANSLLKVLEEPPPQVVF  146 (325)
T ss_pred             CCEEEEeccccccccc---ccCCCcCHHHHHHHHHHHhhCccc-CCceEEEEechhhCCHH-HHHHHHHHHHhCcCCCEE
Confidence            3333333211100000   000112222222233333332222 34689999999987543 355566666666555545


Q ss_pred             EEEEee
Q 017573          173 GVFSAT  178 (369)
Q Consensus       173 i~~saT  178 (369)
                      +++|..
T Consensus       147 Ilvth~  152 (325)
T PRK08699        147 LLVSHA  152 (325)
T ss_pred             EEEeCC
Confidence            554433

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.10  E-value=0.026  Score=53.35  Aligned_cols=21  Identities=24%  Similarity=0.126  Sum_probs=16.6

Q ss_pred             cEEEEcCCCChhhHHHHHHHH
Q 017573           35 DVIQQAQSGTGKTATFCSGIL   55 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~~~~~   55 (369)
                      ..++.||.|+|||.++...+-
T Consensus        40 a~Lf~Gp~G~GKTtlA~~lA~   60 (585)
T PRK14950         40 AYLFTGPRGVGKTSTARILAK   60 (585)
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            359999999999988755443

>KOG0738 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=96.10  E-value=0.04  Score=47.69  Aligned_cols=17  Identities=35%  Similarity=0.374  Sum_probs=15.4

Q ss_pred             CcEEEEcCCCChhhHHH
Q 017573           34 LDVIQQAQSGTGKTATF   50 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~   50 (369)
                      +.++..+|+|+|||+.+
T Consensus       246 kgvLm~GPPGTGKTlLA  262 (491)
T KOG0738|consen  246 KGVLMVGPPGTGKTLLA  262 (491)
T ss_pred             ceeeeeCCCCCcHHHHH
Confidence            78999999999999765

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily

Probab=96.06  E-value=0.045  Score=46.32  Aligned_cols=33  Identities=21%  Similarity=0.261  Sum_probs=23.4

Q ss_pred             CcHhhhhhhhccc----cC-CcEEEEcCCCChhhHHHH
Q 017573           19 PSAIQQRGIVPFC----KG-LDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        19 ~~~~Q~~~~~~~~----~~-~~~li~~~tG~GKT~~~~   51 (369)
                      +++.+.+++..+.    .+ ..+++.||+|+|||..+-
T Consensus        24 ~~~~~~~~~~~l~~~~~~~~~~~~l~G~~G~GKTtl~~   61 (269)
T TIGR03015        24 PSKGHKRAMAYLEYGLSQREGFILITGEVGAGKTTLIR   61 (269)
T ss_pred             CCHHHHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHHH
Confidence            5556666776553    22 358899999999997754

Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.

>PRK06620 hypothetical protein; Validated

Probab=96.06  E-value=0.017  Score=46.92  Aligned_cols=18  Identities=22%  Similarity=0.268  Sum_probs=15.0

Q ss_pred             CcEEEEcCCCChhhHHHH
Q 017573           34 LDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~   51 (369)
                      ..++++||+|+|||..+.
T Consensus        45 ~~l~l~Gp~G~GKThLl~   62 (214)
T PRK06620         45 FTLLIKGPSSSGKTYLTK   62 (214)
T ss_pred             ceEEEECCCCCCHHHHHH
Confidence            458999999999997653

>PRK13342 recombination factor protein RarA; Reviewed

Probab=96.05  E-value=0.045  Score=49.46  Aligned_cols=18  Identities=33%  Similarity=0.309  Sum_probs=15.5

Q ss_pred             CcEEEEcCCCChhhHHHH
Q 017573           34 LDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~   51 (369)
                      .++++.||+|+|||..+-
T Consensus        37 ~~ilL~GppGtGKTtLA~   54 (413)
T PRK13342         37 SSMILWGPPGTGKTTLAR   54 (413)
T ss_pred             ceEEEECCCCCCHHHHHH
Confidence            478999999999997764

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=96.05  E-value=0.066  Score=43.39  Aligned_cols=39  Identities=15%  Similarity=0.161  Sum_probs=29.1

Q ss_pred             cCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCC
Q 017573           32 KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPT   73 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~   73 (369)
                      .|.-+.+.+|+|+|||..++..+.+....+.   +++|+.-.
T Consensus        11 ~g~i~~i~G~~GsGKT~l~~~~~~~~~~~g~---~v~yi~~e   49 (209)
T TIGR02237        11 RGTITQIYGPPGSGKTNICMILAVNAARQGK---KVVYIDTE   49 (209)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhCCC---eEEEEECC
Confidence            3466899999999999888766666554433   78887764

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=96.01  E-value=0.032  Score=49.43  Aligned_cols=20  Identities=25%  Similarity=0.129  Sum_probs=15.6

Q ss_pred             CcEEEEcCCCChhhHHHHHH
Q 017573           34 LDVIQQAQSGTGKTATFCSG   53 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~   53 (369)
                      +..++.||+|+|||..+...
T Consensus        37 ~~~Ll~G~~G~GKt~~a~~l   56 (355)
T TIGR02397        37 HAYLFSGPRGTGKTSIARIF   56 (355)
T ss_pred             eEEEEECCCCCCHHHHHHHH
Confidence            34799999999999776433

This model represents the well-conserved first ~ 365 amino acids of the translation of the dnaX gene. The full-length product of the dnaX gene in the model bacterium E. coli is the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the exterme thermophile Thermus thermophilis.

>COG3972 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=96.01  E-value=0.052  Score=48.46  Aligned_cols=69  Identities=13%  Similarity=0.048  Sum_probs=50.3

Q ss_pred             CCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhc
Q 017573           18 KPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALG   88 (369)
Q Consensus        18 ~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~   88 (369)
                      .+-..|.++.-..-.|.. .|.+=.|||||.+.+.-+.+. ..+.+..++++-+-++.|..++.+...+|+
T Consensus       162 nfD~~Q~kaa~~~~~G~q-rIrGLAGSGKT~~La~Kaa~l-h~knPd~~I~~Tfftk~L~s~~r~lv~~F~  230 (660)
T COG3972         162 NFDTDQTKAAFQSGFGKQ-RIRGLAGSGKTELLAHKAAEL-HSKNPDSRIAFTFFTKILASTMRTLVPEFF  230 (660)
T ss_pred             cccchhheeeeecCCchh-hhhcccCCCchhHHHHHHHHH-hcCCCCceEEEEeehHHHHHHHHHHHHHHH
Confidence            344567777655555655 788999999998765555544 334445589999999999999888777764

>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily

Probab=96.00  E-value=0.079  Score=48.10  Aligned_cols=117  Identities=18%  Similarity=0.167  Sum_probs=58.1

Q ss_pred             ccccCCcEEEEcCCCChhhHHHHHHHHHhh-hccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEE-ECCcchHH
Q 017573           29 PFCKGLDVIQQAQSGTGKTATFCSGILQQL-DYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHAC-VGGTSVRE  106 (369)
Q Consensus        29 ~~~~~~~~li~~~tG~GKT~~~~~~~~~~~-~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~-~~~~~~~~  106 (369)
                      -+..|.-+++.|+||+|||..++..+.+.. ..+.   +++|++.- .-..|+..++-....  ++....+ .+.....+
T Consensus       190 G~~~g~liviag~pg~GKT~~al~ia~~~a~~~g~---~v~~fSlE-m~~~~l~~Rl~~~~~--~v~~~~~~~~~l~~~~  263 (421)
T TIGR03600       190 GLVKGDLIVIGARPSMGKTTLALNIAENVALREGK---PVLFFSLE-MSAEQLGERLLASKS--GINTGNIRTGRFNDSD  263 (421)
T ss_pred             CCCCCceEEEEeCCCCCHHHHHHHHHHHHHHhCCC---cEEEEECC-CCHHHHHHHHHHHHc--CCCHHHHhcCCCCHHH
Confidence            344456789999999999988776665554 2222   67777632 233444433322211  2221111 12222122


Q ss_pred             HHH------HHccCCcEEEe-----ccHHHHHHHHcCCCCCCCccEEEEechhHhhc
Q 017573          107 DQR------ILQAGVHVVVG-----TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLS  152 (369)
Q Consensus       107 ~~~------~~~~~~~iiv~-----t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~  152 (369)
                      +..      .+. +..+.|.     |.+.+....++.......+++||+|=.|.+..
T Consensus       264 ~~~~~~~~~~l~-~~~l~i~d~~~~t~~~i~~~~r~~~~~~~~~~lvvIDyLql~~~  319 (421)
T TIGR03600       264 FNRLLNAVDRLS-EKDLYIDDTGGLTVAQIRSIARRIKRKKGGLDLIVVDYIQLMAP  319 (421)
T ss_pred             HHHHHHHHHHHh-cCCEEEECCCCCCHHHHHHHHHHHHHhcCCCCEEEEecccccCC
Confidence            211      111 2345553     33444443332211122478999999988753

Members of this family are phage (or prophage-region) homologs of the bacterial homohexameric replicative helicase DnaB. Some phage may rely on host DnaB, while others encode their own verions. This model describes the largest phage-specific clade among the close homologs of DnaB, but there are, or course, other DnaB homologs from phage that fall outside the scope of this model.

>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]

Probab=96.00  E-value=0.02  Score=48.87  Aligned_cols=46  Identities=26%  Similarity=0.311  Sum_probs=31.3

Q ss_pred             CCCHHHHHHHH--hCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHH
Q 017573            2 GLQENLLRGIY--AYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATF   50 (369)
Q Consensus         2 ~l~~~i~~~l~--~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~   50 (369)
                      ||.++|+..-+  ..+..+|--|++-.++   ..+.+++.+|+|+|||+.+
T Consensus       155 GL~~Qi~EirE~VELPL~~PElF~~~GI~---PPKGVLLYGPPGTGKTLLA  202 (406)
T COG1222         155 GLDEQIQEIREVVELPLKNPELFEELGID---PPKGVLLYGPPGTGKTLLA  202 (406)
T ss_pred             CHHHHHHHHHHHhcccccCHHHHHHcCCC---CCCceEeeCCCCCcHHHHH
Confidence            45555544333  3466666666665553   3799999999999999875

>TIGR03689 pup_AAA proteasome ATPase

Probab=95.98  E-value=0.057  Score=49.58  Aligned_cols=18  Identities=28%  Similarity=0.267  Sum_probs=16.0

Q ss_pred             CCcEEEEcCCCChhhHHH
Q 017573           33 GLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~   50 (369)
                      .+++++.+|+|+|||..+
T Consensus       216 p~GILLyGPPGTGKT~LA  233 (512)
T TIGR03689       216 PKGVLLYGPPGCGKTLIA  233 (512)
T ss_pred             CcceEEECCCCCcHHHHH
Confidence            578999999999999765

In the Actinobacteria, as shown for Mycobacterium tuberculosis, some proteins are modified by ligation between an epsilon-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup, the Pup ligase PafA, and structural components of the proteasome. This protein forms hexameric rings with ATPase activity.

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=95.97  E-value=0.013  Score=50.48  Aligned_cols=57  Identities=18%  Similarity=0.257  Sum_probs=36.6

Q ss_pred             CcHhhhhhhhccc-cCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHH
Q 017573           19 PSAIQQRGIVPFC-KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTREL   76 (369)
Q Consensus        19 ~~~~Q~~~~~~~~-~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l   76 (369)
                      +.+.|.+.+..+. .+++++|+|+||||||..+ -+++..+.......+++.+=...++
T Consensus       129 ~~~~~~~~L~~~v~~~~nilI~G~tGSGKTTll-~aL~~~i~~~~~~~rivtiEd~~El  186 (323)
T PRK13833        129 MTEAQASVIRSAIDSRLNIVISGGTGSGKTTLA-NAVIAEIVASAPEDRLVILEDTAEI  186 (323)
T ss_pred             CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHHH-HHHHHHHhcCCCCceEEEecCCccc
Confidence            5567776666555 4688999999999999764 4555554332223366665555554

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.95  E-value=0.065  Score=49.26  Aligned_cols=19  Identities=32%  Similarity=0.179  Sum_probs=15.2

Q ss_pred             EEEEcCCCChhhHHHHHHH
Q 017573           36 VIQQAQSGTGKTATFCSGI   54 (369)
Q Consensus        36 ~li~~~tG~GKT~~~~~~~   54 (369)
                      .++.||.|+|||.++.+.+
T Consensus        41 yLf~Gp~G~GKTtlAr~lA   59 (486)
T PRK14953         41 YIFAGPRGTGKTTIARILA   59 (486)
T ss_pred             EEEECCCCCCHHHHHHHHH
Confidence            5789999999998765443

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=95.95  E-value=0.016  Score=49.64  Aligned_cols=57  Identities=19%  Similarity=0.260  Sum_probs=36.5

Q ss_pred             CcHhhhhhhhccc-cCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHH
Q 017573           19 PSAIQQRGIVPFC-KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTREL   76 (369)
Q Consensus        19 ~~~~Q~~~~~~~~-~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l   76 (369)
                      +.+.|.+.+..+. .++++++.|+||||||..+ .+++..+.......+++.+=...++
T Consensus       117 ~~~~~~~~L~~~v~~~~~ilI~G~tGSGKTTll-~al~~~i~~~~~~~ri~tiEd~~El  174 (299)
T TIGR02782       117 MTAAQRDVLREAVLARKNILVVGGTGSGKTTLA-NALLAEIAKNDPTDRVVIIEDTREL  174 (299)
T ss_pred             CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHHH-HHHHHHhhccCCCceEEEECCchhh
Confidence            4445555555544 4689999999999999764 4555555443223367776666554

The TrbB protein is found in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer. TrbB is a homolog of the vir system VirB11 ATPase, and the Flp pilus sytem ATPase TadA.

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=95.93  E-value=0.12  Score=46.19  Aligned_cols=24  Identities=25%  Similarity=0.158  Sum_probs=18.4

Q ss_pred             cCCcEEEEcCCCChhhHHHHHHHH
Q 017573           32 KGLDVIQQAQSGTGKTATFCSGIL   55 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~~~~~   55 (369)
                      .++-+.+.||+|+|||......+.
T Consensus       190 ~g~vi~lvGpnG~GKTTtlakLA~  213 (420)
T PRK14721        190 QGGVYALIGPTGVGKTTTTAKLAA  213 (420)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHH
Confidence            456789999999999977644433

>PRK06904 replicative DNA helicase; Validated

Probab=95.91  E-value=0.15  Score=46.70  Aligned_cols=117  Identities=17%  Similarity=0.091  Sum_probs=58.9

Q ss_pred             cccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEE-EC-CcchHHH
Q 017573           30 FCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHAC-VG-GTSVRED  107 (369)
Q Consensus        30 ~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~-~~-~~~~~~~  107 (369)
                      +..|.-+++.|.||.|||..++-.+.+.....  +.+++|++.- --..|+..++-.....  +....+ .+ .....++
T Consensus       218 l~~G~LiiIaarPg~GKTafalnia~~~a~~~--g~~Vl~fSlE-Ms~~ql~~Rlla~~s~--v~~~~i~~g~~l~~~e~  292 (472)
T PRK06904        218 LQPSDLIIVAARPSMGKTTFAMNLCENAAMAS--EKPVLVFSLE-MPAEQIMMRMLASLSR--VDQTKIRTGQNLDQQDW  292 (472)
T ss_pred             cCCCcEEEEEeCCCCChHHHHHHHHHHHHHhc--CCeEEEEecc-CCHHHHHHHHHHhhCC--CCHHHhccCCCCCHHHH
Confidence            33456689999999999987765555443321  2256666543 4445555544332221  111111 12 1222222


Q ss_pred             HH------HHccCCcEEEe-----ccHHHHHHHHcCCCCCCCccEEEEechhHhh
Q 017573          108 QR------ILQAGVHVVVG-----TPGRVFDMLRRQSLRPDYIKMFVLDEADEML  151 (369)
Q Consensus       108 ~~------~~~~~~~iiv~-----t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~  151 (369)
                      .+      .+.....+.|-     |.+.+....++.......+++||||-.+.+.
T Consensus       293 ~~~~~a~~~l~~~~~l~I~d~~~~t~~~i~~~~r~~~~~~~~~~lvvIDYLqli~  347 (472)
T PRK06904        293 AKISSTVGMFKQKPNLYIDDSSGLTPTELRSRARRVYRENGGLSLIMVDYLQLMR  347 (472)
T ss_pred             HHHHHHHHHHhcCCCEEEECCCCCCHHHHHHHHHHHHHhCCCCCEEEEecHHhcC
Confidence            21      12223446663     4555544333221111247899999999775

>PF03796 DnaB_C: DnaB-like helicase C terminal domain; InterPro: IPR007694 The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork

Probab=95.90  E-value=0.053  Score=45.64  Aligned_cols=42  Identities=24%  Similarity=0.142  Sum_probs=30.8

Q ss_pred             cccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCC
Q 017573           30 FCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPT   73 (369)
Q Consensus        30 ~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~   73 (369)
                      +..|.-+++.|.||.|||..++-.+.+.+....  ..++|++.-
T Consensus        16 ~~~g~L~vi~a~pg~GKT~~~l~ia~~~a~~~~--~~vly~SlE   57 (259)
T PF03796_consen   16 LRPGELTVIAARPGVGKTAFALQIALNAALNGG--YPVLYFSLE   57 (259)
T ss_dssp             B-TT-EEEEEESTTSSHHHHHHHHHHHHHHTTS--SEEEEEESS
T ss_pred             CCcCcEEEEEecccCCchHHHHHHHHHHHHhcC--CeEEEEcCC
Confidence            345567899999999999888877777766532  278888864

Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis. ; GO: 0003678 DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication; PDB: 1Q57_E 1E0K_D 1E0J_B 1CR2_A 1CR4_A 1CR1_A 1CR0_A 1MI8_A 2R6D_B 2R6C_C ....

>PF05729 NACHT: NACHT domain

Probab=95.89  E-value=0.073  Score=41.09  Aligned_cols=26  Identities=15%  Similarity=0.127  Sum_probs=18.0

Q ss_pred             cEEEEcCCCChhhHHHHHHHHHhhhc
Q 017573           35 DVIQQAQSGTGKTATFCSGILQQLDY   60 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~~~~~~~~~~   60 (369)
                      -++|.|++|+|||..+...+......
T Consensus         2 ~l~I~G~~G~GKStll~~~~~~~~~~   27 (166)
T PF05729_consen    2 VLWISGEPGSGKSTLLRKLAQQLAEE   27 (166)
T ss_pred             EEEEECCCCCChHHHHHHHHHHHHhc
Confidence            36899999999997764444433333

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=95.88  E-value=0.097  Score=48.36  Aligned_cols=51  Identities=18%  Similarity=0.148  Sum_probs=38.9

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHh
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRAL   87 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~   87 (369)
                      |.-+++.+|+|+|||..++..+.+.+..+.   +++|++ ..+-..|..+.+..+
T Consensus       263 gs~~li~G~~G~GKt~l~~~f~~~~~~~ge---~~~y~s-~eEs~~~i~~~~~~l  313 (484)
T TIGR02655       263 DSIILATGATGTGKTLLVSKFLENACANKE---RAILFA-YEESRAQLLRNAYSW  313 (484)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHCCC---eEEEEE-eeCCHHHHHHHHHHc
Confidence            356899999999999988877777766554   788877 446667777777665

Members of this family are the circadian clock protein KaiC, part of the kaiABC operon that controls circadian rhythm. It may be universal in Cyanobacteria. Each member has two copies of the KaiC domain (Pfam model pfam06745), which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor.

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=95.87  E-value=0.08  Score=51.15  Aligned_cols=79  Identities=19%  Similarity=0.287  Sum_probs=65.1

Q ss_pred             cCCCeEEEeCCHhhHHHHHHHHhh----CCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEec-CCcCCCCCCCCcEEE
Q 017573          234 AITQSVIFVNTRRKVDWLTDKMRS----RDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTD-LLARGIDVQQVSLVI  308 (369)
Q Consensus       234 ~~~k~lv~~~~~~~~~~~~~~l~~----~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~-~~~~G~d~~~~~~vi  308 (369)
                      .+.++++.+|+..-|...++.+++    .+.++..++|+++..+|.++++...+|+.+|+|+|. .+...+.+.++..||
T Consensus       309 ~g~q~lilaPT~~LA~Q~~~~l~~l~~~~~i~v~ll~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~~v~~~~l~lvV  388 (681)
T PRK10917        309 AGYQAALMAPTEILAEQHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQDDVEFHNLGLVI  388 (681)
T ss_pred             cCCeEEEEeccHHHHHHHHHHHHHHHhhcCcEEEEEcCCCCHHHHHHHHHHHhCCCCCEEEchHHHhcccchhcccceEE
Confidence            456899999999988877666554    468899999999999999999999999999999998 455567788888888


Q ss_pred             EecC
Q 017573          309 NYDL  312 (369)
Q Consensus       309 ~~~~  312 (369)
                      +-..
T Consensus       389 IDE~  392 (681)
T PRK10917        389 IDEQ  392 (681)
T ss_pred             Eech
Confidence            6543

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=95.85  E-value=0.03  Score=49.84  Aligned_cols=24  Identities=33%  Similarity=0.490  Sum_probs=18.2

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHhh
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQL   58 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~~   58 (369)
                      .+++|.||+|+|||.++ ..+++.+
T Consensus        41 ~~i~I~G~~GtGKT~l~-~~~~~~l   64 (365)
T TIGR02928        41 SNVFIYGKTGTGKTAVT-KYVMKEL   64 (365)
T ss_pred             CcEEEECCCCCCHHHHH-HHHHHHH
Confidence            67999999999999765 3444444

Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=95.84  E-value=0.049  Score=47.49  Aligned_cols=39  Identities=10%  Similarity=0.290  Sum_probs=24.9

Q ss_pred             CccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEEe
Q 017573          138 YIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSA  177 (369)
Q Consensus       138 ~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~sa  177 (369)
                      ..+++|+||+|.+.... ...+.+.+..-|+...+++.|.
T Consensus       110 ~~kvviI~~a~~~~~~a-~NaLLK~LEEPp~~~~~Il~t~  148 (329)
T PRK08058        110 NKKVYIIEHADKMTASA-ANSLLKFLEEPSGGTTAILLTE  148 (329)
T ss_pred             CceEEEeehHhhhCHHH-HHHHHHHhcCCCCCceEEEEeC
Confidence            46899999999985432 4455555555555555555443

>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]

Probab=95.83  E-value=0.014  Score=57.53  Aligned_cols=99  Identities=15%  Similarity=0.140  Sum_probs=74.0

Q ss_pred             cCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCc-EEEEecCCcCCCCCCCCcEEEEecC
Q 017573          234 AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSR-VLITTDLLARGIDVQQVSLVINYDL  312 (369)
Q Consensus       234 ~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~-vli~t~~~~~G~d~~~~~~vi~~~~  312 (369)
                      ...++|+|+.-......+...+.-.+.....-.+   .++....+..|.+  ++ +++-++..+.|+|+-.+.+|+..+|
T Consensus      1220 ~qekvIvfsqws~~ldV~e~~~~~N~I~~~~~~~---t~d~~dc~~~fk~--I~clll~~~~~~~GLNL~eA~Hvfl~eP 1294 (1394)
T KOG0298|consen 1220 EQEKVIVFSQWSVVLDVKELRYLMNLIKKQLDGE---TEDFDDCIICFKS--IDCLLLFVSKGSKGLNLIEATHVFLVEP 1294 (1394)
T ss_pred             cCceEEEEEehHHHHHHHHHHHHhhhhHhhhccC---Ccchhhhhhhccc--ceEEEEEeccCcccccHHhhhhhheecc
Confidence            3458899988877777777777665544333222   3344556666665  54 5567888899999999999999999


Q ss_pred             CCCccchhhhhcccccCCCceeEEE
Q 017573          313 PTQPENYLHRIGRSGRFGRKGVAIN  337 (369)
Q Consensus       313 ~~~~~~~~Q~~GR~~R~~~~~~~~~  337 (369)
                      ..++..-.|++||+.|.|+.....+
T Consensus      1295 iLN~~~E~QAigRvhRiGQ~~pT~V 1319 (1394)
T KOG0298|consen 1295 ILNPGDEAQAIGRVHRIGQKRPTFV 1319 (1394)
T ss_pred             ccCchHHHhhhhhhhhcccccchhh
Confidence            9999999999999999998755443

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.83  E-value=0.04  Score=52.19  Aligned_cols=24  Identities=21%  Similarity=0.080  Sum_probs=18.2

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHh
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQ   57 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~   57 (369)
                      ...++.||.|+|||..+...+-..
T Consensus        39 ~a~Lf~Gp~G~GKttlA~~lAk~L   62 (620)
T PRK14948         39 PAYLFTGPRGTGKTSSARILAKSL   62 (620)
T ss_pred             ceEEEECCCCCChHHHHHHHHHHh
Confidence            456999999999998875544433

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=95.81  E-value=0.068  Score=46.18  Aligned_cols=60  Identities=12%  Similarity=0.166  Sum_probs=35.1

Q ss_pred             EEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEEeeC
Q 017573          117 VVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATM  179 (369)
Q Consensus       117 iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~saT~  179 (369)
                      |-|-....+.+.+...... ...+++|+|++|.+.... ...+.+++..-| ...++++|..+
T Consensus       104 I~id~ir~i~~~l~~~p~~-~~~kVvII~~ae~m~~~a-aNaLLK~LEEPp-~~~fILi~~~~  163 (314)
T PRK07399        104 IRLEQIREIKRFLSRPPLE-APRKVVVIEDAETMNEAA-ANALLKTLEEPG-NGTLILIAPSP  163 (314)
T ss_pred             CcHHHHHHHHHHHccCccc-CCceEEEEEchhhcCHHH-HHHHHHHHhCCC-CCeEEEEECCh
Confidence            3344444555555554444 346999999999885333 455566666655 55555555443

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=95.79  E-value=0.027  Score=47.92  Aligned_cols=38  Identities=18%  Similarity=0.169  Sum_probs=24.6

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhc-cCCCccEEEEcC
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDY-GLVQCQALVLAP   72 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~-~~~~~~~liv~P   72 (369)
                      ++.+.+.+|+|+|||.++...+...... +.  .++.++.-
T Consensus       194 ~~vi~~vGptGvGKTTt~~kLa~~~~~~~g~--~~V~li~~  232 (282)
T TIGR03499       194 GGVIALVGPTGVGKTTTLAKLAARFVLEHGN--KKVALITT  232 (282)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHHcCC--CeEEEEEC
Confidence            4568899999999998765554444333 21  15665553

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=95.77  E-value=0.015  Score=50.16  Aligned_cols=57  Identities=18%  Similarity=0.275  Sum_probs=36.4

Q ss_pred             CcHhhhhhhhcc-ccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHH
Q 017573           19 PSAIQQRGIVPF-CKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTREL   76 (369)
Q Consensus        19 ~~~~Q~~~~~~~-~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l   76 (369)
                      +.+.|.+.+... ..++++++.|+||||||.. +.+++..+.......+++.+-...++
T Consensus       133 ~~~~~~~~L~~~v~~~~~ilI~G~tGSGKTTl-l~aL~~~~~~~~~~~rivtIEd~~El  190 (319)
T PRK13894        133 MTAAQREAIIAAVRAHRNILVIGGTGSGKTTL-VNAIINEMVIQDPTERVFIIEDTGEI  190 (319)
T ss_pred             CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHH-HHHHHHhhhhcCCCceEEEEcCCCcc
Confidence            456777777654 4568999999999999955 34444443222222266666666554

>COG4962 CpaF Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]

Probab=95.74  E-value=0.014  Score=49.68  Aligned_cols=58  Identities=16%  Similarity=0.143  Sum_probs=41.9

Q ss_pred             CCCCCcHhhhhhhhccccCC-cEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHH
Q 017573           15 GFEKPSAIQQRGIVPFCKGL-DVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTREL   76 (369)
Q Consensus        15 ~~~~~~~~Q~~~~~~~~~~~-~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l   76 (369)
                      .|..+++-|...+..+...+ ++++++.||||||.. +-++...+....   +++.+=-+.+|
T Consensus       154 ~~gt~~~~~a~~L~~av~~r~NILisGGTGSGKTTl-LNal~~~i~~~e---RvItiEDtaEL  212 (355)
T COG4962         154 IFGTMIRRAAKFLRRAVGIRCNILISGGTGSGKTTL-LNALSGFIDSDE---RVITIEDTAEL  212 (355)
T ss_pred             HcCCcCHHHHHHHHHHHhhceeEEEeCCCCCCHHHH-HHHHHhcCCCcc---cEEEEeehhhh
Confidence            45678899999998888775 999999999999965 334444443333   67776666554

>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]

Probab=95.72  E-value=0.18  Score=44.47  Aligned_cols=27  Identities=33%  Similarity=0.500  Sum_probs=19.7

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHhhhcc
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQLDYG   61 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~~~~~   61 (369)
                      .++++.|+||+|||.++ ..++..+...
T Consensus        43 ~n~~iyG~~GTGKT~~~-~~v~~~l~~~   69 (366)
T COG1474          43 SNIIIYGPTGTGKTATV-KFVMEELEES   69 (366)
T ss_pred             ccEEEECCCCCCHhHHH-HHHHHHHHhh
Confidence            57999999999999775 4444454443

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=95.71  E-value=0.03  Score=53.38  Aligned_cols=21  Identities=24%  Similarity=0.093  Sum_probs=16.4

Q ss_pred             cEEEEcCCCChhhHHHHHHHH
Q 017573           35 DVIQQAQSGTGKTATFCSGIL   55 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~~~~~   55 (369)
                      ..++.||.|+|||.++-..+.
T Consensus        42 AYLF~GP~GtGKTt~AriLAk   62 (725)
T PRK07133         42 AYLFSGPRGTGKTSVAKIFAN   62 (725)
T ss_pred             EEEEECCCCCcHHHHHHHHHH
Confidence            368999999999988754433

>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed

Probab=95.69  E-value=0.065  Score=51.70  Aligned_cols=18  Identities=28%  Similarity=0.242  Sum_probs=15.6

Q ss_pred             CcEEEEcCCCChhhHHHH
Q 017573           34 LDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~   51 (369)
                      .++++.||+|+|||..+-
T Consensus        53 ~slLL~GPpGtGKTTLA~   70 (725)
T PRK13341         53 GSLILYGPPGVGKTTLAR   70 (725)
T ss_pred             ceEEEECCCCCCHHHHHH
Confidence            478999999999997764

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=95.68  E-value=0.027  Score=47.39  Aligned_cols=53  Identities=21%  Similarity=0.228  Sum_probs=39.6

Q ss_pred             ccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHh
Q 017573           31 CKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRAL   87 (369)
Q Consensus        31 ~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~   87 (369)
                      ..++.++|.+++|+|||..++-.+.+.+..+.   ++++|+-. +...+..+.+.++
T Consensus        21 p~g~~~lI~G~pGsGKT~f~~qfl~~~~~~ge---~vlyvs~~-e~~~~l~~~~~~~   73 (260)
T COG0467          21 PRGSVVLITGPPGTGKTIFALQFLYEGAREGE---PVLYVSTE-ESPEELLENARSF   73 (260)
T ss_pred             cCCcEEEEEcCCCCcHHHHHHHHHHHHHhcCC---cEEEEEec-CCHHHHHHHHHHc
Confidence            34688999999999999988888887777644   78888764 4455555666554

>PRK08506 replicative DNA helicase; Provisional

Probab=95.67  E-value=0.14  Score=46.97  Aligned_cols=115  Identities=22%  Similarity=0.154  Sum_probs=59.7

Q ss_pred             cccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEE-ECCcchHHHH
Q 017573           30 FCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHAC-VGGTSVREDQ  108 (369)
Q Consensus        30 ~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~-~~~~~~~~~~  108 (369)
                      +..|.-+++.|.||.|||..++-.+.+.+..+   .++++++.- --..|+..++-....  ++....+ .+.....++.
T Consensus       189 ~~~G~LivIaarpg~GKT~fal~ia~~~~~~g---~~V~~fSlE-Ms~~ql~~Rlla~~s--~v~~~~i~~~~l~~~e~~  262 (472)
T PRK08506        189 FNKGDLIIIAARPSMGKTTLCLNMALKALNQD---KGVAFFSLE-MPAEQLMLRMLSAKT--SIPLQNLRTGDLDDDEWE  262 (472)
T ss_pred             CCCCceEEEEcCCCCChHHHHHHHHHHHHhcC---CcEEEEeCc-CCHHHHHHHHHHHhc--CCCHHHHhcCCCCHHHHH
Confidence            33456789999999999988877776665433   267776543 344555544433211  1111111 1222222221


Q ss_pred             H------HHccCCcEEEe-----ccHHHHHHHHcCCCCCCCccEEEEechhHhh
Q 017573          109 R------ILQAGVHVVVG-----TPGRVFDMLRRQSLRPDYIKMFVLDEADEML  151 (369)
Q Consensus       109 ~------~~~~~~~iiv~-----t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~  151 (369)
                      .      .+. +..+.|-     |.+.+....++.......+++||||=.+.+.
T Consensus       263 ~~~~a~~~l~-~~~l~I~d~~~~ti~~I~~~~r~l~~~~~~~~lvvIDyLql~~  315 (472)
T PRK08506        263 RLSDACDELS-KKKLFVYDSGYVNIHQVRAQLRKLKSQHPEIGLAVIDYLQLMS  315 (472)
T ss_pred             HHHHHHHHHH-cCCeEEECCCCCCHHHHHHHHHHHHHhCCCCCEEEEcChhhcc
Confidence            1      122 2345543     4445544333321112247899999999775

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=95.65  E-value=0.48  Score=41.02  Aligned_cols=36  Identities=19%  Similarity=0.139  Sum_probs=23.1

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEc
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLA   71 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~   71 (369)
                      ++-+.+.+|+|+|||..+...+......   +.+++++.
T Consensus       114 ~~vi~lvGpnGsGKTTt~~kLA~~l~~~---g~~V~Li~  149 (318)
T PRK10416        114 PFVILVVGVNGVGKTTTIGKLAHKYKAQ---GKKVLLAA  149 (318)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHHHhc---CCeEEEEe
Confidence            3457899999999998765444333222   22666665

>COG0210 UvrD Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]

Probab=95.65  E-value=0.037  Score=53.49  Aligned_cols=70  Identities=21%  Similarity=0.195  Sum_probs=58.2

Q ss_pred             CCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCC-CccEEEEcCCHHHHHHHHHHHHHhcc
Q 017573           18 KPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLV-QCQALVLAPTRELAQQIEKVMRALGD   89 (369)
Q Consensus        18 ~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~-~~~~liv~P~~~l~~q~~~~~~~~~~   89 (369)
                      .+++-|++++...  ...++|.|+.|||||.+..--+.+.+..+.. ...++.++=|+.-+.++.+++.+...
T Consensus         2 ~Ln~~Q~~av~~~--~gp~lV~AGaGsGKT~vlt~Ria~li~~~~v~p~~Il~vTFTnkAA~em~~Rl~~~~~   72 (655)
T COG0210           2 KLNPEQREAVLHP--DGPLLVLAGAGSGKTRVLTERIAYLIAAGGVDPEQILAITFTNKAAAEMRERLLKLLG   72 (655)
T ss_pred             CCCHHHHHHHhcC--CCCeEEEECCCCCchhhHHHHHHHHHHcCCcChHHeeeeechHHHHHHHHHHHHHHhC
Confidence            5889999999776  7889999999999999988888877776433 33689999999889999988888764

>PRK04328 hypothetical protein; Provisional

Probab=95.64  E-value=0.027  Score=47.01  Aligned_cols=52  Identities=23%  Similarity=0.244  Sum_probs=36.7

Q ss_pred             cCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHh
Q 017573           32 KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRAL   87 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~   87 (369)
                      .|..+++.+++|+|||..++..+.+.+..+.   +++|++- .+-..+..+.+..+
T Consensus        22 ~gs~ili~G~pGsGKT~l~~~fl~~~~~~ge---~~lyis~-ee~~~~i~~~~~~~   73 (249)
T PRK04328         22 ERNVVLLSGGPGTGKSIFSQQFLWNGLQMGE---PGVYVAL-EEHPVQVRRNMRQF   73 (249)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHHhcCC---cEEEEEe-eCCHHHHHHHHHHc
Confidence            3567899999999999887777777666554   7888774 33444555555554

>PF03237 Terminase_6: Terminase-like family; InterPro: IPR004921 The terminase is a component of the molecular motor that translocates genomic DNA into empty capsids during DNA packaging []

Probab=95.62  E-value=0.34  Score=43.12  Aligned_cols=144  Identities=15%  Similarity=0.085  Sum_probs=61.9

Q ss_pred             EEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHH-HHH---HHHHHHHhccccCcEEEEE--ECCcchHHHHHH
Q 017573           37 IQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTREL-AQQ---IEKVMRALGDYLGVKVHAC--VGGTSVREDQRI  110 (369)
Q Consensus        37 li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l-~~q---~~~~~~~~~~~~~~~v~~~--~~~~~~~~~~~~  110 (369)
                      ++.++.|+|||......++..+...+....++++ |+..- ...   ........... .+.....  ....-      .
T Consensus         1 ~i~~~r~~GKT~~~~~~~~~~~~~~~~~~~vi~~-~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~------~   72 (384)
T PF03237_consen    1 LINGGRGSGKTTLIAIWFLWWALTRPPGRRVIIA-STYRQARDIFGRFWKGIIELLPS-WFEIKFNEWNDRKI------I   72 (384)
T ss_dssp             -EEE-SSS-HHHHHHHHHHHHHHSSSS--EEEEE-ESSHHHHHHHHHHHHHHHHTS-T-TTS--EEEE-SSEE------E
T ss_pred             CCcCCccccHHHHHHHHHHHHHhhCCCCcEEEEe-cCHHHHHHHHHHhHHHHHHHHHH-hcCcccccCCCCcE------E
Confidence            5789999999988777677666555443345555 65554 443   22333333333 2222221  11111      0


Q ss_pred             HccCCcEEEeccHHH--HHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEEeeCCh--hHHHH
Q 017573          111 LQAGVHVVVGTPGRV--FDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMPP--EALEI  186 (369)
Q Consensus       111 ~~~~~~iiv~t~~~l--~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~saT~~~--~~~~~  186 (369)
                      +.++..|.+.+.+.-  ..-+.     ...++.+++||+-......+...+........... .+..|.|+.+  .....
T Consensus        73 ~~nG~~i~~~~~~~~~~~~~~~-----G~~~~~i~iDE~~~~~~~~~~~~~~~~~~~~~~~~-~~~~s~p~~~~~~~~~~  146 (384)
T PF03237_consen   73 LPNGSRIQFRGADSPDSGDNIR-----GFEYDLIIIDEAAKVPDDAFSELIRRLRATWGGSI-RMYISTPPNPGGWFYEI  146 (384)
T ss_dssp             ETTS-EEEEES-----SHHHHH-----TS--SEEEEESGGGSTTHHHHHHHHHHHHCSTT---EEEEEE---SSSHHHHH
T ss_pred             ecCceEEEEecccccccccccc-----ccccceeeeeecccCchHHHHHHHHhhhhcccCcc-eEEeecCCCCCCceeee
Confidence            134455666664321  11111     13478999999887755544444444433333222 2244554433  33344


Q ss_pred             HHHhcCCC
Q 017573          187 TRKFMNKP  194 (369)
Q Consensus       187 ~~~~~~~~  194 (369)
                      ........
T Consensus       147 ~~~~~~~~  154 (384)
T PF03237_consen  147 FQRNLDDD  154 (384)
T ss_dssp             HHHHHCTS
T ss_pred             eehhhcCC
Confidence            44444443

The large subunit heterodimerises with the small terminase protein, which is docked on the capsid portal protein. The latter forms a ring through which genomic DNA is translocated into the capsid. The terminase protein may have or induce an endonuclease activity to cleave DNA after encapsidation. This entry represents a family of terminase large subunits found in a variety of the Caudovirales and prophage regions of bacterial genomes. Homologues are also found in Gene Transfer Agents (GTA) [], including ORFg2 (RCAP_rcc01683) of the GTA of Rhodobacter capsulatus (Rhodopseudomonas capsulata) [see Fig.1, in ].; PDB: 2O0K_A 3CPE_A 2O0J_A 2O0H_A 3C6H_A 3C6A_A.

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=95.60  E-value=0.042  Score=46.14  Aligned_cols=38  Identities=18%  Similarity=0.036  Sum_probs=29.3

Q ss_pred             cCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcC
Q 017573           32 KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAP   72 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P   72 (369)
                      .+.-++|.+++|+|||..++..+.+.+..+.   +++|++-
T Consensus        35 ~gs~~lI~G~pGtGKT~l~~qf~~~~a~~Ge---~vlyis~   72 (259)
T TIGR03878        35 AYSVINITGVSDTGKSLMVEQFAVTQASRGN---PVLFVTV   72 (259)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHHhCCC---cEEEEEe
Confidence            3566899999999999888777776655443   7888884

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>TIGR00416 sms DNA repair protein RadA

Probab=95.58  E-value=0.11  Score=47.44  Aligned_cols=51  Identities=22%  Similarity=0.182  Sum_probs=34.1

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHh
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRAL   87 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~   87 (369)
                      |.-+++.+++|+|||..++..+......+   .+++|+..- +...|......++
T Consensus        94 GsvilI~G~pGsGKTTL~lq~a~~~a~~g---~kvlYvs~E-Es~~qi~~ra~rl  144 (454)
T TIGR00416        94 GSLILIGGDPGIGKSTLLLQVACQLAKNQ---MKVLYVSGE-ESLQQIKMRAIRL  144 (454)
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHHHhcC---CcEEEEECc-CCHHHHHHHHHHc
Confidence            35579999999999988766655544433   278998764 3445555555443

The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=95.54  E-value=0.11  Score=47.39  Aligned_cols=24  Identities=21%  Similarity=0.003  Sum_probs=18.2

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHh
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQ   57 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~   57 (369)
                      ...++.||+|+|||.++...+-..
T Consensus        40 ha~Lf~Gp~G~GKtt~A~~lAk~l   63 (451)
T PRK06305         40 HAYLFSGIRGTGKTTLARIFAKAL   63 (451)
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHh
Confidence            347899999999998875554443

>PF01443 Viral_helicase1: Viral (Superfamily 1) RNA helicase; InterPro: IPR000606 This entry includes RNA and DNA helicases

Probab=95.52  E-value=0.02  Score=47.26  Aligned_cols=15  Identities=20%  Similarity=0.556  Sum_probs=12.8

Q ss_pred             EEEEcCCCChhhHHH
Q 017573           36 VIQQAQSGTGKTATF   50 (369)
Q Consensus        36 ~li~~~tG~GKT~~~   50 (369)
                      ++|.|++|+|||...
T Consensus         1 ~vv~G~pGsGKSt~i   15 (234)
T PF01443_consen    1 IVVHGVPGSGKSTLI   15 (234)
T ss_pred             CEEEcCCCCCHHHHH
Confidence            478999999999754

Some of the members are found in positive-strand single stranded RNA viruses. The helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis [].; GO: 0004386 helicase activity

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=95.49  E-value=0.15  Score=46.50  Aligned_cols=25  Identities=24%  Similarity=0.147  Sum_probs=18.9

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHh
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQ   57 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~   57 (369)
                      ++-+.+.||+|+|||+++...+...
T Consensus       256 g~Vi~LvGpnGvGKTTTiaKLA~~~  280 (484)
T PRK06995        256 GGVFALMGPTGVGKTTTTAKLAARC  280 (484)
T ss_pred             CcEEEEECCCCccHHHHHHHHHHHH
Confidence            4568899999999998865554433

>PRK08006 replicative DNA helicase; Provisional

Probab=95.42  E-value=0.34  Score=44.49  Aligned_cols=117  Identities=19%  Similarity=0.085  Sum_probs=58.5

Q ss_pred             cccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEE-ECCcchHHHH
Q 017573           30 FCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHAC-VGGTSVREDQ  108 (369)
Q Consensus        30 ~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~-~~~~~~~~~~  108 (369)
                      +..|.-++|.|.||.|||..++-.+.+.....  +.+++|++.- --..|+..++-....  ++....+ .+.....++.
T Consensus       221 l~~G~LiiIaarPgmGKTafalnia~~~a~~~--g~~V~~fSlE-M~~~ql~~Rlla~~~--~v~~~~i~~~~l~~~e~~  295 (471)
T PRK08006        221 LQPSDLIIVAARPSMGKTTFAMNLCENAAMLQ--DKPVLIFSLE-MPGEQIMMRMLASLS--RVDQTRIRTGQLDDEDWA  295 (471)
T ss_pred             CCCCcEEEEEeCCCCCHHHHHHHHHHHHHHhc--CCeEEEEecc-CCHHHHHHHHHHHhc--CCCHHHhhcCCCCHHHHH
Confidence            33456679999999999988776665544321  2256666533 334444444433211  1221111 1222223322


Q ss_pred             HH------HccCCcEEEe-----ccHHHHHHHHcCCCCCCCccEEEEechhHhh
Q 017573          109 RI------LQAGVHVVVG-----TPGRVFDMLRRQSLRPDYIKMFVLDEADEML  151 (369)
Q Consensus       109 ~~------~~~~~~iiv~-----t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~  151 (369)
                      ++      +.....+.|-     |...+....++.......+++||+|=.|.+.
T Consensus       296 ~~~~a~~~~~~~~~l~I~d~~~~t~~~i~~~~r~~~~~~~~~~lvvIDYLqli~  349 (471)
T PRK08006        296 RISGTMGILLEKRNMYIDDSSGLTPTEVRSRARRIFREHGGLSLIMIDYLQLMR  349 (471)
T ss_pred             HHHHHHHHHHhcCCEEEECCCCCCHHHHHHHHHHHHHhcCCCCEEEEccHHHcc
Confidence            21      1123445554     4444443333211112247999999999875

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=95.41  E-value=0.13  Score=50.14  Aligned_cols=23  Identities=26%  Similarity=0.193  Sum_probs=17.8

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFCSGIL   55 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~   55 (369)
                      ..+.++.||+|+|||..+-..+.
T Consensus       203 ~~n~lL~G~pG~GKT~l~~~la~  225 (731)
T TIGR02639       203 KNNPLLVGEPGVGKTAIAEGLAL  225 (731)
T ss_pred             CCceEEECCCCCCHHHHHHHHHH
Confidence            36899999999999987643333

>PRK14873 primosome assembly protein PriA; Provisional

Probab=95.31  E-value=0.2  Score=47.99  Aligned_cols=91  Identities=20%  Similarity=0.140  Sum_probs=70.9

Q ss_pred             hhHHHHHHHHHhc--cCCCeEEEeCCHhhHHHHHHHHhhCC--CeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCc
Q 017573          221 WKLETLCDLYETL--AITQSVIFVNTRRKVDWLTDKMRSRD--HTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLA  296 (369)
Q Consensus       221 ~~~~~l~~~~~~~--~~~k~lv~~~~~~~~~~~~~~l~~~~--~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~  296 (369)
                      .|.+...+++...  .++.+||.++.+..+..+.+.|+...  ..+..+|+++++.+|.+.+....+|+.+|+|+|... 
T Consensus       172 GKTevyl~~i~~~l~~Gk~vLvLvPEi~lt~q~~~rl~~~f~~~~v~~lhS~l~~~~R~~~w~~~~~G~~~IViGtRSA-  250 (665)
T PRK14873        172 DWARRLAAAAAATLRAGRGALVVVPDQRDVDRLEAALRALLGAGDVAVLSAGLGPADRYRRWLAVLRGQARVVVGTRSA-  250 (665)
T ss_pred             cHHHHHHHHHHHHHHcCCeEEEEecchhhHHHHHHHHHHHcCCCcEEEECCCCCHHHHHHHHHHHhCCCCcEEEEccee-
Confidence            3444444444332  35689999999999999999998663  579999999999999999999999999999999853 


Q ss_pred             CCCCCCCCcEEEEecC
Q 017573          297 RGIDVQQVSLVINYDL  312 (369)
Q Consensus       297 ~G~d~~~~~~vi~~~~  312 (369)
                      .=..+++...||+.+-
T Consensus       251 vFaP~~~LgLIIvdEE  266 (665)
T PRK14873        251 VFAPVEDLGLVAIWDD  266 (665)
T ss_pred             EEeccCCCCEEEEEcC
Confidence            2356667777776653

>cd01128 rho_factor Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase

Probab=95.30  E-value=0.043  Score=45.51  Aligned_cols=31  Identities=26%  Similarity=0.296  Sum_probs=22.8

Q ss_pred             ccccCCcEEEEcCCCChhhHHHHHHHHHhhhc
Q 017573           29 PFCKGLDVIQQAQSGTGKTATFCSGILQQLDY   60 (369)
Q Consensus        29 ~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~   60 (369)
                      .+..|+.+++.+|.|+|||.. +-.+++.+..
T Consensus        12 ~i~~Gqr~~I~G~~G~GKTTL-lr~I~n~l~~   42 (249)
T cd01128          12 PIGKGQRGLIVAPPKAGKTTL-LQSIANAITK   42 (249)
T ss_pred             ccCCCCEEEEECCCCCCHHHH-HHHHHhcccc
Confidence            445789999999999999965 3445555443

It is a homohexamer. Each monomer consists of an N-terminal domain of the OB fold, which is responsible for binding to cysteine rich nucleotides. This alignment is of the C-terminal ATP binding domain.

>PRK08840 replicative DNA helicase; Provisional

Probab=95.30  E-value=0.33  Score=44.49  Aligned_cols=123  Identities=19%  Similarity=0.089  Sum_probs=60.0

Q ss_pred             hhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEE-ECCc
Q 017573           24 QRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHAC-VGGT  102 (369)
Q Consensus        24 ~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~-~~~~  102 (369)
                      .+.+.-+..|+-+++.|.||.|||..++-.+.+.....  +.+++|+..- --..|+...+-....  ++....+ .+..
T Consensus       208 D~~~~G~~~g~LiviaarPg~GKTafalnia~~~a~~~--~~~v~~fSlE-Ms~~ql~~Rlla~~s--~v~~~~i~~~~l  282 (464)
T PRK08840        208 NKKTAGLQGSDLIIVAARPSMGKTTFAMNLCENAAMDQ--DKPVLIFSLE-MPAEQLMMRMLASLS--RVDQTKIRTGQL  282 (464)
T ss_pred             HHhhcCCCCCceEEEEeCCCCchHHHHHHHHHHHHHhC--CCeEEEEecc-CCHHHHHHHHHHhhC--CCCHHHHhcCCC
Confidence            33333344566789999999999987765555543221  2256666543 334444444432211  1111111 1222


Q ss_pred             chHHHHHH------HccCCcEEEe-----ccHHHHHHHHcCCCCCCCccEEEEechhHhh
Q 017573          103 SVREDQRI------LQAGVHVVVG-----TPGRVFDMLRRQSLRPDYIKMFVLDEADEML  151 (369)
Q Consensus       103 ~~~~~~~~------~~~~~~iiv~-----t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~  151 (369)
                      ...++.+.      +.....+.|-     |...+....++.......+++||+|-.|.+.
T Consensus       283 ~~~e~~~~~~a~~~l~~~~~l~I~d~~~~ti~~i~~~~r~~~~~~~~~~lvvIDYLql~~  342 (464)
T PRK08840        283 DDEDWARISSTMGILMEKKNMYIDDSSGLTPTEVRSRARRIAREHGGLSMIMVDYLQLMR  342 (464)
T ss_pred             CHHHHHHHHHHHHHHHhcCCEEEECCCCCCHHHHHHHHHHHHHhcCCCCEEEEccHHhcC
Confidence            22232221      2122345553     3344433332221111247899999999875

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=95.29  E-value=0.054  Score=47.78  Aligned_cols=38  Identities=13%  Similarity=0.095  Sum_probs=24.6

Q ss_pred             cCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEE
Q 017573           32 KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVL   70 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv   70 (369)
                      .+..+++.+|||||||... .+++..+.......+++.+
T Consensus       148 ~~GlilI~G~TGSGKTT~l-~al~~~i~~~~~~~~Ivti  185 (372)
T TIGR02525       148 AAGLGLICGETGSGKSTLA-ASIYQHCGETYPDRKIVTY  185 (372)
T ss_pred             cCCEEEEECCCCCCHHHHH-HHHHHHHHhcCCCceEEEE
Confidence            4567899999999999764 4555555433222245544

Members of this protein family are predicted ATPases associated with plasmid transfer loci in bacteria. This family is most similar to the DotB ATPase of a type-IV secretion-like system of obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii (TIGR02524).

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=95.28  E-value=0.15  Score=48.92  Aligned_cols=79  Identities=18%  Similarity=0.271  Sum_probs=64.7

Q ss_pred             cCCCeEEEeCCHhhHHHHHHHHhh----CCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEec-CCcCCCCCCCCcEEE
Q 017573          234 AITQSVIFVNTRRKVDWLTDKMRS----RDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTD-LLARGIDVQQVSLVI  308 (369)
Q Consensus       234 ~~~k~lv~~~~~~~~~~~~~~l~~----~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~-~~~~G~d~~~~~~vi  308 (369)
                      .+.++++.+|+..-|...++.+++    .+.++..++|+++..++..+++...+|+.+|+|+|. .+...+++.++..||
T Consensus       283 ~g~qvlilaPT~~LA~Q~~~~~~~l~~~~gi~v~lltg~~~~~~r~~~~~~i~~g~~~IiVgT~~ll~~~~~~~~l~lvV  362 (630)
T TIGR00643       283 AGYQVALMAPTEILAEQHYNSLRNLLAPLGIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQEKVEFKRLALVI  362 (630)
T ss_pred             cCCcEEEECCHHHHHHHHHHHHHHHhcccCcEEEEEecCCCHHHHHHHHHHHhCCCCCEEEecHHHHhccccccccceEE
Confidence            456899999999988877666654    478999999999999999999999999999999998 444557777888887


Q ss_pred             EecC
Q 017573          309 NYDL  312 (369)
Q Consensus       309 ~~~~  312 (369)
                      +-..
T Consensus       363 IDEa  366 (630)
T TIGR00643       363 IDEQ  366 (630)
T ss_pred             Eech
Confidence            6553

>KOG0742 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=95.28  E-value=0.069  Score=46.61  Aligned_cols=17  Identities=29%  Similarity=0.364  Sum_probs=15.6

Q ss_pred             CcEEEEcCCCChhhHHH
Q 017573           34 LDVIQQAQSGTGKTATF   50 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~   50 (369)
                      +|+++.+|+|+|||..+
T Consensus       385 RNilfyGPPGTGKTm~A  401 (630)
T KOG0742|consen  385 RNILFYGPPGTGKTMFA  401 (630)
T ss_pred             hheeeeCCCCCCchHHH
Confidence            78999999999999765

>PRK05580 primosome assembly protein PriA; Validated

Probab=95.25  E-value=0.31  Score=47.11  Aligned_cols=77  Identities=17%  Similarity=0.223  Sum_probs=64.2

Q ss_pred             CCCeEEEeCCHhhHHHHHHHHhhC-CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecC
Q 017573          235 ITQSVIFVNTRRKVDWLTDKMRSR-DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDL  312 (369)
Q Consensus       235 ~~k~lv~~~~~~~~~~~~~~l~~~-~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~  312 (369)
                      ++++|+.+|++..+..+.+.|++. +..+..+||+++..+|.+.+....+|+.+|+|+|.... -..+.++..+|+.+.
T Consensus       190 g~~vLvLvPt~~L~~Q~~~~l~~~fg~~v~~~~s~~s~~~r~~~~~~~~~g~~~IVVgTrsal-~~p~~~l~liVvDEe  267 (679)
T PRK05580        190 GKQALVLVPEIALTPQMLARFRARFGAPVAVLHSGLSDGERLDEWRKAKRGEAKVVIGARSAL-FLPFKNLGLIIVDEE  267 (679)
T ss_pred             CCeEEEEeCcHHHHHHHHHHHHHHhCCCEEEEECCCCHHHHHHHHHHHHcCCCCEEEeccHHh-cccccCCCEEEEECC
Confidence            568999999999999999988764 67899999999999999999999999999999998432 245667888877654

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=95.24  E-value=0.13  Score=50.43  Aligned_cols=19  Identities=32%  Similarity=0.282  Sum_probs=16.4

Q ss_pred             cCCcEEEEcCCCChhhHHH
Q 017573           32 KGLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~   50 (369)
                      .++.+++.||+|+|||..+
T Consensus       211 ~~~giLL~GppGtGKT~la  229 (733)
T TIGR01243       211 PPKGVLLYGPPGTGKTLLA  229 (733)
T ss_pred             CCceEEEECCCCCChHHHH
Confidence            4678999999999999764

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.

>PRK13851 type IV secretion system protein VirB11; Provisional

Probab=95.24  E-value=0.027  Score=49.09  Aligned_cols=43  Identities=19%  Similarity=0.271  Sum_probs=29.3

Q ss_pred             cccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHH
Q 017573           30 FCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTREL   76 (369)
Q Consensus        30 ~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l   76 (369)
                      +..+++++|.||||||||..+ -+++..+....   +++.+=...++
T Consensus       159 v~~~~nilI~G~tGSGKTTll-~aLl~~i~~~~---rivtiEd~~El  201 (344)
T PRK13851        159 VVGRLTMLLCGPTGSGKTTMS-KTLISAIPPQE---RLITIEDTLEL  201 (344)
T ss_pred             HHcCCeEEEECCCCccHHHHH-HHHHcccCCCC---CEEEECCCccc
Confidence            335799999999999999663 45555554332   66666666554

>KOG0730 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=95.23  E-value=0.34  Score=45.17  Aligned_cols=33  Identities=24%  Similarity=0.329  Sum_probs=23.4

Q ss_pred             CCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHH
Q 017573           15 GFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        15 ~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~   50 (369)
                      +..+|-.+.+-.+   ...+.+++.+|+|+|||+++
T Consensus       453 p~~~pe~F~r~Gi---~ppkGVLlyGPPGC~KT~lA  485 (693)
T KOG0730|consen  453 PLKHPEKFARFGI---SPPKGVLLYGPPGCGKTLLA  485 (693)
T ss_pred             hhhchHHHHHhcC---CCCceEEEECCCCcchHHHH
Confidence            4444544444443   23589999999999999876

>CHL00176 ftsH cell division protein; Validated

Probab=95.22  E-value=0.15  Score=48.45  Aligned_cols=18  Identities=33%  Similarity=0.313  Sum_probs=15.7

Q ss_pred             CCcEEEEcCCCChhhHHH
Q 017573           33 GLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~   50 (369)
                      .+++++.+|+|+|||..+
T Consensus       216 p~gVLL~GPpGTGKT~LA  233 (638)
T CHL00176        216 PKGVLLVGPPGTGKTLLA  233 (638)
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            357999999999999775

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=95.20  E-value=0.055  Score=46.78  Aligned_cols=18  Identities=22%  Similarity=0.219  Sum_probs=15.4

Q ss_pred             CcEEEEcCCCChhhHHHH
Q 017573           34 LDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~   51 (369)
                      .++++.||+|+|||..+.
T Consensus        31 ~~~ll~Gp~G~GKT~la~   48 (305)
T TIGR00635        31 DHLLLYGPPGLGKTTLAH   48 (305)
T ss_pred             CeEEEECCCCCCHHHHHH
Confidence            569999999999997653

RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.

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

Probab=95.20  E-value=0.086  Score=51.35  Aligned_cols=73  Identities=21%  Similarity=0.256  Sum_probs=58.1

Q ss_pred             hHHHHHHHHHhccCCCeEEEeCCHhhHHHHHHHHhhCC-----CeeEE-ecCCCCHHHHHHHHHHHhcCCCcEEEEecC
Q 017573          222 KLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRD-----HTVSA-THGDMDQNTRDIIMREFRSGSSRVLITTDL  294 (369)
Q Consensus       222 ~~~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~~-----~~~~~-~~~~~~~~~r~~~~~~f~~~~~~vli~t~~  294 (369)
                      ..-.+..+.-...++++++.+|+...+...++.|++..     ..+.. +|+.++..+++++++++.+|+.+|+|+|..
T Consensus       112 Tfg~~~sl~~a~kgkr~yii~PT~~Lv~Q~~~kl~~~~e~~~~~~~~~~yh~~l~~~ekee~le~i~~gdfdIlitTs~  190 (1187)
T COG1110         112 TFGLLMSLYLAKKGKRVYIIVPTTTLVRQVYERLKKFAEDAGSLDVLVVYHSALPTKEKEEALERIESGDFDILITTSQ  190 (1187)
T ss_pred             HHHHHHHHHHHhcCCeEEEEecCHHHHHHHHHHHHHHHhhcCCcceeeeeccccchHHHHHHHHHHhcCCccEEEEeHH
Confidence            34445555556667899999999988888888776552     33333 999999999999999999999999999973

>COG0552 FtsY Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=95.20  E-value=0.89  Score=38.98  Aligned_cols=130  Identities=22%  Similarity=0.259  Sum_probs=68.2

Q ss_pred             cEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCC--HHHHHHHHHHHHHhccccCcEEEEEE-CCcchHHHHHHH
Q 017573           35 DVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPT--RELAQQIEKVMRALGDYLGVKVHACV-GGTSVREDQRIL  111 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~--~~l~~q~~~~~~~~~~~~~~~v~~~~-~~~~~~~~~~~~  111 (369)
                      -+++.+..|+|||.+..-.+......+.   ++++.+.-  |+=+.   +++..|....+..+.... |+.+        
T Consensus       141 Vil~vGVNG~GKTTTIaKLA~~l~~~g~---~VllaA~DTFRAaAi---EQL~~w~er~gv~vI~~~~G~Dp--------  206 (340)
T COG0552         141 VILFVGVNGVGKTTTIAKLAKYLKQQGK---SVLLAAGDTFRAAAI---EQLEVWGERLGVPVISGKEGADP--------  206 (340)
T ss_pred             EEEEEecCCCchHhHHHHHHHHHHHCCC---eEEEEecchHHHHHH---HHHHHHHHHhCCeEEccCCCCCc--------
Confidence            3799999999999875444443333332   56665542  23332   233333333455554421 2222        


Q ss_pred             ccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhcc-CcHHHHHHHHhhCCccC------cEEEEEeeCChhHH
Q 017573          112 QAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSR-GFKDQIYDIFQLLPAKV------QVGVFSATMPPEAL  184 (369)
Q Consensus       112 ~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~-~~~~~~~~~~~~~~~~~------~~i~~saT~~~~~~  184 (369)
                         +.|+   ++.+....      ..++|+|++|=+-++-+. +.-..+.++.+-+.+..      .++.+-||...+..
T Consensus       207 ---AaVa---fDAi~~Ak------ar~~DvvliDTAGRLhnk~nLM~EL~KI~rV~~k~~~~ap~e~llvlDAttGqnal  274 (340)
T COG0552         207 ---AAVA---FDAIQAAK------ARGIDVVLIDTAGRLHNKKNLMDELKKIVRVIKKDDPDAPHEILLVLDATTGQNAL  274 (340)
T ss_pred             ---HHHH---HHHHHHHH------HcCCCEEEEeCcccccCchhHHHHHHHHHHHhccccCCCCceEEEEEEcccChhHH
Confidence               1111   11222211      233689999999887543 34455555555554432      34445889887766


Q ss_pred             HHHHHh
Q 017573          185 EITRKF  190 (369)
Q Consensus       185 ~~~~~~  190 (369)
                      ...+.+
T Consensus       275 ~QAk~F  280 (340)
T COG0552         275 SQAKIF  280 (340)
T ss_pred             HHHHHH
Confidence            555444

>PRK07004 replicative DNA helicase; Provisional

Probab=95.19  E-value=0.23  Score=45.55  Aligned_cols=116  Identities=14%  Similarity=0.056  Sum_probs=56.6

Q ss_pred             cccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEE-ECCcchHHHH
Q 017573           30 FCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHAC-VGGTSVREDQ  108 (369)
Q Consensus        30 ~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~-~~~~~~~~~~  108 (369)
                      +..|.-+++.|.||+|||..++-.+.+.....  +.++++++. .--..|+..++-....  ++....+ .|.....++.
T Consensus       210 ~~~g~liviaarpg~GKT~~al~ia~~~a~~~--~~~v~~fSl-EM~~~ql~~R~la~~~--~v~~~~i~~g~l~~~e~~  284 (460)
T PRK07004        210 MHGGELIIVAGRPSMGKTAFSMNIGEYVAVEY--GLPVAVFSM-EMPGTQLAMRMLGSVG--RLDQHRMRTGRLTDEDWP  284 (460)
T ss_pred             CCCCceEEEEeCCCCCccHHHHHHHHHHHHHc--CCeEEEEeC-CCCHHHHHHHHHHhhc--CCCHHHHhcCCCCHHHHH
Confidence            33456689999999999987766555443321  115666653 2333444444422111  1111111 1222222222


Q ss_pred             H------HHccCCcEEEe-----ccHHHHHHHHcCCCCCCCccEEEEechhHhh
Q 017573          109 R------ILQAGVHVVVG-----TPGRVFDMLRRQSLRPDYIKMFVLDEADEML  151 (369)
Q Consensus       109 ~------~~~~~~~iiv~-----t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~  151 (369)
                      .      .+ .+..+.|.     |+..+....++-......+++||+|=.+.+.
T Consensus       285 ~~~~a~~~l-~~~~l~I~d~~~~~~~~i~~~~r~l~~~~~~~~lviIDYLql~~  337 (460)
T PRK07004        285 KLTHAVQKM-SEAQLFIDETGGLNPMELRSRARRLARQCGKLGLIIIDYLQLMS  337 (460)
T ss_pred             HHHHHHHHH-hcCCEEEECCCCCCHHHHHHHHHHHHHhCCCCCEEEEChhhhcc
Confidence            1      12 23456653     4444433332211111236899999999875

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

Probab=95.15  E-value=0.24  Score=46.38  Aligned_cols=86  Identities=20%  Similarity=0.282  Sum_probs=70.1

Q ss_pred             HHHHHHhccCCCeEEEeCCH----hhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEec-CCcCCCC
Q 017573          226 LCDLYETLAITQSVIFVNTR----RKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTD-LLARGID  300 (369)
Q Consensus       226 l~~~~~~~~~~k~lv~~~~~----~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~-~~~~G~d  300 (369)
                      +..+..-.++.++.+.+|+.    .+...+.+.|...+..+.++.|.+....|.++++...+|+++++|+|. .+.+.++
T Consensus       302 laml~ai~~G~Q~ALMAPTEILA~QH~~~~~~~l~~~~i~V~lLtG~~kgk~r~~~l~~l~~G~~~ivVGTHALiQd~V~  381 (677)
T COG1200         302 LAMLAAIEAGYQAALMAPTEILAEQHYESLRKWLEPLGIRVALLTGSLKGKARKEILEQLASGEIDIVVGTHALIQDKVE  381 (677)
T ss_pred             HHHHHHHHcCCeeEEeccHHHHHHHHHHHHHHHhhhcCCeEEEeecccchhHHHHHHHHHhCCCCCEEEEcchhhhccee
Confidence            33333333556888999985    566677888888899999999999999999999999999999999998 5566789


Q ss_pred             CCCCcEEEEec
Q 017573          301 VQQVSLVINYD  311 (369)
Q Consensus       301 ~~~~~~vi~~~  311 (369)
                      +.++-.||+-.
T Consensus       382 F~~LgLVIiDE  392 (677)
T COG1200         382 FHNLGLVIIDE  392 (677)
T ss_pred             ecceeEEEEec
Confidence            88888888654

>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=95.15  E-value=0.028  Score=50.51  Aligned_cols=42  Identities=21%  Similarity=0.274  Sum_probs=30.4

Q ss_pred             CcHhhhhhhhccccC--CcEEEEcCCCChhhHHHHHHHHHhhhcc
Q 017573           19 PSAIQQRGIVPFCKG--LDVIQQAQSGTGKTATFCSGILQQLDYG   61 (369)
Q Consensus        19 ~~~~Q~~~~~~~~~~--~~~li~~~tG~GKT~~~~~~~~~~~~~~   61 (369)
                      +.+.|.+.+..+.+.  .-+++.||||||||.+. ..++..+...
T Consensus       242 ~~~~~~~~~~~~~~~p~GliLvTGPTGSGKTTTL-Y~~L~~ln~~  285 (500)
T COG2804         242 MSPFQLARLLRLLNRPQGLILVTGPTGSGKTTTL-YAALSELNTP  285 (500)
T ss_pred             CCHHHHHHHHHHHhCCCeEEEEeCCCCCCHHHHH-HHHHHHhcCC
Confidence            377888888777765  45799999999999774 4555555443

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=95.11  E-value=0.19  Score=44.99  Aligned_cols=18  Identities=33%  Similarity=0.309  Sum_probs=15.9

Q ss_pred             CCcEEEEcCCCChhhHHH
Q 017573           33 GLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~   50 (369)
                      .+++++.||+|+|||..+
T Consensus       165 p~gvLL~GppGtGKT~lA  182 (389)
T PRK03992        165 PKGVLLYGPPGTGKTLLA  182 (389)
T ss_pred             CCceEEECCCCCChHHHH
Confidence            478999999999999775

>cd01393 recA_like RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=95.09  E-value=0.082  Score=43.41  Aligned_cols=43  Identities=14%  Similarity=0.054  Sum_probs=29.3

Q ss_pred             cCCcEEEEcCCCChhhHHHHHHHHHhhhcc---CCCccEEEEcCCH
Q 017573           32 KGLDVIQQAQSGTGKTATFCSGILQQLDYG---LVQCQALVLAPTR   74 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~~~~~~~~~~~---~~~~~~liv~P~~   74 (369)
                      .++-+.+.+|+|+|||..++..+...+..+   ....+++++....
T Consensus        18 ~g~v~~I~G~~GsGKT~l~~~ia~~~~~~~~~~g~~~~v~yi~~e~   63 (226)
T cd01393          18 TGRITEIFGEFGSGKTQLCLQLAVEAQLPGELGGLEGKVVYIDTEG   63 (226)
T ss_pred             CCcEEEEeCCCCCChhHHHHHHHHHhhcccccCCCcceEEEEecCC
Confidence            356789999999999988776665554332   0113788887654

RecA couples ATP hydrolysis to DNA strand exchange. While prokaryotes have a single RecA protein, eukaryotes have multiple RecA homologs such as Rad51, DMC1 and Rad55/57. Archaea have the RecA-like homologs radA and radB.

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=95.02  E-value=0.03  Score=48.67  Aligned_cols=39  Identities=15%  Similarity=0.181  Sum_probs=26.5

Q ss_pred             ccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCC
Q 017573           31 CKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPT   73 (369)
Q Consensus        31 ~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~   73 (369)
                      ..+++++|+|+||||||... -+++..+....   +++.+=-+
T Consensus       158 ~~~~nili~G~tgSGKTTll-~aL~~~ip~~~---ri~tiEd~  196 (332)
T PRK13900        158 ISKKNIIISGGTSTGKTTFT-NAALREIPAIE---RLITVEDA  196 (332)
T ss_pred             HcCCcEEEECCCCCCHHHHH-HHHHhhCCCCC---eEEEecCC
Confidence            35799999999999999663 55555554432   55554333

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=95.01  E-value=0.096  Score=39.54  Aligned_cols=116  Identities=18%  Similarity=0.239  Sum_probs=57.9

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHc-
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQ-  112 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~-  112 (369)
                      -.+.+.+++|+|||..+ .-+.+.+....-+ -.=+++|-          .++-....|+++..+..+........-.. 
T Consensus         6 mki~ITG~PGvGKtTl~-~ki~e~L~~~g~k-vgGf~t~E----------VR~gGkR~GF~Ivdl~tg~~~~la~~~~~~   73 (179)
T COG1618           6 MKIFITGRPGVGKTTLV-LKIAEKLREKGYK-VGGFITPE----------VREGGKRIGFKIVDLATGEEGILARVGFSR   73 (179)
T ss_pred             eEEEEeCCCCccHHHHH-HHHHHHHHhcCce-eeeEEeee----------eecCCeEeeeEEEEccCCceEEEEEcCCCC
Confidence            46899999999999765 4555555543222 34455663          44444555777666654332110000000 


Q ss_pred             cCCcEEEeccHHHH----HHHHcCCCCCCCccEEEEechhHhh--ccCcHHHHHHHHh
Q 017573          113 AGVHVVVGTPGRVF----DMLRRQSLRPDYIKMFVLDEADEML--SRGFKDQIYDIFQ  164 (369)
Q Consensus       113 ~~~~iiv~t~~~l~----~~~~~~~~~~~~~~~viiDE~H~~~--~~~~~~~~~~~~~  164 (369)
                      ....=+....+.+.    ..+++..   ..-|++|+||+--+.  ...|.+.+..+++
T Consensus        74 ~rvGkY~V~v~~le~i~~~al~rA~---~~aDvIIIDEIGpMElks~~f~~~ve~vl~  128 (179)
T COG1618          74 PRVGKYGVNVEGLEEIAIPALRRAL---EEADVIIIDEIGPMELKSKKFREAVEEVLK  128 (179)
T ss_pred             cccceEEeeHHHHHHHhHHHHHHHh---hcCCEEEEecccchhhccHHHHHHHHHHhc
Confidence            01112222223332    2222211   114899999998764  3335555555443

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.96  E-value=0.14  Score=48.61  Aligned_cols=39  Identities=13%  Similarity=0.225  Sum_probs=24.1

Q ss_pred             CccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEEee
Q 017573          138 YIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSAT  178 (369)
Q Consensus       138 ~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~saT  178 (369)
                      ..+++|+||+|.+.... ...+.+.+...+....+|+ .+|
T Consensus       121 ~~KVvIIdea~~Ls~~a-~naLLK~LEepp~~tifIL-~tt  159 (614)
T PRK14971        121 KYKIYIIDEVHMLSQAA-FNAFLKTLEEPPSYAIFIL-ATT  159 (614)
T ss_pred             CcEEEEEECcccCCHHH-HHHHHHHHhCCCCCeEEEE-EeC
Confidence            46899999999985432 3445555555555454444 444

>TIGR00665 DnaB replicative DNA helicase

Probab=94.96  E-value=0.34  Score=44.24  Aligned_cols=114  Identities=17%  Similarity=0.027  Sum_probs=57.1

Q ss_pred             ccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEE-ECCcchHHHH-
Q 017573           31 CKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHAC-VGGTSVREDQ-  108 (369)
Q Consensus        31 ~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~-~~~~~~~~~~-  108 (369)
                      ..|.-++|.|+||+|||..++-.+.+.....  +.++++++.- .-..+..+++-.....  +....+ .+.....++. 
T Consensus       193 ~~G~l~vi~g~pg~GKT~~~l~~a~~~a~~~--g~~vl~~SlE-m~~~~i~~R~~~~~~~--v~~~~~~~g~l~~~~~~~  267 (434)
T TIGR00665       193 QPSDLIILAARPSMGKTAFALNIAENAAIKE--GKPVAFFSLE-MSAEQLAMRMLSSESR--VDSQKLRTGKLSDEDWEK  267 (434)
T ss_pred             CCCeEEEEEeCCCCChHHHHHHHHHHHHHhC--CCeEEEEeCc-CCHHHHHHHHHHHhcC--CCHHHhccCCCCHHHHHH
Confidence            3456689999999999988776666544321  1267777643 3334444444332221  111111 1222222221 


Q ss_pred             -----HHHccCCcEEEe-----ccHHHHHHHHcCCCCCCCccEEEEechhHhh
Q 017573          109 -----RILQAGVHVVVG-----TPGRVFDMLRRQSLRPDYIKMFVLDEADEML  151 (369)
Q Consensus       109 -----~~~~~~~~iiv~-----t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~  151 (369)
                           ..+. +..+.|.     |.+.+...+++.... .++++||+|=.+.+.
T Consensus       268 ~~~a~~~l~-~~~l~i~d~~~~~~~~i~~~i~~~~~~-~~~~~vvID~l~~i~  318 (434)
T TIGR00665       268 LTSAAGKLS-EAPLYIDDTPGLTITELRAKARRLKRE-HGLGLIVIDYLQLMS  318 (434)
T ss_pred             HHHHHHHHh-cCCEEEECCCCCCHHHHHHHHHHHHHh-cCCCEEEEcchHhcC
Confidence                 1122 2334542     344554433322111 237999999998875

This model describes the helicase DnaB, a homohexameric protein required for DNA replication. The homohexamer can form a ring around a single strand of DNA near a replication fork. An intein of 400 residues is found at a conserved location in DnaB of Synechocystis PCC6803, Rhodothermus marinus (both experimentally confirmed), and Mycobacterium tuberculosis. The intein removes itself by a self-splicing reaction. The seed alignment contains inteins so that the model built from the seed alignment will model a low cost at common intein insertion sites.

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=94.93  E-value=0.41  Score=46.64  Aligned_cols=22  Identities=27%  Similarity=0.169  Sum_probs=17.6

Q ss_pred             CCcEEEEcCCCChhhHHHHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFCSGI   54 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~   54 (369)
                      ..+.++.||+|+|||..+-..+
T Consensus       207 ~~n~LLvGppGvGKT~lae~la  228 (758)
T PRK11034        207 KNNPLLVGESGVGKTAIAEGLA  228 (758)
T ss_pred             CCCeEEECCCCCCHHHHHHHHH
Confidence            3589999999999998764443

>PRK12608 transcription termination factor Rho; Provisional

Probab=94.91  E-value=0.31  Score=42.74  Aligned_cols=38  Identities=21%  Similarity=0.173  Sum_probs=25.7

Q ss_pred             hhhhhhhccc---cCCcEEEEcCCCChhhHHHHHHHHHhhhc
Q 017573           22 IQQRGIVPFC---KGLDVIQQAQSGTGKTATFCSGILQQLDY   60 (369)
Q Consensus        22 ~Q~~~~~~~~---~~~~~li~~~tG~GKT~~~~~~~~~~~~~   60 (369)
                      .-.++++.+.   +|++.+|.||.|+|||..+. .+++.+..
T Consensus       119 ~~~RvID~l~PiGkGQR~LIvG~pGtGKTTLl~-~la~~i~~  159 (380)
T PRK12608        119 LSMRVVDLVAPIGKGQRGLIVAPPRAGKTVLLQ-QIAAAVAA  159 (380)
T ss_pred             hhHhhhhheeecCCCceEEEECCCCCCHHHHHH-HHHHHHHh
Confidence            3344555554   57999999999999997653 34444443

>KOG0734 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=94.88  E-value=0.12  Score=46.75  Aligned_cols=46  Identities=24%  Similarity=0.252  Sum_probs=29.1

Q ss_pred             ccEEEEechhHhhccC-------cHHHHHHHHh---hCCccCcEEEEEeeCChhHH
Q 017573          139 IKMFVLDEADEMLSRG-------FKDQIYDIFQ---LLPAKVQVGVFSATMPPEAL  184 (369)
Q Consensus       139 ~~~viiDE~H~~~~~~-------~~~~~~~~~~---~~~~~~~~i~~saT~~~~~~  184 (369)
                      ..+|.|||.+.+...-       ..+.++.++.   .+.++.-+|.+.||--++..
T Consensus       397 PcIIFIDEiDavG~kR~~~~~~y~kqTlNQLLvEmDGF~qNeGiIvigATNfpe~L  452 (752)
T KOG0734|consen  397 PCIIFIDEIDAVGGKRNPSDQHYAKQTLNQLLVEMDGFKQNEGIIVIGATNFPEAL  452 (752)
T ss_pred             CeEEEEechhhhcccCCccHHHHHHHHHHHHHHHhcCcCcCCceEEEeccCChhhh
Confidence            4789999999875321       1233444443   34556678999999765543

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family

Probab=94.88  E-value=0.073  Score=43.68  Aligned_cols=52  Identities=21%  Similarity=0.236  Sum_probs=37.4

Q ss_pred             cCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHh
Q 017573           32 KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRAL   87 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~   87 (369)
                      .+.-+++.+++|+|||..++..+.+.+..+.   +++|++... -..+..+.+..+
T Consensus        15 ~g~~~li~G~~G~GKt~~~~~~~~~~~~~g~---~~~y~s~e~-~~~~l~~~~~~~   66 (224)
T TIGR03880        15 EGHVIVVIGEYGTGKTTFSLQFLYQGLKNGE---KAMYISLEE-REERILGYAKSK   66 (224)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhCCC---eEEEEECCC-CHHHHHHHHHHc
Confidence            3567899999999999887766666665543   788887654 456666666655

This model represents a rather narrowly distributed archaeal protein family in which members have a single copy of the KaiC domain. This stands in contrast to the circadian clock protein KaiC itself, with two copies of the domain. Members are expected to have weak ATPase activity, by homology to the autokinase/autophosphorylase KaiC itself.

>TIGR02688 conserved hypothetical protein TIGR02688

Probab=94.85  E-value=0.13  Score=45.72  Aligned_cols=49  Identities=22%  Similarity=0.215  Sum_probs=30.3

Q ss_pred             CHHHHHHHHhCCCCC--CcHhhh-h----hhhccccCCcEEEEcCCCChhhHHHHH
Q 017573            4 QENLLRGIYAYGFEK--PSAIQQ-R----GIVPFCKGLDVIQQAQSGTGKTATFCS   52 (369)
Q Consensus         4 ~~~i~~~l~~~~~~~--~~~~Q~-~----~~~~~~~~~~~li~~~tG~GKT~~~~~   52 (369)
                      .+|+-=-+...|+..  +.+-|+ .    .++.+.++.|++..+|+|+|||-.+..
T Consensus       173 dEWid~LlrSiG~~P~~~~~r~k~~~L~rl~~fve~~~Nli~lGp~GTGKThla~~  228 (449)
T TIGR02688       173 EEWIDVLIRSIGYEPEGFEARQKLLLLARLLPLVEPNYNLIELGPKGTGKSYIYNN  228 (449)
T ss_pred             HHHHHHHHHhcCCCcccCChHHHHHHHHhhHHHHhcCCcEEEECCCCCCHHHHHHH
Confidence            345555566666622  222111 1    114455789999999999999976654

Members of this family are uncharacterized proteins sporadically distributed in bacteria and archaea, about 470 amino acids in length. Several members of this family appear in public databases with annotation as ATP-dependent protease La, despite the lack of similarity to families TIGR00763 (ATP-dependent protease La) or pfam02190 (ATP-dependent protease La (LON) domain). This protein is repeatedly found downstream of another uncharacterized protein of about 880 amino acids in length, described by model TIGR02687.

>PRK05748 replicative DNA helicase; Provisional

Probab=94.84  E-value=0.37  Score=44.19  Aligned_cols=115  Identities=11%  Similarity=0.037  Sum_probs=57.4

Q ss_pred             ccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEE-ECCcchHHHHH
Q 017573           31 CKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHAC-VGGTSVREDQR  109 (369)
Q Consensus        31 ~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~-~~~~~~~~~~~  109 (369)
                      ..|.-++|.|+||.|||..++-.+.+.....  +.++++++.- .-..|+..++-.....  +....+ .+.....++..
T Consensus       201 ~~G~livIaarpg~GKT~~al~ia~~~a~~~--g~~v~~fSlE-ms~~~l~~R~l~~~~~--v~~~~i~~~~l~~~e~~~  275 (448)
T PRK05748        201 QPNDLIIVAARPSVGKTAFALNIAQNVATKT--DKNVAIFSLE-MGAESLVMRMLCAEGN--IDAQRLRTGQLTDDDWPK  275 (448)
T ss_pred             CCCceEEEEeCCCCCchHHHHHHHHHHHHhC--CCeEEEEeCC-CCHHHHHHHHHHHhcC--CCHHHhhcCCCCHHHHHH
Confidence            3456689999999999988776666544321  1156666533 3344554444322111  111111 12222222211


Q ss_pred             ------HHccCCcEEEe-----ccHHHHHHHHcCCCCCCCccEEEEechhHhh
Q 017573          110 ------ILQAGVHVVVG-----TPGRVFDMLRRQSLRPDYIKMFVLDEADEML  151 (369)
Q Consensus       110 ------~~~~~~~iiv~-----t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~  151 (369)
                            .+. +..+.|.     |.+.+...+++......++++||+|=.|.+.
T Consensus       276 ~~~a~~~l~-~~~~~i~d~~~~ti~~i~~~~r~~~~~~~~~~~vvIDyL~li~  327 (448)
T PRK05748        276 LTIAMGSLS-DAPIYIDDTPGIKVTEIRARCRRLAQEHGGLGLILIDYLQLIQ  327 (448)
T ss_pred             HHHHHHHHh-cCCEEEECCCCCCHHHHHHHHHHHHHhcCCCCEEEEccchhcC
Confidence                  122 2345553     3444544333211111147899999999875

>TIGR00595 priA primosomal protein N'

Probab=94.82  E-value=0.15  Score=47.34  Aligned_cols=77  Identities=14%  Similarity=0.192  Sum_probs=63.5

Q ss_pred             CCCeEEEeCCHhhHHHHHHHHhhC-CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecC
Q 017573          235 ITQSVIFVNTRRKVDWLTDKMRSR-DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDL  312 (369)
Q Consensus       235 ~~k~lv~~~~~~~~~~~~~~l~~~-~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~  312 (369)
                      ++++|+.+|.+..+..+++.|++. +..+..+||+++..+|.+.+....+|+.+|+|+|...- -..++++..||+.+.
T Consensus        25 g~~vLvlvP~i~L~~Q~~~~l~~~f~~~v~vlhs~~~~~er~~~~~~~~~g~~~IVVGTrsal-f~p~~~l~lIIVDEe  102 (505)
T TIGR00595        25 GKSVLVLVPEIALTPQMIQRFKYRFGSQVAVLHSGLSDSEKLQAWRKVKNGEILVVIGTRSAL-FLPFKNLGLIIVDEE  102 (505)
T ss_pred             CCeEEEEeCcHHHHHHHHHHHHHHhCCcEEEEECCCCHHHHHHHHHHHHcCCCCEEECChHHH-cCcccCCCEEEEECC
Confidence            568999999999999998888764 66889999999999999999999999999999997432 245667888876653

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).

>PF06733 DEAD_2: DEAD_2; InterPro: IPR010614 This represents a conserved region within a number of RAD3-like DNA-binding helicases that are seemingly ubiquitous - members include proteins of eukaryotic, bacterial and archaeal origin

Probab=94.81  E-value=0.015  Score=45.62  Aligned_cols=41  Identities=22%  Similarity=0.333  Sum_probs=27.5

Q ss_pred             HccCCcEEEeccHHHHHHHHcCC---CCCCCccEEEEechhHhhc
Q 017573          111 LQAGVHVVVGTPGRVFDMLRRQS---LRPDYIKMFVLDEADEMLS  152 (369)
Q Consensus       111 ~~~~~~iiv~t~~~l~~~~~~~~---~~~~~~~~viiDE~H~~~~  152 (369)
                      ....++|+|+++..++.......   +... -.+||+||||.+.+
T Consensus       116 ~~~~adivi~~y~yl~~~~~~~~~~~~~~~-~~ivI~DEAHNL~~  159 (174)
T PF06733_consen  116 LAKNADIVICNYNYLFDPSIRKSLFGIDLK-DNIVIFDEAHNLED  159 (174)
T ss_dssp             CGGG-SEEEEETHHHHSHHHHHHHCT--CC-CEEEEETTGGGCGG
T ss_pred             hcccCCEEEeCHHHHhhHHHHhhhcccccc-CcEEEEecccchHH
Confidence            34568999999999876543322   2233 37899999999864

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.

>PF12846 AAA_10: AAA-like domain

Probab=94.79  E-value=0.044  Score=47.23  Aligned_cols=40  Identities=18%  Similarity=0.338  Sum_probs=28.8

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHH
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRE   75 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~   75 (369)
                      +.+++|.|+||+|||..+...+...+..+.   .++++=|..+
T Consensus         1 n~h~~i~G~tGsGKT~~~~~l~~~~~~~g~---~~~i~D~~g~   40 (304)
T PF12846_consen    1 NPHTLILGKTGSGKTTLLKNLLEQLIRRGP---RVVIFDPKGD   40 (304)
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHHHHcCC---CEEEEcCCch
Confidence            468999999999999887755555555553   6777755533

>COG2812 DnaX DNA polymerase III, gamma/tau subunits [DNA replication, recombination, and repair]

Probab=94.73  E-value=0.073  Score=48.69  Aligned_cols=17  Identities=24%  Similarity=0.272  Sum_probs=14.6

Q ss_pred             CcEEEEcCCCChhhHHH
Q 017573           34 LDVIQQAQSGTGKTATF   50 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~   50 (369)
                      ...++.+|-|+|||.++
T Consensus        39 hAYlfsG~RGvGKTt~A   55 (515)
T COG2812          39 HAYLFSGPRGVGKTTIA   55 (515)
T ss_pred             hhhhhcCCCCcCchhHH
Confidence            45699999999999876

>PHA00012 I assembly protein

Probab=94.71  E-value=1.2  Score=38.28  Aligned_cols=27  Identities=30%  Similarity=0.329  Sum_probs=22.7

Q ss_pred             EEEEcCCCChhhHHHHHHHHHhhhccC
Q 017573           36 VIQQAQSGTGKTATFCSGILQQLDYGL   62 (369)
Q Consensus        36 ~li~~~tG~GKT~~~~~~~~~~~~~~~   62 (369)
                      -++.|-+|+|||+.+...+...+.++.
T Consensus         4 ylITGkPGSGKSl~aV~~I~~~L~~Gr   30 (361)
T PHA00012          4 YVVTGKLGAGKTLVAVSRIQDKLVKGC   30 (361)
T ss_pred             EEEecCCCCCchHHHHHHHHHHHHcCC
Confidence            478999999999998888888777663

>TIGR02784 addA_alphas double-strand break repair helicase AddA, alphaproteobacterial type

Probab=94.65  E-value=0.089  Score=54.19  Aligned_cols=100  Identities=17%  Similarity=0.134  Sum_probs=64.4

Q ss_pred             cCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccC-cEE-------EEEECC-c
Q 017573           32 KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLG-VKV-------HACVGG-T  102 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~-~~v-------~~~~~~-~  102 (369)
                      ..++++|.|+.|||||.+...-++..+..+....++++|+-|+.-+.++.+++.+...... ..-       ....+. .
T Consensus         9 p~~~~~~~a~agsgkt~~l~~~~~~~~~~~~~~~~i~~~t~t~~aa~em~~Ri~~~L~~~~~~~~~~l~~~l~~~~~~~~   88 (1141)
T TIGR02784         9 PKTSAWVSANAGSGKTHVLTQRVIRLLLNGVPPSKILCLTYTKAAAAEMQNRVFDRLGEWAVLDDAELRARLEALEGKRP   88 (1141)
T ss_pred             CCCCEEEEEECCCCHHHHHHHHHHHHHHcCCCCCeEEEEecCHHHHHHHHHHHHHHHHHHhcCChHHHHHHHHHhcCCCC
Confidence            3688999999999999988777777776554445899999999999888887766543210 000       000000 0


Q ss_pred             ch---H----HHHHHHccCCcEEEeccHHHHHHHHc
Q 017573          103 SV---R----EDQRILQAGVHVVVGTPGRVFDMLRR  131 (369)
Q Consensus       103 ~~---~----~~~~~~~~~~~iiv~t~~~l~~~~~~  131 (369)
                      ..   .    ...+.+.+...+-|.|.+.|...+.+
T Consensus        89 ~~~~l~~ar~l~~~~l~~~~~l~I~Ti~sf~~~l~r  124 (1141)
T TIGR02784        89 DAAKLAEARRLFARALETPGGLKIQTIHAFCESLLH  124 (1141)
T ss_pred             ChHHHHHHHHHHHHHHhCCCCceEeeHHHHHHHHHH
Confidence            00   0    11133445567889999999765544

AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination. The term AddAB is used broadly, with AddA homologous between the alphaproteobacteria (as modeled here) and the Firmicutes, while the partner AddB proteins show no strong homology across the two groups of species.

>PRK08760 replicative DNA helicase; Provisional

Probab=94.64  E-value=0.29  Score=45.06  Aligned_cols=114  Identities=15%  Similarity=0.072  Sum_probs=57.9

Q ss_pred             cCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHH--
Q 017573           32 KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQR--  109 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~--  109 (369)
                      .|.-++|.|.||.|||..++-.+.+......  .+++|++.- .-..|+..++........... ...+.....++..  
T Consensus       228 ~G~LivIaarPg~GKTafal~iA~~~a~~~g--~~V~~fSlE-Ms~~ql~~Rl~a~~s~i~~~~-i~~g~l~~~e~~~~~  303 (476)
T PRK08760        228 PTDLIILAARPAMGKTTFALNIAEYAAIKSK--KGVAVFSME-MSASQLAMRLISSNGRINAQR-LRTGALEDEDWARVT  303 (476)
T ss_pred             CCceEEEEeCCCCChhHHHHHHHHHHHHhcC--CceEEEecc-CCHHHHHHHHHHhhCCCcHHH-HhcCCCCHHHHHHHH
Confidence            3456799999999999887766655543311  156666543 334455555544322211111 1112222222211  


Q ss_pred             ----HHccCCcEEEe-----ccHHHHHHHHcCCCCCCCccEEEEechhHhh
Q 017573          110 ----ILQAGVHVVVG-----TPGRVFDMLRRQSLRPDYIKMFVLDEADEML  151 (369)
Q Consensus       110 ----~~~~~~~iiv~-----t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~  151 (369)
                          .+. +..+.|.     |++.+....++... ...+++||||=.+.+.
T Consensus       304 ~a~~~l~-~~~l~I~d~~~~t~~~I~~~~r~l~~-~~~~~lVvIDyLql~~  352 (476)
T PRK08760        304 GAIKMLK-ETKIFIDDTPGVSPEVLRSKCRRLKR-EHDLGLIVIDYLQLMS  352 (476)
T ss_pred             HHHHHHh-cCCEEEeCCCCCCHHHHHHHHHHHHH-hcCCCEEEEecHHhcC
Confidence                122 2345544     34555443333211 1337999999999774

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=94.62  E-value=0.067  Score=49.40  Aligned_cols=53  Identities=25%  Similarity=0.221  Sum_probs=39.1

Q ss_pred             cCCcEEEEcCCCChhhHHHHHHHHHhhhc-cCCCccEEEEcCCHHHHHHHHHHHHHhc
Q 017573           32 KGLDVIQQAQSGTGKTATFCSGILQQLDY-GLVQCQALVLAPTRELAQQIEKVMRALG   88 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~~~~~~~~~~-~~~~~~~liv~P~~~l~~q~~~~~~~~~   88 (369)
                      .+...+|.+++|+|||..++..+.+.+.+ +.   +++|++-- +-..++.+++..+.
T Consensus        20 ~g~~~Li~G~pGsGKT~la~qfl~~g~~~~ge---~~lyvs~e-E~~~~l~~~~~~~G   73 (484)
T TIGR02655        20 IGRSTLVSGTSGTGKTLFSIQFLYNGIIHFDE---PGVFVTFE-ESPQDIIKNARSFG   73 (484)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHHHhCCC---CEEEEEEe-cCHHHHHHHHHHcC
Confidence            35778999999999998887777765554 44   78888854 55566666666653

Members of this family are the circadian clock protein KaiC, part of the kaiABC operon that controls circadian rhythm. It may be universal in Cyanobacteria. Each member has two copies of the KaiC domain (Pfam model pfam06745), which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor.

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=94.62  E-value=0.23  Score=46.14  Aligned_cols=18  Identities=33%  Similarity=0.313  Sum_probs=15.8

Q ss_pred             CCcEEEEcCCCChhhHHH
Q 017573           33 GLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~   50 (369)
                      .+++++.+|+|+|||..+
T Consensus        88 ~~giLL~GppGtGKT~la  105 (495)
T TIGR01241        88 PKGVLLVGPPGTGKTLLA  105 (495)
T ss_pred             CCcEEEECCCCCCHHHHH
Confidence            467999999999999775

HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH.

>PF03969 AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654 ATPase family gene 1 (AFG1) ATPase is a 377 amino acid putative protein with an ATPase motif typical of the protein family including SEC18p PAS1, CDC48-VCP and TBP

Probab=94.56  E-value=0.58  Score=41.31  Aligned_cols=18  Identities=22%  Similarity=0.202  Sum_probs=15.8

Q ss_pred             CCcEEEEcCCCChhhHHH
Q 017573           33 GLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~   50 (369)
                      .+++.++|+.|.|||..+
T Consensus        62 ~~GlYl~G~vG~GKT~Lm   79 (362)
T PF03969_consen   62 PKGLYLWGPVGRGKTMLM   79 (362)
T ss_pred             CceEEEECCCCCchhHHH
Confidence            578999999999999754

AFG1 also has substantial homology to these proteins outside the ATPase domain []. This family of proteins contains a P-loop motif.; GO: 0005524 ATP binding

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

Probab=94.50  E-value=0.27  Score=47.16  Aligned_cols=92  Identities=20%  Similarity=0.225  Sum_probs=70.3

Q ss_pred             chhhhHHHHHHHHHhc--cCCCeEEEeCCHhhHHHHHHHHhhC-CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecC
Q 017573          218 KEEWKLETLCDLYETL--AITQSVIFVNTRRKVDWLTDKMRSR-DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDL  294 (369)
Q Consensus       218 ~~~~~~~~l~~~~~~~--~~~k~lv~~~~~~~~~~~~~~l~~~-~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~  294 (369)
                      +.+.|.+...+++...  .++.+|+.+|.+.....+.+.|+.. +.++..+|+++++.+|...+.+..+|+.+|+|+|..
T Consensus       226 TGSGKTEvYl~~i~~~L~~GkqvLvLVPEI~Ltpq~~~rf~~rFg~~v~vlHS~Ls~~er~~~W~~~~~G~~~vVIGtRS  305 (730)
T COG1198         226 TGSGKTEVYLEAIAKVLAQGKQVLVLVPEIALTPQLLARFKARFGAKVAVLHSGLSPGERYRVWRRARRGEARVVIGTRS  305 (730)
T ss_pred             CCCcHHHHHHHHHHHHHHcCCEEEEEeccccchHHHHHHHHHHhCCChhhhcccCChHHHHHHHHHHhcCCceEEEEech
Confidence            3344555555544432  3468999999999888887777655 789999999999999999999999999999999975


Q ss_pred             CcCCCCCCCCcEEEEe
Q 017573          295 LARGIDVQQVSLVINY  310 (369)
Q Consensus       295 ~~~G~d~~~~~~vi~~  310 (369)
                      + .=..++++..||+.
T Consensus       306 A-lF~Pf~~LGLIIvD  320 (730)
T COG1198         306 A-LFLPFKNLGLIIVD  320 (730)
T ss_pred             h-hcCchhhccEEEEe
Confidence            3 23456677777754

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

Probab=94.48  E-value=0.38  Score=48.04  Aligned_cols=78  Identities=14%  Similarity=0.230  Sum_probs=64.8

Q ss_pred             ccCCCeEEEeCCHhhH----HHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEec-CCcCCCCCCCCcEE
Q 017573          233 LAITQSVIFVNTRRKV----DWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTD-LLARGIDVQQVSLV  307 (369)
Q Consensus       233 ~~~~k~lv~~~~~~~~----~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~-~~~~G~d~~~~~~v  307 (369)
                      ..++.+.|.+|+.=-|    +.+.+.++...+++..++.-.+.++...+++...+|.++|+|+|- .++.++-+.++-.+
T Consensus       641 ~~GKQVAvLVPTTlLA~QHy~tFkeRF~~fPV~I~~LSRF~s~kE~~~il~~la~G~vDIvIGTHrLL~kdv~FkdLGLl  720 (1139)
T COG1197         641 MDGKQVAVLVPTTLLAQQHYETFKERFAGFPVRIEVLSRFRSAKEQKEILKGLAEGKVDIVIGTHRLLSKDVKFKDLGLL  720 (1139)
T ss_pred             cCCCeEEEEcccHHhHHHHHHHHHHHhcCCCeeEEEecccCCHHHHHHHHHHHhcCCccEEEechHhhCCCcEEecCCeE
Confidence            3556889999996544    556666666688999999999999999999999999999999997 78888888888888


Q ss_pred             EEe
Q 017573          308 INY  310 (369)
Q Consensus       308 i~~  310 (369)
                      |+-
T Consensus       721 IID  723 (1139)
T COG1197         721 IID  723 (1139)
T ss_pred             EEe
Confidence            753

>PRK09087 hypothetical protein; Validated

Probab=94.47  E-value=0.16  Score=41.58  Aligned_cols=38  Identities=3%  Similarity=0.037  Sum_probs=23.4

Q ss_pred             cEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEEeeC
Q 017573          140 KMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATM  179 (369)
Q Consensus       140 ~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~saT~  179 (369)
                      +++++|++|.+.  .....+..+++.+......+.+|++.
T Consensus        89 ~~l~iDDi~~~~--~~~~~lf~l~n~~~~~g~~ilits~~  126 (226)
T PRK09087         89 GPVLIEDIDAGG--FDETGLFHLINSVRQAGTSLLMTSRL  126 (226)
T ss_pred             CeEEEECCCCCC--CCHHHHHHHHHHHHhCCCeEEEECCC
Confidence            489999999763  22456777776665533334445553

>KOG1807 consensus Helicases [Replication, recombination and repair]

Probab=94.45  E-value=0.051  Score=51.01  Aligned_cols=67  Identities=19%  Similarity=-0.018  Sum_probs=51.9

Q ss_pred             CcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhcc---CCCccEEEEcCCHHHHHHHHHHHH
Q 017573           19 PSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYG---LVQCQALVLAPTRELAQQIEKVMR   85 (369)
Q Consensus        19 ~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~---~~~~~~liv~P~~~l~~q~~~~~~   85 (369)
                      +-.-|+.|+......+-.++++|+|+|||++.+.++-..+...   ....+++++|-+..-+.|.-..+.
T Consensus       379 ldsSq~~A~qs~ltyelsliqgppGTgkt~vtlkav~tLL~n~s~~~~~epIlvvC~Tnhavdq~ligiy  448 (1025)
T KOG1807|consen  379 LDSSQQFAKQSKLTYELSLIQGPPGTGKTLVTLKAVDTLLLNSSGYTEPEPILVVCLTNHAVDQYLIGIY  448 (1025)
T ss_pred             ecHHHHHHHHHHhhhhhheeecCCCCCceeehHHHHHHHHhcccccccccceeeeehhhHHHHHHHHHHH
Confidence            4456999999888899999999999999998877766665443   112279999999888888766554

>KOG0737 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=94.44  E-value=0.91  Score=39.35  Aligned_cols=19  Identities=26%  Similarity=0.286  Sum_probs=16.8

Q ss_pred             cCCcEEEEcCCCChhhHHH
Q 017573           32 KGLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~   50 (369)
                      ..+++++.+|+|+|||..+
T Consensus       126 p~kGiLL~GPpG~GKTmlA  144 (386)
T KOG0737|consen  126 PPKGILLYGPPGTGKTMLA  144 (386)
T ss_pred             CCccceecCCCCchHHHHH
Confidence            4588999999999999876

>PRK05917 DNA polymerase III subunit delta'; Validated

Probab=94.44  E-value=0.48  Score=40.16  Aligned_cols=43  Identities=19%  Similarity=0.232  Sum_probs=29.1

Q ss_pred             CCccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEEeeCC
Q 017573          137 DYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMP  180 (369)
Q Consensus       137 ~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~saT~~  180 (369)
                      ...+++|+|++|.+.... ...+.+++..-|+...++++|..+.
T Consensus        94 ~~~kv~ii~~ad~mt~~A-aNaLLK~LEEPp~~~~fiL~~~~~~  136 (290)
T PRK05917         94 SPYKIYIIHEADRMTLDA-ISAFLKVLEDPPQHGVIILTSAKPQ  136 (290)
T ss_pred             CCceEEEEechhhcCHHH-HHHHHHHhhcCCCCeEEEEEeCChh
Confidence            346899999999986433 5566666666666666666665543

>PF06309 Torsin: Torsin; InterPro: IPR010448 This family consists of several eukaryotic torsin proteins

Probab=94.44  E-value=0.19  Score=36.43  Aligned_cols=51  Identities=12%  Similarity=0.057  Sum_probs=32.9

Q ss_pred             EEEcCCCChhhHHHHHHHHHhhhccCCCccEEEE-----cCCHHHHHHHHHHHHHh
Q 017573           37 IQQAQSGTGKTATFCSGILQQLDYGLVQCQALVL-----APTRELAQQIEKVMRAL   87 (369)
Q Consensus        37 li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv-----~P~~~l~~q~~~~~~~~   87 (369)
                      -+.|+||+|||.++-+.+-+....+....-+...     .|....+.+-.++++++
T Consensus        57 SfHG~tGtGKn~v~~liA~~ly~~G~~S~~V~~f~~~~hFP~~~~v~~Yk~~L~~~  112 (127)
T PF06309_consen   57 SFHGWTGTGKNFVSRLIAEHLYKSGMKSPFVHQFIATHHFPHNSNVDEYKEQLKSW  112 (127)
T ss_pred             EeecCCCCcHHHHHHHHHHHHHhcccCCCceeeecccccCCCchHHHHHHHHHHHH
Confidence            4899999999999877766666665544333222     35556665555555554

Torsion dystonia is an autosomal dominant movement disorder characterised by involuntary, repetitive muscle contractions and twisted postures. The most severe early-onset form of dystonia has been linked to mutations in the human DYT1 (TOR1A) gene encoding a protein termed torsinA. While causative genetic alterations have been identified, the function of torsin proteins and the molecular mechanism underlying dystonia remain unknown. Phylogenetic analysis of the torsin protein family indicates these proteins share distant sequence similarity with the large and diverse family of AAA ATPase, central region containing proteins () proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia [].; GO: 0005524 ATP binding, 0051085 chaperone mediated protein folding requiring cofactor

>PF01637 Arch_ATPase: Archaeal ATPase; InterPro: IPR011579 This domain has been found in a number of bacterial and archaeal proteins, all of which contain a conserved P-loop motif that is involved in binding ATP

Probab=94.41  E-value=0.048  Score=44.87  Aligned_cols=25  Identities=20%  Similarity=0.403  Sum_probs=18.4

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhh
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQL   58 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~   58 (369)
                      ++.++|.||.|+|||.. +..+...+
T Consensus        20 ~~~~~l~G~rg~GKTsL-l~~~~~~~   44 (234)
T PF01637_consen   20 SQHILLYGPRGSGKTSL-LKEFINEL   44 (234)
T ss_dssp             SSEEEEEESTTSSHHHH-HHHHHHHC
T ss_pred             CcEEEEEcCCcCCHHHH-HHHHHHHh
Confidence            47789999999999975 33444444

; GO: 0005524 ATP binding; PDB: 2FNA_A 2QEN_A.

>PRK04841 transcriptional regulator MalT; Provisional

Probab=94.39  E-value=0.22  Score=50.34  Aligned_cols=41  Identities=15%  Similarity=0.302  Sum_probs=32.4

Q ss_pred             cEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEEeeCC
Q 017573          140 KMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMP  180 (369)
Q Consensus       140 ~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~saT~~  180 (369)
                      -++|+|++|.+.+......+..+....+++..+++.|-+.+
T Consensus       123 ~~lvlDD~h~~~~~~~~~~l~~l~~~~~~~~~lv~~sR~~~  163 (903)
T PRK04841        123 LYLVIDDYHLITNPEIHEAMRFFLRHQPENLTLVVLSRNLP  163 (903)
T ss_pred             EEEEEeCcCcCCChHHHHHHHHHHHhCCCCeEEEEEeCCCC
Confidence            58999999998656556678888888888888888777643

>PF03266 NTPase_1: NTPase; InterPro: IPR004948 This entry represents a family of nucleoside-triphosphatases which have activity towards ATP, GTP, CTP, TTP and UTP and may hydrolyse nucleoside diphosphates with lower efficiency []

Probab=94.39  E-value=0.023  Score=44.10  Aligned_cols=34  Identities=24%  Similarity=0.388  Sum_probs=19.4

Q ss_pred             CccEEEEechhHhh--ccCcHHHHHHHHhhCCccCcEEE
Q 017573          138 YIKMFVLDEADEML--SRGFKDQIYDIFQLLPAKVQVGV  174 (369)
Q Consensus       138 ~~~~viiDE~H~~~--~~~~~~~~~~~~~~~~~~~~~i~  174 (369)
                      .-+++|+||+=.+.  ...|.+.+..+++   +...+++
T Consensus        95 ~~~liviDEIG~mEl~~~~F~~~v~~~l~---s~~~vi~  130 (168)
T PF03266_consen   95 SSDLIVIDEIGKMELKSPGFREAVEKLLD---SNKPVIG  130 (168)
T ss_dssp             CCHEEEE---STTCCC-CHHHHHHHHHHC---TTSEEEE
T ss_pred             CCCEEEEeccchhhhcCHHHHHHHHHHHc---CCCcEEE
Confidence            35899999998774  4456666666666   3444554

It includes proteins from bacteria to human, and the function was determined first in a hyperthermophilic bacterium to be an NTPase []. The structure of one member-sequence represents a variation of the RecA fold, and implies that the function might be that of a DNA/RNA modifying enzyme []. The sequence carries both a Walker A and Walker B motif which together are characteristic of ATPases or GTPases. The protein exhibits an increased expression profile in human liver cholangiocarcinoma when compared to normal tissue [].; GO: 0005524 ATP binding, 0016740 transferase activity, 0019204 nucleotide phosphatase activity; PDB: 1YE8_A 2I3B_A.

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.37  E-value=0.25  Score=43.98  Aligned_cols=20  Identities=20%  Similarity=0.104  Sum_probs=16.1

Q ss_pred             CcEEEEcCCCChhhHHHHHH
Q 017573           34 LDVIQQAQSGTGKTATFCSG   53 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~   53 (369)
                      ...+++||+|+|||..+...
T Consensus        40 ~~~L~~G~~G~GKt~~a~~l   59 (367)
T PRK14970         40 QALLFCGPRGVGKTTCARIL   59 (367)
T ss_pred             eEEEEECCCCCCHHHHHHHH
Confidence            36889999999999776443

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=94.35  E-value=0.35  Score=48.21  Aligned_cols=78  Identities=21%  Similarity=0.276  Sum_probs=64.2

Q ss_pred             cCCCeEEEeCCHhhHHHHHHHHhhC----CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEec-CCcCCCCCCCCcEEE
Q 017573          234 AITQSVIFVNTRRKVDWLTDKMRSR----DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTD-LLARGIDVQQVSLVI  308 (369)
Q Consensus       234 ~~~k~lv~~~~~~~~~~~~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~-~~~~G~d~~~~~~vi  308 (369)
                      .+.++++.+|+...|...++.+++.    +.++..+++..+..++.++++.+.+|+.+|+|+|. .+...+.+.++..+|
T Consensus       499 ~g~qvlvLvPT~~LA~Q~~~~f~~~~~~~~i~v~~Lsg~~~~~e~~~~~~~l~~g~~dIVIGTp~ll~~~v~f~~L~llV  578 (926)
T TIGR00580       499 DGKQVAVLVPTTLLAQQHFETFKERFANFPVTIELLSRFRSAKEQNEILKELASGKIDILIGTHKLLQKDVKFKDLGLLI  578 (926)
T ss_pred             hCCeEEEEeCcHHHHHHHHHHHHHHhccCCcEEEEEeccccHHHHHHHHHHHHcCCceEEEchHHHhhCCCCcccCCEEE
Confidence            3468999999999998887776653    56788999999999999999999999999999998 444557778888887


Q ss_pred             Eec
Q 017573          309 NYD  311 (369)
Q Consensus       309 ~~~  311 (369)
                      +-.
T Consensus       579 IDE  581 (926)
T TIGR00580       579 IDE  581 (926)
T ss_pred             eec
Confidence            654

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.

>COG0541 Ffh Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=94.32  E-value=1  Score=40.02  Aligned_cols=130  Identities=15%  Similarity=0.226  Sum_probs=71.9

Q ss_pred             EEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCC--HHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHcc
Q 017573           36 VIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPT--RELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQA  113 (369)
Q Consensus        36 ~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~--~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~  113 (369)
                      ++.++=-|||||+++.-.+......   +.++++|+.-  |.-+.   ++++.+....+..+.....+.. +.+      
T Consensus       103 ImmvGLQGsGKTTt~~KLA~~lkk~---~~kvllVaaD~~RpAA~---eQL~~La~q~~v~~f~~~~~~~-Pv~------  169 (451)
T COG0541         103 ILMVGLQGSGKTTTAGKLAKYLKKK---GKKVLLVAADTYRPAAI---EQLKQLAEQVGVPFFGSGTEKD-PVE------  169 (451)
T ss_pred             EEEEeccCCChHhHHHHHHHHHHHc---CCceEEEecccCChHHH---HHHHHHHHHcCCceecCCCCCC-HHH------
Confidence            7888999999998875555443332   2377777642  23332   3344443334555544311111 111      


Q ss_pred             CCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhh-ccCcHHHHHHHHhhCCccCcEEEEEeeCChhHHHHHHHh
Q 017573          114 GVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEML-SRGFKDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKF  190 (369)
Q Consensus       114 ~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~-~~~~~~~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~  190 (369)
                            ..-+. ......     ..+|++|+|=+-++. +...-.++..+...+.+.--++.+-|+...+.......|
T Consensus       170 ------Iak~a-l~~ak~-----~~~DvvIvDTAGRl~ide~Lm~El~~Ik~~~~P~E~llVvDam~GQdA~~~A~aF  235 (451)
T COG0541         170 ------IAKAA-LEKAKE-----EGYDVVIVDTAGRLHIDEELMDELKEIKEVINPDETLLVVDAMIGQDAVNTAKAF  235 (451)
T ss_pred             ------HHHHH-HHHHHH-----cCCCEEEEeCCCcccccHHHHHHHHHHHhhcCCCeEEEEEecccchHHHHHHHHH
Confidence                  00111 122222     236889999887654 444557777777788777767777887776655554443

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=94.25  E-value=0.24  Score=48.56  Aligned_cols=18  Identities=33%  Similarity=0.292  Sum_probs=15.7

Q ss_pred             CCcEEEEcCCCChhhHHH
Q 017573           33 GLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~   50 (369)
                      .+.+++.||+|+|||..+
T Consensus       487 ~~giLL~GppGtGKT~la  504 (733)
T TIGR01243       487 PKGVLLFGPPGTGKTLLA  504 (733)
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            467999999999999775

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.

>PF00437 T2SE: Type II/IV secretion system protein; InterPro: IPR001482 A number of bacterial proteins, some of which are involved in a general secretion pathway (GSP) for the export of proteins (also called the type II pathway) belong to this group [, ]

Probab=94.24  E-value=0.052  Score=46.00  Aligned_cols=42  Identities=14%  Similarity=0.290  Sum_probs=28.2

Q ss_pred             ccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHH
Q 017573           31 CKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRE   75 (369)
Q Consensus        31 ~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~   75 (369)
                      ..++++++.|+||||||..+ .+++..+...  ..+++.+-...+
T Consensus       125 ~~~~~ili~G~tGSGKTT~l-~all~~i~~~--~~~iv~iEd~~E  166 (270)
T PF00437_consen  125 RGRGNILISGPTGSGKTTLL-NALLEEIPPE--DERIVTIEDPPE  166 (270)
T ss_dssp             HTTEEEEEEESTTSSHHHHH-HHHHHHCHTT--TSEEEEEESSS-
T ss_pred             ccceEEEEECCCccccchHH-HHHhhhcccc--ccceEEeccccc
Confidence            34689999999999999765 5556565554  125666555444

These proteins are probably located in the cytoplasm and, on the basis of the presence of a conserved P-loop region IPR001687 from INTERPRO, bind ATP.; GO: 0005524 ATP binding, 0006810 transport, 0005622 intracellular; PDB: 1NLZ_C 2PT7_B 1OPX_A 1NLY_A 1G6O_B 2OAQ_2 2OAP_1 2JNQ_A 2JMZ_A 2GZA_B ....

>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases

Probab=94.24  E-value=0.091  Score=41.67  Aligned_cols=41  Identities=17%  Similarity=0.231  Sum_probs=29.0

Q ss_pred             CCcHhhhhhhhccc-cCCcEEEEcCCCChhhHHHHHHHHHhhh
Q 017573           18 KPSAIQQRGIVPFC-KGLDVIQQAQSGTGKTATFCSGILQQLD   59 (369)
Q Consensus        18 ~~~~~Q~~~~~~~~-~~~~~li~~~tG~GKT~~~~~~~~~~~~   59 (369)
                      .+.+.|.+.+.... .++.+++.+|||+|||..+ -+++..+.
T Consensus         9 ~~~~~~~~~l~~~v~~g~~i~I~G~tGSGKTTll-~aL~~~i~   50 (186)
T cd01130           9 TFSPLQAAYLWLAVEARKNILISGGTGSGKTTLL-NALLAFIP   50 (186)
T ss_pred             CCCHHHHHHHHHHHhCCCEEEEECCCCCCHHHHH-HHHHhhcC
Confidence            45666777776655 4688999999999999754 34444443

The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to plant cells. The pilus is a fibrous cell surface organelle, which mediates adhesion between bacteria during conjugative transfer or between bacteria and host eukaryotic cells during infection. VirB11- related ATPases include the archaeal flagella biosynthesis protein and the pilus assembly proteins CpaF/TadA and TrbB. This alignment contains the C-terminal domain, which is the ATPase.

>PHA03372 DNA packaging terminase subunit 1; Provisional

Probab=94.22  E-value=0.22  Score=46.10  Aligned_cols=127  Identities=16%  Similarity=0.124  Sum_probs=74.0

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHH----HHhccccCcEEEEEECCcchHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVM----RALGDYLGVKVHACVGGTSVREDQ  108 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~----~~~~~~~~~~v~~~~~~~~~~~~~  108 (369)
                      .+..+...|-.-|||.... +++..+...-.+-++.|++..+-..+-..+++    ++|.+...  +....+        
T Consensus       202 QkaTVFLVPRRHGKTWf~V-piIsllL~s~~gI~IGYvAHqKhvs~~Vf~EI~~~lrrwF~~~~--vi~~k~--------  270 (668)
T PHA03372        202 QKATVFLVPRRHGKTWFII-PIISFLLKNIIGISIGYVAHQKHVSQFVLKEVEFRCRRMFPRKH--TIENKD--------  270 (668)
T ss_pred             ccceEEEecccCCceehHH-HHHHHHHHhhcCceEEEEeeHHHHHHHHHHHHHHHHhhhcCccc--eeeecC--------
Confidence            4667888999999997643 44444444444558999999887666655544    44433211  111111        


Q ss_pred             HHHccCCcEEEecc-----HHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCC-ccCcEEEEEeeCC
Q 017573          109 RILQAGVHVVVGTP-----GRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLP-AKVQVGVFSATMP  180 (369)
Q Consensus       109 ~~~~~~~~iiv~t~-----~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~-~~~~~i~~saT~~  180 (369)
                            ..|.+.-|     -.+......+....+.++++++||+|-+.    ...+..++-.+. +++++|++|.|-.
T Consensus       271 ------~tI~~s~pg~Kst~~fasc~n~NsiRGQ~fnll~VDEA~FI~----~~a~~tilgfm~q~~~KiIfISS~Ns  338 (668)
T PHA03372        271 ------NVISIDHRGAKSTALFASCYNTNSIRGQNFHLLLVDEAHFIK----KDAFNTILGFLAQNTTKIIFISSTNT  338 (668)
T ss_pred             ------cEEEEecCCCcceeeehhhccCccccCCCCCEEEEehhhccC----HHHHHHhhhhhcccCceEEEEeCCCC
Confidence                  11222211     11123344456677789999999999763    234444544443 4677899888853

>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP)

Probab=94.22  E-value=0.081  Score=44.50  Aligned_cols=46  Identities=17%  Similarity=0.242  Sum_probs=30.3

Q ss_pred             HHHhCCCCCCcHhhhhhhhcccc--CCcEEEEcCCCChhhHHHHHHHHHhhh
Q 017573           10 GIYAYGFEKPSAIQQRGIVPFCK--GLDVIQQAQSGTGKTATFCSGILQQLD   59 (369)
Q Consensus        10 ~l~~~~~~~~~~~Q~~~~~~~~~--~~~~li~~~tG~GKT~~~~~~~~~~~~   59 (369)
                      .|.+.|+   .+.|.+.+..+..  +..+++.+|||||||..+ .+++..+.
T Consensus        58 ~l~~lg~---~~~~~~~l~~~~~~~~GlilisG~tGSGKTT~l-~all~~i~  105 (264)
T cd01129          58 DLEKLGL---KPENLEIFRKLLEKPHGIILVTGPTGSGKTTTL-YSALSELN  105 (264)
T ss_pred             CHHHcCC---CHHHHHHHHHHHhcCCCEEEEECCCCCcHHHHH-HHHHhhhC
Confidence            3555553   5567777766554  346899999999999764 34444443

It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which contains an ATP binding site and a tetracysteine motif. This subgroup also includes PillB and HofB.

>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=94.18  E-value=0.041  Score=46.28  Aligned_cols=19  Identities=21%  Similarity=0.289  Sum_probs=16.2

Q ss_pred             CCcEEEEcCCCChhhHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~   51 (369)
                      ..|+++.+|||||||+.+.
T Consensus        97 KSNILLiGPTGsGKTlLAq  115 (408)
T COG1219          97 KSNILLIGPTGSGKTLLAQ  115 (408)
T ss_pred             eccEEEECCCCCcHHHHHH
Confidence            3679999999999998763

>PHA00350 putative assembly protein

Probab=94.13  E-value=0.61  Score=41.45  Aligned_cols=26  Identities=19%  Similarity=0.176  Sum_probs=19.9

Q ss_pred             EEEEcCCCChhhHHHHH-HHHHhhhcc
Q 017573           36 VIQQAQSGTGKTATFCS-GILQQLDYG   61 (369)
Q Consensus        36 ~li~~~tG~GKT~~~~~-~~~~~~~~~   61 (369)
                      .++.|.+|||||..++- .++.++.++
T Consensus         4 ~l~tG~pGSGKT~~aV~~~i~palk~G   30 (399)
T PHA00350          4 YAIVGRPGSYKSYEAVVYHIIPALKDG   30 (399)
T ss_pred             EEEecCCCCchhHHHHHHHHHHHHHCC
Confidence            47899999999988775 466666555

>KOG0729 consensus 26S proteasome regulatory complex, ATPase RPT1 [Posttranslational modification, protein turnover, chaperones]

Probab=94.13  E-value=0.18  Score=41.46  Aligned_cols=41  Identities=22%  Similarity=0.183  Sum_probs=28.0

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQI   80 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~   80 (369)
                      .+.+++.+|+|+|||+++      +...+... -++|-+-.++|++..
T Consensus       211 pkgvllygppgtgktl~a------ravanrtd-acfirvigselvqky  251 (435)
T KOG0729|consen  211 PKGVLLYGPPGTGKTLCA------RAVANRTD-ACFIRVIGSELVQKY  251 (435)
T ss_pred             CCceEEeCCCCCchhHHH------HHHhcccC-ceEEeehhHHHHHHH
Confidence            589999999999999986      22222222 466666666776543

>KOG1513 consensus Nuclear helicase MOP-3/SNO (DEAD-box superfamily) [Transcription; Signal transduction mechanisms]

Probab=94.05  E-value=0.049  Score=51.40  Aligned_cols=63  Identities=24%  Similarity=0.381  Sum_probs=50.2

Q ss_pred             HHHHHhcCCCcEEEEecCCcCCCCCCCCcEE--------EEecCCCCccchhhhhcccccCCCc-eeEEEEe
Q 017573          277 IMREFRSGSSRVLITTDLLARGIDVQQVSLV--------INYDLPTQPENYLHRIGRSGRFGRK-GVAINFV  339 (369)
Q Consensus       277 ~~~~f~~~~~~vli~t~~~~~G~d~~~~~~v--------i~~~~~~~~~~~~Q~~GR~~R~~~~-~~~~~~~  339 (369)
                      --+.|.+|+..|-|-+.+.+.|+.+...+.|        |.+.+|||....+|.+||..|.++- +.-|+|.
T Consensus       849 EKqrFM~GeK~vAIISEAaSSGiSLQsDrRv~NqRRRvHiTLELPWSADrAIQQFGRTHRSNQVsaPEYvFl  920 (1300)
T KOG1513|consen  849 EKQRFMDGEKLVAIISEAASSGISLQSDRRVQNQRRRVHITLELPWSADRAIQQFGRTHRSNQVSAPEYVFL  920 (1300)
T ss_pred             HHhhhccccceeeeeehhhccCceeecchhhhhhhheEEEEEECCcchhHHHHHhcccccccccCCCeEEEE
Confidence            4467889999999999999999998765444        5688999999999999999998764 3344443

>KOG0780 consensus Signal recognition particle, subunit Srp54 [Intracellular trafficking, secretion, and vesicular transport]

Probab=94.01  E-value=0.27  Score=42.74  Aligned_cols=130  Identities=13%  Similarity=0.162  Sum_probs=71.1

Q ss_pred             EEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCH--HHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHcc
Q 017573           36 VIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTR--ELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQA  113 (369)
Q Consensus        36 ~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~--~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~  113 (369)
                      +.+.+=.|+|||.+..-.++.+-.++.   ++.++|.-.  +=+   .++++......++.+...+  +..+.       
T Consensus       104 imfVGLqG~GKTTtc~KlA~y~kkkG~---K~~LvcaDTFRagA---fDQLkqnA~k~~iP~ygsy--te~dp-------  168 (483)
T KOG0780|consen  104 IMFVGLQGSGKTTTCTKLAYYYKKKGY---KVALVCADTFRAGA---FDQLKQNATKARVPFYGSY--TEADP-------  168 (483)
T ss_pred             EEEEeccCCCcceeHHHHHHHHHhcCC---ceeEEeecccccch---HHHHHHHhHhhCCeeEecc--cccch-------
Confidence            688999999999887666655544444   777777542  222   2233332222234433311  11110       


Q ss_pred             CCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhh-ccCcHHHHHHHHhhCCccCcEEEEEeeCChhHHHHHHHh
Q 017573          114 GVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEML-SRGFKDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKF  190 (369)
Q Consensus       114 ~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~-~~~~~~~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~  190 (369)
                         +.|+     ..-+.+  +..++|++||+|-.-+.. +.+..+++..+.+.+.+..-++.+-|+...........+
T Consensus       169 ---v~ia-----~egv~~--fKke~fdvIIvDTSGRh~qe~sLfeEM~~v~~ai~Pd~vi~VmDasiGQaae~Qa~aF  236 (483)
T KOG0780|consen  169 ---VKIA-----SEGVDR--FKKENFDVIIVDTSGRHKQEASLFEEMKQVSKAIKPDEIIFVMDASIGQAAEAQARAF  236 (483)
T ss_pred             ---HHHH-----HHHHHH--HHhcCCcEEEEeCCCchhhhHHHHHHHHHHHhhcCCCeEEEEEeccccHhHHHHHHHH
Confidence               0011     011111  233457999999776653 233456667777777777767778888776655544433

>TIGR02012 tigrfam_recA protein RecA

Probab=93.99  E-value=0.14  Score=44.15  Aligned_cols=43  Identities=16%  Similarity=0.088  Sum_probs=31.2

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHH
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQ   79 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q   79 (369)
                      .-+.|.+|+|+|||..++..+.+....+.   +++|+..-.++..+
T Consensus        56 ~iteI~G~~GsGKTtLaL~~~~~~~~~g~---~v~yId~E~~~~~~   98 (321)
T TIGR02012        56 RIIEIYGPESSGKTTLALHAIAEAQKAGG---TAAFIDAEHALDPV   98 (321)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHcCC---cEEEEcccchhHHH
Confidence            55789999999999888777666655433   78888665554443

This model describes orthologs of the recA protein. RecA promotes hybridization of homolgous regions of DNA. A segment of ssDNA can be hybridized to another ssDNA region, or to a dsDNA region. ATP is hydrolyzed in the process. Part of the SOS respones, it is regulated by LexA via autocatalytic cleavage.

>PF13555 AAA_29: P-loop containing region of AAA domain

Probab=93.97  E-value=0.016  Score=36.13  Aligned_cols=18  Identities=22%  Similarity=0.418  Sum_probs=15.3

Q ss_pred             CCcEEEEcCCCChhhHHH
Q 017573           33 GLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~   50 (369)
                      +...++.+++|+|||...
T Consensus        23 g~~tli~G~nGsGKSTll   40 (62)
T PF13555_consen   23 GDVTLITGPNGSGKSTLL   40 (62)
T ss_pred             CcEEEEECCCCCCHHHHH
Confidence            457999999999999754

>COG1132 MdlB ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]

Probab=93.96  E-value=0.52  Score=44.79  Aligned_cols=21  Identities=29%  Similarity=0.368  Sum_probs=17.0

Q ss_pred             cccCCcEEEEcCCCChhhHHH
Q 017573           30 FCKGLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        30 ~~~~~~~li~~~tG~GKT~~~   50 (369)
                      +..|+.+-+.||+|+|||..+
T Consensus       352 i~~Ge~vaiVG~sGsGKSTl~  372 (567)
T COG1132         352 IEPGEKVAIVGPSGSGKSTLI  372 (567)
T ss_pred             EcCCCEEEEECCCCCCHHHHH
Confidence            446788889999999998654

>KOG0740 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=93.94  E-value=0.89  Score=40.61  Aligned_cols=78  Identities=22%  Similarity=0.202  Sum_probs=42.4

Q ss_pred             ccEEEEechhHhhccC-------c-HHHHHHHHhh----CCccCcEEEEEeeCChh-HHHHHHHhcCCCEEEEecCcccc
Q 017573          139 IKMFVLDEADEMLSRG-------F-KDQIYDIFQL----LPAKVQVGVFSATMPPE-ALEITRKFMNKPVRILVKRDELT  205 (369)
Q Consensus       139 ~~~viiDE~H~~~~~~-------~-~~~~~~~~~~----~~~~~~~i~~saT~~~~-~~~~~~~~~~~~~~~~~~~~~~~  205 (369)
                      ..++.+||+|.+...-       . ......+...    ..+..+++.++||-.+. ..+-+.+-+.             
T Consensus       246 PsvifidEidslls~Rs~~e~e~srr~ktefLiq~~~~~s~~~drvlvigaTN~P~e~Dea~~Rrf~-------------  312 (428)
T KOG0740|consen  246 PSVIFIDEIDSLLSKRSDNEHESSRRLKTEFLLQFDGKNSAPDDRVLVIGATNRPWELDEAARRRFV-------------  312 (428)
T ss_pred             CeEEEechhHHHHhhcCCcccccchhhhhHHHhhhccccCCCCCeEEEEecCCCchHHHHHHHHHhh-------------
Confidence            5788899999876321       1 1111111111    12345788889997553 3333333222             


Q ss_pred             ccceeEEEEEccchhhhHHHHHHHHHhc
Q 017573          206 LEGIKQFYVNVEKEEWKLETLCDLYETL  233 (369)
Q Consensus       206 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~  233 (369)
                          ...++..+........+..++...
T Consensus       313 ----kr~yiplPd~etr~~~~~~ll~~~  336 (428)
T KOG0740|consen  313 ----KRLYIPLPDYETRSLLWKQLLKEQ  336 (428)
T ss_pred             ----ceeeecCCCHHHHHHHHHHHHHhC
Confidence                233455566666777777777765

>PRK09165 replicative DNA helicase; Provisional

Probab=93.94  E-value=0.56  Score=43.49  Aligned_cols=116  Identities=11%  Similarity=0.037  Sum_probs=57.9

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhccC------------CCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEEC
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDYGL------------VQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVG  100 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~~~------------~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~  100 (369)
                      |.-++|.|.||.|||..++-.+.+......            .+.+++|++. ..-..|+..++-.......... ...+
T Consensus       217 g~livIaarpg~GKT~~al~ia~~~a~~~~~~~~~~~~~~~~~g~~vl~fSl-EMs~~ql~~R~la~~s~v~~~~-i~~~  294 (497)
T PRK09165        217 SDLIILAGRPSMGKTALATNIAFNAAKAYRREAQPDGSKKAVNGGVVGFFSL-EMSAEQLATRILSEQSEISSSK-IRRG  294 (497)
T ss_pred             CceEEEEeCCCCChHHHHHHHHHHHHHhhcccccccccccccCCCeEEEEeC-cCCHHHHHHHHHHHhcCCCHHH-HhcC
Confidence            455799999999999877665555443210            1235666653 3444555555533322211111 1112


Q ss_pred             CcchHHHHHHHc-----cCCcEEEe-----ccHHHHHHHHcCCCCCCCccEEEEechhHhh
Q 017573          101 GTSVREDQRILQ-----AGVHVVVG-----TPGRVFDMLRRQSLRPDYIKMFVLDEADEML  151 (369)
Q Consensus       101 ~~~~~~~~~~~~-----~~~~iiv~-----t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~  151 (369)
                      .....++.....     ....+.|-     |.+.+....++... ...+++||||=.|.+.
T Consensus       295 ~l~~~e~~~l~~a~~~l~~~~l~I~d~~~~ti~~i~~~ir~l~~-~~~~~lvvIDyLqli~  354 (497)
T PRK09165        295 KISEEDFEKLVDASQELQKLPLYIDDTPALSISQLRARARRLKR-QHGLDLLVVDYLQLIR  354 (497)
T ss_pred             CCCHHHHHHHHHHHHHHhcCCeEEeCCCCCCHHHHHHHHHHHHH-hcCCCEEEEcchHhcc
Confidence            222222221111     12345543     34455444433211 2347999999999775

>KOG0732 consensus AAA+-type ATPase containing the bromodomain [Posttranslational modification, protein turnover, chaperones]

Probab=93.93  E-value=0.43  Score=47.31  Aligned_cols=68  Identities=22%  Similarity=0.341  Sum_probs=40.3

Q ss_pred             EeccHHHHHHHHcCCCCCCCccEEEEechhHhhc----------cCcHHHHHHHHhhCCccCcEEEEEeeCChhHHHHH
Q 017573          119 VGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLS----------RGFKDQIYDIFQLLPAKVQVGVFSATMPPEALEIT  187 (369)
Q Consensus       119 v~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~----------~~~~~~~~~~~~~~~~~~~~i~~saT~~~~~~~~~  187 (369)
                      |+..+.=+.++.... ......++.+||++-+.-          .+....+..++..++...|++.++||..++..+-.
T Consensus       345 vgEaERqlrllFeeA-~k~qPSIIffdeIdGlapvrSskqEqih~SIvSTLLaLmdGldsRgqVvvigATnRpda~dpa  422 (1080)
T KOG0732|consen  345 VGEAERQLRLLFEEA-QKTQPSIIFFDEIDGLAPVRSSKQEQIHASIVSTLLALMDGLDSRGQVVVIGATNRPDAIDPA  422 (1080)
T ss_pred             cCcHHHHHHHHHHHH-hccCceEEeccccccccccccchHHHhhhhHHHHHHHhccCCCCCCceEEEcccCCccccchh
Confidence            344444344443322 222357899999994321          11224455566677889999999999887665433

>cd01394 radB RadB

Probab=93.89  E-value=0.092  Score=42.86  Aligned_cols=36  Identities=19%  Similarity=0.160  Sum_probs=27.1

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEc
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLA   71 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~   71 (369)
                      +.-+.+.+++|+|||..++..+.+....+.   +++|+.
T Consensus        19 g~i~~i~G~~GsGKT~l~~~~a~~~~~~g~---~v~yi~   54 (218)
T cd01394          19 GTVTQVYGPPGTGKTNIAIQLAVETAGQGK---KVAYID   54 (218)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhcCC---eEEEEE
Confidence            455899999999999888777666554433   788874

The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.

>PRK05595 replicative DNA helicase; Provisional

Probab=93.83  E-value=0.73  Score=42.19  Aligned_cols=115  Identities=17%  Similarity=0.145  Sum_probs=56.5

Q ss_pred             cccCCcEEEEcCCCChhhHHHHHHHHHhh-hccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEE-ECCcchHHH
Q 017573           30 FCKGLDVIQQAQSGTGKTATFCSGILQQL-DYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHAC-VGGTSVRED  107 (369)
Q Consensus        30 ~~~~~~~li~~~tG~GKT~~~~~~~~~~~-~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~-~~~~~~~~~  107 (369)
                      +..|.-++|.|.||.|||..++-.+.+.. ..+.   +++++..- .-..|+..++-....  ++....+ .+.....++
T Consensus       198 ~~~g~liviaarpg~GKT~~al~ia~~~a~~~g~---~vl~fSlE-ms~~~l~~R~~a~~~--~v~~~~~~~~~l~~~e~  271 (444)
T PRK05595        198 FQKGDMILIAARPSMGKTTFALNIAEYAALREGK---SVAIFSLE-MSKEQLAYKLLCSEA--NVDMLRLRTGNLEDKDW  271 (444)
T ss_pred             CCCCcEEEEEecCCCChHHHHHHHHHHHHHHcCC---cEEEEecC-CCHHHHHHHHHHHhc--CCCHHHHhcCCCCHHHH
Confidence            33456678999999999987766655433 3332   67777653 233444444332211  1211111 122222222


Q ss_pred             HHHHc-----cCCcEEEe-----ccHHHHHHHHcCCCCCCCccEEEEechhHhh
Q 017573          108 QRILQ-----AGVHVVVG-----TPGRVFDMLRRQSLRPDYIKMFVLDEADEML  151 (369)
Q Consensus       108 ~~~~~-----~~~~iiv~-----t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~  151 (369)
                      .....     ....+.|-     |.+.+....++... ..++++||+|=.|.+.
T Consensus       272 ~~~~~~~~~l~~~~l~i~d~~~~t~~~i~~~~r~~~~-~~~~~~vvIDylql~~  324 (444)
T PRK05595        272 ENIARASGPLAAAKIFIDDTAGVSVMEMRSKCRRLKI-EHGIDMILIDYLQLMS  324 (444)
T ss_pred             HHHHHHHHHHhcCCEEEECCCCCCHHHHHHHHHHHHH-hcCCCEEEEeHHHhcc
Confidence            11110     12234443     33444333333211 1337999999999875

>cd00983 recA RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=93.82  E-value=0.15  Score=43.99  Aligned_cols=43  Identities=14%  Similarity=0.088  Sum_probs=32.3

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHH
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQ   79 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q   79 (369)
                      .-+.+.+|+|+|||..++..+.+....+.   +++|+.+-.++-.+
T Consensus        56 ~iteI~Gp~GsGKTtLal~~~~~~~~~g~---~~vyId~E~~~~~~   98 (325)
T cd00983          56 RIIEIYGPESSGKTTLALHAIAEAQKLGG---TVAFIDAEHALDPV   98 (325)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHcCC---CEEEECccccHHHH
Confidence            45789999999999888777766655433   88998876665544

RecA couples ATP hydrolysis to DNA strand exchange.

>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C

Probab=93.80  E-value=0.2  Score=39.94  Aligned_cols=62  Identities=19%  Similarity=0.097  Sum_probs=37.9

Q ss_pred             hhhccc-cCCcEEEEcCCCChhhHHHHHHHHHhhhcc-------CCCccEEEEcCCHHHHHHHHHHHHHhc
Q 017573           26 GIVPFC-KGLDVIQQAQSGTGKTATFCSGILQQLDYG-------LVQCQALVLAPTRELAQQIEKVMRALG   88 (369)
Q Consensus        26 ~~~~~~-~~~~~li~~~tG~GKT~~~~~~~~~~~~~~-------~~~~~~liv~P~~~l~~q~~~~~~~~~   88 (369)
                      ++.-+. .|.-.++.||+|+|||..++-.+.+.....       ..+.+++++..-.. ..++.+.+....
T Consensus        24 li~g~~~~g~l~~i~g~~g~GKT~~~~~l~~~~~~g~~~~g~~~~~~~~Vl~i~~E~~-~~~~~~rl~~~~   93 (193)
T PF13481_consen   24 LIDGLLPRGELTLIAGPPGSGKTTLALQLAAALATGRPFLGELPPRPGRVLYISLEDS-ESQIARRLRALL   93 (193)
T ss_dssp             EETTEE-TTSEEEEEECSTSSHHHHHHHHHHHHHT---TT---------EEEEESSS--HHHHHHHHHHHH
T ss_pred             eECCcccCCeEEEEEeCCCCCHHHHHHHHHHHHHhCCccCCcccccCceEEEEeccCC-HHHHHHHHHHHh
Confidence            334444 567799999999999988766666555311       12347888876544 556667776654

>cd01131 PilT Pilus retraction ATPase PilT

Probab=93.80  E-value=0.099  Score=41.92  Aligned_cols=36  Identities=17%  Similarity=0.367  Sum_probs=22.0

Q ss_pred             cEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcC
Q 017573           35 DVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAP   72 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P   72 (369)
                      -+++.+|||||||... ..++..+..... .+++.+-.
T Consensus         3 lilI~GptGSGKTTll-~~ll~~~~~~~~-~~i~t~e~   38 (198)
T cd01131           3 LVLVTGPTGSGKSTTL-AAMIDYINKNKT-HHILTIED   38 (198)
T ss_pred             EEEEECCCCCCHHHHH-HHHHHHhhhcCC-cEEEEEcC
Confidence            4789999999999774 344444443222 24454443

PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism known as twitching motility.

>CHL00095 clpC Clp protease ATP binding subunit

Probab=93.80  E-value=0.26  Score=48.89  Aligned_cols=23  Identities=26%  Similarity=0.124  Sum_probs=18.1

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFCSGIL   55 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~   55 (369)
                      ..+.++.||+|+|||.++-..+.
T Consensus       200 ~~n~lL~G~pGvGKTal~~~la~  222 (821)
T CHL00095        200 KNNPILIGEPGVGKTAIAEGLAQ  222 (821)
T ss_pred             cCCeEEECCCCCCHHHHHHHHHH
Confidence            36899999999999987644433

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=93.79  E-value=0.057  Score=45.44  Aligned_cols=29  Identities=28%  Similarity=0.324  Sum_probs=22.3

Q ss_pred             hhhhhccccCCcEEEEcCCCChhhHHHHH
Q 017573           24 QRGIVPFCKGLDVIQQAQSGTGKTATFCS   52 (369)
Q Consensus        24 ~~~~~~~~~~~~~li~~~tG~GKT~~~~~   52 (369)
                      ++++..+..++++++.||+|+|||..+..
T Consensus        12 ~~~l~~l~~g~~vLL~G~~GtGKT~lA~~   40 (262)
T TIGR02640        12 SRALRYLKSGYPVHLRGPAGTGKTTLAMH   40 (262)
T ss_pred             HHHHHHHhcCCeEEEEcCCCCCHHHHHHH
Confidence            34444555689999999999999987643

Members of this family are the GvpN protein associated with the production of gas vesicles produced in some prokaryotes to give cells buoyancy. This family belongs to a larger family of ATPases (pfam07728).

>COG1074 RecB ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]

Probab=93.74  E-value=0.13  Score=52.68  Aligned_cols=56  Identities=30%  Similarity=0.391  Sum_probs=45.9

Q ss_pred             cCCcEEEEcCCCChhhHHHHHHHHHhhhcc--CCCccEEEEcCCHHHHHHHHHHHHHh
Q 017573           32 KGLDVIQQAQSGTGKTATFCSGILQQLDYG--LVQCQALVLAPTRELAQQIEKVMRAL   87 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~~~~~~~~~~~--~~~~~~liv~P~~~l~~q~~~~~~~~   87 (369)
                      .+++++|.|..|||||.+...-+++.+..+  -.-..+|+|+.|++-+..+..++.+-
T Consensus        15 ~~~~~lveASAGSGKT~vL~~r~lrlLl~~~~~~v~~ILvvTFT~aAa~Emk~RI~~~   72 (1139)
T COG1074          15 PGQSVLVEASAGTGKTFVLAERVLRLLLEGGPLDVDEILVVTFTKAAAAEMKERIRDR   72 (1139)
T ss_pred             CCCcEEEEEcCCCCchhHHHHHHHHHHhhcCCCChhHeeeeeccHHHHHHHHHHHHHH
Confidence            468999999999999999888888887764  23347999999999888888877653

>COG0464 SpoVK ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]

Probab=93.73  E-value=0.63  Score=43.35  Aligned_cols=20  Identities=30%  Similarity=0.222  Sum_probs=16.7

Q ss_pred             cCCcEEEEcCCCChhhHHHH
Q 017573           32 KGLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~   51 (369)
                      ..+.+++.||+|+|||+.+-
T Consensus       275 ~~~giLl~GpPGtGKT~lAk  294 (494)
T COG0464         275 PPKGVLLYGPPGTGKTLLAK  294 (494)
T ss_pred             CCCeeEEECCCCCCHHHHHH
Confidence            34689999999999998763

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=93.72  E-value=0.52  Score=40.94  Aligned_cols=38  Identities=11%  Similarity=0.234  Sum_probs=23.8

Q ss_pred             CccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEE
Q 017573          138 YIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFS  176 (369)
Q Consensus       138 ~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~s  176 (369)
                      ..+++|+||+|.+.... ...+.+.+...|+...+++.|
T Consensus        93 ~~kv~iI~~ad~m~~~a-~naLLK~LEepp~~t~~il~~  130 (313)
T PRK05564         93 DKKVIIIYNSEKMTEQA-QNAFLKTIEEPPKGVFIILLC  130 (313)
T ss_pred             CceEEEEechhhcCHHH-HHHHHHHhcCCCCCeEEEEEe
Confidence            46899999999885433 345555555555455455444

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=93.69  E-value=0.11  Score=42.73  Aligned_cols=38  Identities=16%  Similarity=0.181  Sum_probs=28.5

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCC
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPT   73 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~   73 (369)
                      |.-+.+.+++|+|||..++..+.+.+..+.   +++|+.--
T Consensus        23 g~i~~i~G~~GsGKT~l~~~la~~~~~~~~---~v~yi~~e   60 (225)
T PRK09361         23 GTITQIYGPPGSGKTNICLQLAVEAAKNGK---KVIYIDTE   60 (225)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHCCC---eEEEEECC
Confidence            456799999999999887777666655433   78887654

>PRK10436 hypothetical protein; Provisional

Probab=93.68  E-value=0.095  Score=47.74  Aligned_cols=40  Identities=23%  Similarity=0.227  Sum_probs=27.6

Q ss_pred             CcHhhhhhhhcccc--CCcEEEEcCCCChhhHHHHHHHHHhhh
Q 017573           19 PSAIQQRGIVPFCK--GLDVIQQAQSGTGKTATFCSGILQQLD   59 (369)
Q Consensus        19 ~~~~Q~~~~~~~~~--~~~~li~~~tG~GKT~~~~~~~~~~~~   59 (369)
                      +.+.|.+.+..+..  +.-+++.+|||||||... .+++..+.
T Consensus       202 ~~~~~~~~l~~~~~~~~GliLvtGpTGSGKTTtL-~a~l~~~~  243 (462)
T PRK10436        202 MTPAQLAQFRQALQQPQGLILVTGPTGSGKTVTL-YSALQTLN  243 (462)
T ss_pred             cCHHHHHHHHHHHHhcCCeEEEECCCCCChHHHH-HHHHHhhC
Confidence            35566667766553  466899999999999875 34454543

>PRK05636 replicative DNA helicase; Provisional

Probab=93.67  E-value=0.75  Score=42.65  Aligned_cols=114  Identities=15%  Similarity=0.116  Sum_probs=53.7

Q ss_pred             cCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEE-ECCcchHHHHHH
Q 017573           32 KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHAC-VGGTSVREDQRI  110 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~-~~~~~~~~~~~~  110 (369)
                      .|.-+++.|.||.|||..++-.+.+.....  +.++++++. .--..|+..++-....  ++....+ .+.....++.++
T Consensus       264 ~G~Liiiaarpg~GKT~~al~~a~~~a~~~--g~~v~~fSl-EMs~~ql~~R~ls~~s--~v~~~~i~~g~l~~~e~~~~  338 (505)
T PRK05636        264 GGQMIIVAARPGVGKSTLALDFMRSASIKH--NKASVIFSL-EMSKSEIVMRLLSAEA--EVRLSDMRGGKMDEDAWEKL  338 (505)
T ss_pred             CCceEEEEeCCCCCHHHHHHHHHHHHHHhC--CCeEEEEEe-eCCHHHHHHHHHHHhc--CCCHHHHhcCCCCHHHHHHH
Confidence            345578999999999987765554433222  125666643 2223333333322111  1111111 122222222211


Q ss_pred             H-----ccCCcEEEe-----ccHHHHHHHHcCCCCCCCccEEEEechhHhh
Q 017573          111 L-----QAGVHVVVG-----TPGRVFDMLRRQSLRPDYIKMFVLDEADEML  151 (369)
Q Consensus       111 ~-----~~~~~iiv~-----t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~  151 (369)
                      .     ..+..+.|-     |.+.+....++... ...+++||||=.|.+.
T Consensus       339 ~~a~~~l~~~~l~I~d~~~~ti~~I~~~~r~~~~-~~~~~lvvIDYLql~~  388 (505)
T PRK05636        339 VQRLGKIAQAPIFIDDSANLTMMEIRSKARRLKQ-KHDLKLIVVDYLQLMS  388 (505)
T ss_pred             HHHHHHHhcCCEEEECCCCCCHHHHHHHHHHHHH-hcCCCEEEEcchHhcC
Confidence            1     112345553     33344333332111 1237999999999875

>PRK10865 protein disaggregation chaperone; Provisional

Probab=93.65  E-value=0.43  Score=47.44  Aligned_cols=22  Identities=23%  Similarity=0.169  Sum_probs=17.4

Q ss_pred             CcEEEEcCCCChhhHHHHHHHH
Q 017573           34 LDVIQQAQSGTGKTATFCSGIL   55 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~   55 (369)
                      .+.++.||+|+|||..+-..+.
T Consensus       200 ~n~lL~G~pGvGKT~l~~~la~  221 (857)
T PRK10865        200 NNPVLIGEPGVGKTAIVEGLAQ  221 (857)
T ss_pred             CceEEECCCCCCHHHHHHHHHH
Confidence            5899999999999987643333

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=93.58  E-value=0.47  Score=47.27  Aligned_cols=19  Identities=26%  Similarity=0.314  Sum_probs=16.3

Q ss_pred             CcEEEEcCCCChhhHHHHH
Q 017573           34 LDVIQQAQSGTGKTATFCS   52 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~   52 (369)
                      .+.++.||+|+|||.++-.
T Consensus       195 ~n~lL~G~pGvGKT~l~~~  213 (852)
T TIGR03346       195 NNPVLIGEPGVGKTAIVEG  213 (852)
T ss_pred             CceEEEcCCCCCHHHHHHH
Confidence            6889999999999977643

Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins.

>KOG1132 consensus Helicase of the DEAD superfamily [Replication, recombination and repair]

Probab=93.57  E-value=1.9  Score=41.74  Aligned_cols=42  Identities=19%  Similarity=0.336  Sum_probs=33.3

Q ss_pred             hCCCCCCcHhhhhhhhccc----cCCcEEEEcCCCChhhHHHHHHHH
Q 017573           13 AYGFEKPSAIQQRGIVPFC----KGLDVIQQAQSGTGKTATFCSGIL   55 (369)
Q Consensus        13 ~~~~~~~~~~Q~~~~~~~~----~~~~~li~~~tG~GKT~~~~~~~~   55 (369)
                      .|+| +||+.|......++    ...+.++..|||+|||++.+-..+
T Consensus        17 ~fP~-qpY~~Q~a~M~rvl~~L~~~q~~llESPTGTGKSLsLLCS~L   62 (945)
T KOG1132|consen   17 EFPF-QPYPTQLAFMTRVLSCLDRKQNGLLESPTGTGKSLSLLCSTL   62 (945)
T ss_pred             eccC-CcchHHHHHHHHHHHHHHHhhhhhccCCCCCCccHHHHHHHH
Confidence            4676 78999988777665    458899999999999987654444

>PF08423 Rad51: Rad51; InterPro: IPR013632 This domain is found at the C terminus of the DNA repair and recombination protein Rad51

Probab=93.56  E-value=0.18  Score=42.15  Aligned_cols=41  Identities=15%  Similarity=0.058  Sum_probs=26.5

Q ss_pred             cEEEEcCCCChhhHHHHHHHHHhh-hc--cCCCccEEEEcCCHH
Q 017573           35 DVIQQAQSGTGKTATFCSGILQQL-DY--GLVQCQALVLAPTRE   75 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~~~~~~~~-~~--~~~~~~~liv~P~~~   75 (369)
                      =.=+++|.|+|||-.++..++... ..  +..+.+++|+.-...
T Consensus        40 itEi~G~~gsGKTql~l~l~~~~~l~~~~~g~~~~vvyidTe~~   83 (256)
T PF08423_consen   40 ITEIVGESGSGKTQLCLQLAVNVQLPEEIGGLGGKVVYIDTEGT   83 (256)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHTTSGGCTTSSSSEEEEEESSSS
T ss_pred             EEEEEEecccccchHHHHHHHHhhcccccccCCCceEEEeCCCC
Confidence            356899999999966655444433 22  233447999875543

It is critical for DNA binding []. Rad51 is a homologue of the bacterial RecA protein. Rad51 and RecA share a core ATPase domain.; PDB: 2ZUC_A 2Z43_C 2ZUD_B 2DFL_A 2ZUB_A 2BKE_A 2KZ3_A 2CVH_B 2CVF_B 1SZP_D ....

>PRK06321 replicative DNA helicase; Provisional

Probab=93.53  E-value=1.5  Score=40.39  Aligned_cols=113  Identities=17%  Similarity=0.073  Sum_probs=56.6

Q ss_pred             cCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEE-ECCcchHHHHH-
Q 017573           32 KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHAC-VGGTSVREDQR-  109 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~-~~~~~~~~~~~-  109 (369)
                      .|.-++|.|.||.|||..++-.+.+.....  +.++++++. .--..|+..++-....  ++....+ .+.....++.+ 
T Consensus       225 ~G~LiiiaarPgmGKTafal~ia~~~a~~~--g~~v~~fSL-EMs~~ql~~Rlla~~s--~v~~~~i~~~~l~~~e~~~~  299 (472)
T PRK06321        225 PSNLMILAARPAMGKTALALNIAENFCFQN--RLPVGIFSL-EMTVDQLIHRIICSRS--EVESKKISVGDLSGRDFQRI  299 (472)
T ss_pred             CCcEEEEEeCCCCChHHHHHHHHHHHHHhc--CCeEEEEec-cCCHHHHHHHHHHhhc--CCCHHHhhcCCCCHHHHHHH
Confidence            346678999999999987766544433221  125666653 2334444444432211  2221111 12222223321 


Q ss_pred             -----HHccCCcEEEe-----ccHHHHHHHHcCCCCCCCccEEEEechhHhh
Q 017573          110 -----ILQAGVHVVVG-----TPGRVFDMLRRQSLRPDYIKMFVLDEADEML  151 (369)
Q Consensus       110 -----~~~~~~~iiv~-----t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~  151 (369)
                           .+. +..+.|-     |.+.+....++-.. ...+++||||=.+.+.
T Consensus       300 ~~a~~~l~-~~~~~idd~~~~ti~~i~~~~r~~~~-~~~~~lvvIDyLql~~  349 (472)
T PRK06321        300 VSVVNEMQ-EHTLLIDDQPGLKITDLRARARRMKE-SYDIQFLIIDYLQLLS  349 (472)
T ss_pred             HHHHHHHH-cCCEEEeCCCCCCHHHHHHHHHHHHH-hcCCCEEEEcchHHcC
Confidence                 122 2345554     44455443333211 2347899999999875

>cd01125 repA Hexameric Replicative Helicase RepA

Probab=93.51  E-value=0.82  Score=37.90  Aligned_cols=37  Identities=19%  Similarity=0.034  Sum_probs=25.0

Q ss_pred             cEEEEcCCCChhhHHHHHHHHHhhh---------ccCCCccEEEEc
Q 017573           35 DVIQQAQSGTGKTATFCSGILQQLD---------YGLVQCQALVLA   71 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~~~~~~~~~---------~~~~~~~~liv~   71 (369)
                      -.++.||.|+|||..++..++....         ....+.+++|+.
T Consensus         3 ~~ll~g~~G~GKS~lal~la~~va~G~~~~g~~~~~~~~~~Vlyi~   48 (239)
T cd01125           3 VSALVAPGGTGKSSLLLVLALAMALGKNLFGGGLKVTEPGRVVYLS   48 (239)
T ss_pred             eeEEEcCCCCCHHHHHHHHHHHHhcCccccCCccccCCCceEEEEE
Confidence            4689999999999887766554321         111233788888

RepA is encoded by a plasmid, which is found in most Gram negative bacteria. RepA is a 5'-3' DNA helicase which can utilize ATP, GTP and CTP to a lesser extent.

>KOG0744 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=93.41  E-value=0.84  Score=38.89  Aligned_cols=67  Identities=19%  Similarity=0.264  Sum_probs=37.2

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhcc---CCCccEEEEcCCH-----------HHHHHHHHHHHHhccccCcEEEEE
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDYG---LVQCQALVLAPTR-----------ELAQQIEKVMRALGDYLGVKVHAC   98 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~~---~~~~~~liv~P~~-----------~l~~q~~~~~~~~~~~~~~~v~~~   98 (369)
                      ++-++++||+|+|||.. +-++++.+.-.   ......+|=..+-           -|+.++.+.+.++...-+.-|.++
T Consensus       177 NRliLlhGPPGTGKTSL-CKaLaQkLSIR~~~~y~~~~liEinshsLFSKWFsESgKlV~kmF~kI~ELv~d~~~lVfvL  255 (423)
T KOG0744|consen  177 NRLILLHGPPGTGKTSL-CKALAQKLSIRTNDRYYKGQLIEINSHSLFSKWFSESGKLVAKMFQKIQELVEDRGNLVFVL  255 (423)
T ss_pred             eeEEEEeCCCCCChhHH-HHHHHHhheeeecCccccceEEEEehhHHHHHHHhhhhhHHHHHHHHHHHHHhCCCcEEEEE
Confidence            46689999999999954 44555554211   1111234434333           345555555555555555556555


Q ss_pred             EC
Q 017573           99 VG  100 (369)
Q Consensus        99 ~~  100 (369)
                      ..
T Consensus       256 ID  257 (423)
T KOG0744|consen  256 ID  257 (423)
T ss_pred             eH
Confidence            53

>KOG0701 consensus dsRNA-specific nuclease Dicer and related ribonucleases [RNA processing and modification]

Probab=93.32  E-value=0.045  Score=56.24  Aligned_cols=93  Identities=26%  Similarity=0.404  Sum_probs=75.8

Q ss_pred             CeEEEeCCHhhHHHHHHHHhhCCC-eeEEecCCCC-----------HHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCC
Q 017573          237 QSVIFVNTRRKVDWLTDKMRSRDH-TVSATHGDMD-----------QNTRDIIMREFRSGSSRVLITTDLLARGIDVQQV  304 (369)
Q Consensus       237 k~lv~~~~~~~~~~~~~~l~~~~~-~~~~~~~~~~-----------~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~  304 (369)
                      ..++|++....+....+.+...+. .+..+.|.+.           ...+.+++..|.....++|++|.++.+|+|++.+
T Consensus       294 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~k~~~~~~~~~~~~vl~~~~~~~ln~L~~~~~~~e~~d~~~~  373 (1606)
T KOG0701|consen  294 SGIIFVDQRYTAYVLLELLREIFSNDPLFVTGASGANLWKSFKNELELRQAEVLRRFHFHELNLLIATSVLEEGVDVPKC  373 (1606)
T ss_pred             hheeecccchHHHHHHHHHHHhhccCcceeeccccCccchhhHHHHHhhhHHHHHHHhhhhhhHHHHHHHHHhhcchhhh
Confidence            458999999999998888876632 3333444321           2235778888888999999999999999999999


Q ss_pred             cEEEEecCCCCccchhhhhcccccC
Q 017573          305 SLVINYDLPTQPENYLHRIGRSGRF  329 (369)
Q Consensus       305 ~~vi~~~~~~~~~~~~Q~~GR~~R~  329 (369)
                      +.++.++.+.....|+|..||+.+.
T Consensus       374 ~~~~~~~~~~~~~~~vq~~~r~~~~  398 (1606)
T KOG0701|consen  374 NLVVLFDAPTYYRSYVQKKGRARAA  398 (1606)
T ss_pred             hhheeccCcchHHHHHHhhcccccc
Confidence            9999999999999999999999765

>KOG2228 consensus Origin recognition complex, subunit 4 [Replication, recombination and repair]

Probab=93.28  E-value=1.7  Score=37.33  Aligned_cols=65  Identities=17%  Similarity=0.379  Sum_probs=33.7

Q ss_pred             HHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCc-cCcEEEEEeeCChhHHHHHH
Q 017573          124 RVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPA-KVQVGVFSATMPPEALEITR  188 (369)
Q Consensus       124 ~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~-~~~~i~~saT~~~~~~~~~~  188 (369)
                      .++..+..+....+.--++|+||++-+.......-+.++++...+ ..++..+.-|-.-+..+..+
T Consensus       123 ~lL~~L~~~~~~t~~~ViFIldEfDlf~~h~rQtllYnlfDisqs~r~Piciig~Ttrld~lE~LE  188 (408)
T KOG2228|consen  123 KLLEALKKGDETTSGKVIFILDEFDLFAPHSRQTLLYNLFDISQSARAPICIIGVTTRLDILELLE  188 (408)
T ss_pred             HHHHHHhcCCCCCCceEEEEeehhhccccchhhHHHHHHHHHHhhcCCCeEEEEeeccccHHHHHH
Confidence            344444544333333346889999988766555555565555432 23344444444334444433

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	369
2zu6_A	388	Crystal Structure Of The Eif4a-Pdcd4 Complex Length		1e-156
3eiq_A	414	Crystal Structure Of Pdcd4-eif4a Length = 414		1e-155
2xb2_A	411	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		1e-148
2hyi_C	413	Structure Of The Human Exon Junction Complex With A		1e-148
2j0q_A	410	The Crystal Structure Of The Exon Junction Complex		1e-148
2hxy_A	391	Crystal Structure Of Human Apo-Eif4aiii Length = 39		1e-148
2j0u_B	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		1e-147
2j0u_A	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		1e-147
2vso_A	395	Crystal Structure Of A Translation Initiation Compl		1e-130
1fuu_A	394	Yeast Initiation Factor 4a Length = 394		1e-125
1s2m_A	400	Crystal Structure Of The Dead Box Protein Dhh1p Len		3e-79
3bor_A	237	Crystal Structure Of The Deadc Domain Of Human Tran		2e-78
2g9n_A	221	Structure Of The Dead Domain Of Human Eukaryotic In		2e-72
3pew_A	395	S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3		5e-72
3pey_A	395	S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length		7e-72
1qde_A	224	Crystal Structure Of The Atpase Domain Of Translati		7e-70
3fmp_B	479	Crystal Structure Of The Nucleoporin Nup214 In Comp		2e-69
3g0h_A	424	Human Dead-box Rna Helicase Ddx19, In Complex With		3e-69
1xtk_A	390	Structure Of Decd To Dead Mutation Of Human Uap56 L		3e-69
3ews_A	445	Human Dead-Box Rna-Helicase Ddx19 In Complex With A		3e-69
3fht_A	412	Crystal Structure Of Human Dbp5 In Complex With Amp		4e-69
1xti_A	391	Structure Of Wildtype Human Uap56 Length = 391		9e-69
1xtj_A	386	Structure Of Human Uap56 In Complex With Adp Length		1e-68
3fho_B	508	Structure Of S. Pombe Dbp5 Length = 508		5e-67
1qva_A	223	Yeast Initiation Factor 4a N-Terminal Domain Length		9e-65
1hv8_A	367	Crystal Structure Of A Dead Box Protein From The Hy		2e-56
1fuk_A	165	Crystal Structure Of The Carboxy Terminal Domain Of		2e-53
2i4i_A	417	Crystal Structure Of Human Dead-Box Rna Helicase Dd		1e-50
2db3_A	434	Structural Basis For Rna Unwinding By The Dead-Box		2e-48
2z0m_A	337	Crystal Structure Of Hypothetical Atp-Dependent Rna		7e-42
3sqx_A	512	Structure Of Mss116p (Nte And C-Tail Double Deletio		7e-37
3i5x_A	563	Structure Of Mss116p Bound To Ssrna And Amp-Pnp Len		9e-37
3sqw_A	579	Structure Of Mss116p (Nte Deletion) Bound To Ssrna		1e-36
2kbf_A	187	Solution Structure Of Carboxyl-Terminal Domain Of D		4e-36
1t6n_A	220	Crystal Structure Of The N-Terminal Domain Of Human		7e-36
2rb4_A	175	Crystal Structure Of The Helicase Domain Of Human D		1e-35
3peu_A	188	S. Cerevisiae Dbp5 L327v C-Terminal Domain Bound To		3e-35
1vec_A	206	Crystal Structure Of The N-Terminal Domain Of RckP5		3e-35
3gfp_A	189	Structure Of The C-Terminal Domain Of The Dead-Box		4e-35
2wax_A	193	Structure Of The Human Ddx6 C-Terminal Domain In Co		8e-34
2oxc_A	230	Human Dead-Box Rna Helicase Ddx20, Dead Domain In C		2e-32
2kbe_A	226	Solution Structure Of Amino-Terminal Domain Of Dbp5		9e-29
2gxq_A	207	Hera N-Terminal Domain In Complex With Amp, Crystal		3e-28
2hjv_A	163	Structure Of The Second Domain (Residues 207-368) O		3e-28
3mwj_A	207	Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Ap		6e-28
3fhc_B	235	Crystal Structure Of Human Dbp5 In Complex With Nup		2e-27
3fmo_B	300	Crystal Structure Of The Nucleoporin Nup214 In Comp		4e-27
1t5i_A	172	Crystal Structure Of The C-Terminal Domain Of Uap56		1e-25
3ber_A	249	Human Dead-Box Rna-Helicase Ddx47, Conserved Domain		2e-24
1wrb_A	253	Crystal Structure Of The N-Terminal Reca-Like Domai		4e-24
1q0u_A	219	Crystal Structure Of The Bstdead N-Terminal Domain		7e-23
2jgn_A	185	Ddx3 Helicase Domain Length = 185		5e-21
2yjt_D	170	Crystal Structure Of E. Coli Dead-Box Protein Srmb		2e-20
3fe2_A	242	Human Dead-Box Rna Helicase Ddx5 (P68), Conserved D		2e-20
4a4d_A	253	Crystal Structure Of The N-Terminal Domain Of The H		3e-20
3ly5_A	262	Ddx18 Dead-Domain Length = 262		5e-20
2p6n_A	191	Human Dead-box Rna Helicase Ddx41, Helicase Domain		1e-18
2pl3_A	236	Human Dead-Box Rna Helicase Ddx10, Dead Domain In C		2e-18
3iuy_A	228	Crystal Structure Of Ddx53 Dead-Box Domain Length =		2e-17
3i32_A	300	Dimeric Structure Of A Hera Helicase Fragment Inclu		3e-16
3eaq_A	212	Novel Dimerization Motif In The Dead Box Rna Helica		2e-15
4db4_A	256	Mss116p Dead-Box Helicase Domain 2 Bound To A Chima		7e-15
4db2_C	257	Mss116p Dead-Box Helicase Domain 2 Bound To An Rna		7e-15
4db2_A	257	Mss116p Dead-Box Helicase Domain 2 Bound To An Rna		8e-15
3dkp_A	245	Human Dead-Box Rna-Helicase Ddx52, Conserved Domain		2e-14
1oyy_A	523	Structure Of The Recq Catalytic Core Bound To Atp-G		3e-09
1oyw_A	523	Structure Of The Recq Catalytic Core Length = 523		4e-09
4gl2_A	699	Structural Basis For Dsrna Duplex Backbone Recognit		2e-05
1gm5_A	780	Structure Of Recg Bound To Three-Way Dna Junction L		1e-04
4ay2_A	687	Capturing 5' Tri-Phosphorylated Rna Duplex By Rig-I		2e-04
3tmi_A	695	Structural Basis For Rna Recognition And Activation		2e-04
2ykg_A	696	Structural Insights Into Rna Recognition By Rig-I L		2e-04
2v1x_A	591	Crystal Structure Of Human Recq-Like Dna Helicase L		2e-04
4i1s_A	243	Melanoma Differentiation Associated Protein-5 Helic		7e-04

>pdb|2ZU6|A Chain A, Crystal Structure Of The Eif4a-Pdcd4 Complex Length = 388

Iteration: 1
 Score =  548 bits (1411), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 276/370 (74%), Positives = 313/370 (84%), Gaps = 1/370 (0%)
Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
           M L E+LLRGIYAYGFEKPSAIQQR I+P  KG DVI QAQSGTGKTATF   ILQQ++ 
Sbjct: 19  MNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIEL 78
Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVR-EDQRILQAGVHVVV 119
            L   QALVLAPTRELAQQI+KV+ ALGDY+G   HAC+GGT+VR E Q++     H++V
Sbjct: 79  DLKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIV 138
Query: 120 GTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATM 179
           GTPGRVFDML R+ L P YIKMFVLDEADEMLSRGFKDQIYDIFQ L +  QV + SATM
Sbjct: 139 GTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVVLLSATM 198
Query: 180 PPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSV 239
           P + LE+T+KFM  P+RILVK++ELTLEGI+QFY+NVE+EEWKL+TLCDLYETL ITQ+V
Sbjct: 199 PSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLCDLYETLTITQAV 258
Query: 240 IFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGI 299
           IF+NTRRKVDWLT+KM +RD TVSA HGDMDQ  RD+IMREFRSGSSRVLITTDLLARGI
Sbjct: 259 IFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGI 318
Query: 300 DVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIE 359
           DVQQVSLVINYDLPT  ENY+HRIGR GRFGRKGVAIN VT +D+R L DI+ FYN  IE
Sbjct: 319 DVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTEEDKRTLRDIETFYNTSIE 378
Query: 360 ELPSNVADLL 369
           E+P NVADL+
Sbjct: 379 EMPLNVADLI 388

>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a Length = 414

Iteration: 1
 Score =  545 bits (1405), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 276/370 (74%), Positives = 313/370 (84%), Gaps = 1/370 (0%)
Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
           M L E+LLRGIYAYGFEKPSAIQQR I+P  KG DVI QAQSGTGKTATF   ILQQ++ 
Sbjct: 45  MNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIEL 104
Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVR-EDQRILQAGVHVVV 119
            L   QALVLAPTRELAQQI+KV+ ALGDY+G   HAC+GGT+VR E Q++     H++V
Sbjct: 105 DLKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIV 164
Query: 120 GTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATM 179
           GTPGRVFDML R+ L P YIKMFVLDEADEMLSRGFKDQIYDIFQ L +  QV + SATM
Sbjct: 165 GTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVVLLSATM 224
Query: 180 PPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSV 239
           P + LE+T+KFM  P+RILVK++ELTLEGI+QFY+NVE+EEWKL+TLCDLYETL ITQ+V
Sbjct: 225 PSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLCDLYETLTITQAV 284
Query: 240 IFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGI 299
           IF+NTRRKVDWLT+KM +RD TVSA HGDMDQ  RD+IMREFRSGSSRVLITTDLLARGI
Sbjct: 285 IFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGI 344
Query: 300 DVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIE 359
           DVQQVSLVINYDLPT  ENY+HRIGR GRFGRKGVAIN VT +D+R L DI+ FYN  IE
Sbjct: 345 DVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTEEDKRTLRDIETFYNTSIE 404
Query: 360 ELPSNVADLL 369
           E+P NVADL+
Sbjct: 405 EMPLNVADLI 414

>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 =  521 bits (1342), Expect = e-148,   Method: Compositional matrix adjust.
 Identities = 251/369 (68%), Positives = 302/369 (81%)
Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
           MGL+E+LLRGIYAYGFEKPSAIQQR I    KG DVI Q+QSGTGKTATF   +LQ LD 
Sbjct: 43  MGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDI 102
Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG 120
            + + QAL+LAPTRELA QI+K + ALGDY+ V+ HAC+GGT+V ED R L  G HVV G
Sbjct: 103 QVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAG 162
Query: 121 TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMP 180
           TPGRVFDM+RR+SLR   IKM VLDEADEML++GFK+QIYD+++ LP   QV + SAT+P
Sbjct: 163 TPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLP 222
Query: 181 PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVI 240
            E LE+T KFM  P+RILVKRDELTLEGIKQF+V VE+EEWK +TLCDLY+TL ITQ+VI
Sbjct: 223 HEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVI 282
Query: 241 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 300
           F NT+RKVDWLT+KMR  + TVS+ HGDM Q  R+ IM+EFRSG+SRVLI+TD+ ARG+D
Sbjct: 283 FCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLD 342
Query: 301 VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEE 360
           V QVSL+INYDLP   E Y+HRIGRSGR+GRKGVAINFV  DD R+L DI+++Y+  I+E
Sbjct: 343 VPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDE 402
Query: 361 LPSNVADLL 369
           +P NVADL+
Sbjct: 403 MPMNVADLI 411

>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 =  521 bits (1342), Expect = e-148,   Method: Compositional matrix adjust.
 Identities = 251/369 (68%), Positives = 302/369 (81%)
Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
           MGL+E+LLRGIYAYGFEKPSAIQQR I    KG DVI Q+QSGTGKTATF   +LQ LD 
Sbjct: 43  MGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDI 102
Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG 120
            + + QAL+LAPTRELA QI+K + ALGDY+ V+ HAC+GGT+V ED R L  G HVV G
Sbjct: 103 QVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAG 162
Query: 121 TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMP 180
           TPGRVFDM+RR+SLR   IKM VLDEADEML++GFK+QIYD+++ LP   QV + SAT+P
Sbjct: 163 TPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLP 222
Query: 181 PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVI 240
            E LE+T KFM  P+RILVKRDELTLEGIKQF+V VE+EEWK +TLCDLY+TL ITQ+VI
Sbjct: 223 HEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVI 282
Query: 241 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 300
           F NT+RKVDWLT+KMR  + TVS+ HGDM Q  R+ IM+EFRSG+SRVLI+TD+ ARG+D
Sbjct: 283 FCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLD 342
Query: 301 VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEE 360
           V QVSL+INYDLP   E Y+HRIGRSGR+GRKGVAINFV  DD R+L DI+++Y+  I+E
Sbjct: 343 VPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDE 402
Query: 361 LPSNVADLL 369
           +P NVADL+
Sbjct: 403 MPMNVADLI 411

>pdb|2J0Q|A Chain A, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 410

Iteration: 1
 Score =  521 bits (1342), Expect = e-148,   Method: Compositional matrix adjust.
 Identities = 251/369 (68%), Positives = 302/369 (81%)
Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
           MGL+E+LLRGIYAYGFEKPSAIQQR I    KG DVI Q+QSGTGKTATF   +LQ LD 
Sbjct: 42  MGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDI 101
Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG 120
            + + QAL+LAPTRELA QI+K + ALGDY+ V+ HAC+GGT+V ED R L  G HVV G
Sbjct: 102 QVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAG 161
Query: 121 TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMP 180
           TPGRVFDM+RR+SLR   IKM VLDEADEML++GFK+QIYD+++ LP   QV + SAT+P
Sbjct: 162 TPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLP 221
Query: 181 PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVI 240
            E LE+T KFM  P+RILVKRDELTLEGIKQF+V VE+EEWK +TLCDLY+TL ITQ+VI
Sbjct: 222 HEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVI 281
Query: 241 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 300
           F NT+RKVDWLT+KMR  + TVS+ HGDM Q  R+ IM+EFRSG+SRVLI+TD+ ARG+D
Sbjct: 282 FCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLD 341
Query: 301 VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEE 360
           V QVSL+INYDLP   E Y+HRIGRSGR+GRKGVAINFV  DD R+L DI+++Y+  I+E
Sbjct: 342 VPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDE 401
Query: 361 LPSNVADLL 369
           +P NVADL+
Sbjct: 402 MPMNVADLI 410

>pdb|2HXY|A Chain A, Crystal Structure Of Human Apo-Eif4aiii Length = 391

Iteration: 1
 Score =  520 bits (1339), Expect = e-148,   Method: Compositional matrix adjust.
 Identities = 251/369 (68%), Positives = 302/369 (81%)
Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
           MGL+E+LLRGIYAYGFEKPSAIQQR I    KG DVI Q+QSGTGKTATF   +LQ LD 
Sbjct: 21  MGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDI 80
Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG 120
            + + QAL+LAPTRELA QI+K + ALGDY+ V+ HAC+GGT+V ED R L  G HVV G
Sbjct: 81  QVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAG 140
Query: 121 TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMP 180
           TPGRVFDM+RR+SLR   IKM VLDEADEML++GFK+QIYD+++ LP   QV + SAT+P
Sbjct: 141 TPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLP 200
Query: 181 PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVI 240
            E LE+T KFM  P+RILVKRDELTLEGIKQF+V VE+EEWK +TLCDLY+TL ITQ+VI
Sbjct: 201 HEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVI 260
Query: 241 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 300
           F NT+RKVDWLT+KMR  + TVS+ HGDM Q  R+ IM+EFRSG+SRVLI+TD+ ARG+D
Sbjct: 261 FCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLD 320
Query: 301 VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEE 360
           V QVSL+INYDLP   E Y+HRIGRSGR+GRKGVAINFV  DD R+L DI+++Y+  I+E
Sbjct: 321 VPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDE 380
Query: 361 LPSNVADLL 369
           +P NVADL+
Sbjct: 381 MPMNVADLI 389

>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score =  518 bits (1335), Expect = e-147,   Method: Compositional matrix adjust.
 Identities = 249/369 (67%), Positives = 302/369 (81%)
Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
           MGL+E+LLRGIYAYGFEKPSAIQQR I    KG DVI Q+QSGTGKTATF   +LQ LD 
Sbjct: 6   MGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSVSVLQCLDI 65
Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG 120
            + + QAL+LAPTRELA Q++K + ALGDY+ V+ HAC+GGT+V ED R L  G HVV G
Sbjct: 66  QVRETQALILAPTRELAVQVQKGLLALGDYMNVQSHACIGGTNVGEDIRKLDYGQHVVAG 125
Query: 121 TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMP 180
           TPGRVFDM+RR+SLR   IKM VLDEADEML++GFK+QIYD+++ LP   QV + SAT+P
Sbjct: 126 TPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLP 185
Query: 181 PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVI 240
            E LE+T KFM  P+RILVKRDELTLEGIKQF+V VE+EEWK +TLCDLY+TL ITQ+VI
Sbjct: 186 HEVLEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVI 245
Query: 241 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 300
           F NT+RKVDWLT+KMR  + TVS+ HGDM Q  R+ IM+EFRSG+SRVLI+TD+ ARG+D
Sbjct: 246 FCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLD 305
Query: 301 VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEE 360
           V QVSL+INYDLP   E Y+HRIGRSGR+GRKGVA+NFV  DD R+L DI+++Y+  I+E
Sbjct: 306 VPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAVNFVKNDDIRVLRDIEQYYSTQIDE 365
Query: 361 LPSNVADLL 369
           +P NVADL+
Sbjct: 366 MPMNVADLI 374

>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score =  518 bits (1334), Expect = e-147,   Method: Compositional matrix adjust.
 Identities = 249/369 (67%), Positives = 302/369 (81%)
Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
           MGL+E+LLRGIYAYGFEKPSAIQQR I    KG DVI Q+QSGTGKTATF   +LQ LD 
Sbjct: 6   MGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSVSVLQCLDI 65
Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG 120
            + + QAL+LAPTRELA Q++K + ALGDY+ V+ HAC+GGT+V ED R L  G HVV G
Sbjct: 66  QVRETQALILAPTRELAVQVQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAG 125
Query: 121 TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMP 180
           TPGRVFDM+RR+SLR   IKM VLDEADEML++GFK+QIYD+++ LP   QV + SAT+P
Sbjct: 126 TPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLP 185
Query: 181 PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVI 240
            E LE+T KFM  P+RILVKRDELTLEGIKQF+V VE+EEWK +TLCDLY+TL ITQ+VI
Sbjct: 186 HEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVI 245
Query: 241 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 300
           F NT+RKVDWLT+KMR  + TVS+ HGDM Q  R+ IM+EFRSG+SRVLI+TD+ ARG+D
Sbjct: 246 FCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLD 305
Query: 301 VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEE 360
           V QVSL+INYDLP   E Y+HRIGRSGR+GRKGVA+NFV  DD R+L DI+++Y+  I+E
Sbjct: 306 VPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAVNFVKNDDIRVLRDIEQYYSTQIDE 365
Query: 361 LPSNVADLL 369
           +P NVADL+
Sbjct: 366 MPMNVADLI 374

>pdb|2VSO|A Chain A, Crystal Structure Of A Translation Initiation Complex Length = 395

Iteration: 1
 Score =  462 bits (1188), Expect = e-130,   Method: Compositional matrix adjust.
 Identities = 240/369 (65%), Positives = 292/369 (79%), Gaps = 1/369 (0%)
Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
           M L ENLLRG++ YGFE+PSAIQQR I+P  +G DV+ QAQSGTGKT TF    LQ++D 
Sbjct: 27  MELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDT 86
Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG 120
            +   QAL+LAPTRELA QI+KV+ AL  ++ +KVHAC+GGTS  ED   L+    +VVG
Sbjct: 87  SVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLRDA-QIVVG 145
Query: 121 TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMP 180
           TPGRVFD ++R+  R D IKMF+LDEADEMLS GFK+QIY IF LLP   QV + SATMP
Sbjct: 146 TPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTTQVVLLSATMP 205
Query: 181 PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVI 240
            + LE+T KFM  PVRILVK+DELTLEGIKQFYVNVE+EE+K E L DLY+++++TQ+VI
Sbjct: 206 NDVLEVTTKFMRNPVRILVKKDELTLEGIKQFYVNVEEEEYKYECLTDLYDSISVTQAVI 265
Query: 241 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 300
           F NTRRKV+ LT K+R+   TVSA + D+ Q  RD IM+EFRSGSSR+LI+TDLLARGID
Sbjct: 266 FCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGID 325
Query: 301 VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEE 360
           VQQVSLVINYDLP   ENY+HRIGR GRFGRKGVAINFVT +D   + +++KFY+  IEE
Sbjct: 326 VQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELEKFYSTQIEE 385
Query: 361 LPSNVADLL 369
           LPS++A LL
Sbjct: 386 LPSDIATLL 394

>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a Length = 394

Iteration: 1
 Score =  443 bits (1139), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 234/367 (63%), Positives = 282/367 (76%), Gaps = 1/367 (0%)
Query: 3   LQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGL 62
           L ENLLRG++ YGFE+PSAIQQR I P  +G DV+ QAQSGTGKT TF    LQ++D  +
Sbjct: 28  LDENLLRGVFGYGFEEPSAIQQRAIXPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSV 87
Query: 63  VQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTP 122
              QAL LAPTRELA QI+KV+ AL  +  +KVHAC+GGTS  ED   L+    +VVGTP
Sbjct: 88  KAPQALXLAPTRELALQIQKVVXALAFHXDIKVHACIGGTSFVEDAEGLRDA-QIVVGTP 146
Query: 123 GRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMPPE 182
           GRVFD ++R+  R D IK F+LDEADE LS GFK+QIY IF LLP   QV + SAT P +
Sbjct: 147 GRVFDNIQRRRFRTDKIKXFILDEADEXLSSGFKEQIYQIFTLLPPTTQVVLLSATXPND 206
Query: 183 ALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFV 242
            LE+T KF   PVRILVK+DELTLEGIKQFYVNVE+EE+K E L DLY+++++TQ+VIF 
Sbjct: 207 VLEVTTKFXRNPVRILVKKDELTLEGIKQFYVNVEEEEYKYECLTDLYDSISVTQAVIFC 266
Query: 243 NTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQ 302
           NTRRKV+ LT K+R+   TVSA + D+ Q  RD I +EFRSGSSR+LI+TDLLARGIDVQ
Sbjct: 267 NTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIXKEFRSGSSRILISTDLLARGIDVQ 326
Query: 303 QVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELP 362
           QVSLVINYDLP   ENY+HRIGR GRFGRKGVAINFVT +D     +++KFY+  IEELP
Sbjct: 327 QVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAXRELEKFYSTQIEELP 386
Query: 363 SNVADLL 369
           S++A LL
Sbjct: 387 SDIATLL 393

>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p Length = 400

Iteration: 1
 Score =  291 bits (746), Expect = 3e-79,   Method: Compositional matrix adjust.
 Identities = 154/363 (42%), Positives = 217/363 (59%), Gaps = 2/363 (0%)
Query: 3   LQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGL 62
           L+  LL GI+  GFEKPS IQ+  I     G D++ +A++GTGKTA F    L+++   L
Sbjct: 28  LKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKL 87
Query: 63  VQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTP 122
            + QAL++ PTRELA Q  +V+R LG + G+      GGT++R+D   L   VH++VGTP
Sbjct: 88  NKIQALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLNETVHILVGTP 147
Query: 123 GRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMPPE 182
           GRV D+  R+        +F++DEAD+MLSR FK  I  I   LP   Q  +FSAT P  
Sbjct: 148 GRVLDLASRKVADLSDCSLFIMDEADKMLSRDFKTIIEQILSFLPPTHQSLLFSATFPLT 207
Query: 183 ALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFV 242
             E   K ++KP  I +  +ELTL+GI Q+Y  VE E  KL  L  L+  L I Q++IF 
Sbjct: 208 VKEFMVKHLHKPYEINL-MEELTLKGITQYYAFVE-ERQKLHCLNTLFSKLQINQAIIFC 265
Query: 243 NTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQ 302
           N+  +V+ L  K+    ++   +H  M Q  R+ +  EFR G  R L+ +DLL RGID+Q
Sbjct: 266 NSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQ 325
Query: 303 QVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELP 362
            V++VIN+D P   E YLHRIGRSGRFG  G+AIN +  +D   L+ I++     I  +P
Sbjct: 326 AVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWNDRFNLYKIEQELGTEIAAIP 385
Query: 363 SNV 365
           + +
Sbjct: 386 ATI 388

>pdb|3BOR|A Chain A, Crystal Structure Of The Deadc Domain Of Human Translation Initiation Factor 4a-2 Length = 237

Iteration: 1
 Score =  289 bits (739), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 141/203 (69%), Positives = 165/203 (81%), Gaps = 1/203 (0%)
Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
           M L+E+LLRGIYAYGFEKPSAIQQR I+P  KG DVI QAQSGTGKTATF   ILQQL+ 
Sbjct: 35  MNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQLEI 94
Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQA-GVHVVV 119
              + QALVLAPTRELAQQI+KV+ ALGDY+G   HAC+GGT+VR + + LQA   H+VV
Sbjct: 95  EFKETQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRNEMQKLQAEAPHIVV 154
Query: 120 GTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATM 179
           GTPGRVFDML R+ L P +IKMFVLDEADEMLSRGFKDQIY+IFQ L   +QV + SATM
Sbjct: 155 GTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSRGFKDQIYEIFQKLNTSIQVVLLSATM 214
Query: 180 PPEALEITRKFMNKPVRILVKRD 202
           P + LE+T+KFM  P+RILVK++
Sbjct: 215 PTDVLEVTKKFMRDPIRILVKKE 237

>pdb|2G9N|A Chain A, Structure Of The Dead Domain Of Human Eukaryotic Initiation Factor 4a, Eif4a Length = 221

Iteration: 1
 Score =  269 bits (688), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 133/200 (66%), Positives = 152/200 (76%), Gaps = 1/200 (0%)
Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
           M L E+LLRGIYAYGFE PSAIQQR I+P   G DVI QAQSGTG TATF   ILQQ++ 
Sbjct: 20  MNLSESLLRGIYAYGFEXPSAIQQRAILPCIXGYDVIAQAQSGTGXTATFAISILQQIEL 79
Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQA-GVHVVV 119
            L   QALVLAPTRELAQQI+ V+ ALGDY+G   HAC+GGT+VR + + LQ    H++V
Sbjct: 80  DLXATQALVLAPTRELAQQIQXVVMALGDYMGASCHACIGGTNVRAEVQXLQMEAPHIIV 139
Query: 120 GTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATM 179
           GTPGRVFDML R+ L P YI MFVLDEADEMLSRGF DQIYDIFQ L +  QV + SATM
Sbjct: 140 GTPGRVFDMLNRRYLSPXYIXMFVLDEADEMLSRGFXDQIYDIFQXLNSNTQVVLLSATM 199
Query: 180 PPEALEITRKFMNKPVRILV 199
           P + LE+T  FM  P+RILV
Sbjct: 200 PSDVLEVTXXFMRDPIRILV 219

>pdb|3PEW|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score =  268 bits (684), Expect = 5e-72,   Method: Compositional matrix adjust.
 Identities = 147/364 (40%), Positives = 222/364 (60%), Gaps = 14/364 (3%)
Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGL--DVIQQAQSGTGKTATFCSGILQQL 58
           +GL   LL+GIYA  F+KPS IQ+R +         ++I Q+QSGTGKTA F   +L ++
Sbjct: 10  LGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRV 69
Query: 59  DYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVV 118
           +      QA+ LAP+RELA+Q  +V++ +G +  +     V  +  +  Q        V+
Sbjct: 70  NPEDASPQAICLAPSRELARQTLEVVQEMGKFTKITSQLIVPDSFEKNKQ----INAQVI 125
Query: 119 VGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSR-GFKDQIYDIFQLLPAKVQVGVFSA 177
           VGTPG V D++RR+ ++   IK+FVLDEAD ML + G  DQ   + + LP   Q+ +FSA
Sbjct: 126 VGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVKRFLPKDTQLVLFSA 185
Query: 178 TMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQ 237
           T      +  +K +     + ++ +E+ ++ IKQ Y++ + E  K + L +LY  + I  
Sbjct: 186 TFADAVRQYAKKIVPNANTLELQTNEVNVDAIKQLYMDCKNEADKFDVLTELYGVMTIGS 245
Query: 238 SVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLAR 297
           S+IFV T++  + L  K++S  H VS  HGD+    RD ++ +FR G S+VLITT++LAR
Sbjct: 246 SIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLAR 305
Query: 298 GIDVQQVSLVINYDLPT------QPENYLHRIGRSGRFGRKGVAINFV-TRDDERMLFDI 350
           GID+  VS+V+NYDLPT       P  Y+HRIGR+GRFGRKGVAI+FV  ++   +L  I
Sbjct: 306 GIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDKNSFNILSAI 365
Query: 351 QKFY 354
           QK++
Sbjct: 366 QKYF 369

>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score =  267 bits (682), Expect = 7e-72,   Method: Compositional matrix adjust.
 Identities = 147/364 (40%), Positives = 222/364 (60%), Gaps = 14/364 (3%)
Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGL--DVIQQAQSGTGKTATFCSGILQQL 58
           +GL   LL+GIYA  F+KPS IQ+R +         ++I Q+QSGTGKTA F   +L ++
Sbjct: 10  LGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRV 69
Query: 59  DYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVV 118
           +      QA+ LAP+RELA+Q  +V++ +G +  +     V  +  +  Q        V+
Sbjct: 70  NPEDASPQAICLAPSRELARQTLEVVQEMGKFTKITSQLIVPDSFEKNKQ----INAQVI 125
Query: 119 VGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSR-GFKDQIYDIFQLLPAKVQVGVFSA 177
           VGTPG V D++RR+ ++   IK+FVLDEAD ML + G  DQ   + + LP   Q+ +FSA
Sbjct: 126 VGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVKRFLPKDTQLVLFSA 185
Query: 178 TMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQ 237
           T      +  +K +     + ++ +E+ ++ IKQ Y++ + E  K + L +LY  + I  
Sbjct: 186 TFADAVRQYAKKIVPNANTLELQTNEVNVDAIKQLYMDCKNEADKFDVLTELYGLMTIGS 245
Query: 238 SVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLAR 297
           S+IFV T++  + L  K++S  H VS  HGD+    RD ++ +FR G S+VLITT++LAR
Sbjct: 246 SIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLAR 305
Query: 298 GIDVQQVSLVINYDLPT------QPENYLHRIGRSGRFGRKGVAINFV-TRDDERMLFDI 350
           GID+  VS+V+NYDLPT       P  Y+HRIGR+GRFGRKGVAI+FV  ++   +L  I
Sbjct: 306 GIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDKNSFNILSAI 365
Query: 351 QKFY 354
           QK++
Sbjct: 366 QKYF 369

>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 =  260 bits (665), Expect = 7e-70,   Method: Compositional matrix adjust.
 Identities = 130/207 (62%), Positives = 157/207 (75%), Gaps = 1/207 (0%)
Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
           M L ENLLRG++ YGFE+PSAIQQR I+P  +G DV+ QAQSGTGKT TF    LQ++D 
Sbjct: 19  MELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDT 78
Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG 120
            +   QAL+LAPTRELA QI+KV+ AL  ++ +KVHAC+GGTS  ED   L+    +VVG
Sbjct: 79  SVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLR-DAQIVVG 137
Query: 121 TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMP 180
           TPGRVFD ++R+  R D IKMF+LDEADEMLS GFK+QIY IF LLP   QV + SATMP
Sbjct: 138 TPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTTQVVLLSATMP 197
Query: 181 PEALEITRKFMNKPVRILVKRDELTLE 207
            + LE+T KFM  PVRILVK+DELTLE
Sbjct: 198 NDVLEVTTKFMRNPVRILVKKDELTLE 224

>pdb|3FMP|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex With The Dead- Box Helicase Ddx19 Length = 479

Iteration: 1
 Score =  259 bits (662), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 151/378 (39%), Positives = 226/378 (59%), Gaps = 17/378 (4%)
Query: 3   LQENLLRGIYAYGFEKPSAIQQRGIVPFCKG---LDVIQQAQSGTGKTATFCSGILQQLD 59
           L+  LL+G+YA GF +PS IQ+  + P        ++I Q+QSGTGKTA F   +L Q++
Sbjct: 99  LKPQLLQGVYAMGFNRPSKIQENAL-PLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVE 157
Query: 60  YGLVQCQALVLAPTRELAQQIEKVMRALGD-YLGVKVHACVGGTSVREDQRILQAGVHVV 118
                 Q L L+PT ELA Q  KV+  +G  Y  +K+   V G  +   Q+I +    +V
Sbjct: 158 PANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKISE---QIV 214
Query: 119 VGTPGRVFDMLRR-QSLRPDYIKMFVLDEADEMLS-RGFKDQIYDIFQLLPAKVQVGVFS 176
           +GTPG V D   + + + P  IK+FVLDEAD M++ +G +DQ   I ++LP   Q+ +FS
Sbjct: 215 IGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFS 274
Query: 177 ATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAIT 236
           AT      +  +K +  P  I +KR+E TL+ IKQ+YV     + K + LC+LY  + I 
Sbjct: 275 ATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVLCSSRDEKFQALCNLYGAITIA 334
Query: 237 QSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLA 296
           Q++IF +TR+   WL  ++    H V+   G+M    R  ++  FR G  +VL+TT++ A
Sbjct: 335 QAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCA 394
Query: 297 RGIDVQQVSLVINYDLPT----QPEN--YLHRIGRSGRFGRKGVAINFV-TRDDERMLFD 349
           RGIDV+QVS+VIN+DLP      P+N  YLHRIGR+GRFG++G+A+N V ++    +L  
Sbjct: 395 RGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHSMNILNR 454
Query: 350 IQKFYNVVIEELPSNVAD 367
           IQ+ +N  IE L ++  D
Sbjct: 455 IQEHFNKKIERLDTDDLD 472

>pdb|3G0H|A Chain A, Human Dead-box Rna Helicase Ddx19, In Complex With An Atp-analogue And Rna Length = 424

Iteration: 1
 Score =  258 bits (660), Expect = 3e-69,   Method: Compositional matrix adjust.
 Identities = 151/378 (39%), Positives = 226/378 (59%), Gaps = 17/378 (4%)
Query: 3   LQENLLRGIYAYGFEKPSAIQQRGIVPFCKG---LDVIQQAQSGTGKTATFCSGILQQLD 59
           L+  LL+G+YA GF +PS IQ+  + P        ++I Q+QSGTGKTA F   +L Q++
Sbjct: 48  LKPQLLQGVYAMGFNRPSKIQENAL-PLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVE 106
Query: 60  YGLVQCQALVLAPTRELAQQIEKVMRALGD-YLGVKVHACVGGTSVREDQRILQAGVHVV 118
                 Q L L+PT ELA Q  KV+  +G  Y  +K+   V G  +   Q+I +    +V
Sbjct: 107 PANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKISE---QIV 163
Query: 119 VGTPGRVFDMLRR-QSLRPDYIKMFVLDEADEMLS-RGFKDQIYDIFQLLPAKVQVGVFS 176
           +GTPG V D   + + + P  IK+FVLDEAD M++ +G +DQ   I ++LP   Q+ +FS
Sbjct: 164 IGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFS 223
Query: 177 ATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAIT 236
           AT      +  +K +  P  I +KR+E TL+ IKQ+YV     + K + LC+LY  + I 
Sbjct: 224 ATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVLCSSRDEKFQALCNLYGAITIA 283
Query: 237 QSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLA 296
           Q++IF +TR+   WL  ++    H V+   G+M    R  ++  FR G  +VL+TT++ A
Sbjct: 284 QAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCA 343
Query: 297 RGIDVQQVSLVINYDLPT----QPEN--YLHRIGRSGRFGRKGVAINFV-TRDDERMLFD 349
           RGIDV+QVS+VIN+DLP      P+N  YLHRIGR+GRFG++G+A+N V ++    +L  
Sbjct: 344 RGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHSMNILNR 403
Query: 350 IQKFYNVVIEELPSNVAD 367
           IQ+ +N  IE L ++  D
Sbjct: 404 IQEHFNKKIERLDTDDLD 421

>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56 Length = 390

Iteration: 1
 Score =  258 bits (660), Expect = 3e-69,   Method: Compositional matrix adjust.
 Identities = 147/368 (39%), Positives = 217/368 (58%), Gaps = 6/368 (1%)
Query: 3   LQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGL 62
           L+  LLR I   GFE PS +Q   I     G+DV+ QA+SG GKTA F    LQQL+   
Sbjct: 14  LKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVT 73
Query: 63  VQCQALVLAPTRELAQQIEKVMRALGDYL-GVKVHACVGGTSVREDQRILQAGV-HVVVG 120
            Q   LV+  TRELA QI K       Y+  VKV    GG S+++D+ +L+    H+VVG
Sbjct: 74  GQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVG 133
Query: 121 TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSR-GFKDQIYDIFQLLPAKVQVGVFSATM 179
           TPGR+  + R +SL   +IK F+LDEAD+ML +   +  + +IF++ P + QV +FSAT+
Sbjct: 134 TPGRILALARNKSLNLKHIKHFILDEADKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATL 193
Query: 180 PPEALEITRKFMNKPVRILVKRD-ELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQS 238
             E   + RKFM  P+ I V  + +LTL G++Q+YV + K+  K   L DL + L   Q 
Sbjct: 194 SKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKL-KDNEKNRKLFDLLDVLEFNQV 252
Query: 239 VIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARG 298
           VIFV + ++   L   +  ++    A H  M Q  R    ++F+    R+L+ T+L  RG
Sbjct: 253 VIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRG 312
Query: 299 IDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVT-RDDERMLFDIQKFYNVV 357
           +D+++V++  NYD+P   + YLHR+ R+GRFG KG+AI FV+  +D ++L D+Q  + V 
Sbjct: 313 MDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVN 372
Query: 358 IEELPSNV 365
           I ELP  +
Sbjct: 373 ISELPDEI 380

>pdb|3EWS|A Chain A, Human Dead-Box Rna-Helicase Ddx19 In Complex With Adp Length = 445

Iteration: 1
 Score =  258 bits (659), Expect = 3e-69,   Method: Compositional matrix adjust.
 Identities = 151/378 (39%), Positives = 226/378 (59%), Gaps = 17/378 (4%)
Query: 3   LQENLLRGIYAYGFEKPSAIQQRGIVPFCKG---LDVIQQAQSGTGKTATFCSGILQQLD 59
           L+  LL+G+YA GF +PS IQ+  + P        ++I Q+QSGTGKTA F   +L Q++
Sbjct: 69  LKPQLLQGVYAMGFNRPSKIQENAL-PLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVE 127
Query: 60  YGLVQCQALVLAPTRELAQQIEKVMRALGD-YLGVKVHACVGGTSVREDQRILQAGVHVV 118
                 Q L L+PT ELA Q  KV+  +G  Y  +K+   V G  +   Q+I +    +V
Sbjct: 128 PANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKISE---QIV 184
Query: 119 VGTPGRVFDMLRR-QSLRPDYIKMFVLDEADEML-SRGFKDQIYDIFQLLPAKVQVGVFS 176
           +GTPG V D   + + + P  IK+FVLDEAD M+ ++G +DQ   I ++LP   Q+ +FS
Sbjct: 185 IGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFS 244
Query: 177 ATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAIT 236
           AT      +  +K +  P  I +KR+E TL+ IKQ+YV     + K + LC+LY  + I 
Sbjct: 245 ATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVLCSSRDEKFQALCNLYGAITIA 304
Query: 237 QSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLA 296
           Q++IF +TR+   WL  ++    H V+   G+M    R  ++  FR G  +VL+TT++ A
Sbjct: 305 QAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCA 364
Query: 297 RGIDVQQVSLVINYDLPT----QPEN--YLHRIGRSGRFGRKGVAINFV-TRDDERMLFD 349
           RGIDV+QVS+VIN+DLP      P+N  YLHRIGR+GRFG++G+A+N V ++    +L  
Sbjct: 365 RGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHSMNILNR 424
Query: 350 IQKFYNVVIEELPSNVAD 367
           IQ+ +N  IE L ++  D
Sbjct: 425 IQEHFNKKIERLDTDDLD 442

>pdb|3FHT|A Chain A, Crystal Structure Of Human Dbp5 In Complex With Amppnp And Rna Length = 412

Iteration: 1
 Score =  258 bits (659), Expect = 4e-69,   Method: Compositional matrix adjust.
 Identities = 151/378 (39%), Positives = 226/378 (59%), Gaps = 17/378 (4%)
Query: 3   LQENLLRGIYAYGFEKPSAIQQRGIVPFCKG---LDVIQQAQSGTGKTATFCSGILQQLD 59
           L+  LL+G+YA GF +PS IQ+  + P        ++I Q+QSGTGKTA F   +L Q++
Sbjct: 32  LKPQLLQGVYAMGFNRPSKIQENAL-PLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVE 90
Query: 60  YGLVQCQALVLAPTRELAQQIEKVMRALGD-YLGVKVHACVGGTSVREDQRILQAGVHVV 118
                 Q L L+PT ELA Q  KV+  +G  Y  +K+   V G  +   Q+I +    +V
Sbjct: 91  PANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKISE---QIV 147
Query: 119 VGTPGRVFDMLRR-QSLRPDYIKMFVLDEADEML-SRGFKDQIYDIFQLLPAKVQVGVFS 176
           +GTPG V D   + + + P  IK+FVLDEAD M+ ++G +DQ   I ++LP   Q+ +FS
Sbjct: 148 IGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFS 207
Query: 177 ATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAIT 236
           AT      +  +K +  P  I +KR+E TL+ IKQ+YV     + K + LC+LY  + I 
Sbjct: 208 ATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVLCSSRDEKFQALCNLYGAITIA 267
Query: 237 QSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLA 296
           Q++IF +TR+   WL  ++    H V+   G+M    R  ++  FR G  +VL+TT++ A
Sbjct: 268 QAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCA 327
Query: 297 RGIDVQQVSLVINYDLPT----QPEN--YLHRIGRSGRFGRKGVAINFV-TRDDERMLFD 349
           RGIDV+QVS+VIN+DLP      P+N  YLHRIGR+GRFG++G+A+N V ++    +L  
Sbjct: 328 RGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHSMNILNR 387
Query: 350 IQKFYNVVIEELPSNVAD 367
           IQ+ +N  IE L ++  D
Sbjct: 388 IQEHFNKKIERLDTDDLD 405

>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56 Length = 391

Iteration: 1
 Score =  257 bits (656), Expect = 9e-69,   Method: Compositional matrix adjust.
 Identities = 146/368 (39%), Positives = 216/368 (58%), Gaps = 6/368 (1%)
Query: 3   LQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGL 62
           L+  LLR I   GFE PS +Q   I     G+DV+ QA+SG GKTA F    LQQL+   
Sbjct: 15  LKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVT 74
Query: 63  VQCQALVLAPTRELAQQIEKVMRALGDYL-GVKVHACVGGTSVREDQRILQAGV-HVVVG 120
            Q   LV+  TRELA QI K       Y+  VKV    GG S+++D+ +L+    H+VVG
Sbjct: 75  GQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVG 134
Query: 121 TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSR-GFKDQIYDIFQLLPAKVQVGVFSATM 179
           TPGR+  + R +SL   +IK F+LDE D+ML +   +  + +IF++ P + QV +FSAT+
Sbjct: 135 TPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATL 194
Query: 180 PPEALEITRKFMNKPVRILVKRD-ELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQS 238
             E   + RKFM  P+ I V  + +LTL G++Q+YV + K+  K   L DL + L   Q 
Sbjct: 195 SKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKL-KDNEKNRKLFDLLDVLEFNQV 253
Query: 239 VIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARG 298
           VIFV + ++   L   +  ++    A H  M Q  R    ++F+    R+L+ T+L  RG
Sbjct: 254 VIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRG 313
Query: 299 IDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVT-RDDERMLFDIQKFYNVV 357
           +D+++V++  NYD+P   + YLHR+ R+GRFG KG+AI FV+  +D ++L D+Q  + V 
Sbjct: 314 MDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVN 373
Query: 358 IEELPSNV 365
           I ELP  +
Sbjct: 374 ISELPDEI 381

>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp Length = 386

Iteration: 1
 Score =  256 bits (655), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 146/368 (39%), Positives = 216/368 (58%), Gaps = 6/368 (1%)
Query: 3   LQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGL 62
           L+  LLR I   GFE PS +Q   I     G+DV+ QA+SG GKTA F    LQQL+   
Sbjct: 15  LKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVT 74
Query: 63  VQCQALVLAPTRELAQQIEKVMRALGDYL-GVKVHACVGGTSVREDQRILQAGV-HVVVG 120
            Q   LV+  TRELA QI K       Y+  VKV    GG S+++D+ +L+    H+VVG
Sbjct: 75  GQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVG 134
Query: 121 TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSR-GFKDQIYDIFQLLPAKVQVGVFSATM 179
           TPGR+  + R +SL   +IK F+LDE D+ML +   +  + +IF++ P + QV +FSAT+
Sbjct: 135 TPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATL 194
Query: 180 PPEALEITRKFMNKPVRILVKRD-ELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQS 238
             E   + RKFM  P+ I V  + +LTL G++Q+YV + K+  K   L DL + L   Q 
Sbjct: 195 SKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKL-KDNEKNRKLFDLLDVLEFNQV 253
Query: 239 VIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARG 298
           VIFV + ++   L   +  ++    A H  M Q  R    ++F+    R+L+ T+L  RG
Sbjct: 254 VIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRG 313
Query: 299 IDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVT-RDDERMLFDIQKFYNVV 357
           +D+++V++  NYD+P   + YLHR+ R+GRFG KG+AI FV+  +D ++L D+Q  + V 
Sbjct: 314 MDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVN 373
Query: 358 IEELPSNV 365
           I ELP  +
Sbjct: 374 ISELPDEI 381

>pdb|1QVA|A Chain A, Yeast Initiation Factor 4a N-Terminal Domain Length = 223

Iteration: 1
 Score =  243 bits (621), Expect = 9e-65,   Method: Compositional matrix adjust.
 Identities = 122/199 (61%), Positives = 148/199 (74%), Gaps = 1/199 (0%)
Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
           M L E LLRG++ YGFE+PSAIQQR I+P  +G DV+ QAQSGTGKT TF    LQ++D 
Sbjct: 26  MELDEQLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDT 85
Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG 120
            +   QAL+LAPTRELA QI+KV+ AL  ++ +KVHAC+GGTS  ED   L+    +VVG
Sbjct: 86  SVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLR-DAQIVVG 144
Query: 121 TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMP 180
           TPGRVFD ++R+  R D IKMF+LDEADEMLS GFK+QIY IF LLP   QV + SATMP
Sbjct: 145 TPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTTQVVLLSATMP 204
Query: 181 PEALEITRKFMNKPVRILV 199
            + LE+T KFM  PVRILV
Sbjct: 205 NDVLEVTTKFMRNPVRILV 223

>pdb|1HV8|A Chain A, Crystal Structure Of A Dead Box Protein From The Hyperthermophile Methanococcus Jannaschii Length = 367

Iteration: 1
 Score =  216 bits (549), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 124/353 (35%), Positives = 197/353 (55%), Gaps = 9/353 (2%)
Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKG-LDVIQQAQSGTGKTATFCSGILQQLD 59
           + L +N+L  I   GFEKP+ IQ + I  F     +++ QA++G+GKTA+F   +++ ++
Sbjct: 11  LNLSDNILNAIRNKGFEKPTDIQXKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVN 70
Query: 60  YGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVV 119
                 +A++L PTRELA Q+   + +L     +K+    GG ++    + L+   ++VV
Sbjct: 71  EN-NGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALK-NANIVV 128
Query: 120 GTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATM 179
           GTPGR+ D + R +L    +K F+LDEADE L+ GF   +  I        ++ +FSAT 
Sbjct: 129 GTPGRILDHINRGTLNLKNVKYFILDEADEXLNXGFIKDVEKILNACNKDKRILLFSATX 188
Query: 180 PPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSV 239
           P E L + +K+      I  K +      I+Q YV V + E + E LC L +       +
Sbjct: 189 PREILNLAKKYXGDYSFIKAKINA----NIEQSYVEVNENE-RFEALCRLLKNKEFY-GL 242
Query: 240 IFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGI 299
           +F  T+R    L   +R       A HGD+ Q+ R+ ++R F+    R+LI TD+ +RGI
Sbjct: 243 VFCKTKRDTKELASXLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVXSRGI 302
Query: 300 DVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQK 352
           DV  ++ VINY LP  PE+Y HRIGR+GR G+KG AI+ + R + + L  I++
Sbjct: 303 DVNDLNCVINYHLPQNPESYXHRIGRTGRAGKKGKAISIINRREYKKLRYIER 355

>pdb|1FUK|A Chain A, Crystal Structure Of The Carboxy Terminal Domain Of Yeast Eif4a Length = 165

Iteration: 1
 Score =  206 bits (524), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 112/164 (68%), Positives = 137/164 (83%)
Query: 206 LEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSAT 265
           LEGIKQFYVNVE+EE+K E L DLY+++++TQ+VIF NTRRKV+ LT K+R+   TVSA 
Sbjct: 1   LEGIKQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAI 60
Query: 266 HGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGR 325
           + D+ Q  RD IM+EFRSGSSR+LI+TDLLARGIDVQQVSLVINYDLP   ENY+HRIGR
Sbjct: 61  YSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGR 120
Query: 326 SGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPSNVADLL 369
            GRFGRKGVAINFVT +D   + +++KFY+  IEELPS++A LL
Sbjct: 121 GGRFGRKGVAINFVTNEDVGAMRELEKFYSTQIEELPSDIATLL 164

>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x Length = 417

Iteration: 1
 Score =  197 bits (500), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 128/375 (34%), Positives = 197/375 (52%), Gaps = 22/375 (5%)
Query: 16  FEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQL----------------D 59
           + +P+ +Q+  I    +  D++  AQ+G+GKTA F   IL Q+                 
Sbjct: 35  YTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYSDGPGEALRAMKENGR 94
Query: 60  YGLVQCQ--ALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHV 117
           YG  +    +LVLAPTRELA QI +  R       V+     GG  + +  R L+ G H+
Sbjct: 95  YGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRPCVVYGGADIGQQIRDLERGCHL 154
Query: 118 VVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQ--LLPAK--VQVG 173
           +V TPGR+ DM+ R  +  D+ K  VLDEAD ML  GF+ QI  I +   +P K      
Sbjct: 155 LVATPGRLVDMMERGKIGLDFCKYLVLDEADRMLDMGFEPQIRRIVEQDTMPPKGVRHTM 214
Query: 174 VFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETL 233
           +FSAT P E   + R F+++ + + V R   T E I Q  V VE+ + +   L  L  T 
Sbjct: 215 MFSATFPKEIQMLARDFLDEYIFLAVGRVGSTSENITQKVVWVEESDKRSFLLDLLNATG 274
Query: 234 AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTD 293
             + +++FV T++  D L D +    +  ++ HGD  Q  R+  + +FRSG S +L+ T 
Sbjct: 275 KDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATA 334
Query: 294 LLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKF 353
           + ARG+D+  V  VIN+DLP+  E Y+HRIGR+GR G  G+A +F    +  +  D+   
Sbjct: 335 VAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINITKDLLDL 394
Query: 354 YNVVIEELPSNVADL 368
                +E+PS + ++
Sbjct: 395 LVEAKQEVPSWLENM 409

>pdb|2DB3|A Chain A, Structural Basis For Rna Unwinding By The Dead-Box Protein Drosophila Vasa Length = 434

Iteration: 1
 Score =  189 bits (480), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 114/352 (32%), Positives = 190/352 (53%), Gaps = 9/352 (2%)
Query: 3   LQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQL---- 58
           L++ ++  +   G++ P+ IQ+  I     G D++  AQ+G+GKTA F   IL +L    
Sbjct: 63  LRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPILSKLLEDP 122
Query: 59  -DYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHV 117
            +  L + Q ++++PTRELA QI    R       +K+    GGTS R     +  G HV
Sbjct: 123 HELELGRPQVVIVSPTRELAIQIFNEARKFAFESYLKIGIVYGGTSFRHQNECITRGCHV 182
Query: 118 VVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKV--QVGVF 175
           V+ TPGR+ D + R  +  +  +  VLDEAD ML  GF + +  I   +  +   Q  +F
Sbjct: 183 VIATPGRLLDFVDRTFITFEDTRFVVLDEADRMLDMGFSEDMRRIMTHVTMRPEHQTLMF 242
Query: 176 SATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAI 235
           SAT P E   +  +F+   V + +         +KQ    V K   + + +  L E    
Sbjct: 243 SATFPEEIQRMAGEFLKNYVFVAIGIVGGACSDVKQTIYEVNKYAKRSKLIEILSEQADG 302
Query: 236 TQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLL 295
           T  ++FV T+R  D+L   +  ++   ++ HGD  Q+ R+  +R+F++GS +VLI T + 
Sbjct: 303 T--IVFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATSVA 360
Query: 296 ARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERML 347
           +RG+D++ +  VINYD+P++ ++Y+HRIGR+GR G  G A +F   + +R +
Sbjct: 361 SRGLDIKNIKHVINYDMPSKIDDYVHRIGRTGRVGNNGRATSFFDPEKDRAI 412

>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna Helicase From Sulfolobus Tokodaii Length = 337

Iteration: 1
 Score =  167 bits (424), Expect = 7e-42,   Method: Compositional matrix adjust.
 Identities = 111/340 (32%), Positives = 183/340 (53%), Gaps = 23/340 (6%)
Query: 3   LQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGL 62
           + E + + I   GF+  + +Q + I    +G +V+ +A++G+GKTA +   IL+      
Sbjct: 1   MNEKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILE------ 54
Query: 63  VQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVRED-QRILQAGVHVVVGT 121
           +  ++LV+ PTREL +Q+   +R +G Y+  KV    GG   +    R+  A   +VV T
Sbjct: 55  LGMKSLVVTPTRELTRQVASHIRDIGRYMDTKVAEVYGGMPYKAQINRVRNA--DIVVAT 112
Query: 122 PGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMPP 181
           PGR+ D+  +  +     ++ ++DEAD M   GF D I  I      +   G+FSAT+P 
Sbjct: 113 PGRLLDLWSKGVIDLSSFEIVIIDEADLMFEMGFIDDIKIILAQTSNRKITGLFSATIPE 172
Query: 182 EALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEW--KLETLCDLYETLAITQSV 239
           E  ++ + F+     I      + L  ++  +V+V K++W  K++ L +  +   I    
Sbjct: 173 EIRKVVKDFITNYEEI---EACIGLANVEHKFVHV-KDDWRSKVQALRENKDKGVI---- 224
Query: 240 IFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGI 299
           +FV TR +V  L   +R  D+ +    GD+ Q+ R+  +  FR G   +LITTD+ +RG+
Sbjct: 225 VFVRTRNRVAKL---VRLFDNAIE-LRGDLPQSVRNRNIDAFREGEYDMLITTDVASRGL 280
Query: 300 DVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFV 339
           D+  V  VIN+D P     Y+HRIGR+GR GRKG AI F+
Sbjct: 281 DIPLVEKVINFDAPQDLRTYIHRIGRTGRMGRKGEAITFI 320

>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 =  151 bits (381), Expect = 7e-37,   Method: Compositional matrix adjust.
 Identities = 114/387 (29%), Positives = 200/387 (51%), Gaps = 31/387 (8%)
Query: 3   LQENLLRGIYAYGFEKPSAIQQRGIVPF--CKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
           L + + + I    F   + +QQ+ I P    +  DVI +A++GTGKT  F   I Q L  
Sbjct: 28  LDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLIN 87
Query: 61  GLVQCQ----ALVLAPTRELAQQIEKVMRALGDY-LGVKVHACV---GGTSVRED-QRIL 111
                Q    A+++APTR+LA QIE  ++ + D   G+K +ACV   GGT  R    ++ 
Sbjct: 88  TKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMN 147
Query: 112 QAGVHVVVGTPGRVFDMLRRQSLRP-DYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAK- 169
           +   ++V+ TPGR+ D+L + S +   ++   VLDEAD +L  GF+D +  I  +L  K 
Sbjct: 148 KLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGILNEKN 207
Query: 170 ------VQVGVFSATMPPEALEITRKFMNKPVRILV----KRDELTLEGIKQFYVNVEKE 219
                 ++  +FSAT+  +  ++    MNK   + +    K +    E I Q  V  EK 
Sbjct: 208 SKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEKF 267
Query: 220 EWKLETLCD-----LYETLAITQSVIFVNTRRKVDWLTDKMRS---RDHTVSATHGDMDQ 271
              +    +     + E  +  +++IF  T +   +L   +++   +D  +   HG + Q
Sbjct: 268 ANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQ 327
Query: 272 NTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGR 331
           N R  +++ F+   S +L+ TD+ ARG+D   V  V+   +P++  NY+HRIGR+ R G+
Sbjct: 328 NKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGK 387
Query: 332 KGVAINFVTRDDERMLFDIQKFYNVVI 358
           +G ++ F+ +D+   + +++   N+VI
Sbjct: 388 EGSSVLFICKDELPFVRELEDAKNIVI 414

>pdb|3I5X|A Chain A, Structure Of Mss116p Bound To Ssrna And Amp-Pnp Length = 563

Iteration: 1
 Score =  150 bits (380), Expect = 9e-37,   Method: Compositional matrix adjust.
 Identities = 114/387 (29%), Positives = 200/387 (51%), Gaps = 31/387 (8%)
Query: 3   LQENLLRGIYAYGFEKPSAIQQRGIVPF--CKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
           L + + + I    F   + +QQ+ I P    +  DVI +A++GTGKT  F   I Q L  
Sbjct: 79  LDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLIN 138
Query: 61  GLVQCQ----ALVLAPTRELAQQIEKVMRALGDY-LGVKVHACV---GGTSVRED-QRIL 111
                Q    A+++APTR+LA QIE  ++ + D   G+K +ACV   GGT  R    ++ 
Sbjct: 139 TKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMN 198
Query: 112 QAGVHVVVGTPGRVFDMLRRQSLRP-DYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAK- 169
           +   ++V+ TPGR+ D+L + S +   ++   VLDEAD +L  GF+D +  I  +L  K 
Sbjct: 199 KLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGILNEKN 258
Query: 170 ------VQVGVFSATMPPEALEITRKFMNKPVRILV----KRDELTLEGIKQFYVNVEKE 219
                 ++  +FSAT+  +  ++    MNK   + +    K +    E I Q  V  EK 
Sbjct: 259 SKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEKF 318
Query: 220 EWKLETLCD-----LYETLAITQSVIFVNTRRKVDWLTDKMRS---RDHTVSATHGDMDQ 271
              +    +     + E  +  +++IF  T +   +L   +++   +D  +   HG + Q
Sbjct: 319 ANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQ 378
Query: 272 NTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGR 331
           N R  +++ F+   S +L+ TD+ ARG+D   V  V+   +P++  NY+HRIGR+ R G+
Sbjct: 379 NKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGK 438
Query: 332 KGVAINFVTRDDERMLFDIQKFYNVVI 358
           +G ++ F+ +D+   + +++   N+VI
Sbjct: 439 EGSSVLFICKDELPFVRELEDAKNIVI 465

>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And Amp-Pnp Length = 579

Iteration: 1
 Score =  150 bits (378), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 114/387 (29%), Positives = 200/387 (51%), Gaps = 31/387 (8%)
Query: 3   LQENLLRGIYAYGFEKPSAIQQRGIVPF--CKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
           L + + + I    F   + +QQ+ I P    +  DVI +A++GTGKT  F   I Q L  
Sbjct: 28  LDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLIN 87
Query: 61  GLVQCQ----ALVLAPTRELAQQIEKVMRALGDY-LGVKVHACV---GGTSVRED-QRIL 111
                Q    A+++APTR+LA QIE  ++ + D   G+K +ACV   GGT  R    ++ 
Sbjct: 88  TKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMN 147
Query: 112 QAGVHVVVGTPGRVFDMLRRQSLRP-DYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAK- 169
           +   ++V+ TPGR+ D+L + S +   ++   VLDEAD +L  GF+D +  I  +L  K 
Sbjct: 148 KLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGILNEKN 207
Query: 170 ------VQVGVFSATMPPEALEITRKFMNKPVRILV----KRDELTLEGIKQFYVNVEKE 219
                 ++  +FSAT+  +  ++    MNK   + +    K +    E I Q  V  EK 
Sbjct: 208 SKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEKF 267
Query: 220 EWKLETLCD-----LYETLAITQSVIFVNTRRKVDWLTDKMRS---RDHTVSATHGDMDQ 271
              +    +     + E  +  +++IF  T +   +L   +++   +D  +   HG + Q
Sbjct: 268 ANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQ 327
Query: 272 NTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGR 331
           N R  +++ F+   S +L+ TD+ ARG+D   V  V+   +P++  NY+HRIGR+ R G+
Sbjct: 328 NKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGK 387
Query: 332 KGVAINFVTRDDERMLFDIQKFYNVVI 358
           +G ++ F+ +D+   + +++   N+VI
Sbjct: 388 EGSSVLFICKDELPFVRELEDAKNIVI 414

>pdb|2KBF|A Chain A, Solution Structure Of Carboxyl-Terminal Domain Of Dbp5p Length = 187

Iteration: 1
 Score =  148 bits (374), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 76/174 (43%), Positives = 116/174 (66%), Gaps = 8/174 (4%)
Query: 202 DELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHT 261
           +E+ ++ IKQ Y++ + E  K + L +LY  + I  S+IFV T++  + L  K++S  H 
Sbjct: 2   NEVNVDAIKQLYMDCKNEADKFDVLTELYGLMTIGSSIIFVATKKTANVLYGKLKSEGHE 61
Query: 262 VSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPT------Q 315
           VS  HGD+    RD ++ +FR G S+VLITT++LARGID+  VS+V+NYDLPT       
Sbjct: 62  VSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQAD 121
Query: 316 PENYLHRIGRSGRFGRKGVAINFV-TRDDERMLFDIQKFY-NVVIEELPSNVAD 367
           P  Y+HRIGR+GRFGRKGVAI+FV  ++   +L  IQK++ ++ +  +P++  D
Sbjct: 122 PATYIHRIGRTGRFGRKGVAISFVHDKNSFNILSAIQKYFGDIEMTRVPTDDWD 175

>pdb|1T6N|A Chain A, Crystal Structure Of The N-Terminal Domain Of Human Uap56 Length = 220

Iteration: 1
 Score =  147 bits (372), Expect = 7e-36,   Method: Compositional matrix adjust.
 Identities = 85/200 (42%), Positives = 117/200 (58%), Gaps = 3/200 (1%)
Query: 3   LQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGL 62
           L+  LLR I   GFE PS +Q   I     G+DV+ QA+SG GKTA F    LQQL+   
Sbjct: 21  LKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVT 80
Query: 63  VQCQALVLAPTRELAQQIEKVMRALGDYL-GVKVHACVGGTSVREDQRILQAGV-HVVVG 120
            Q   LV+  TRELA QI K       Y+  VKV    GG S+++D+ +L+    H+VVG
Sbjct: 81  GQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVG 140
Query: 121 TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSR-GFKDQIYDIFQLLPAKVQVGVFSATM 179
           TPGR+  + R +SL   +IK F+LDE D+ML +   +  + +IF++ P + QV +FSAT+
Sbjct: 141 TPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATL 200
Query: 180 PPEALEITRKFMNKPVRILV 199
             E   + RKFM  P+ I V
Sbjct: 201 SKEIRPVCRKFMQDPMEIFV 220

>pdb|2RB4|A Chain A, Crystal Structure Of The Helicase Domain Of Human Ddx25 Rna Helicase Length = 175

Iteration: 1
 Score =  147 bits (371), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 74/170 (43%), Positives = 107/170 (62%), Gaps = 6/170 (3%)
Query: 204 LTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVS 263
           LTL  I+Q+YV  E  + K + LC++Y ++ I Q++IF  TRR   WLT +M    H VS
Sbjct: 3   LTLNNIRQYYVLCEHRKDKYQALCNIYGSITIGQAIIFCQTRRNAKWLTVEMIQDGHQVS 62
Query: 264 ATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP------E 317
              G++    R  I++ FR G  +VLITT++ ARGIDV+QV++V+N+DLP +       E
Sbjct: 63  LLSGELTVEQRASIIQRFRDGKEKVLITTNVCARGIDVKQVTIVVNFDLPVKQGEEPDYE 122
Query: 318 NYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPSNVAD 367
            YLHRIGR+GRFG+KG+A N +  D+   L  IQ  +N  I++L +   D
Sbjct: 123 TYLHRIGRTGRFGKKGLAFNMIEVDELPSLMKIQDHFNSSIKQLNAEDMD 172

>pdb|3PEU|A Chain A, S. Cerevisiae Dbp5 L327v C-Terminal Domain Bound To Gle1 H337r And Ip6 Length = 188

Iteration: 1
 Score =  145 bits (367), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 74/160 (46%), Positives = 105/160 (65%), Gaps = 7/160 (4%)
Query: 202 DELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHT 261
           +E+ ++ IKQ Y + + E  K + L +LY    I  S+IFV T++  + L  K++S  H 
Sbjct: 3   NEVNVDAIKQLYXDCKNEADKFDVLTELYGVXTIGSSIIFVATKKTANVLYGKLKSEGHE 62
Query: 262 VSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPT------Q 315
           VS  HGD+    RD ++ +FR G S+VLITT++LARGID+  VS V+NYDLPT       
Sbjct: 63  VSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSXVVNYDLPTLANGQAD 122
Query: 316 PENYLHRIGRSGRFGRKGVAINFV-TRDDERMLFDIQKFY 354
           P  Y+HRIGR+GRFGRKGVAI+FV  ++   +L  IQK++
Sbjct: 123 PATYIHRIGRTGRFGRKGVAISFVHDKNSFNILSAIQKYF 162

>pdb|1VEC|A Chain A, Crystal Structure Of The N-Terminal Domain Of RckP54, A Human Dead-Box Protein Length = 206

Iteration: 1
 Score =  145 bits (366), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 75/196 (38%), Positives = 119/196 (60%), Gaps = 1/196 (0%)
Query: 3   LQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGL 62
           L+  LL GI+  G+EKPS IQ+  I     G D++ +A++GTGK+  +   +L++LD   
Sbjct: 10  LKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKK 69
Query: 63  VQCQALVLAPTRELAQQIEKVMRALGDYLG-VKVHACVGGTSVREDQRILQAGVHVVVGT 121
              QA+V+ PTRELA Q+ ++   +  ++G  KV A  GGT++R+D   L   VHVV+ T
Sbjct: 70  DNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIAT 129
Query: 122 PGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMPP 181
           PGR+ D++++   + D+++M VLDEAD++LS+ F   + DI   LP   Q+ ++SAT P 
Sbjct: 130 PGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNRQILLYSATFPL 189
Query: 182 EALEITRKFMNKPVRI 197
              +     + KP  I
Sbjct: 190 SVQKFMNSHLEKPYEI 205

>pdb|3GFP|A Chain A, Structure Of The C-Terminal Domain Of The Dead-Box Protein Dbp5 Length = 189

Iteration: 1
 Score =  145 bits (365), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 74/160 (46%), Positives = 105/160 (65%), Gaps = 7/160 (4%)
Query: 202 DELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHT 261
           +E+ ++ IKQ Y + + E  K + L +LY    I  S+IFV T++  + L  K++S  H 
Sbjct: 4   NEVNVDAIKQLYXDCKNEADKFDVLTELYGLXTIGSSIIFVATKKTANVLYGKLKSEGHE 63
Query: 262 VSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPT------Q 315
           VS  HGD+    RD ++ +FR G S+VLITT++LARGID+  VS V+NYDLPT       
Sbjct: 64  VSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSXVVNYDLPTLANGQAD 123
Query: 316 PENYLHRIGRSGRFGRKGVAINFV-TRDDERMLFDIQKFY 354
           P  Y+HRIGR+GRFGRKGVAI+FV  ++   +L  IQK++
Sbjct: 124 PATYIHRIGRTGRFGRKGVAISFVHDKNSFNILSAIQKYF 163

>pdb|2WAX|A Chain A, Structure Of The Human Ddx6 C-Terminal Domain In Complex With An Edc3-Fdf Peptide Length = 193

Iteration: 1
 Score =  140 bits (354), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 71/164 (43%), Positives = 101/164 (61%), Gaps = 1/164 (0%)
Query: 202 DELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHT 261
           +ELTL+G+ Q+Y  V  E  K+  L  L+  L I QS+IF N+ ++V+ L  K+    ++
Sbjct: 12  EELTLKGVTQYYAYV-TERQKVHCLNTLFSRLQINQSIIFCNSSQRVELLAKKISQLGYS 70
Query: 262 VSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLH 321
               H  M Q  R+ +  +FR+G  R L+ TDL  RGID+Q V++VIN+D P   E YLH
Sbjct: 71  CFYIHAKMRQEHRNRVFHDFRNGLCRNLVCTDLFTRGIDIQAVNVVINFDFPKLAETYLH 130
Query: 322 RIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPSNV 365
           RIGRSGRFG  G+AIN +T DD   L  I++     I+ +PSN+
Sbjct: 131 RIGRSGRFGHLGLAINLITYDDRFNLKSIEEQLGTEIKPIPSNI 174

>pdb|2OXC|A Chain A, Human Dead-Box Rna Helicase Ddx20, Dead Domain In Complex With Adp Length = 230

Iteration: 1
 Score =  136 bits (343), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 79/194 (40%), Positives = 115/194 (59%), Gaps = 3/194 (1%)
Query: 3   LQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGL 62
           L   +L G+ A GFE+PS +Q + I     GLD+I QA+SGTGKT  F +  L  L    
Sbjct: 31  LSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDSLVLEN 90
Query: 63  VQCQALVLAPTRELAQQIEKVMRALGDYL-GVKVHACVGGTSVREDQRILQAGVHVVVGT 121
           +  Q L+LAPTRE+A QI  V+ A+G  + G++ H  +GGT + +D+  L+   H+ VG+
Sbjct: 91  LSTQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRLKK-CHIAVGS 149
Query: 122 PGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRG-FKDQIYDIFQLLPAKVQVGVFSATMP 180
           PGR+  ++    L P  I++F+LDEAD++L  G F++QI  I+  LPA  Q+   SAT P
Sbjct: 150 PGRIKQLIELDYLNPGSIRLFILDEADKLLEEGSFQEQINWIYSSLPASKQMLAVSATYP 209
Query: 181 PEALEITRKFMNKP 194
                   K+M  P
Sbjct: 210 EFLANALTKYMRDP 223

>pdb|2KBE|A Chain A, Solution Structure Of Amino-Terminal Domain Of Dbp5p Length = 226

Iteration: 1
 Score =  124 bits (311), Expect = 9e-29,   Method: Compositional matrix adjust.
 Identities = 73/181 (40%), Positives = 110/181 (60%), Gaps = 7/181 (3%)
Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGL--DVIQQAQSGTGKTATFCSGILQQL 58
           +GL   LL+GIYA  F+KPS IQ+R +         ++I Q+QSGTGKTA F   +L ++
Sbjct: 27  LGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRV 86
Query: 59  DYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVV 118
           +      QA+ LAP+RELA+Q  +V++ +G +  +     V   S  ++++I      V+
Sbjct: 87  NPEDASPQAICLAPSRELARQTLEVVQEMGKFTKITSQLIVPD-SFEKNKQI---NAQVI 142
Query: 119 VGTPGRVFDMLRRQSLRPDYIKMFVLDEADEML-SRGFKDQIYDIFQLLPAKVQVGVFSA 177
           VGTPG V D++RR+ ++   IK+FVLDEAD ML  +G  DQ   + + LP   Q+ +FSA
Sbjct: 143 VGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVKRFLPKDTQLVLFSA 202
Query: 178 T 178
           T
Sbjct: 203 T 203

>pdb|2GXQ|A Chain A, Hera N-Terminal Domain In Complex With Amp, Crystal Form 1 Length = 207

Iteration: 1
 Score =  122 bits (306), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 74/198 (37%), Positives = 108/198 (54%), Gaps = 5/198 (2%)
Query: 3   LQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGL 62
           L+  +L  ++  G   P+ IQ   +    +G D+I QA++GTGKT  F   I ++L    
Sbjct: 8   LKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAERLAPSQ 67
Query: 63  V---QCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVV 119
               + +ALVL PTRELA Q+   + A+  +L  KV A  GGT   + +  L  G   VV
Sbjct: 68  ERGRKPRALVLTPTRELALQVASELTAVAPHL--KVVAVYGGTGYGKQKEALLRGADAVV 125
Query: 120 GTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATM 179
            TPGR  D LR+  L    +++ VLDEADEMLS GF++++  +    P   Q  +FSAT+
Sbjct: 126 ATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSMGFEEEVEALLSATPPSRQTLLFSATL 185
Query: 180 PPEALEITRKFMNKPVRI 197
           P  A  +  ++M  PV I
Sbjct: 186 PSWAKRLAERYMKNPVLI 203

>pdb|2HJV|A Chain A, Structure Of The Second Domain (Residues 207-368) Of The Bacillus Subtilis Yxin Protein Length = 163

Iteration: 1
 Score =  122 bits (306), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 65/160 (40%), Positives = 96/160 (60%), Gaps = 1/160 (0%)
Query: 204 LTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVS 263
           LT   I+   + V +EE K   L D+  T      +IF  T+  V+ LTD++    +   
Sbjct: 5   LTTRNIEHAVIQV-REENKFSLLKDVLMTENPDSCIIFCRTKEHVNQLTDELDDLGYPCD 63
Query: 264 ATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRI 323
             HG M Q  R  +M EF+ G  R L+ TD+ ARGID++ +SLVINYDLP + E+Y+HR 
Sbjct: 64  KIHGGMIQEDRFDVMNEFKRGEYRYLVATDVAARGIDIENISLVINYDLPLEKESYVHRT 123
Query: 324 GRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPS 363
           GR+GR G KG AI+FVT  ++R L DI+++    I+++ +
Sbjct: 124 GRTGRAGNKGKAISFVTAFEKRFLADIEEYIGFEIQKIEA 163

>pdb|3MWJ|A Chain A, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Apo Form Length = 207

Iteration: 1
 Score =  121 bits (303), Expect = 6e-28,   Method: Compositional matrix adjust.
 Identities = 73/198 (36%), Positives = 108/198 (54%), Gaps = 5/198 (2%)
Query: 3   LQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGL 62
           L+  +L  ++  G   P+ I+   +    +G D+I QA++GTGKT  F   I ++L    
Sbjct: 8   LKPEILEALHGRGLTTPTPIEAAALPLALEGKDLIGQARTGTGKTLAFALPIAERLAPSQ 67
Query: 63  V---QCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVV 119
               + +ALVL PTRELA Q+   + A+  +L  KV A  GGT   + +  L  G   VV
Sbjct: 68  ERGRKPRALVLTPTRELALQVASELTAVAPHL--KVVAVYGGTGYGKQKEALLRGADAVV 125
Query: 120 GTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATM 179
            TPGR  D LR+  L    +++ VLDEADEMLS GF++++  +    P   Q  +FSAT+
Sbjct: 126 ATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSMGFEEEVEALLSATPPSRQTLLFSATL 185
Query: 180 PPEALEITRKFMNKPVRI 197
           P  A  +  ++M  PV I
Sbjct: 186 PSWAKRLAERYMKNPVLI 203

>pdb|3FHC|B Chain B, Crystal Structure Of Human Dbp5 In Complex With Nup214 Length = 235

Iteration: 1
 Score =  119 bits (299), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 79/207 (38%), Positives = 118/207 (57%), Gaps = 10/207 (4%)
Query: 3   LQENLLRGIYAYGFEKPSAIQQRGIVPFC---KGLDVIQQAQSGTGKTATFCSGILQQLD 59
           L+  LL+G+YA GF +PS IQ+  + P        ++I Q+QSGTGKTA F   +L Q++
Sbjct: 32  LKPQLLQGVYAMGFNRPSKIQENAL-PLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVE 90
Query: 60  YGLVQCQALVLAPTRELAQQIEKVMRALGD-YLGVKVHACVGGTSVREDQRILQAGVHVV 118
                 Q L L+PT ELA Q  KV+  +G  Y  +K+   V G  +   Q+I +    +V
Sbjct: 91  PANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKISE---QIV 147
Query: 119 VGTPGRVFDMLRR-QSLRPDYIKMFVLDEADEML-SRGFKDQIYDIFQLLPAKVQVGVFS 176
           +GTPG V D   + + + P  IK+FVLDEAD M+ ++G +DQ   I ++LP   Q+ +FS
Sbjct: 148 IGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFS 207
Query: 177 ATMPPEALEITRKFMNKPVRILVKRDE 203
           AT      +  +K +  P  I +KR+E
Sbjct: 208 ATFEDSVWKFAQKVVPDPNVIKLKREE 234

>pdb|3FMO|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex With The Dead- Box Helicase Ddx19 Length = 300

Iteration: 1
 Score =  119 bits (297), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 78/206 (37%), Positives = 117/206 (56%), Gaps = 10/206 (4%)
Query: 3   LQENLLRGIYAYGFEKPSAIQQRGIVPFC---KGLDVIQQAQSGTGKTATFCSGILQQLD 59
           L+  LL+G+YA GF +PS IQ+  + P        ++I Q+QSGTGKTA F   +L Q++
Sbjct: 99  LKPQLLQGVYAMGFNRPSKIQENAL-PLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVE 157
Query: 60  YGLVQCQALVLAPTRELAQQIEKVMRALGD-YLGVKVHACVGGTSVREDQRILQAGVHVV 118
                 Q L L+PT ELA Q  KV+  +G  Y  +K+   V G  +   Q+I +    +V
Sbjct: 158 PANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKISE---QIV 214
Query: 119 VGTPGRVFDMLRR-QSLRPDYIKMFVLDEADEMLS-RGFKDQIYDIFQLLPAKVQVGVFS 176
           +GTPG V D   + + + P  IK+FVLDEAD M++ +G +DQ   I ++LP   Q+ +FS
Sbjct: 215 IGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFS 274
Query: 177 ATMPPEALEITRKFMNKPVRILVKRD 202
           AT      +  +K +  P  I +KR+
Sbjct: 275 ATFEDSVWKFAQKVVPDPNVIKLKRE 300

>pdb|1T5I|A Chain A, Crystal Structure Of The C-Terminal Domain Of Uap56 Length = 172

Iteration: 1
 Score =  113 bits (283), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 59/162 (36%), Positives = 96/162 (59%), Gaps = 2/162 (1%)
Query: 205 TLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSA 264
           +L G++Q+YV + K+  K   L DL + L   Q VIFV + ++   L   +  ++    A
Sbjct: 2   SLHGLQQYYVKL-KDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIA 60
Query: 265 THGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIG 324
            H  M Q  R    ++F+    R+L+ T+L  RG+D+++V++  NYD+P   + YLHR+ 
Sbjct: 61  IHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVA 120
Query: 325 RSGRFGRKGVAINFVT-RDDERMLFDIQKFYNVVIEELPSNV 365
           R+GRFG KG+AI FV+  +D ++L D+Q  + V I ELP  +
Sbjct: 121 RAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEI 162

>pdb|3BER|A Chain A, Human Dead-Box Rna-Helicase Ddx47, Conserved Domain I In Complex With Amp Length = 249

Iteration: 1
 Score =  109 bits (273), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 67/200 (33%), Positives = 103/200 (51%), Gaps = 1/200 (0%)
Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
           +G+ + L       G+ KP+ IQ   I    +G D+I  A++G+GKT  F   IL  L  
Sbjct: 48  LGVTDVLCEACDQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPILNALLE 107
Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG 120
              +  ALVL PTRELA QI +   ALG  +GV+    VGG         L    H+++ 
Sbjct: 108 TPQRLFALVLTPTRELAFQISEQFEALGSSIGVQSAVIVGGIDSMSQSLALAKKPHIIIA 167
Query: 121 TPGRVFDMLRR-QSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATM 179
           TPGR+ D L   +      +K  V+DEAD +L+  F+ ++  I +++P   +  +FSATM
Sbjct: 168 TPGRLIDHLENTKGFNLRALKYLVMDEADRILNMDFETEVDKILKVIPRDRKTFLFSATM 227
Query: 180 PPEALEITRKFMNKPVRILV 199
             +  ++ R  +  PV+  V
Sbjct: 228 TKKVQKLQRAALKNPVKCAV 247

>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 =  108 bits (271), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 73/226 (32%), Positives = 112/226 (49%), Gaps = 17/226 (7%)
Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATF---------C 51
           + L   +   I    +++P+ IQ+  I    +  D++  AQ+G+GKTA F         C
Sbjct: 28  LKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVC 87
Query: 52  SGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACV--GGTSVREDQR 109
             + QQ        + L+LAPTRELA QI    +     L   + +CV  GG       R
Sbjct: 88  QDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFS--LNTPLRSCVVYGGADTHSQIR 145
Query: 110 ILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQL--LP 167
            +Q G H++V TPGR+ D + +  +  ++ K  VLDEAD ML  GF+ QI  I +   +P
Sbjct: 146 EVQMGCHLLVATPGRLVDFIEKNKISLEFCKYIVLDEADRMLDMGFEPQIRKIIEESNMP 205
Query: 168 AKV--QVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQ 211
           + +  Q  +FSAT P E  ++   F+   + + V R   T + IKQ
Sbjct: 206 SGINRQTLMFSATFPKEIQKLAADFLYNYIFMTVGRVGSTSDSIKQ 251

>pdb|1Q0U|A Chain A, Crystal Structure Of The Bstdead N-Terminal Domain Length = 219

Iteration: 1
 Score =  104 bits (260), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 65/201 (32%), Positives = 100/201 (49%), Gaps = 4/201 (1%)
Query: 3   LQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGL 62
            Q  ++  I    F KP+ IQ+R I    +G   + Q+Q+GTGKT  +   I +++    
Sbjct: 11  FQPFIIEAIKTLRFYKPTEIQERIIPGALRGESXVGQSQTGTGKTHAYLLPIXEKIKPER 70
Query: 63  VQCQALVLAPTRELAQQIE----KVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVV 118
            + QA++ APTRELA QI     K+ +       +     +GGT  ++    L    H+V
Sbjct: 71  AEVQAVITAPTRELATQIYHETLKITKFCPKDRXIVARCLIGGTDKQKALEKLNVQPHIV 130
Query: 119 VGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSAT 178
           +GTPGR+ D +R Q+L      + V+DEAD  L  GF   +  I    P  +Q  VFSAT
Sbjct: 131 IGTPGRINDFIREQALDVHTAHILVVDEADLXLDXGFITDVDQIAARXPKDLQXLVFSAT 190
Query: 179 MPPEALEITRKFMNKPVRILV 199
           +P +     +K+   P  + V
Sbjct: 191 IPEKLKPFLKKYXENPTFVHV 211

>pdb|2JGN|A Chain A, Ddx3 Helicase Domain Length = 185

Iteration: 1
 Score = 98.6 bits (244), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 56/159 (35%), Positives = 88/159 (55%)
Query: 205 TLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSA 264
           T E I Q  V VE+ + +   L  L  T   + +++FV T++  D L D +    +  ++
Sbjct: 16  TSENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTS 75
Query: 265 THGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIG 324
            HGD  Q  R+  + +FRSG S +L+ T + ARG+D+  V  VIN+DLP+  E Y+HRIG
Sbjct: 76  IHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIG 135
Query: 325 RSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPS 363
           R+GR G  G+A +F    +  +  D+        +E+PS
Sbjct: 136 RTGRVGNLGLATSFFNERNINITKDLLDLLVEAKQEVPS 174

>pdb|2YJT|D Chain D, Crystal Structure Of E. Coli Dead-Box Protein Srmb Bound To Regulator Of Ribonuclease Activity A (Rraa) Length = 170

Iteration: 1
 Score = 97.1 bits (240), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 56/161 (34%), Positives = 84/161 (52%), Gaps = 3/161 (1%)
Query: 209 IKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGD 268
           I Q+Y   +  E K   L  L +    T+S++FV  R +V  L + +R          G+
Sbjct: 4   IHQWYYRADDLEHKTALLVHLLKQPEATRSIVFVRKRERVHELANWLREAGINNCYLEGE 63
Query: 269 MDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGR 328
           M Q  R+  ++    G   VL+ TD+ ARGID+  VS V N+D+P   + YLHRIGR+ R
Sbjct: 64  MVQGKRNEAIKRLTEGRVNVLVATDVAARGIDIPDVSHVFNFDMPRSGDTYLHRIGRTAR 123
Query: 329 FGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPSNVADLL 369
            GRKG AI+ V   D  +L  + ++   + E + + V D L
Sbjct: 124 AGRKGTAISLVEAHDHLLLGKVGRY---IEEPIKARVIDEL 161

>pdb|3FE2|A Chain A, Human Dead-Box Rna Helicase Ddx5 (P68), Conserved Domain I In Complex With Adp Length = 242

Iteration: 1
 Score = 96.7 bits (239), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 67/207 (32%), Positives = 100/207 (48%), Gaps = 11/207 (5%)
Query: 6   NLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY----- 60
           N++  I    F +P+AIQ +G      GLD++  AQ+G+GKT ++    +  +++     
Sbjct: 39  NVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPFLE 98
Query: 61  ---GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHV 117
              G +    LVLAPTRELAQQ+++V         +K     GG       R L+ GV +
Sbjct: 99  RGDGPI---CLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIRDLERGVEI 155
Query: 118 VVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSA 177
            + TPGR+ D L             VLDEAD ML  GF+ QI  I   +    Q  ++SA
Sbjct: 156 CIATPGRLIDFLECGKTNLRRTTYLVLDEADRMLDMGFEPQIRKIVDQIRPDRQTLMWSA 215
Query: 178 TMPPEALEITRKFMNKPVRILVKRDEL 204
           T P E  ++   F+   + I +   EL
Sbjct: 216 TWPKEVRQLAEDFLKDYIHINIGALEL 242

>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 = 95.9 bits (237), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 65/200 (32%), Positives = 97/200 (48%), Gaps = 11/200 (5%)
Query: 6   NLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY----- 60
           N++  I    F +P+AIQ +G      GLD++  AQ+G+GKT ++    +  +++     
Sbjct: 53  NVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPFLE 112
Query: 61  ---GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHV 117
              G +    LVLAPTRELAQQ+++V         +K     GG       R L+ GV +
Sbjct: 113 RGDGPI---CLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIRDLERGVEI 169
Query: 118 VVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSA 177
            + TPGR+ D L             VLDEAD ML  GF+ QI  I   +    Q  ++SA
Sbjct: 170 CIATPGRLIDFLECGKTNLRRTTYLVLDEADRMLDMGFEPQIRKIVDQIRPDRQTLMWSA 229
Query: 178 TMPPEALEITRKFMNKPVRI 197
           T P E  ++   F+   + I
Sbjct: 230 TWPKEVRQLAEDFLKDYIHI 249

>pdb|3LY5|A Chain A, Ddx18 Dead-Domain Length = 262

Iteration: 1
 Score = 95.1 bits (235), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 58/184 (31%), Positives = 101/184 (54%), Gaps = 11/184 (5%)
Query: 3   LQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATF---CSGILQQLD 59
           + EN L+ I   GF   + IQ + I P  +G D++  A++G+GKT  F      ++ +L 
Sbjct: 61  VNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLR 120
Query: 60  YGLVQCQA-LVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVV 118
           +        L+L+PTRELA Q   V++ L  +        +GG++   + + L  G++++
Sbjct: 121 FMPRNGTGVLILSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQKLGNGINII 180
Query: 119 VGTPGRVFDMLRRQSLRPDY----IKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGV 174
           V TPGR+ D ++     P +    ++  V+DEAD +L  GF++++  I +LLP + Q  +
Sbjct: 181 VATPGRLLDHMQNT---PGFMYKNLQCLVIDEADRILDVGFEEELKQIIKLLPTRRQTML 237
Query: 175 FSAT 178
           FSAT
Sbjct: 238 FSAT 241

>pdb|2P6N|A Chain A, Human Dead-box Rna Helicase Ddx41, Helicase Domain Length = 191

Iteration: 1
 Score = 90.5 bits (223), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 42/116 (36%), Positives = 65/116 (56%), Gaps = 1/116 (0%)
Query: 239 VIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARG 298
           +IF   +  VD + + +  +     A HG  DQ  R   +  FR G   VL+ TD+ ++G
Sbjct: 58  LIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVASKG 117
Query: 299 IDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRD-DERMLFDIQKF 353
           +D   +  VINYD+P + ENY+HRIGR+G  G  G+A  F+ +  DE +L D++  
Sbjct: 118 LDFPAIQHVINYDMPEEIENYVHRIGRTGCSGNTGIATTFINKACDESVLMDLKAL 173

>pdb|2PL3|A Chain A, Human Dead-Box Rna Helicase Ddx10, Dead Domain In Complex With Adp Length = 236

Iteration: 1
 Score = 90.5 bits (223), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 63/204 (30%), Positives = 104/204 (50%), Gaps = 10/204 (4%)
Query: 3   LQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGL 62
           L +  L+G+    +   + IQ++ I    +G DV+  A++G+GKT  F   +L+ L Y L
Sbjct: 32  LSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEAL-YRL 90
Query: 63  VQCQA-----LVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVR-EDQRILQAGVH 116
                     L+++PTRELA Q  +V+R +G          +GG  ++ E +RI    ++
Sbjct: 91  QWTSTDGLGVLIISPTRELAYQTFEVLRKVGKNHDFSAGLIIGGKDLKHEAERI--NNIN 148
Query: 117 VVVGTPGRVFDMLRRQ-SLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVF 175
           ++V TPGR+   +    S     ++M VLDEAD +L  GF D +  + + LP K Q  +F
Sbjct: 149 ILVCTPGRLLQHMDETVSFHATDLQMLVLDEADRILDMGFADTMNAVIENLPKKRQTLLF 208
Query: 176 SATMPPEALEITRKFMNKPVRILV 199
           SAT      ++ R  +  P  + V
Sbjct: 209 SATQTKSVKDLARLSLKNPEYVWV 232

>pdb|3IUY|A Chain A, Crystal Structure Of Ddx53 Dead-Box Domain Length = 228

Iteration: 1
 Score = 86.7 bits (213), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 62/200 (31%), Positives = 95/200 (47%), Gaps = 7/200 (3%)
Query: 6   NLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQC 65
           +LL+ I   G  KP+ IQ +      +G+D+I  AQ+GTGKT ++       LD   +  
Sbjct: 30  DLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIHLDSQPISR 89
Query: 66  Q------ALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVV 119
           +       LVL PTRELA  +E        Y G+K     GG +       +  GV +++
Sbjct: 90  EQRNGPGMLVLTPTRELALHVEAECSKYS-YKGLKSICIYGGRNRNGQIEDISKGVDIII 148
Query: 120 GTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATM 179
            TPGR+ D+    S+    I   V+DEAD+ML   F+ QI  I   +    Q  + SAT 
Sbjct: 149 ATPGRLNDLQMNNSVNLRSITYLVIDEADKMLDMEFEPQIRKILLDVRPDRQTVMTSATW 208
Query: 180 PPEALEITRKFMNKPVRILV 199
           P    ++   ++  P+ + V
Sbjct: 209 PDTVRQLALSYLKDPMIVYV 228

>pdb|3I32|A Chain A, Dimeric Structure Of A Hera Helicase Fragment Including The C-Terminal Reca Domain, The Dimerization Domain, And The Rna Binding Domain Length = 300

Iteration: 1
 Score = 82.4 bits (202), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 37/100 (37%), Positives = 58/100 (58%)
Query: 222 KLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREF 281
           +LE L DL    +  ++++F  T+ + + +   +    H   A HGDM Q  R+ +M  F
Sbjct: 15  RLEVLSDLLYVASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQGERERVMGAF 74
Query: 282 RSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLH 321
           R G  RVL+ TD+ ARG+D+ QV LV++Y +P + E Y H
Sbjct: 75  RQGEVRVLVATDVAARGLDIPQVDLVVHYRMPDRAEAYQH 114

>pdb|3EAQ|A Chain A, Novel Dimerization Motif In The Dead Box Rna Helicase Hera Form 2, Complete Dimer, Symmetric Length = 212

Iteration: 1
 Score = 79.7 bits (195), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 36/100 (36%), Positives = 58/100 (58%)
Query: 222 KLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREF 281
           +LE L DL    +  ++++F  T+ + + +   +    H   A HGD+ Q  R+ ++  F
Sbjct: 18  RLEVLSDLLYVASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAF 77
Query: 282 RSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLH 321
           R G  RVL+ TD+ ARG+D+ QV LV++Y LP + E Y H
Sbjct: 78  RQGEVRVLVATDVAARGLDIPQVDLVVHYRLPDRAEAYQH 117

>pdb|4DB4|A Chain A, Mss116p Dead-Box Helicase Domain 2 Bound To A Chimaeric Rna-Dna Duplex Length = 256

Iteration: 1
 Score = 78.2 bits (191), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 37/125 (29%), Positives = 74/125 (59%), Gaps = 3/125 (2%)
Query: 237 QSVIFVNTRRKVDWLTDKMRS---RDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTD 293
           +++IF  T +   +L   +++   +D  +   HG + QN R  +++ F+   S +L+ TD
Sbjct: 35  KAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTD 94
Query: 294 LLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKF 353
           + ARG+D   V  V+   +P++  NY+HRIGR+ R G++G ++ F+ +D+   + +++  
Sbjct: 95  VGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRELEDA 154
Query: 354 YNVVI 358
            N+VI
Sbjct: 155 KNIVI 159

>pdb|4DB2|C Chain C, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex Length = 257

Iteration: 1
 Score = 78.2 bits (191), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 37/125 (29%), Positives = 74/125 (59%), Gaps = 3/125 (2%)
Query: 237 QSVIFVNTRRKVDWLTDKMRS---RDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTD 293
           +++IF  T +   +L   +++   +D  +   HG + QN R  +++ F+   S +L+ TD
Sbjct: 35  KAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTD 94
Query: 294 LLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKF 353
           + ARG+D   V  V+   +P++  NY+HRIGR+ R G++G ++ F+ +D+   + +++  
Sbjct: 95  VGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRELEDA 154
Query: 354 YNVVI 358
            N+VI
Sbjct: 155 KNIVI 159

>pdb|4DB2|A Chain A, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex Length = 257

Iteration: 1
 Score = 78.2 bits (191), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 37/125 (29%), Positives = 74/125 (59%), Gaps = 3/125 (2%)
Query: 237 QSVIFVNTRRKVDWLTDKMRS---RDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTD 293
           +++IF  T +   +L   +++   +D  +   HG + QN R  +++ F+   S +L+ TD
Sbjct: 35  KAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTD 94
Query: 294 LLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKF 353
           + ARG+D   V  V+   +P++  NY+HRIGR+ R G++G ++ F+ +D+   + +++  
Sbjct: 95  VGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRELEDA 154
Query: 354 YNVVI 358
            N+VI
Sbjct: 155 KNIVI 159

>pdb|3DKP|A Chain A, Human Dead-Box Rna-Helicase Ddx52, Conserved Domain I In Complex With Adp Length = 245

Iteration: 1
 Score = 76.6 bits (187), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 54/185 (29%), Positives = 95/185 (51%), Gaps = 8/185 (4%)
Query: 3   LQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGL 62
           +   LL+ I   GF+ P+ IQ + I     G +++  A +G+GKT  F   IL QL    
Sbjct: 36  INSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMQLKQPA 95
Query: 63  VQ-CQALVLAPTRELAQQIEKVMRALGDYLGVKVHAC-VGGTSVREDQRILQAGVHVVVG 120
            +  +AL+++PTRELA QI + +  + +  G ++H       + ++          ++V 
Sbjct: 96  NKGFRALIISPTRELASQIHRELIKISEGTGFRIHMIHKAAVAAKKFGPKSSKKFDILVT 155
Query: 121 TPGRVFDMLRRQSLRPDY--IKMFVLDEADEML---SRGFKDQIYDIFQLLPA-KVQVGV 174
           TP R+  +L++     D   ++  V+DE+D++      GF+DQ+  IF    + KV+  +
Sbjct: 156 TPNRLIYLLKQDPPGIDLASVEWLVVDESDKLFEDGKTGFRDQLASIFLACTSHKVRRAM 215
Query: 175 FSATM 179
           FSAT 
Sbjct: 216 FSATF 220

>pdb|1OYY|A Chain A, Structure Of The Recq Catalytic Core Bound To Atp-Gamma-S Length = 523

Iteration: 1
 Score = 59.3 bits (142), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 28/105 (26%), Positives = 55/105 (52%)
Query: 239 VIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARG 298
           +I+ N+R KV+    +++S+  + +A H  ++ N R  +  +F+    ++++ T     G
Sbjct: 240 IIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMG 299
Query: 299 IDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDD 343
           I+   V  V+++D+P   E+Y    GR+GR G    A+ F    D
Sbjct: 300 INKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPAD 344

>pdb|1OYW|A Chain A, Structure Of The Recq Catalytic Core Length = 523

Iteration: 1
 Score = 59.3 bits (142), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 29/109 (26%), Positives = 55/109 (50%)
Query: 239 VIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARG 298
           +I+ N+R KV+    +++S+  + +A H  ++ N R  +  +F+    ++++ T     G
Sbjct: 240 IIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGXG 299
Query: 299 IDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERML 347
           I+   V  V+++D+P   E+Y    GR+GR G    A  F    D   L
Sbjct: 300 INKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAXLFYDPADXAWL 348

>pdb|4GL2|A Chain A, Structural Basis For Dsrna Duplex Backbone Recognition By Mda5 Length = 699

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 45/198 (22%), Positives = 80/198 (40%), Gaps = 33/198 (16%)
Query: 158 QIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDE-------LTLEGIK 210
           QI D  +++ A   +  F      +   +    + KP+++    DE       L  E  K
Sbjct: 312 QINDTIRMIDAYTHLETFYNEEKDKKFAVIEDDLKKPLKL----DETDRFLMTLFFENNK 367
Query: 211 QFYVNVEKEEWKLETLCDLYETL--------AITQSVIFVNTRRKV----DWLTDKMR-- 256
                 E  E++ E L  L  T+           + +IF  TR+       W+T+  +  
Sbjct: 368 MLKRLAENPEYENEKLTKLRNTIMEQYTRTEESARGIIFTKTRQSAYALSQWITENEKFA 427
Query: 257 ----SRDHTVSATHGD----MDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVI 308
                  H + A H      M QN +  ++ +FR+G   +LI T +   G+D+++ ++VI
Sbjct: 428 EVGVKAHHLIGAGHSSEFKPMTQNEQKEVISKFRTGKINLLIATTVAEEGLDIKECNIVI 487
Query: 309 NYDLPTQPENYLHRIGRS 326
            Y L T     +   GR+
Sbjct: 488 RYGLVTNEIAMVQARGRA 505

>pdb|1GM5|A Chain A, Structure Of Recg Bound To Three-Way Dna Junction Length = 780

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 70/324 (21%), Positives = 140/324 (43%), Gaps = 45/324 (13%)
Query: 32  KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYL 91
           K ++ + Q   G+GKT      IL   + G    Q   + PT  LA  I+   R +  + 
Sbjct: 388 KPMNRLLQGDVGSGKTVVAQLAILDNYEAGF---QTAFMVPTSILA--IQHYRRTVESFS 442
Query: 92  GVKVHAC--VGGTSVREDQRI---LQAG-VHVVVGTPGRVFDMLRRQSLR---PDYIKMF 142
              +H    +G T+  E ++I   L+ G + VV+GT   + + +  ++L     D    F
Sbjct: 443 KFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQEDVHFKNLGLVIIDEQHRF 502
Query: 143 VLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMPPEA--------LEITRKFMNKP 194
            + + + ++++G               V   V SAT  P +        L++T      P
Sbjct: 503 GVKQREALMNKG-------------KMVDTLVMSATPIPRSMALAFYGDLDVTVIDEMPP 549
Query: 195 VRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDK 254
            R  V+   + ++ + + Y  V +E  +      +Y  +  +  +   +     ++L+ +
Sbjct: 550 GRKEVQTMLVPMDRVNEVYEFVRQEVMRGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKE 609
Query: 255 MRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPT 314
           +   +  +   HG + Q  +D +M EF  G   +L++T ++  GIDV + ++++      
Sbjct: 610 VFP-EFKLGLMHGRLSQEEKDRVMLEFAEGRYDILVSTTVIEVGIDVPRANVMV----IE 664
Query: 315 QPENY----LHRI-GRSGRFGRKG 333
            PE +    LH++ GR GR G++ 
Sbjct: 665 NPERFGLAQLHQLRGRVGRGGQEA 688

>pdb|4AY2|A Chain A, Capturing 5' Tri-Phosphorylated Rna Duplex By Rig-I Length = 687

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 39/131 (29%), Positives = 60/131 (45%), Gaps = 17/131 (12%)
Query: 198 LVKRDELTLEGIKQFYVNVEKEEWKLETLC----DLYETLAITQSVIFVNTRRKVDWLTD 253
           L +R E  L+ ++    +   E  KLE LC    + Y     T +++FV TR  VD L +
Sbjct: 348 LTQRFEEKLQELESVSRDPSNENPKLEDLCFILQEEYHLNPETITILFVKTRALVDALKN 407
Query: 254 ------KMRSRDHTVSATHGDMDQNT------RDIIMREFR-SGSSRVLITTDLLARGID 300
                 K+      +    G  +QNT      +  I+  F+ SG   +LI T +   GID
Sbjct: 408 WIEGNPKLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAFKASGDHNILIATSVADEGID 467
Query: 301 VQQVSLVINYD 311
           + Q +LVI Y+
Sbjct: 468 IAQCNLVILYE 478

>pdb|3TMI|A Chain A, Structural Basis For Rna Recognition And Activation Of Rig-I Length = 695

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 39/131 (29%), Positives = 60/131 (45%), Gaps = 17/131 (12%)
Query: 198 LVKRDELTLEGIKQFYVNVEKEEWKLETLC----DLYETLAITQSVIFVNTRRKVDWLTD 253
           L +R E  L+ ++    +   E  KLE LC    + Y     T +++FV TR  VD L +
Sbjct: 356 LTQRFEEKLQELESVSRDPSNENPKLEDLCFILQEEYHLNPETITILFVKTRALVDALKN 415
Query: 254 ------KMRSRDHTVSATHGDMDQNT------RDIIMREFR-SGSSRVLITTDLLARGID 300
                 K+      +    G  +QNT      +  I+  F+ SG   +LI T +   GID
Sbjct: 416 WIEGNPKLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAFKASGDHNILIATSVADEGID 475
Query: 301 VQQVSLVINYD 311
           + Q +LVI Y+
Sbjct: 476 IAQCNLVILYE 486

>pdb|2YKG|A Chain A, Structural Insights Into Rna Recognition By Rig-I Length = 696

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 39/131 (29%), Positives = 60/131 (45%), Gaps = 17/131 (12%)
Query: 198 LVKRDELTLEGIKQFYVNVEKEEWKLETLC----DLYETLAITQSVIFVNTRRKVDWLTD 253
           L +R E  L+ ++    +   E  KLE LC    + Y     T +++FV TR  VD L +
Sbjct: 357 LTQRFEEKLQELESVSRDPSNENPKLEDLCFILQEEYHLNPETITILFVKTRALVDALKN 416
Query: 254 ------KMRSRDHTVSATHGDMDQNT------RDIIMREFR-SGSSRVLITTDLLARGID 300
                 K+      +    G  +QNT      +  I+  F+ SG   +LI T +   GID
Sbjct: 417 WIEGNPKLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAFKASGDHNILIATSVADEGID 476
Query: 301 VQQVSLVINYD 311
           + Q +LVI Y+
Sbjct: 477 IAQCNLVILYE 487

>pdb|2V1X|A Chain A, Crystal Structure Of Human Recq-Like Dna Helicase Length = 591

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/98 (22%), Positives = 47/98 (47%)
Query: 239 VIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARG 298
           +I+  +++  + +T  +++      A H +++   +  + R++ +   +V++ T     G
Sbjct: 271 IIYCFSQKDSEQVTVSLQNLGIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATVAFGMG 330
Query: 299 IDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAI 336
           ID   V  VI++ +    ENY    GR+GR   K   I
Sbjct: 331 IDKPDVRFVIHHSMSKSMENYYQESGRAGRDDMKADCI 368

>pdb|4I1S|A Chain A, Melanoma Differentiation Associated Protein-5 Helicase Domain Complex With Inhibitor Non-structural Protein V Length = 243

Iteration: 1
 Score = 41.6 bits (96), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 31/121 (25%), Positives = 53/121 (43%), Gaps = 22/121 (18%)
Query: 216 VEKEEWKLETLCDLYETLA--------ITQSVIFVNTRRKV----DWLTDKMR------S 257
            E  E++ E L  L  T+           + +IF  TR+       W+TD  +       
Sbjct: 123 AENPEYENEKLTKLRNTIXEHFTRTEESARGIIFTKTRQSAYALSQWITDNKKFAEVGVK 182
Query: 258 RDHTVSATHGD----MDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLP 313
             H + A H        QN +  ++ +FR+G   +LI T +   G+D+++ ++VI Y L 
Sbjct: 183 AHHLIGAGHSSEFKPXTQNEQREVISKFRTGKINLLIATTVAEEGLDIKECNIVIRYGLV 242
Query: 314 T 314
           T
Sbjct: 243 T 243

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	369
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	0.0
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	0.0
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	0.0
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	0.0
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	0.0
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	0.0
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	0.0
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	0.0
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	0.0
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	1e-136
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	1e-135
3bor_A	237	Human initiation factor 4A-II; translation initiat	1e-132
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	1e-129
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	1e-122
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	1e-120
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	1e-116
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	1e-116
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	1e-110
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	1e-110
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	1e-107
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	1e-107
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	1e-103
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	1e-101
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	1e-101
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	2e-97
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	6e-91
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	3e-79
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	5e-71
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	7e-69
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	2e-59
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	3e-58
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	3e-57
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	3e-56
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	9e-55
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	3e-54
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	8e-54
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	2e-53
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	7e-53
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	8e-45
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	3e-44
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	3e-24
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	1e-15
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	5e-17
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	6e-15
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	5e-14
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	3e-13
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	3e-11
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	7e-06
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	1e-10
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	8e-04
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	2e-10
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	2e-06
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	3e-10
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	7e-05
1yks_A	440	Genome polyprotein [contains: flavivirin protease	1e-09
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	1e-09
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	1e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-09
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-08
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	7e-08
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	3e-07
3b6e_A	216	Interferon-induced helicase C domain-containing P;	3e-07
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	7e-07
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	9e-07
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	1e-06
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	4e-06
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	7e-06
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	2e-05
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	4e-05
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	4e-05
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	1e-04
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	2e-04

>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 =  693 bits (1792), Expect = 0.0
 Identities = 251/369 (68%), Positives = 302/369 (81%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
           MGL+E+LLRGIYAYGFEKPSAIQQR I    KG DVI Q+QSGTGKTATF   +LQ LD 
Sbjct: 42  MGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDI 101

Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG 120
            + + QAL+LAPTRELA QI+K + ALGDY+ V+ HAC+GGT+V ED R L  G HVV G
Sbjct: 102 QVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAG 161

Query: 121 TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMP 180
           TPGRVFDM+RR+SLR   IKM VLDEADEML++GFK+QIYD+++ LP   QV + SAT+P
Sbjct: 162 TPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLP 221

Query: 181 PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVI 240
            E LE+T KFM  P+RILVKRDELTLEGIKQF+V VE+EEWK +TLCDLY+TL ITQ+VI
Sbjct: 222 HEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVI 281

Query: 241 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 300
           F NT+RKVDWLT+KMR  + TVS+ HGDM Q  R+ IM+EFRSG+SRVLI+TD+ ARG+D
Sbjct: 282 FCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLD 341

Query: 301 VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEE 360
           V QVSL+INYDLP   E Y+HRIGRSGR+GRKGVAINFV  DD R+L DI+++Y+  I+E
Sbjct: 342 VPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDE 401

Query: 361 LPSNVADLL 369
           +P NVADL+
Sbjct: 402 MPMNVADLI 410

>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 =  689 bits (1781), Expect = 0.0
 Identities = 276/370 (74%), Positives = 313/370 (84%), Gaps = 1/370 (0%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
           M L E+LLRGIYAYGFEKPSAIQQR I+P  KG DVI QAQSGTGKTATF   ILQQ++ 
Sbjct: 45  MNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIEL 104

Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQA-GVHVVV 119
            L   QALVLAPTRELAQQI+KV+ ALGDY+G   HAC+GGT+VR + + LQ    H++V
Sbjct: 105 DLKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIV 164

Query: 120 GTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATM 179
           GTPGRVFDML R+ L P YIKMFVLDEADEMLSRGFKDQIYDIFQ L +  QV + SATM
Sbjct: 165 GTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVVLLSATM 224

Query: 180 PPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSV 239
           P + LE+T+KFM  P+RILVK++ELTLEGI+QFY+NVE+EEWKL+TLCDLYETL ITQ+V
Sbjct: 225 PSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLCDLYETLTITQAV 284

Query: 240 IFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGI 299
           IF+NTRRKVDWLT+KM +RD TVSA HGDMDQ  RD+IMREFRSGSSRVLITTDLLARGI
Sbjct: 285 IFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGI 344

Query: 300 DVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIE 359
           DVQQVSLVINYDLPT  ENY+HRIGR GRFGRKGVAIN VT +D+R L DI+ FYN  IE
Sbjct: 345 DVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTEEDKRTLRDIETFYNTSIE 404

Query: 360 ELPSNVADLL 369
           E+P NVADL+
Sbjct: 405 EMPLNVADLI 414

>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 =  685 bits (1770), Expect = 0.0
 Identities = 240/369 (65%), Positives = 292/369 (79%), Gaps = 1/369 (0%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
           M L ENLLRG++ YGFE+PSAIQQR I+P  +G DV+ QAQSGTGKT TF    LQ++D 
Sbjct: 26  MELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDT 85

Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG 120
            +   QAL+LAPTRELA QI+KV+ AL  ++ +KVHAC+GGTS  ED   L+    +VVG
Sbjct: 86  SVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLR-DAQIVVG 144

Query: 121 TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMP 180
           TPGRVFD ++R+  R D IKMF+LDEADEMLS GFK+QIY IF LLP   QV + SATMP
Sbjct: 145 TPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTTQVVLLSATMP 204

Query: 181 PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVI 240
            + LE+T KFM  PVRILVK+DELTLEGIKQFYVNVE+EE+K E L DLY+++++TQ+VI
Sbjct: 205 NDVLEVTTKFMRNPVRILVKKDELTLEGIKQFYVNVEEEEYKYECLTDLYDSISVTQAVI 264

Query: 241 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 300
           F NTRRKV+ LT K+R+   TVSA + D+ Q  RD IM+EFRSGSSR+LI+TDLLARGID
Sbjct: 265 FCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGID 324

Query: 301 VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEE 360
           VQQVSLVINYDLP   ENY+HRIGR GRFGRKGVAINFVT +D   + +++KFY+  IEE
Sbjct: 325 VQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELEKFYSTQIEE 384

Query: 361 LPSNVADLL 369
           LPS++A LL
Sbjct: 385 LPSDIATLL 393

>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 =  651 bits (1681), Expect = 0.0
 Identities = 155/369 (42%), Positives = 218/369 (59%), Gaps = 2/369 (0%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
             L+  LL GI+  GFEKPS IQ+  I     G D++ +A++GTGKTA F    L+++  
Sbjct: 26  FYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKP 85

Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG 120
            L + QAL++ PTRELA Q  +V+R LG + G+      GGT++R+D   L   VH++VG
Sbjct: 86  KLNKIQALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLNETVHILVG 145

Query: 121 TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMP 180
           TPGRV D+  R+        +F++DEAD+MLSR FK  I  I   LP   Q  +FSAT P
Sbjct: 146 TPGRVLDLASRKVADLSDCSLFIMDEADKMLSRDFKTIIEQILSFLPPTHQSLLFSATFP 205

Query: 181 PEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVI 240
               E   K ++KP  I +  +ELTL+GI Q+Y  VE E  KL  L  L+  L I Q++I
Sbjct: 206 LTVKEFMVKHLHKPYEINLM-EELTLKGITQYYAFVE-ERQKLHCLNTLFSKLQINQAII 263

Query: 241 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID 300
           F N+  +V+ L  K+    ++   +H  M Q  R+ +  EFR G  R L+ +DLL RGID
Sbjct: 264 FCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRGID 323

Query: 301 VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEE 360
           +Q V++VIN+D P   E YLHRIGRSGRFG  G+AIN +  +D   L+ I++     I  
Sbjct: 324 IQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWNDRFNLYKIEQELGTEIAA 383

Query: 361 LPSNVADLL 369
           +P+ +   L
Sbjct: 384 IPATIDKSL 392

>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 =  633 bits (1635), Expect = 0.0
 Identities = 148/381 (38%), Positives = 223/381 (58%), Gaps = 15/381 (3%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGL--DVIQQAQSGTGKTATFCSGILQQL 58
           + L+  LL+G+YA GF +PS IQ+  +         ++I Q+QSGTGKTA F   +L Q+
Sbjct: 30  LRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQV 89

Query: 59  DYGLVQCQALVLAPTRELAQQIEKVMRALGDYL-GVKVHACVGGTSVREDQRILQAGVHV 117
           +      Q L L+PT ELA Q  KV+  +G +   +K+   V G  +   Q+I      +
Sbjct: 90  EPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKI---SEQI 146

Query: 118 VVGTPGRVFDMLRR-QSLRPDYIKMFVLDEADEMLS-RGFKDQIYDIFQLLPAKVQVGVF 175
           V+GTPG V D   + + + P  IK+FVLDEAD M++ +G +DQ   I ++LP   Q+ +F
Sbjct: 147 VIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLF 206

Query: 176 SATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAI 235
           SAT      +  +K +  P  I +KR+E TL+ IKQ+YV     + K + LC+LY  + I
Sbjct: 207 SATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVLCSSRDEKFQALCNLYGAITI 266

Query: 236 TQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLL 295
            Q++IF +TR+   WL  ++    H V+   G+M    R  ++  FR G  +VL+TT++ 
Sbjct: 267 AQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVC 326

Query: 296 ARGIDVQQVSLVINYDLPTQP------ENYLHRIGRSGRFGRKGVAINFVT-RDDERMLF 348
           ARGIDV+QVS+VIN+DLP         E YLHRIGR+GRFG++G+A+N V  +    +L 
Sbjct: 327 ARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHSMNILN 386

Query: 349 DIQKFYNVVIEELPSNVADLL 369
            IQ+ +N  IE L ++  D +
Sbjct: 387 RIQEHFNKKIERLDTDDLDEI 407

>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 =  631 bits (1629), Expect = 0.0
 Identities = 148/381 (38%), Positives = 223/381 (58%), Gaps = 15/381 (3%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGL--DVIQQAQSGTGKTATFCSGILQQL 58
           + L+  LL+G+YA GF +PS IQ+  +         ++I Q+QSGTGKTA F   +L Q+
Sbjct: 97  LRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQV 156

Query: 59  DYGLVQCQALVLAPTRELAQQIEKVMRALGDYL-GVKVHACVGGTSVREDQRILQAGVHV 117
           +      Q L L+PT ELA Q  KV+  +G +   +K+   V G  +   Q+I      +
Sbjct: 157 EPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKI---SEQI 213

Query: 118 VVGTPGRVFDMLRR-QSLRPDYIKMFVLDEADEMLS-RGFKDQIYDIFQLLPAKVQVGVF 175
           V+GTPG V D   + + + P  IK+FVLDEAD M++ +G +DQ   I ++LP   Q+ +F
Sbjct: 214 VIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLF 273

Query: 176 SATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAI 235
           SAT      +  +K +  P  I +KR+E TL+ IKQ+YV     + K + LC+LY  + I
Sbjct: 274 SATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVLCSSRDEKFQALCNLYGAITI 333

Query: 236 TQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLL 295
            Q++IF +TR+   WL  ++    H V+   G+M    R  ++  FR G  +VL+TT++ 
Sbjct: 334 AQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVC 393

Query: 296 ARGIDVQQVSLVINYDLPTQP------ENYLHRIGRSGRFGRKGVAINFVT-RDDERMLF 348
           ARGIDV+QVS+VIN+DLP         E YLHRIGR+GRFG++G+A+N V  +    +L 
Sbjct: 394 ARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHSMNILN 453

Query: 349 DIQKFYNVVIEELPSNVADLL 369
            IQ+ +N  IE L ++  D +
Sbjct: 454 RIQEHFNKKIERLDTDDLDEI 474

>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 =  626 bits (1616), Expect = 0.0
 Identities = 149/380 (39%), Positives = 231/380 (60%), Gaps = 15/380 (3%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGL--DVIQQAQSGTGKTATFCSGILQQL 58
           +GL   LL+GIYA  F+KPS IQ+R +         ++I Q+QSGTGKTA F   +L ++
Sbjct: 10  LGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRV 69

Query: 59  DYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVV 118
           +      QA+ LAP+RELA+Q  +V++ +G +  +     V  +  +  Q        V+
Sbjct: 70  NPEDASPQAICLAPSRELARQTLEVVQEMGKFTKITSQLIVPDSFEKNKQI----NAQVI 125

Query: 119 VGTPGRVFDMLRRQSLRPDYIKMFVLDEADEML-SRGFKDQIYDIFQLLPAKVQVGVFSA 177
           VGTPG V D++RR+ ++   IK+FVLDEAD ML  +G  DQ   + + LP   Q+ +FSA
Sbjct: 126 VGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVKRFLPKDTQLVLFSA 185

Query: 178 TMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQ 237
           T      +  +K +     + ++ +E+ ++ IKQ Y++ + E  K + L +LY  + I  
Sbjct: 186 TFADAVRQYAKKIVPNANTLELQTNEVNVDAIKQLYMDCKNEADKFDVLTELYGLMTIGS 245

Query: 238 SVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLAR 297
           S+IFV T++  + L  K++S  H VS  HGD+    RD ++ +FR G S+VLITT++LAR
Sbjct: 246 SIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLAR 305

Query: 298 GIDVQQVSLVINYDLPTQ------PENYLHRIGRSGRFGRKGVAINFVT-RDDERMLFDI 350
           GID+  VS+V+NYDLPT       P  Y+HRIGR+GRFGRKGVAI+FV  ++   +L  I
Sbjct: 306 GIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDKNSFNILSAI 365

Query: 351 QKFY-NVVIEELPSNVADLL 369
           QK++ ++ +  +P++  D +
Sbjct: 366 QKYFGDIEMTRVPTDDWDEV 385

>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 1xtj_A* 1xtk_A Length = 391

 Score =  598 bits (1545), Expect = 0.0
 Identities = 146/370 (39%), Positives = 216/370 (58%), Gaps = 6/370 (1%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
             L+  LLR I   GFE PS +Q   I     G+DV+ QA+SG GKTA F    LQQL+ 
Sbjct: 13  FLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEP 72

Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYL-GVKVHACVGGTSVREDQRILQAGV-HVV 118
              Q   LV+  TRELA QI K       Y+  VKV    GG S+++D+ +L+    H+V
Sbjct: 73  VTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIV 132

Query: 119 VGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSR-GFKDQIYDIFQLLPAKVQVGVFSA 177
           VGTPGR+  + R +SL   +IK F+LDE D+ML +   +  + +IF++ P + QV +FSA
Sbjct: 133 VGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSA 192

Query: 178 TMPPEALEITRKFMNKPVRILVKRD-ELTLEGIKQFYVNVEKEEWKLETLCDLYETLAIT 236
           T+  E   + RKFM  P+ I V  + +LTL G++Q+YV + K+  K   L DL + L   
Sbjct: 193 TLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKL-KDNEKNRKLFDLLDVLEFN 251

Query: 237 QSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLA 296
           Q VIFV + ++   L   +  ++    A H  M Q  R    ++F+    R+L+ T+L  
Sbjct: 252 QVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFG 311

Query: 297 RGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVT-RDDERMLFDIQKFYN 355
           RG+D+++V++  NYD+P   + YLHR+ R+GRFG KG+AI FV+  +D ++L D+Q  + 
Sbjct: 312 RGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFE 371

Query: 356 VVIEELPSNV 365
           V I ELP  +
Sbjct: 372 VNISELPDEI 381

>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 =  392 bits (1010), Expect = e-136
 Identities = 129/365 (35%), Positives = 204/365 (55%), Gaps = 15/365 (4%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKG-LDVIQQAQSGTGKTATFCSGILQQLD 59
           + L +N+L  I   GFEKP+ IQ + I  F     +++ QA++G+GKTA+F   +++ ++
Sbjct: 11  LNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVN 70

Query: 60  YGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVV 119
                 +A++L PTRELA Q+   + +L     +K+    GG ++    + L+   ++VV
Sbjct: 71  EN-NGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALK-NANIVV 128

Query: 120 GTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATM 179
           GTPGR+ D + R +L    +K F+LDEADEML+ GF   +  I        ++ +FSATM
Sbjct: 129 GTPGRILDHINRGTLNLKNVKYFILDEADEMLNMGFIKDVEKILNACNKDKRILLFSATM 188

Query: 180 PPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLC---DLYETLAIT 236
           P E L + +K+M     I  K        I+Q YV V  E  + E LC      E   + 
Sbjct: 189 PREILNLAKKYMGDYSFIKAK----INANIEQSYVEV-NENERFEALCRLLKNKEFYGL- 242

Query: 237 QSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLA 296
              +F  T+R    L   +R       A HGD+ Q+ R+ ++R F+    R+LI TD+++
Sbjct: 243 ---VFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVMS 299

Query: 297 RGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNV 356
           RGIDV  ++ VINY LP  PE+Y+HRIGR+GR G+KG AI+ + R + + L  I++   +
Sbjct: 300 RGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKKGKAISIINRREYKKLRYIERAMKL 359

Query: 357 VIEEL 361
            I++L
Sbjct: 360 KIKKL 364

>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 =  384 bits (989), Expect = e-135
 Identities = 130/207 (62%), Positives = 157/207 (75%), Gaps = 1/207 (0%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
           M L ENLLRG++ YGFE+PSAIQQR I+P  +G DV+ QAQSGTGKT TF    LQ++D 
Sbjct: 19  MELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDT 78

Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG 120
            +   QAL+LAPTRELA QI+KV+ AL  ++ +KVHAC+GGTS  ED   L+    +VVG
Sbjct: 79  SVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLR-DAQIVVG 137

Query: 121 TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMP 180
           TPGRVFD ++R+  R D IKMF+LDEADEMLS GFK+QIY IF LLP   QV + SATMP
Sbjct: 138 TPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTTQVVLLSATMP 197

Query: 181 PEALEITRKFMNKPVRILVKRDELTLE 207
            + LE+T KFM  PVRILVK+DELTLE
Sbjct: 198 NDVLEVTTKFMRNPVRILVKKDELTLE 224

>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 =  376 bits (968), Expect = e-132
 Identities = 141/203 (69%), Positives = 165/203 (81%), Gaps = 1/203 (0%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
           M L+E+LLRGIYAYGFEKPSAIQQR I+P  KG DVI QAQSGTGKTATF   ILQQL+ 
Sbjct: 35  MNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQLEI 94

Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQA-GVHVVV 119
              + QALVLAPTRELAQQI+KV+ ALGDY+G   HAC+GGT+VR + + LQA   H+VV
Sbjct: 95  EFKETQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRNEMQKLQAEAPHIVV 154

Query: 120 GTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATM 179
           GTPGRVFDML R+ L P +IKMFVLDEADEMLSRGFKDQIY+IFQ L   +QV + SATM
Sbjct: 155 GTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSRGFKDQIYEIFQKLNTSIQVVLLSATM 214

Query: 180 PPEALEITRKFMNKPVRILVKRD 202
           P + LE+T+KFM  P+RILVK++
Sbjct: 215 PTDVLEVTKKFMRDPIRILVKKE 237

>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 =  373 bits (960), Expect = e-129
 Identities = 103/351 (29%), Positives = 175/351 (49%), Gaps = 18/351 (5%)

Query: 3   LQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGL 62
           + E + + I   GF+  + +Q + I    +G +V+ +A++G+GKTA +   IL+      
Sbjct: 1   MNEKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILEL----- 55

Query: 63  VQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTP 122
              ++LV+ PTREL +Q+   +R +G Y+  KV    GG   +     ++    +VV TP
Sbjct: 56  -GMKSLVVTPTRELTRQVASHIRDIGRYMDTKVAEVYGGMPYKAQINRVR-NADIVVATP 113

Query: 123 GRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMPPE 182
           GR+ D+  +  +     ++ ++DEAD M   GF D I  I      +   G+FSAT+P E
Sbjct: 114 GRLLDLWSKGVIDLSSFEIVIIDEADLMFEMGFIDDIKIILAQTSNRKITGLFSATIPEE 173

Query: 183 ALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFV 242
             ++ + F+     I      + L  ++  +V+V+       +             ++FV
Sbjct: 174 IRKVVKDFITNYEEIEAC---IGLANVEHKFVHVKD---DWRSKVQALRENKDKGVIVFV 227

Query: 243 NTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQ 302
            TR +V  L     +         GD+ Q+ R+  +  FR G   +LITTD+ +RG+D+ 
Sbjct: 228 RTRNRVAKLVRLFDN----AIELRGDLPQSVRNRNIDAFREGEYDMLITTDVASRGLDIP 283

Query: 303 QVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKF 353
            V  VIN+D P     Y+HRIGR+GR GRKG AI F+   +  +  +++K 
Sbjct: 284 LVEKVINFDAPQDLRTYIHRIGRTGRMGRKGEAITFILN-EYWLEKEVKKV 333

>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 =  362 bits (932), Expect = e-122
 Identities = 108/393 (27%), Positives = 194/393 (49%), Gaps = 31/393 (7%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVP--FCKGLDVIQQAQSGTGKTATFCSGILQQL 58
             L + + + I    F   + +QQ+ I P    +  DVI +A++GTGKT  F   I Q L
Sbjct: 26  GVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHL 85

Query: 59  DYGLVQ----CQALVLAPTRELAQQIEKVMRALGDY----LGVKVHACVGGTSV-REDQR 109
                      +A+++APTR+LA QIE  ++ + D           + VGGT       +
Sbjct: 86  INTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNK 145

Query: 110 ILQAGVHVVVGTPGRVFDMLRRQSLR-PDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPA 168
           + +   ++V+ TPGR+ D+L + S +   ++   VLDEAD +L  GF+D +  I  +L  
Sbjct: 146 MNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGILNE 205

Query: 169 K-------VQVGVFSATMPPEALEITRKFMNKPVRILV----KRDELTLEGIKQFYVNVE 217
           K       ++  +FSAT+  +  ++    MNK   + +    K +    E I Q  V  E
Sbjct: 206 KNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISE 265

Query: 218 KEEWKL-----ETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRS---RDHTVSATHGDM 269
           K    +          + E  +  +++IF  T +   +L   +++   +D  +   HG +
Sbjct: 266 KFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKI 325

Query: 270 DQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRF 329
            QN R  +++ F+   S +L+ TD+ ARG+D   V  V+   +P++  NY+HRIGR+ R 
Sbjct: 326 TQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARS 385

Query: 330 GRKGVAINFVTRDDERMLFDIQKFYNVVIEELP 362
           G++G ++ F+ +D+   + +++   N+VI +  
Sbjct: 386 GKEGSSVLFICKDELPFVRELEDAKNIVIAKQE 418

>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 =  358 bits (920), Expect = e-120
 Identities = 109/392 (27%), Positives = 193/392 (49%), Gaps = 31/392 (7%)

Query: 2   GLQENLLRGIYAYGFEKPSAIQQRGIVPF--CKGLDVIQQAQSGTGKTATFCSGILQQLD 59
            L + + + I    F   + +QQ+ I P    +  DVI +A++GTGKT  F   I Q L 
Sbjct: 78  VLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLI 137

Query: 60  YGLVQ----CQALVLAPTRELAQQIEKVMRALGDY----LGVKVHACVGGTSVREDQRIL 111
                     +A+++APTR+LA QIE  ++ + D           + VGGT  R     +
Sbjct: 138 NTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKM 197

Query: 112 Q-AGVHVVVGTPGRVFDMLRRQSLR-PDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAK 169
                ++V+ TPGR+ D+L + S +   ++   VLDEAD +L  GF+D +  I  +L  K
Sbjct: 198 NKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGILNEK 257

Query: 170 -------VQVGVFSATMPPEALEITRKFMNKPVRILV----KRDELTLEGIKQFYVNVEK 218
                  ++  +FSAT+  +  ++    MNK   + +    K +    E I Q  V  EK
Sbjct: 258 NSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEK 317

Query: 219 EEWKL-----ETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRS---RDHTVSATHGDMD 270
               +          + E  +  +++IF  T +   +L   +++   +D  +   HG + 
Sbjct: 318 FANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKIT 377

Query: 271 QNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFG 330
           QN R  +++ F+   S +L+ TD+ ARG+D   V  V+   +P++  NY+HRIGR+ R G
Sbjct: 378 QNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSG 437

Query: 331 RKGVAINFVTRDDERMLFDIQKFYNVVIEELP 362
           ++G ++ F+ +D+   + +++   N+VI +  
Sbjct: 438 KEGSSVLFICKDELPFVRELEDAKNIVIAKQE 469

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19 Length = 165

 Score =  334 bits (859), Expect = e-116
 Identities = 112/164 (68%), Positives = 137/164 (83%)

Query: 206 LEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSAT 265
           LEGIKQFYVNVE+EE+K E L DLY+++++TQ+VIF NTRRKV+ LT K+R+   TVSA 
Sbjct: 1   LEGIKQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAI 60

Query: 266 HGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGR 325
           + D+ Q  RD IM+EFRSGSSR+LI+TDLLARGIDVQQVSLVINYDLP   ENY+HRIGR
Sbjct: 61  YSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGR 120

Query: 326 SGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPSNVADLL 369
            GRFGRKGVAINFVT +D   + +++KFY+  IEELPS++A LL
Sbjct: 121 GGRFGRKGVAINFVTNEDVGAMRELEKFYSTQIEELPSDIATLL 164

>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 =  336 bits (865), Expect = e-116
 Identities = 79/202 (39%), Positives = 118/202 (58%), Gaps = 3/202 (1%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
           + L   +L G+ A GFE+PS +Q + I     GLD+I QA+SGTGKT  F +  L  L  
Sbjct: 29  LLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDSLVL 88

Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYL-GVKVHACVGGTSVREDQRILQAGVHVVV 119
             +  Q L+LAPTRE+A QI  V+ A+G  + G++ H  +GGT + +D+  L+   H+ V
Sbjct: 89  ENLSTQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRLK-KCHIAV 147

Query: 120 GTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRG-FKDQIYDIFQLLPAKVQVGVFSAT 178
           G+PGR+  ++    L P  I++F+LDEAD++L  G F++QI  I+  LPA  Q+   SAT
Sbjct: 148 GSPGRIKQLIELDYLNPGSIRLFILDEADKLLEEGSFQEQINWIYSSLPASKQMLAVSAT 207

Query: 179 MPPEALEITRKFMNKPVRILVK 200
            P        K+M  P  + + 
Sbjct: 208 YPEFLANALTKYMRDPTFVRLN 229

>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 =  324 bits (832), Expect = e-110
 Identities = 76/207 (36%), Positives = 115/207 (55%), Gaps = 8/207 (3%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGL--DVIQQAQSGTGKTATFCSGILQQL 58
           + L+  LL+G+YA GF +PS IQ+  +         ++I Q+QSGTGKTA F   +L Q+
Sbjct: 97  LRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQV 156

Query: 59  DYGLVQCQALVLAPTRELAQQIEKVMRALGDYL-GVKVHACVGGTSVREDQRILQAGVHV 117
           +      Q L L+PT ELA Q  KV+  +G +   +K+   V G  +   Q+I      +
Sbjct: 157 EPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKI---SEQI 213

Query: 118 VVGTPGRVFDMLRRQ-SLRPDYIKMFVLDEADEMLS-RGFKDQIYDIFQLLPAKVQVGVF 175
           V+GTPG V D   +   + P  IK+FVLDEAD M++ +G +DQ   I ++LP   Q+ +F
Sbjct: 214 VIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLF 273

Query: 176 SATMPPEALEITRKFMNKPVRILVKRD 202
           SAT      +  +K +  P  I +KR+
Sbjct: 274 SATFEDSVWKFAQKVVPDPNVIKLKRE 300

>2rb4_A ATP-dependent RNA helicase DDX25; rossmann fold, structural genomics, structural consortium, SGC, alternative initiation, ATP-binding, devel protein; 2.80A {Homo sapiens} Length = 175

 Score =  318 bits (818), Expect = e-110
 Identities = 74/173 (42%), Positives = 108/173 (62%), Gaps = 6/173 (3%)

Query: 203 ELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTV 262
            LTL  I+Q+YV  E  + K + LC++Y ++ I Q++IF  TRR   WLT +M    H V
Sbjct: 2   MLTLNNIRQYYVLCEHRKDKYQALCNIYGSITIGQAIIFCQTRRNAKWLTVEMIQDGHQV 61

Query: 263 SATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQ------P 316
           S   G++    R  I++ FR G  +VLITT++ ARGIDV+QV++V+N+DLP +       
Sbjct: 62  SLLSGELTVEQRASIIQRFRDGKEKVLITTNVCARGIDVKQVTIVVNFDLPVKQGEEPDY 121

Query: 317 ENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPSNVADLL 369
           E YLHRIGR+GRFG+KG+A N +  D+   L  IQ  +N  I++L +   D +
Sbjct: 122 ETYLHRIGRTGRFGKKGLAFNMIEVDELPSLMKIQDHFNSSIKQLNAEDMDEI 174

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens} Length = 417

 Score =  319 bits (821), Expect = e-107
 Identities = 125/375 (33%), Positives = 188/375 (50%), Gaps = 24/375 (6%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFC----SGILQ 56
           + + E ++  I    + +P+ +Q+  I    +  D++  AQ+G+GKTA F     S I  
Sbjct: 20  VEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYS 79

Query: 57  QLDYGLVQC--------------QALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGT 102
                 ++                +LVLAPTRELA QI +  R       V+     GG 
Sbjct: 80  DGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRPCVVYGGA 139

Query: 103 SVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDI 162
            + +  R L+ G H++V TPGR+ DM+ R  +  D+ K  VLDEAD ML  GF+ QI  I
Sbjct: 140 DIGQQIRDLERGCHLLVATPGRLVDMMERGKIGLDFCKYLVLDEADRMLDMGFEPQIRRI 199

Query: 163 FQLL--PAKV--QVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEK 218
            +    P K      +FSAT P E   + R F+++ + + V R   T E I Q  V VE+
Sbjct: 200 VEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGRVGSTSENITQKVVWVEE 259

Query: 219 EEWKLETLCDLYETLAITQSV-IFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDII 277
            + K   L DL           +FV T++  D L D +    +  ++ HGD  Q  R+  
Sbjct: 260 SD-KRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEA 318

Query: 278 MREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAIN 337
           + +FRSG S +L+ T + ARG+D+  V  VIN+DLP+  E Y+HRIGR+GR G  G+A +
Sbjct: 319 LHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATS 378

Query: 338 FVTRDDERMLFDIQK 352
           F    +  +  D+  
Sbjct: 379 FFNERNINITKDLLD 393

>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 =  319 bits (820), Expect = e-107
 Identities = 112/354 (31%), Positives = 188/354 (53%), Gaps = 9/354 (2%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFC----SGILQ 56
             L++ ++  +   G++ P+ IQ+  I     G D++  AQ+G+GKTA F     S +L+
Sbjct: 61  ADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPILSKLLE 120

Query: 57  QLDYGLVQ-CQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGV 115
                 +   Q ++++PTRELA QI    R       +K+    GGTS R     +  G 
Sbjct: 121 DPHELELGRPQVVIVSPTRELAIQIFNEARKFAFESYLKIGIVYGGTSFRHQNECITRGC 180

Query: 116 HVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQ--LLPAKVQVG 173
           HVV+ TPGR+ D + R  +  +  +  VLDEAD ML  GF + +  I     +  + Q  
Sbjct: 181 HVVIATPGRLLDFVDRTFITFEDTRFVVLDEADRMLDMGFSEDMRRIMTHVTMRPEHQTL 240

Query: 174 VFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETL 233
           +FSAT P E   +  +F+   V + +         +KQ    V K   K   L ++    
Sbjct: 241 MFSATFPEEIQRMAGEFLKNYVFVAIGIVGGACSDVKQTIYEVNKYA-KRSKLIEILSEQ 299

Query: 234 AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTD 293
           A   +++FV T+R  D+L   +  ++   ++ HGD  Q+ R+  +R+F++GS +VLI T 
Sbjct: 300 A-DGTIVFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATS 358

Query: 294 LLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERML 347
           + +RG+D++ +  VINYD+P++ ++Y+HRIGR+GR G  G A +F   + +R +
Sbjct: 359 VASRGLDIKNIKHVINYDMPSKIDDYVHRIGRTGRVGNNGRATSFFDPEKDRAI 412

>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 =  303 bits (779), Expect = e-103
 Identities = 85/202 (42%), Positives = 117/202 (57%), Gaps = 3/202 (1%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
             L+  LLR I   GFE PS +Q   I     G+DV+ QA+SG GKTA F    LQQL+ 
Sbjct: 19  FLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEP 78

Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYL-GVKVHACVGGTSVREDQRILQAGV-HVV 118
              Q   LV+  TRELA QI K       Y+  VKV    GG S+++D+ +L+    H+V
Sbjct: 79  VTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIV 138

Query: 119 VGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSR-GFKDQIYDIFQLLPAKVQVGVFSA 177
           VGTPGR+  + R +SL   +IK F+LDE D+ML +   +  + +IF++ P + QV +FSA
Sbjct: 139 VGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSA 198

Query: 178 TMPPEALEITRKFMNKPVRILV 199
           T+  E   + RKFM  P+ I V
Sbjct: 199 TLSKEIRPVCRKFMQDPMEIFV 220

>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19 Length = 206

 Score =  297 bits (763), Expect = e-101
 Identities = 75/198 (37%), Positives = 119/198 (60%), Gaps = 1/198 (0%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
             L+  LL GI+  G+EKPS IQ+  I     G D++ +A++GTGK+  +   +L++LD 
Sbjct: 8   YCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDL 67

Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYL-GVKVHACVGGTSVREDQRILQAGVHVVV 119
                QA+V+ PTRELA Q+ ++   +  ++ G KV A  GGT++R+D   L   VHVV+
Sbjct: 68  KKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVI 127

Query: 120 GTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATM 179
            TPGR+ D++++   + D+++M VLDEAD++LS+ F   + DI   LP   Q+ ++SAT 
Sbjct: 128 ATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNRQILLYSATF 187

Query: 180 PPEALEITRKFMNKPVRI 197
           P    +     + KP  I
Sbjct: 188 PLSVQKFMNSHLEKPYEI 205

>1t5i_A C_terminal domain of A probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; 1.90A {Homo sapiens} SCOP: c.37.1.19 Length = 172

 Score =  294 bits (756), Expect = e-101
 Identities = 59/162 (36%), Positives = 96/162 (59%), Gaps = 2/162 (1%)

Query: 205 TLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSA 264
           +L G++Q+YV + K+  K   L DL + L   Q VIFV + ++   L   +  ++    A
Sbjct: 2   SLHGLQQYYVKL-KDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIA 60

Query: 265 THGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIG 324
            H  M Q  R    ++F+    R+L+ T+L  RG+D+++V++  NYD+P   + YLHR+ 
Sbjct: 61  IHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVA 120

Query: 325 RSGRFGRKGVAINFVT-RDDERMLFDIQKFYNVVIEELPSNV 365
           R+GRFG KG+AI FV+  +D ++L D+Q  + V I ELP  +
Sbjct: 121 RAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEI 162

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis} Length = 163

 Score =  285 bits (732), Expect = 2e-97
 Identities = 65/161 (40%), Positives = 96/161 (59%), Gaps = 1/161 (0%)

Query: 203 ELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTV 262
            LT   I+   + V +EE K   L D+  T      +IF  T+  V+ LTD++    +  
Sbjct: 4   GLTTRNIEHAVIQV-REENKFSLLKDVLMTENPDSCIIFCRTKEHVNQLTDELDDLGYPC 62

Query: 263 SATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHR 322
              HG M Q  R  +M EF+ G  R L+ TD+ ARGID++ +SLVINYDLP + E+Y+HR
Sbjct: 63  DKIHGGMIQEDRFDVMNEFKRGEYRYLVATDVAARGIDIENISLVINYDLPLEKESYVHR 122

Query: 323 IGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPS 363
            GR+GR G KG AI+FVT  ++R L DI+++    I+++ +
Sbjct: 123 TGRTGRAGNKGKAISFVTAFEKRFLADIEEYIGFEIQKIEA 163

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A* Length = 414

 Score =  278 bits (712), Expect = 6e-91
 Identities = 64/392 (16%), Positives = 131/392 (33%), Gaps = 50/392 (12%)

Query: 3   LQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGL 62
             E+          +  +  Q+       +G      A +G GKT       L     G 
Sbjct: 6   EYEDFRSFFKKKFGKDLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLARKGK 65

Query: 63  VQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSV----REDQRILQAGVHVV 118
              ++ ++ PT  L +Q  + ++ L D   VK+             + ++   +   H++
Sbjct: 66  ---KSALVFPTVTLVKQTLERLQKLADE-KVKIFGFYSSMKKEEKEKFEKSFEEDDYHIL 121

Query: 119 VGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSAT 178
           V +   V     R+ L         +D+ D +L          +   +P ++    FS  
Sbjct: 122 VFSTQFVSK--NREKLSQKRFDFVFVDDVDAVLKASRNIDTLLMMVGIPEEIIRKAFSTI 179

Query: 179 MPPEALEITRK---------------------FMNKPVRILVKRDELTLEGIKQFYVNVE 217
              +  E  +                           +   V R       I    ++  
Sbjct: 180 KQGKIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLLNFTVGRLVSVARNITHVRISSR 239

Query: 218 KEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDII 277
            +E KL  L +++    +    IF  T  +   L + ++     V  T  + ++N     
Sbjct: 240 SKE-KLVELLEIFRDGIL----IFAQTEEEGKELYEYLKRFKFNVGETWSEFEKN----- 289

Query: 278 MREFRSGSSRVLITTD----LLARGIDV-QQVSLVINYDLP--TQPENYLHRIGRSGRFG 330
             +F+ G   +LI        L RG+D+ +++  VI +  P       Y+   GRS R  
Sbjct: 290 FEDFKVGKINILIGVQAYYGKLTRGVDLPERIKYVIFWGTPSGPDVYTYIQASGRSSRIL 349

Query: 331 RKGV--AINFVTRDDERMLFDIQKFYNVVIEE 360
              +   ++ +  +DE +   ++    ++ EE
Sbjct: 350 NGVLVKGVSVIFEEDEEIFESLKTRLLLIAEE 381

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19 Length = 219

 Score =  241 bits (617), Expect = 3e-79
 Identities = 66/205 (32%), Positives = 105/205 (51%), Gaps = 4/205 (1%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
              Q  ++  I    F KP+ IQ+R I    +G  ++ Q+Q+GTGKT  +   I++++  
Sbjct: 9   FPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKP 68

Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYL----GVKVHACVGGTSVREDQRILQAGVH 116
              + QA++ APTRELA QI      +  +      +     +GGT  ++    L    H
Sbjct: 69  ERAEVQAVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLNVQPH 128

Query: 117 VVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFS 176
           +V+GTPGR+ D +R Q+L      + V+DEAD ML  GF   +  I   +P  +Q+ VFS
Sbjct: 129 IVIGTPGRINDFIREQALDVHTAHILVVDEADLMLDMGFITDVDQIAARMPKDLQMLVFS 188

Query: 177 ATMPPEALEITRKFMNKPVRILVKR 201
           AT+P +     +K+M  P  + V  
Sbjct: 189 ATIPEKLKPFLKKYMENPTFVHVLE 213

>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 =  219 bits (561), Expect = 5e-71
 Identities = 75/204 (36%), Positives = 110/204 (53%), Gaps = 5/204 (2%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
             L+  +L  ++  G   P+ IQ   +    +G D+I QA++GTGKT  F   I ++L  
Sbjct: 6   FPLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAERLAP 65

Query: 61  GLVQC---QALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHV 117
              +    +ALVL PTRELA Q+   + A+  +L  KV A  GGT   + +  L  G   
Sbjct: 66  SQERGRKPRALVLTPTRELALQVASELTAVAPHL--KVVAVYGGTGYGKQKEALLRGADA 123

Query: 118 VVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSA 177
           VV TPGR  D LR+  L    +++ VLDEADEMLS GF++++  +    P   Q  +FSA
Sbjct: 124 VVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSMGFEEEVEALLSATPPSRQTLLFSA 183

Query: 178 TMPPEALEITRKFMNKPVRILVKR 201
           T+P  A  +  ++M  PV I V +
Sbjct: 184 TLPSWAKRLAERYMKNPVLINVIK 207

>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 =  216 bits (551), Expect = 7e-69
 Identities = 67/201 (33%), Positives = 102/201 (50%), Gaps = 1/201 (0%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
           +G+ + L       G+ KP+ IQ   I    +G D+I  A++G+GKT  F   IL  L  
Sbjct: 48  LGVTDVLCEACDQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPILNALLE 107

Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG 120
              +  ALVL PTRELA QI +   ALG  +GV+    VGG         L    H+++ 
Sbjct: 108 TPQRLFALVLTPTRELAFQISEQFEALGSSIGVQSAVIVGGIDSMSQSLALAKKPHIIIA 167

Query: 121 TPGRVFDMLRRQ-SLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATM 179
           TPGR+ D L          +K  V+DEAD +L+  F+ ++  I +++P   +  +FSATM
Sbjct: 168 TPGRLIDHLENTKGFNLRALKYLVMDEADRILNMDFETEVDKILKVIPRDRKTFLFSATM 227

Query: 180 PPEALEITRKFMNKPVRILVK 200
             +  ++ R  +  PV+  V 
Sbjct: 228 TKKVQKLQRAALKNPVKCAVS 248

>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 =  191 bits (487), Expect = 2e-59
 Identities = 59/204 (28%), Positives = 100/204 (49%), Gaps = 6/204 (2%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
             L +  L+G+    +   + IQ++ I    +G DV+  A++G+GKT  F   +L+ L  
Sbjct: 30  FPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEALYR 89

Query: 61  G----LVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVH 116
                      L+++PTRELA Q  +V+R +G          +GG  ++ +   +   ++
Sbjct: 90  LQWTSTDGLGVLIISPTRELAYQTFEVLRKVGKNHDFSAGLIIGGKDLKHEAERIN-NIN 148

Query: 117 VVVGTPGRVFD-MLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVF 175
           ++V TPGR+   M    S     ++M VLDEAD +L  GF D +  + + LP K Q  +F
Sbjct: 149 ILVCTPGRLLQHMDETVSFHATDLQMLVLDEADRILDMGFADTMNAVIENLPKKRQTLLF 208

Query: 176 SATMPPEALEITRKFMNKPVRILV 199
           SAT      ++ R  +  P  + V
Sbjct: 209 SATQTKSVKDLARLSLKNPEYVWV 232

>2yjt_D ATP-dependent RNA helicase SRMB, regulator of ribonuclease activity A; hydrolase inhibitor-hydrolase complex, DEAD box RNA helicase; 2.90A {Escherichia coli} Length = 170

 Score =  185 bits (473), Expect = 3e-58
 Identities = 53/154 (34%), Positives = 80/154 (51%)

Query: 207 EGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATH 266
           + I Q+Y   +  E K   L  L +    T+S++FV  R +V  L + +R          
Sbjct: 2   KKIHQWYYRADDLEHKTALLVHLLKQPEATRSIVFVRKRERVHELANWLREAGINNCYLE 61

Query: 267 GDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRS 326
           G+M Q  R+  ++    G   VL+ TD+ ARGID+  VS V N+D+P   + YLHRIGR+
Sbjct: 62  GEMVQGKRNEAIKRLTEGRVNVLVATDVAARGIDIPDVSHVFNFDMPRSGDTYLHRIGRT 121

Query: 327 GRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEE 360
            R GRKG AI+ V   D  +L  + ++    I+ 
Sbjct: 122 ARAGRKGTAISLVEAHDHLLLGKVGRYIEEPIKA 155

>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 =  185 bits (473), Expect = 3e-57
 Identities = 54/206 (26%), Positives = 99/206 (48%), Gaps = 8/206 (3%)

Query: 2   GLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQL-DY 60
            +   LL+ I   GF+ P+ IQ + I     G +++  A +G+GKT  F   IL QL   
Sbjct: 35  KINSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMQLKQP 94

Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQ-RILQAGVHVVV 119
                +AL+++PTRELA QI + +  + +  G ++H         +           ++V
Sbjct: 95  ANKGFRALIISPTRELASQIHRELIKISEGTGFRIHMIHKAAVAAKKFGPKSSKKFDILV 154

Query: 120 GTPGRVFDMLRRQSLRPD--YIKMFVLDEADEML---SRGFKDQIYDIF-QLLPAKVQVG 173
            TP R+  +L++     D   ++  V+DE+D++      GF+DQ+  IF      KV+  
Sbjct: 155 TTPNRLIYLLKQDPPGIDLASVEWLVVDESDKLFEDGKTGFRDQLASIFLACTSHKVRRA 214

Query: 174 VFSATMPPEALEITRKFMNKPVRILV 199
           +FSAT   +  +  +  ++  + + +
Sbjct: 215 MFSATFAYDVEQWCKLNLDNVISVSI 240

>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 =  183 bits (467), Expect = 3e-56
 Identities = 70/224 (31%), Positives = 106/224 (47%), Gaps = 13/224 (5%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQL-D 59
           + L   +   I    +++P+ IQ+  I    +  D++  AQ+G+GKTA F   I+  L  
Sbjct: 28  LKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVC 87

Query: 60  YGLVQC--------QALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL 111
             L Q         + L+LAPTRELA QI    +       ++     GG       R +
Sbjct: 88  QDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIREV 147

Query: 112 QAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLL----P 167
           Q G H++V TPGR+ D + +  +  ++ K  VLDEAD ML  GF+ QI  I +       
Sbjct: 148 QMGCHLLVATPGRLVDFIEKNKISLEFCKYIVLDEADRMLDMGFEPQIRKIIEESNMPSG 207

Query: 168 AKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQ 211
              Q  +FSAT P E  ++   F+   + + V R   T + IKQ
Sbjct: 208 INRQTLMFSATFPKEIQKLAADFLYNYIFMTVGRVGSTSDSIKQ 251

>3eaq_A Heat resistant RNA dependent ATPase; DEAD box RNA helicase, dimer, ATP-binding, helicase, hydrolase, nucleotide-binding; 2.30A {Thermus thermophilus} PDB: 3ear_A 3eas_A Length = 212

 Score =  178 bits (453), Expect = 9e-55
 Identities = 47/157 (29%), Positives = 80/157 (50%), Gaps = 3/157 (1%)

Query: 209 IKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGD 268
            ++  V       +LE L DL    +  ++++F  T+ + + +   +    H   A HGD
Sbjct: 6   YEEEAVPA-PVRGRLEVLSDLLYVASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGD 64

Query: 269 MDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGR 328
           + Q  R+ ++  FR G  RVL+ TD+ ARG+D+ QV LV++Y LP + E Y HR GR+GR
Sbjct: 65  LSQGERERVLGAFRQGEVRVLVATDVAARGLDIPQVDLVVHYRLPDRAEAYQHRSGRTGR 124

Query: 329 FGRKGVAINFVTRDDERMLFDIQKFYNVVIE--ELPS 363
            GR G  +      + R +  +++      +    P+
Sbjct: 125 AGRGGRVVLLYGPRERRDVEALERAVGRRFKRVNPPT 161

>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 =  177 bits (451), Expect = 3e-54
 Identities = 62/205 (30%), Positives = 95/205 (46%), Gaps = 7/205 (3%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
                +LL+ I   G  KP+ IQ +      +G+D+I  AQ+GTGKT ++       LD 
Sbjct: 25  FQQYPDLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIHLDS 84

Query: 61  GLVQCQ------ALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAG 114
             +  +       LVL PTRELA  +E        Y G+K     GG +       +  G
Sbjct: 85  QPISREQRNGPGMLVLTPTRELALHVEAECSKYS-YKGLKSICIYGGRNRNGQIEDISKG 143

Query: 115 VHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGV 174
           V +++ TPGR+ D+    S+    I   V+DEAD+ML   F+ QI  I   +    Q  +
Sbjct: 144 VDIIIATPGRLNDLQMNNSVNLRSITYLVIDEADKMLDMEFEPQIRKILLDVRPDRQTVM 203

Query: 175 FSATMPPEALEITRKFMNKPVRILV 199
            SAT P    ++   ++  P+ + V
Sbjct: 204 TSATWPDTVRQLALSYLKDPMIVYV 228

>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 =  177 bits (451), Expect = 8e-54
 Identities = 58/201 (28%), Positives = 106/201 (52%), Gaps = 6/201 (2%)

Query: 3   LQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGL 62
           + EN L+ I   GF   + IQ + I P  +G D++  A++G+GKT  F    ++ +    
Sbjct: 61  VNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLR 120

Query: 63  VQCQ----ALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVV 118
              +     L+L+PTRELA Q   V++ L  +        +GG++   + + L  G++++
Sbjct: 121 FMPRNGTGVLILSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQKLGNGINII 180

Query: 119 VGTPGRVFDMLRRQ-SLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSA 177
           V TPGR+ D ++         ++  V+DEAD +L  GF++++  I +LLP + Q  +FSA
Sbjct: 181 VATPGRLLDHMQNTPGFMYKNLQCLVIDEADRILDVGFEEELKQIIKLLPTRRQTMLFSA 240

Query: 178 TMPPEALEITRK-FMNKPVRI 197
           T   +  ++ R     +P+ +
Sbjct: 241 TQTRKVEDLARISLKKEPLYV 261

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus} Length = 300

 Score =  178 bits (452), Expect = 2e-53
 Identities = 48/157 (30%), Positives = 80/157 (50%), Gaps = 3/157 (1%)

Query: 209 IKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGD 268
            ++  V       +LE L DL    +  ++++F  T+ + + +   +    H   A HGD
Sbjct: 3   YEEEAVPA-PVRGRLEVLSDLLYVASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGD 61

Query: 269 MDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGR 328
           M Q  R+ +M  FR G  RVL+ TD+ ARG+D+ QV LV++Y +P + E Y HR GR+GR
Sbjct: 62  MSQGERERVMGAFRQGEVRVLVATDVAARGLDIPQVDLVVHYRMPDRAEAYQHRSGRTGR 121

Query: 329 FGRKGVAINFVTRDDERMLFDIQKFYNVVIE--ELPS 363
            GR G  +      + R +  +++      +    P+
Sbjct: 122 AGRGGRVVLLYGPRERRDVEALERAVGRRFKRVNPPT 158

>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 =  174 bits (443), Expect = 7e-53
 Identities = 68/205 (33%), Positives = 97/205 (47%), Gaps = 7/205 (3%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFC----SGILQ 56
                N++  I    F +P+AIQ +G      GLD++  AQ+G+GKT ++       I  
Sbjct: 34  ANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINH 93

Query: 57  Q--LDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAG 114
           Q  L+ G      LVLAPTRELAQQ+++V         +K     GG       R L+ G
Sbjct: 94  QPFLERG-DGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIRDLERG 152

Query: 115 VHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGV 174
           V + + TPGR+ D L             VLDEAD ML  GF+ QI  I   +    Q  +
Sbjct: 153 VEICIATPGRLIDFLECGKTNLRRTTYLVLDEADRMLDMGFEPQIRKIVDQIRPDRQTLM 212

Query: 175 FSATMPPEALEITRKFMNKPVRILV 199
           +SAT P E  ++   F+   + I +
Sbjct: 213 WSATWPKEVRQLAEDFLKDYIHINI 237

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens} Length = 191

 Score =  152 bits (385), Expect = 8e-45
 Identities = 44/166 (26%), Positives = 76/166 (45%), Gaps = 9/166 (5%)

Query: 190 FMNKPVRILVKRDELTL-------EGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFV 242
             +    + +  + L           + Q    V++E  K+  L +  +       +IF 
Sbjct: 4   HHHHSSGVDLGTENLYFQSMGAASLDVIQEVEYVKEEA-KMVYLLECLQKTP-PPVLIFA 61

Query: 243 NTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQ 302
             +  VD + + +  +     A HG  DQ  R   +  FR G   VL+ TD+ ++G+D  
Sbjct: 62  EKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVASKGLDFP 121

Query: 303 QVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLF 348
            +  VINYD+P + ENY+HRIGR+G  G  G+A  F+ +  +  + 
Sbjct: 122 AIQHVINYDMPEEIENYVHRIGRTGCSGNTGIATTFINKACDESVL 167

>2jgn_A DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosphorylation, nucleotide-binding, hydrolase, RNA-binding, ATP-binding, DNA-binding, nuclear protein; 1.91A {Homo sapiens} Length = 185

 Score =  150 bits (380), Expect = 3e-44
 Identities = 52/145 (35%), Positives = 78/145 (53%), Gaps = 2/145 (1%)

Query: 209 IKQFYVNVEKEEWKLETLCDLYETLAITQSV-IFVNTRRKVDWLTDKMRSRDHTVSATHG 267
           I Q  V VE+ + K   L DL           +FV T++  D L D +    +  ++ HG
Sbjct: 20  ITQKVVWVEESD-KRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHG 78

Query: 268 DMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSG 327
           D  Q  R+  + +FRSG S +L+ T + ARG+D+  V  VIN+DLP+  E Y+HRIGR+G
Sbjct: 79  DRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTG 138

Query: 328 RFGRKGVAINFVTRDDERMLFDIQK 352
           R G  G+A +F    +  +  D+  
Sbjct: 139 RVGNLGLATSFFNERNINITKDLLD 163

>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 =  102 bits (255), Expect = 3e-24
 Identities = 37/210 (17%), Positives = 77/210 (36%), Gaps = 21/210 (10%)

Query: 143 VLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRD 202
            L  A E+L       +    + L  + + G   A+    + +  +K ++          
Sbjct: 281 KLHHAIELLETQGLSALRAYIKKLYEEAKAGSTKASKEIFSDKRMKKAISL--------- 331

Query: 203 ELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRD--- 259
              L   K+  ++  K +   E + +  +    ++ ++F N R     + +++       
Sbjct: 332 ---LVQAKEIGLDHPKMDKLKEIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKDGIKA 388

Query: 260 -----HTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPT 314
                         + Q  + +I+ EF  G   VL+ T +   G+DV +V LV+ Y+   
Sbjct: 389 KRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVATSVGEEGLDVPEVDLVVFYEPVP 448

Query: 315 QPENYLHRIGRSGRFGRKGVAINFVTRDDE 344
                + R GR+GR    G  I  + +   
Sbjct: 449 SAIRSIQRRGRTGR-HMPGRVIILMAKGTR 477

>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 = 77.1 bits (189), Expect = 1e-15
 Identities = 51/339 (15%), Positives = 110/339 (32%), Gaps = 9/339 (2%)

Query: 24  QRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKV 83
           Q  I   CK  + +    +G GKT         +L     +   L+LAPT+ L  Q  + 
Sbjct: 14  QEVIYAKCKETNCLIVLPTGLGKTLIAMMIAEYRLTKYGGK--VLMLAPTKPLVLQHAES 71

Query: 84  MRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFV 143
            R L +    K+ A  G  S  E  +       V+V TP  + + L    +  + + + V
Sbjct: 72  FRRLFNLPPEKIVALTGEKSPEERSKAWAR-AKVIVATPQTIENDLLAGRISLEDVSLIV 130

Query: 144 LDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDE 203
            DEA   +       I   ++       V   +A+      +I     N  +  +  R E
Sbjct: 131 FDEAHRAVGNYAYVFIAREYKRQAKNPLVIGLTASPGSTPEKIMEVINNLGIEHIEYRSE 190

Query: 204 LTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVS 263
            + + ++ +   +  E  +++      E   + + ++    +   +    +  S D    
Sbjct: 191 NSPD-VRPYVKGIRFEWVRVDLPEIYKEVRKLLREMLRDALKPLAETGLLESSSPDIPKK 249

Query: 264 ATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRI 323
                       II  E   G+  +       A  + +     ++     +    Y+ ++
Sbjct: 250 EVL-----RAGQIINEEMAKGNHDLRGLLLYHAMALKLHHAIELLETQGLSALRAYIKKL 304

Query: 324 GRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELP 362
               + G    +    +    +    +      +  + P
Sbjct: 305 YEEAKAGSTKASKEIFSDKRMKKAISLLVQAKEIGLDHP 343

>3o8b_A HCV NS3 protease/helicase; ntpase, RNA, translocation, protein-RNA compl protease/ntpase/helicase, hydrolase; 1.95A {Hepatitis c virus} PDB: 3o8c_A* 3o8d_A* 3o8r_A* 4a92_A* 1cu1_A 2zjo_A* 1a1v_A* 1hei_A 3kqn_A* 3kql_A* 3kqu_A* 3kqh_A 3kqk_A 8ohm_A 2f55_A 1jr6_A 1onb_A Length = 666

 Score = 81.6 bits (201), Expect = 5e-17
 Identities = 54/318 (16%), Positives = 87/318 (27%), Gaps = 67/318 (21%)

Query: 32  KGLDVIQQAQSGTGKTATFCSGILQQL-DYGLVQCQALVLAPTRELAQQIEKVMRALGDY 90
                   A +G+GK+      +       G    + LVL P+          M      
Sbjct: 231 SFQVAHLHAPTGSGKST----KVPAAYAAQGY---KVLVLNPSVAATLGFGAYMSKA--- 280

Query: 91  LGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEM 150
            G+  +   G        R +  G  V   T G+    L           + + DE    
Sbjct: 281 HGIDPNIRTGV-------RTITTGAPVTYSTYGK---FLADGGCSGGAYDIIICDECHST 330

Query: 151 LSRGFKDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIK 210
                   I  +           V  AT  P    +T    N           L+  G  
Sbjct: 331 -DSTTILGIGTVLDQAETAGARLVVLATATPPG-SVTVPHPNIEEVA------LSNTGEI 382

Query: 211 QFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMD 270
            FY      E                  +IF ++++K D L  K+        A +  +D
Sbjct: 383 PFYGKAIPIEA--IRGGR---------HLIFCHSKKKCDELAAKLSGLGINAVAYYRGLD 431

Query: 271 QNTRDIIMREFRSGSSRVLITTDLLARG--IDV-------QQVSLVINYD--------LP 313
                  +    +    V++ TD L  G   D          V+  +++           
Sbjct: 432 -------VSVIPTIGDVVVVATDALMTGYTGDFDSVIDCNTCVTQTVDFSLDPTFTIETT 484

Query: 314 TQP---ENYLHRIGRSGR 328
           T P    +   R GR+GR
Sbjct: 485 TVPQDAVSRSQRRGRTGR 502

>2p6r_A Afuhel308 helicase; protein-DNA complex, SF2 helicase, archaeal helicase, DNA repair,, DNA binding protein/DNA complex; 3.00A {Archaeoglobus fulgidus} SCOP: a.4.5.43 a.289.1.2 c.37.1.19 c.37.1.19 PDB: 2p6u_A Length = 702

 Score = 75.2 bits (185), Expect = 6e-15
 Identities = 65/413 (15%), Positives = 140/413 (33%), Gaps = 91/413 (22%)

Query: 2   GLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYG 61
            +    +  +   G E+    Q   +     G +++    +  GKT      ++++   G
Sbjct: 9   SISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKG 68

Query: 62  LVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGT 121
               ++L + P R LA +  +  +     +G+++    G      D+ +      ++V T
Sbjct: 69  ---GKSLYVVPLRALAGEKYESFKKWEK-IGLRIGISTGDYES-RDEHLGDC--DIIVTT 121

Query: 122 PGRVFDMLRRQSLRPDYIKMFVLDE----ADE--------MLSRGFKDQIYDIFQLLPAK 169
             +   ++R ++     +   V+DE      E        ++++          + +   
Sbjct: 122 SEKADSLIRNRASWIKAVSCLVVDEIHLLDSEKRGATLEILVTK---------MRRMNKA 172

Query: 170 VQ-VGVFSATMP-PEALEITRKFMNKPVRILVKRD----ELTLEGIKQFYVNVEKEEWKL 223
           ++ +G+ SAT P    +    ++++         D     L  EG+      +E  +   
Sbjct: 173 LRVIGL-SATAPNVTEIA---EWLDAD---YYVSDWRPVPLV-EGVL-CEGTLELFDGAF 223

Query: 224 ETLCDL-YETLAIT------QSVIFVNTRRKV----------------------DWLTDK 254
            T   + +E L           ++F +TRR                          L + 
Sbjct: 224 STSRRVKFEELVEECVAENGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEEN 283

Query: 255 MRSRDHTVSAT--------HGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSL 306
                  ++          H  +    R ++   FR G+ +V++ T  LA G+++     
Sbjct: 284 EGEMSRKLAECVRKGAAFHHAGLLNGQRRVVEDAFRRGNIKVVVATPTLAAGVNL-PARR 342

Query: 307 VINYDL--------PTQPENYLHRIGRSGRFG--RKGVAINFVTRDDERMLFD 349
           VI   L          +   Y    GR+GR G   +G AI  V + D  +   
Sbjct: 343 VIVRSLYRFDGYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIVGKRDREIAVK 395

>3dmq_A RNA polymerase-associated protein RAPA; SWF2/SNF2, transcription factor, RNA polymerase recycling, activator, ATP-binding, DNA-binding; 3.20A {Escherichia coli K12} Length = 968

 Score = 72.4 bits (177), Expect = 5e-14
 Identities = 26/153 (16%), Positives = 53/153 (34%), Gaps = 7/153 (4%)

Query: 218 KEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSR-DHTVSATHGDMDQNTRDI 276
             + ++E L     +    + ++          L   +R R     +  H  M    RD 
Sbjct: 486 NFDPRVEWLMGYLTSHRSQKVLVICAKAATALQLEQVLREREGIRAAVFHEGMSIIERDR 545

Query: 277 IMREFRSGSS--RVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKG- 333
               F    +  +VL+ +++ + G + Q  S ++ +DLP  P+    RIGR  R G+   
Sbjct: 546 AAAWFAEEDTGAQVLLCSEIGSEGRNFQFASHMVMFDLPFNPDLLEQRIGRLDRIGQAHD 605

Query: 334 -VAINFVTRD--DERMLFDIQKFYNVVIEELPS 363
                          ++    +  +      P+
Sbjct: 606 IQIHVPYLEKTAQSVLVRWYHEGLDAFEHTCPT 638

>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A* Length = 720

 Score = 69.9 bits (171), Expect = 3e-13
 Identities = 79/422 (18%), Positives = 152/422 (36%), Gaps = 80/422 (18%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGI-VPFCKGLDVIQQAQSGTGKTATFCSGILQQLD 59
           + + E +   +   G E     Q   +     +G + +    + +GKT      ++ ++ 
Sbjct: 6   LRVDERIKSTLKERGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRIL 65

Query: 60  YGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVV 119
                 +A+ + P + LA++  +  +     +G++V    G    +++         +++
Sbjct: 66  TQ--GGKAVYIVPLKALAEEKFQEFQDWEK-IGLRVAMATGDYDSKDEWL---GKYDIII 119

Query: 120 GTPGRVFDMLRRQSLRPDYIKMFVLDE----ADEMLSRGFKDQIYDIFQLLPAKVQ-VGV 174
            T  +   +LR  S     +K+ V DE          RG    +  I   +  K Q +G+
Sbjct: 120 ATAEKFDSLLRHGSSWIKDVKILVADEIHLIGSR--DRG--ATLEVILAHMLGKAQIIGL 175

Query: 175 FSATMP-PEALEITRKFMNKPVRILVKRD----ELTLEGIK--QFYVNVEKEEWKLETLC 227
            SAT+  PE L    +++N     L+  D    +L   G+    F    +    +  +  
Sbjct: 176 -SATIGNPEELA---EWLNAE---LIVSDWRPVKLR-RGVFYQGFVTWEDGSIDRFSSWE 227

Query: 228 DL-YETLA-ITQSVIFVNTRRKV----DWLTDKMRSRDHT-------------------- 261
           +L Y+ +     ++IFVN RRK       L+ K++S                        
Sbjct: 228 ELVYDAIRKKKGALIFVNMRRKAERVALELSKKVKSLLTKPEIRALNELADSLEENPTNE 287

Query: 262 ---------VSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVI---- 308
                    V+  H  + ++ R ++   FR G  + ++ T  L+ GI+      VI    
Sbjct: 288 KLAKAIRGGVAFHHAGLGRDERVLVEENFRKGIIKAVVATPTLSAGINT-PAFRVIIRDI 346

Query: 309 -NYDLPTQPE----NYLHRIGRSGRFG--RKGVAINFVTRDDERMLFDIQKFYNVVIEEL 361
             Y                +GR+GR      G  I   T DD R +     +     E+L
Sbjct: 347 WRYSDFGMERIPIIEVHQMLGRAGRPKYDEVGEGIIVSTSDDPREVM--NHYIFGKPEKL 404

Query: 362 PS 363
            S
Sbjct: 405 FS 406

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A* Length = 696

 Score = 63.8 bits (154), Expect = 3e-11
 Identities = 41/185 (22%), Positives = 71/185 (38%), Gaps = 17/185 (9%)

Query: 185 EITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDL----YETLAITQSVI 240
            +     ++  + L +R E  L+ ++    +   E  KLE LC +    Y     T +++
Sbjct: 344 NVRAAGFDEIEQDLTQRFEEKLQELESVSRDPSNENPKLEDLCFILQEEYHLNPETITIL 403

Query: 241 FVNTRRKVDWLTDKMRSRD------------HTVSATHGDMDQNTRDIIMREFR-SGSSR 287
           FV TR  VD L + +                   +  +  M    +  I+  F+ SG   
Sbjct: 404 FVKTRALVDALKNWIEGNPKLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAFKASGDHN 463

Query: 288 VLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERML 347
           +LI T +   GID+ Q +LVI Y+        +   GR    G K   +       E+  
Sbjct: 464 ILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTRGRGRARGSKCFLLTSNAGVIEKEQ 523

Query: 348 FDIQK 352
            ++ K
Sbjct: 524 INMYK 528

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A* Length = 696

 Score = 46.9 bits (110), Expect = 7e-06
 Identities = 26/149 (17%), Positives = 53/149 (35%), Gaps = 3/149 (2%)

Query: 18  KPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLD--YGLVQCQALVLAPTRE 75
           KP   Q    +P  KG + I  A +G GKT          L       + + +  A    
Sbjct: 13  KPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQIP 72

Query: 76  LAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLR 135
           + +Q + V     +  G +V    G T+       +     +++ TP  + + L++ ++ 
Sbjct: 73  VYEQNKSVFSKYFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTIP 132

Query: 136 P-DYIKMFVLDEADEMLSRGFKDQIYDIF 163
                 + + DE      +   + I   +
Sbjct: 133 SLSIFTLMIFDECHNTSKQHPYNMIMFNY 161

>4a2w_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.70A {Anas platyrhynchos} Length = 936

 Score = 62.3 bits (150), Expect = 1e-10
 Identities = 32/186 (17%), Positives = 62/186 (33%), Gaps = 19/186 (10%)

Query: 185 EITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDL----YETLAITQSVI 240
            +      +  + L  + +     +     +   E  KLE L  +    Y     T++++
Sbjct: 577 NVKNGPYTELEQHLTAKFQEKEPELIALSKDETNENPKLEELVCILDDAYRYNPQTRTLL 636

Query: 241 FVNTRRKVDWLTDKMRS------------RDHTVSATHGDMDQNTRDIIMREFRSGSS-R 287
           F  TR  V  L   M                         M   ++  ++  F++    R
Sbjct: 637 FAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNR 696

Query: 288 VLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERML 347
           +LI T +   GID+ Q +LV+ Y+        +   GR GR       I   ++ +    
Sbjct: 697 LLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GR-AAGSKCILVTSKTEVVEN 754

Query: 348 FDIQKF 353
               ++
Sbjct: 755 EKCNRY 760

>4a2w_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.70A {Anas platyrhynchos} Length = 936

 Score = 40.3 bits (93), Expect = 8e-04
 Identities = 26/142 (18%), Positives = 49/142 (34%), Gaps = 5/142 (3%)

Query: 14  YGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKT---ATFCSGILQQLDYGLVQCQALVL 70
           Y  +K  + Q     P   G + +  A +G+GKT      C    Q +  G  + + + L
Sbjct: 244 YETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGR-KAKVVFL 302

Query: 71  APTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLR 130
           A    + +Q + V +   +  G  V    G          +     ++V TP  + +   
Sbjct: 303 ATKVPVYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFE 362

Query: 131 RQSLRP-DYIKMFVLDEADEML 151
             +L       + + DE     
Sbjct: 363 DGTLTSLSIFTLMIFDECHNTT 384

>4a2q_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.40A {Anas platyrhynchos} Length = 797

 Score = 61.1 bits (147), Expect = 2e-10
 Identities = 32/177 (18%), Positives = 60/177 (33%), Gaps = 19/177 (10%)

Query: 185 EITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDL----YETLAITQSVI 240
            +      +  + L  + +     +     +   E  KLE L  +    Y     T++++
Sbjct: 577 NVKNGPYTELEQHLTAKFQEKEPELIALSKDETNENPKLEELVCILDDAYRYNPQTRTLL 636

Query: 241 FVNTRRKVDWLTDKMRS------------RDHTVSATHGDMDQNTRDIIMREFRSGSS-R 287
           F  TR  V  L   M                         M   ++  ++  F++    R
Sbjct: 637 FAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNR 696

Query: 288 VLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDE 344
           +LI T +   GID+ Q +LV+ Y+        +   GR GR       I   ++ + 
Sbjct: 697 LLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GR-AAGSKCILVTSKTEV 751

>4a2q_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.40A {Anas platyrhynchos} Length = 797

 Score = 48.4 bits (114), Expect = 2e-06
 Identities = 50/372 (13%), Positives = 119/372 (31%), Gaps = 25/372 (6%)

Query: 14  YGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKT---ATFCSGILQQLDYGLVQCQALVL 70
           Y  +K  + Q     P   G + +  A +G+GKT      C    Q +  G  + + + L
Sbjct: 244 YETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGR-KAKVVFL 302

Query: 71  APTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLR 130
           A    + +Q + V +   +  G  V    G          +     ++V TP  + +   
Sbjct: 303 ATKVPVYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFE 362

Query: 131 RQSLRP-DYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVF-----SATMPPEAL 184
             +L       + + DE          + +   +          +      +A++     
Sbjct: 363 DGTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQKFNSASQLPQILGLTASVGVGNA 422

Query: 185 EITRKFMNKPVRILVKRDELTLEGIK------QFYVNVEKEEWKL------ETLCDLYET 232
           +   + +     +    D   +  ++      Q ++N  + + +L           +   
Sbjct: 423 KNIEETIEHICSLCSYLDIQAISTVRENIQELQRFMNKPEIDVRLVKRRIHNPFAAIISN 482

Query: 233 LAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRD-IIMREFRSGSSRVLIT 291
           L ++++   + T   VD L+   +    T +  H  +    +  ++  E +   SR+   
Sbjct: 483 L-MSETEALMRTIYSVDTLSQNSKKDFGTQNYEHWIVVTQRKCRLLQLEDKEEESRICRA 541

Query: 292 TDLLARGIDVQQVSLVINYDLP-TQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDI 350
             +    +     +L+I+ D       +YL     + + G        +T   +    ++
Sbjct: 542 LFICTEHLRKYNDALIISEDARIIDALSYLTEFFTNVKNGPYTELEQHLTAKFQEKEPEL 601

Query: 351 QKFYNVVIEELP 362
                    E P
Sbjct: 602 IALSKDETNENP 613

>4a2p_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.00A {Anas platyrhynchos} PDB: 4a36_A* Length = 556

 Score = 60.7 bits (146), Expect = 3e-10
 Identities = 32/177 (18%), Positives = 60/177 (33%), Gaps = 19/177 (10%)

Query: 185 EITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDL----YETLAITQSVI 240
            +      +  + L  + +     +     +   E  KLE L  +    Y     T++++
Sbjct: 336 NVKNGPYTELEQHLTAKFQEKEPELIALSKDETNENPKLEELVCILDDAYRYNPQTRTLL 395

Query: 241 FVNTRRKVDWLTDKMRS------------RDHTVSATHGDMDQNTRDIIMREFRSGSS-R 287
           F  TR  V  L   M                         M   ++  ++  F++    R
Sbjct: 396 FAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNR 455

Query: 288 VLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDE 344
           +LI T +   GID+ Q +LV+ Y+        +   GR GR       I   ++ + 
Sbjct: 456 LLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GR-AAGSKCILVTSKTEV 510

>4a2p_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.00A {Anas platyrhynchos} PDB: 4a36_A* Length = 556

 Score = 43.8 bits (102), Expect = 7e-05
 Identities = 48/366 (13%), Positives = 114/366 (31%), Gaps = 21/366 (5%)

Query: 18  KPSAIQQRGIVPFCKGLDVIQQAQSGTGKT--ATFCSGILQQLDYGLVQCQALVLAPTRE 75
           K  + Q     P   G + +  A +G+GKT  +        Q      + + + LA    
Sbjct: 7   KARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVP 66

Query: 76  LAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLR 135
           + +Q + V +   +  G  V    G          +     ++V TP  + +     +L 
Sbjct: 67  VYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLT 126

Query: 136 P-DYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVF-----SATMPPEALEITRK 189
                 + + DE          + +   +          +      +A++     +   +
Sbjct: 127 SLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQKFNSASQLPQILGLTASVGVGNAKNIEE 186

Query: 190 FMNKPVRILVKRDELTLEGIK------QFYVNVEKEEWKLETLCDLYETLAITQSVI--- 240
            +     +    D   +  ++      Q ++N  + + +L          AI  +++   
Sbjct: 187 TIEHICSLCSYLDIQAISTVRENIQELQRFMNKPEIDVRLVKRRIHNPFAAIISNLMSET 246

Query: 241 --FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRD-IIMREFRSGSSRVLITTDLLAR 297
              + T   VD L+   +    T +  H  +    +  ++  E +   SR+     +   
Sbjct: 247 EALMRTIYSVDTLSQNSKKDFGTQNYEHWIVVTQRKCRLLQLEDKEEESRICRALFICTE 306

Query: 298 GIDVQQVSLVINYDLPTQPE-NYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNV 356
            +     +L+I+ D       +YL     + + G        +T   +    ++      
Sbjct: 307 HLRKYNDALIISEDARIIDALSYLTEFFTNVKNGPYTELEQHLTAKFQEKEPELIALSKD 366

Query: 357 VIEELP 362
              E P
Sbjct: 367 ETNENP 372

>1yks_A Genome polyprotein [contains: flavivirin protease NS3 catalytic subunit]; helicase, flavivirus, DEAD-BOX, ATPase, rtpase, hydrolase; 1.80A {Yellow fever virus} SCOP: c.37.1.14 c.37.1.14 PDB: 1ymf_A* Length = 440

 Score = 58.7 bits (142), Expect = 1e-09
 Identities = 47/322 (14%), Positives = 99/322 (30%), Gaps = 62/322 (19%)

Query: 32  KGLDVIQQAQSGTGKTATFCSGILQQL--DYGLVQCQALVLAPTRELAQQIEKVMRALGD 89
           KG+  +     G GKT       L Q+  +    + + LVLAPTR +  ++++       
Sbjct: 7   KGMTTVLDFHPGAGKT----RRFLPQILAECARRRLRTLVLAPTRVVLSEMKEAFH---- 58

Query: 90  YLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMF---VLDE 146
             G+ V       S     R +     +           L  + L P  +  +   ++DE
Sbjct: 59  --GLDVKFHTQAFSAHGSGREV-----IDAMCHA----TLTYRMLEPTRVVNWEVIIMDE 107

Query: 147 ADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTL 206
           A  +       + +   +    +    + +AT P  + E    F +    I   + ++  
Sbjct: 108 AHFLDPASIAARGWAAHRARANESATILMTATPPGTSDE----FPHSNGEIEDVQTDIPS 163

Query: 207 EGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATH 266
           E     +  +  ++                    F+ + R  + +   +R    +V   +
Sbjct: 164 EPWNTGHDWILADKRPT---------------AWFLPSIRAANVMAASLRKAGKSVVVLN 208

Query: 267 GDMDQNTRDIIMREFRSGSSRVLITTDLLARG--IDVQQV-----SLVINYD-------- 311
                 T +      +      ++ TD+   G  + V++V     +              
Sbjct: 209 RK----TFEREYPTIKQKKPDFILATDIAEMGANLCVERVLDCRTAFKPVLVDEGRKVAI 264

Query: 312 LPTQPENYLHRIGRSGRFGRKG 333
                 +      R GR GR  
Sbjct: 265 KGPLRISASSAAQRRGRIGRNP 286

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus} Length = 555

 Score = 58.8 bits (141), Expect = 1e-09
 Identities = 40/178 (22%), Positives = 68/178 (38%), Gaps = 19/178 (10%)

Query: 185 EITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDL----YETLAITQSVI 240
           ++     ++  R L +R E  LE +++   +   E  KL  L  +    Y     T++++
Sbjct: 335 DVREAAFDETERELTRRFEEKLEELEKVSRDPSNENPKLRDLYLVLQEEYHLKPETKTIL 394

Query: 241 FVNTRRKVDWLTDKMRSR------------DHTVSATHGDMDQNTRDIIMREFR-SGSSR 287
           FV TR  VD L   +                   +     M    +  ++  FR SG + 
Sbjct: 395 FVKTRALVDALKKWIEENPALSFLKPGILTGRGRTNRATGMTLPAQKCVLEAFRASGDNN 454

Query: 288 VLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDER 345
           +LI T +   GID+ + +LVI Y+        +   GR GR  R        +  D  
Sbjct: 455 ILIATSVADEGIDIAECNLVILYEYVGNVIKMIQTRGR-GR-ARDSKCFLLTSSADVI 510

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus} Length = 555

 Score = 46.0 bits (108), Expect = 1e-05
 Identities = 36/274 (13%), Positives = 83/274 (30%), Gaps = 22/274 (8%)

Query: 23  QQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQ--ALVLAPTRELAQQI 80
           Q    +P  KG + I  A +G GKT          L       +   +  A    + +Q 
Sbjct: 9   QLELALPAKKGKNTIICAPTGCGKTFVSLLICEHHLKKFPCGQKGKVVFFANQIPVYEQQ 68

Query: 81  EKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRP-DYI 139
             V     + LG  + +  G TS     + +     +++ TP  + + L   ++      
Sbjct: 69  ATVFSRYFERLGYNIASISGATSDSVSVQHIIEDNDIIILTPQILVNNLNNGAIPSLSVF 128

Query: 140 KMFVLDEADEMLSRGFKDQIYDIFQLLPAK------VQVGVFSATMPPEALEITRKFMNK 193
            + + DE          +QI   +             QV   +A++     +   + M  
Sbjct: 129 TLMIFDECHNTSKNHPYNQIMFRYLDHKLGESRDPLPQVVGLTASVGVGDAKTAEEAMQH 188

Query: 194 PVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTD 253
             ++    D   +  ++     +E+  +K + +     +             R  +    
Sbjct: 189 ICKLCAALDASVIATVRDNVAELEQVVYKPQKISRKVAS-------------RTSNTFKC 235

Query: 254 KMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSR 287
            +            D+ +    +   + R   ++
Sbjct: 236 IISQLMKETEKLAKDVSEELGKLFQIQNREFGTQ 269

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 58.7 bits (141), Expect = 1e-09
 Identities = 53/314 (16%), Positives = 109/314 (34%), Gaps = 93/314 (29%)

Query: 103 SVREDQRILQAGVHVVVGTPGRVFDMLRRQ-----------SLRPDYIKMFVLDE----- 146
           S  E   I+ +    V GT  R+F  L  +            LR +Y   F++       
Sbjct: 47  SKEEIDHIIMSK-DAVSGTL-RLFWTLLSKQEEMVQKFVEEVLRINY--KFLMSPIKTEQ 102

Query: 147 -ADEMLSRGF---KDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMN-KPVRILV-- 199
               M++R +   +D++Y+  Q+   K  V     +     L++ +  +  +P + ++  
Sbjct: 103 RQPSMMTRMYIEQRDRLYNDNQVFA-KYNV-----SRLQPYLKLRQALLELRPAKNVLID 156

Query: 200 ------K--------RDELTLE----GIKQFYVNV---EKEEWKLETLCDLYETLA---I 235
                 K                    I  F++N+      E  LE L  L   +     
Sbjct: 157 GVLGSGKTWVALDVCLSYKVQCKMDFKI--FWLNLKNCNSPETVLEMLQKLLYQIDPNWT 214

Query: 236 TQSVIFVNTRRKVDWLTDKMR----SRDHTVSATHGDMD--QNTRDIIMREFRSGSSRVL 289
           ++S    N + ++  +  ++R    S+ +        +   QN +      F + S ++L
Sbjct: 215 SRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLL--VLLNVQNAK--AWNAF-NLSCKIL 269

Query: 290 ITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFD 349
           +TT    R    +QV+  ++    T      H +               +T D+ + L  
Sbjct: 270 LTT----R--F-KQVTDFLSAATTTHISLDHHSMT--------------LTPDEVKSLL- 307

Query: 350 IQKFYNVVIEELPS 363
             K+ +   ++LP 
Sbjct: 308 -LKYLDCRPQDLPR 320

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 54.9 bits (131), Expect = 3e-08
 Identities = 50/374 (13%), Positives = 108/374 (28%), Gaps = 113/374 (30%)

Query: 29  PFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALG 88
           P+   L V+   Q+         +      +   + C+ L+   TR          + + 
Sbjct: 242 PYENCLLVLLNVQN---------AKAWNAFN---LSCKILLT--TRF---------KQVT 278

Query: 89  DYLGVKV--HACV----GGTSVREDQRILQAGVH---------VVVGTP---GRVFDMLR 130
           D+L      H  +       +  E + +L   +          V+   P     + + +R
Sbjct: 279 DFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIR 338

Query: 131 RQSLRPDYIKMFVLDEADEMLSRGFKD-------QIYDIFQLLPAKVQVGVFSATMPPEA 183
                 D  K    D+   ++             +++D   + P    +       P   
Sbjct: 339 DGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHI-------PTIL 391

Query: 184 LEI---------TRKFMNKPVRI-LVKRD--ELTLEGIKQFYVNVEKEEWKLETLCDLYE 231
           L +             +NK  +  LV++   E T+  I   Y+ ++    KLE    L+ 
Sbjct: 392 LSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTI-SIPSIYLELKV---KLENEYALHR 447

Query: 232 TLAITQSVIFVNTRRKVDWLTDKMRSRD---------HTVSATHGDMDQNTRDIIMREFR 282
           ++ +       N  +  D         D         H  +  H +     R + + +FR
Sbjct: 448 SI-VDH----YNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFL-DFR 501

Query: 283 SGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRD 342
                  +   +            ++  +   Q + Y                  ++  +
Sbjct: 502 ------FLEQKIRHDSTAWNASGSIL--NTLQQLKFYK----------------PYICDN 537

Query: 343 D---ERMLFDIQKF 353
           D   ER++  I  F
Sbjct: 538 DPKYERLVNAILDF 551

>2v1x_A ATP-dependent DNA helicase Q1; DNA strand annealing, mismatch repair, nucleotide-binding, DNA-binding, polymorphism, nuclear protein, ATPase; HET: ADP; 2.00A {Homo sapiens} PDB: 2wwy_A* Length = 591

 Score = 53.1 bits (128), Expect = 7e-08
 Identities = 32/160 (20%), Positives = 68/160 (42%), Gaps = 16/160 (10%)

Query: 212 FYVNVEKEEWKLETLCDLYETLAITQS----VIFVNTRRKVDWLTDKMRSRDHTVSATHG 267
           +Y   +K     + + D+ + +         +I+  +++  + +T  +++      A H 
Sbjct: 240 YYEVRQKPSNTEDFIEDIVKLINGRYKGQSGIIYCFSQKDSEQVTVSLQNLGIHAGAYHA 299

Query: 268 DMDQNTRDIIMREFRSGSSRVLITTDLLA--RGIDVQQVSLVINYDLPTQPENYLHRIGR 325
           +++   +  + R++ +   +V++ T  +A   GID   V  VI++ +    ENY    GR
Sbjct: 300 NLEPEDKTTVHRKWSANEIQVVVAT--VAFGMGIDKPDVRFVIHHSMSKSMENYYQESGR 357

Query: 326 SGRFGRKGVAINFVTRDD----ERMLF----DIQKFYNVV 357
           +GR   K   I +    D      M+       QK Y +V
Sbjct: 358 AGRDDMKADCILYYGFGDIFRISSMVVMENVGQQKLYEMV 397

>1oyw_A RECQ helicase, ATP-dependent DNA helicase; winged helix, helix-turn-helix, ATP binding, Zn(2+) binding, hydrolase; 1.80A {Escherichia coli} SCOP: a.4.5.43 c.37.1.19 c.37.1.19 PDB: 1oyy_A* Length = 523

 Score = 51.4 bits (124), Expect = 3e-07
 Identities = 29/109 (26%), Positives = 56/109 (51%)

Query: 239 VIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARG 298
           +I+ N+R KV+    +++S+  + +A H  ++ N R  +  +F+    ++++ T     G
Sbjct: 240 IIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMG 299

Query: 299 IDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERML 347
           I+   V  V+++D+P   E+Y    GR+GR G    A+ F    D   L
Sbjct: 300 INKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWL 348

>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H RNA-binding helicase, innate immunity, IFIH1, S genomics; 1.60A {Homo sapiens} Length = 216

 Score = 49.4 bits (118), Expect = 3e-07
 Identities = 16/114 (14%), Positives = 37/114 (32%), Gaps = 9/114 (7%)

Query: 43  GTGKT---ATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACV 99
           G+GKT          L +        + +VL     L +Q+ +           +V    
Sbjct: 58  GSGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEFQPFLKKWYRVIGLS 117

Query: 100 GGTSVREDQRILQAGVHVVVGTPGRVFDML------RRQSLRPDYIKMFVLDEA 147
           G T ++     +     +++ T   + + L          ++     + ++DE 
Sbjct: 118 GDTQLKISFPEVVKSCDIIISTAQILENSLLNLENGEDAGVQLSDFSLIIIDEC 171

>2jlq_A Serine protease subunit NS3; ribonucleoprotein, nucleotide-binding, viral nucleoprotein, endoplasmic reticulum, helicase, hydrolase; 1.67A {Dengue virus 4} PDB: 2jly_A* 2jls_A* 2jlu_A 2jlv_A* 2jlw_A 2jlx_A* 2jlz_A* 2jlr_A* 2bmf_A 2bhr_A Length = 451

 Score = 49.8 bits (119), Expect = 7e-07
 Identities = 53/326 (16%), Positives = 95/326 (29%), Gaps = 73/326 (22%)

Query: 32  KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQA-LVLAPTRELAQQIEKVMRAL-GD 89
           K    I     G GKT      +   +   L++    L+LAPTR +A ++E+ +R L   
Sbjct: 18  KKRLTIMDLHPGAGKTKRI---LPSIVREALLRRLRTLILAPTRVVAAEMEEALRGLPIR 74

Query: 90  YLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIK---MFVLDE 146
           Y    V +   G  +            V +            + L    +    + V+DE
Sbjct: 75  YQTPAVKSDHTGREI------------VDLMCHA----TFTTRLLSSTRVPNYNLIVMDE 118

Query: 147 A-----DEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKR 201
           A       + +RG+     ++ +     +     +AT  P          N P+      
Sbjct: 119 AHFTDPCSVAARGYISTRVEMGEAAAIFM-----TAT--PPGSTDPFPQSNSPI------ 165

Query: 202 DELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHT 261
               +E            +W  +              V FV + +  + + + +R     
Sbjct: 166 --EDIEREIPERSWNTGFDWITDYQGKT---------VWFVPSIKAGNDIANCLRKSGKR 214

Query: 262 VSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARG--IDV-------QQVSLVINYD- 311
           V                 + +      ++TTD+   G            + +  VI  D 
Sbjct: 215 VIQLSRKTFDT----EYPKTKLTDWDFVVTTDISEMGANFRAGRVIDPRRCLKPVILTDG 270

Query: 312 ------LPTQPENYLHRIGRSGRFGR 331
                     P        R GR GR
Sbjct: 271 PERVILAGPIPVTPASAAQRRGRIGR 296

>2fwr_A DNA repair protein RAD25; DNA unwinding, XPB, DNA binding protein; HET: DNA; 2.60A {Archaeoglobus fulgidus} SCOP: c.37.1.19 c.37.1.19 PDB: 2fzl_A* Length = 472

 Score = 49.4 bits (118), Expect = 9e-07
 Identities = 43/326 (13%), Positives = 95/326 (29%), Gaps = 86/326 (26%)

Query: 43  GTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGT 102
           G+GKT    + I +      +    L++ PT  LA+Q ++ +   G+    +      G 
Sbjct: 118 GSGKTHVAMAAINE------LSTPTLIVVPTLALAEQWKERLGIFGE----EYVGEFSGR 167

Query: 103 SVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFK------ 156
                         + V T    +    +   R   +   + DE   + +  +       
Sbjct: 168 IKELKP--------LTVSTYDSAYVNAEKLGNRFMLL---IFDEVHHLPAESYVQIAQMS 216

Query: 157 ----------------DQIYDIFQLL----------------PAKVQVGVFSATMPPEAL 184
                            +   + +++                 AK  +      +  +  
Sbjct: 217 IAPFRLGLTATFEREDGRHEILKEVVGGKVFELFPDSLAGKHLAKYTIKRIFVPLAEDER 276

Query: 185 EITRKFMNKPVRILVKRDE--LTLEGIKQFYVNVEKEEW--------------------K 222
               K      + L  R       E   +  +    +E                     K
Sbjct: 277 VEYEKREKVYKQFLRARGITLRRAEDFNKIVMASGYDERAYEALRAWEEARRIAFNSKNK 336

Query: 223 LETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFR 282
           +  L ++ E     + +IF      V  ++         + A      +  R+ I+  FR
Sbjct: 337 IRKLREILERHRKDKIIIFTRHNELVYRISKVFL-----IPAITHRTSREEREEILEGFR 391

Query: 283 SGSSRVLITTDLLARGIDVQQVSLVI 308
           +G  R ++++ +L  GIDV   ++ +
Sbjct: 392 TGRFRAIVSSQVLDEGIDVPDANVGV 417

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4} Length = 510

 Score = 49.1 bits (116), Expect = 1e-06
 Identities = 51/341 (14%), Positives = 103/341 (30%), Gaps = 42/341 (12%)

Query: 18  KPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELA 77
           +P   Q+  +         I    +  G++          L+    + + L++ PT  L 
Sbjct: 113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENY--EGKILIIVPTTALT 170

Query: 78  QQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPD 137
            Q+         +    +    GG S  +  +       VVVGT               +
Sbjct: 171 TQMADDFVDYRLFSHAMIKKIGGGASKDDKYKN---DAPVVVGT------WQTVVKQPKE 221

Query: 138 YIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMN-KPVR 196
           +   F +   DE      K     I  L     + G  S ++      I +       + 
Sbjct: 222 WFSQFGMMMNDECHLATGKSISSIISGLNNCMFKFG-LSGSLRDGKANIMQYVGMFGEIF 280

Query: 197 ILVKRDELTLEG---------IKQFYVNVEKEEWKLETLCDLYETLAITQ---------- 237
             V   +L  +G         I   Y +    + K +T  +  + +              
Sbjct: 281 KPVTTSKLMEDGQVTELKINSIFLRYPDEFTTKLKGKTYQEEIKIITGLSKRNKWIAKLA 340

Query: 238 ---------SVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRV 288
                    + +          + D +++    V    G++D  TR+I+     +G   +
Sbjct: 341 IKLAQKDENAFVMFKHVSHGKAIFDLIKNEYDKVYYVSGEVDTETRNIMKTLAENGKGII 400

Query: 289 LITT-DLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGR 328
           ++ +  + + GI V+ +  V+           L  IGR  R
Sbjct: 401 IVASYGVFSTGISVKNLHHVVLAHGVKSKIIVLQTIGRVLR 441

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A Length = 431

 Score = 47.5 bits (113), Expect = 4e-06
 Identities = 53/326 (16%), Positives = 98/326 (30%), Gaps = 66/326 (20%)

Query: 32  KGLDVIQQAQSGTGKTATFCSGILQQL--DYGLVQCQALVLAPTRELAQQIEKVMRAL-G 88
           K    +     G GKT      +L QL  +    + + ++LAPTR +A ++ + +R    
Sbjct: 1   KRELTVLDLHPGAGKT-R---RVLPQLVREAVKKRLRTVILAPTRVVASEMYEALRGEPI 56

Query: 89  DYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEA- 147
            Y+   V +   G  +            V           L +    P+Y  ++++DEA 
Sbjct: 57  RYMTPAVQSERTGNEI------------VDFMCHSTFTMKLLQGVRVPNY-NLYIMDEAH 103

Query: 148 ----DEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDE 203
                 + +RG+ +      ++          +AT P             P       DE
Sbjct: 104 FLDPASVAARGYIET-----RVSMGDAGAIFMTATPPGTTEAF-------PPSNSPIIDE 151

Query: 204 LTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVS 263
              E            EW  E              V FV++ ++   +   ++     V 
Sbjct: 152 ---ETRIPDKAWNSGYEWITEFDGRT---------VWFVHSIKQGAEIGTCLQKAGKKVL 199

Query: 264 ATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARG--IDVQQV----SLVINYD------ 311
             +    ++       + +S     +ITTD+   G      +V      +          
Sbjct: 200 YLNRKTFES----EYPKCKSEKWDFVITTDISEMGANFKADRVIDPRKTIKPILLDGRVS 255

Query: 312 -LPTQPENYLHRIGRSGRFGRKGVAI 336
                         R GR GR    +
Sbjct: 256 MQGPIAITPASAAQRRGRIGRNPEKL 281

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus} Length = 673

 Score = 46.8 bits (111), Expect = 7e-06
 Identities = 56/323 (17%), Positives = 91/323 (28%), Gaps = 67/323 (20%)

Query: 32  KGLDVIQQAQSGTGKTATFCSGILQQL--DYGLVQCQALVLAPTRELAQQIEKVMRALGD 89
           K    +     G GKT      IL Q+  D    + +  VLAPTR +A    ++  AL  
Sbjct: 240 KRQLTVLDLHPGAGKT-R---RILPQIIKDAIQKRLRTAVLAPTRVVA---AEMAEALRG 292

Query: 90  YLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDE--- 146
                             QR       V V     +   L      P+Y  +FV+DE   
Sbjct: 293 L--------PVRYLTPAVQREHSGNEIVDVMCHATLTHRLMSPLRVPNY-NLFVMDEAHF 343

Query: 147 --ADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDEL 204
                + +RG+     +  +     +     +AT P  +        N PV  +      
Sbjct: 344 TDPASIAARGYIATRVEAGEAAAIFM-----TATPPGTSDPFPD--TNSPVHDVSSEIP- 395

Query: 205 TLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSA 264
                          EW  +              V FV + +  + +   ++     V  
Sbjct: 396 -------DRAWSSGFEWITDYAGKT---------VWFVASVKMSNEIAQCLQRAGKRVIQ 439

Query: 265 THGDMDQNTRDIIMREFRSGSSRVLITTDLLARG--IDV-------QQVSLVINYD---- 311
            +             + ++G    +ITTD+   G            + V   I  +    
Sbjct: 440 LNRKSYDT----EYPKCKNGDWDFVITTDISEMGANFGASRVIDCRKSVKPTILDEGEGR 495

Query: 312 ---LPTQPENYLHRIGRSGRFGR 331
                           R GR GR
Sbjct: 496 VILSVPSAITSASAAQRRGRVGR 518

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus} Length = 715

 Score = 45.5 bits (108), Expect = 2e-05
 Identities = 76/433 (17%), Positives = 150/433 (34%), Gaps = 87/433 (20%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVP-FCKGLDVIQQAQSGTGKTATFCSGILQQLD 59
           + L  N++  I   G +K +  Q   +     +G  ++  + +G+GKT     GI+  L 
Sbjct: 13  LKLPSNVIEIIKKRGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGIISFLL 72

Query: 60  YGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVV 119
                 +A+ + P R L  +     +     +G KV    G     +          +++
Sbjct: 73  KN--GGKAIYVTPLRALTNEKYLTFKDWEL-IGFKVAMTSGDYDTDDAWL---KNYDIII 126

Query: 120 GTPGRVFDMLRRQSLRPDYIKMFVLDE----ADEMLSRGFKDQIYDIFQLLPAKVQ-VGV 174
            T  ++  + R +    + +  FVLDE     D    RG    + +   +   +   + +
Sbjct: 127 TTYEKLDSLWRHRPEWLNEVNYFVLDELHYLNDP--ERG---PVVESVTIRAKRRNLLAL 181

Query: 175 FSATMP-PEALEITRKFMNK--------PVRI---LVKRDELTLEGIKQFYVNVEKEEWK 222
            SAT+   + +    K++          PV +   ++  +    E    F  N  K+   
Sbjct: 182 -SATISNYKQIA---KWLGAEPVATNWRPVPLIEGVIYPERKKKEYNVIFKDNTTKKVHG 237

Query: 223 LETLCDL-YETLAITQSV-IFVNTRR----------------------------KVDWLT 252
            + +     ++L+    V +F N+R+                            ++D + 
Sbjct: 238 DDAIIAYTLDSLSKNGQVLVFRNSRKMAESTALKIANYMNFVSLDENALSEILKQLDDIE 297

Query: 253 DKMRSRDHTVSAT--------HGDMDQNTRDIIMREFRSGSSRVLITTDLLA-------- 296
           +        + +         H  + +  RD+I   FR    +V++ T  LA        
Sbjct: 298 EGGSDEKELLKSLISKGVAYHHAGLSKALRDLIEEGFRQRKIKVIVATPTLAAGVNLPAR 357

Query: 297 ----RGIDVQQVSLVINYDLPTQPENYLHRIGRSGR--FGRKGVAINFVTRDDERMLFDI 350
                 I      +   YD       Y    GR+GR  F + G +I  V RD E +    
Sbjct: 358 TVIIGDIYRFNKKIAGYYD-EIPIMEYKQMSGRAGRPGFDQIGESI-VVVRDKEDVDRVF 415

Query: 351 QKFYNVVIEELPS 363
           +K+    +E + S
Sbjct: 416 KKYVLSDVEPIES 428

>2whx_A Serine protease/ntpase/helicase NS3; transcription, hydrolase, ATP-binding, reticulum, nucleotidyltransferase, multifunctional enzyme; HET: ADP; 2.20A {Dengue virus 4} PDB: 2vbc_A 2wzq_A Length = 618

 Score = 44.6 bits (105), Expect = 4e-05
 Identities = 50/326 (15%), Positives = 86/326 (26%), Gaps = 73/326 (22%)

Query: 32  KGLDVIQQAQSGTGKTATFCSGILQQL-DYGLVQCQA-LVLAPTRELAQQIEKVMRALGD 89
           K    I     G GKT      IL  +    L +    L+LAPTR +A    ++  AL  
Sbjct: 185 KKRLTIMDLHPGAGKT----KRILPSIVREALKRRLRTLILAPTRVVA---AEMEEALRG 237

Query: 90  YLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIK---MFVLDE 146
                             +        V +            + L    +    + V+DE
Sbjct: 238 L--------PIRYQTPAVKSDHTGREIVDLMCHA----TFTTRLLSSTRVPNYNLIVMDE 285

Query: 147 -----ADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKR 201
                   + +RG+        ++   +      +AT  P          N P+      
Sbjct: 286 AHFTDPCSVAARGYIST-----RVEMGEAAAIFMTAT--PPGSTDPFPQSNSPI------ 332

Query: 202 DELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHT 261
               +E            +W  +              V FV + +  + + + +R     
Sbjct: 333 --EDIEREIPERSWNTGFDWITDYQGKT---------VWFVPSIKAGNDIANCLRKSGKR 381

Query: 262 VSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARG--IDV-------QQVSLVINYD- 311
           V                 + +      ++TTD+   G            + +  VI  D 
Sbjct: 382 VIQLSRKTFDT----EYPKTKLTDWDFVVTTDISEMGANFRAGRVIDPRRCLKPVILTDG 437

Query: 312 ------LPTQPENYLHRIGRSGRFGR 331
                     P        R GR GR
Sbjct: 438 PERVILAGPIPVTPASAAQRRGRIGR 463

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A Length = 677

 Score = 44.5 bits (104), Expect = 4e-05
 Identities = 27/187 (14%), Positives = 63/187 (33%), Gaps = 20/187 (10%)

Query: 191 MNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDW 250
               V  L+      +E   + Y  +         L  L         V F  ++  +  
Sbjct: 280 AIDLVMELMYTTGEEVE--VRDYKRLTPISVLDHALESLDNLRPGDCIVCF--SKNDIYS 335

Query: 251 LTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRV--LITTDLLARGIDVQQVSLVI 308
           ++ ++  R    +  +G +   T+    ++F   +     L+ TD +  G+++    ++ 
Sbjct: 336 VSRQIEIRGLESAVIYGSLPPGTKLAQAKKFNDPNDPCKILVATDAIGMGLNLSIRRIIF 395

Query: 309 N----YDLPTQPENYLHRI---------GRSGRFGRKGVAINFVTRDDERMLFDIQKFYN 355
                  +  + E  L  I         GR+GRF  +      VT  +   L  +++   
Sbjct: 396 YSLIKPSINEKGERELEPITTSQALQIAGRAGRFSSRF-KEGEVTTMNHEDLSLLKEILK 454

Query: 356 VVIEELP 362
             ++ + 
Sbjct: 455 RPVDPIR 461

>2z83_A Helicase/nucleoside triphosphatase; hydrolase, membrane, nucleotide-binding, RNA replication, transmembrane, viral protein; 1.80A {Japanese encephalitis virus} PDB: 2v8o_A 2qeq_A Length = 459

 Score = 42.9 bits (101), Expect = 1e-04
 Identities = 59/319 (18%), Positives = 95/319 (29%), Gaps = 67/319 (21%)

Query: 36  VIQQAQSGTGKTATFCSGILQQL-DYGLVQCQA-LVLAPTRELAQQIEKVMRALGDYLGV 93
            +     G+GKT      IL Q+    + Q     VLAPTR +A    ++  AL    G+
Sbjct: 24  TVLDLHPGSGKT----RKILPQIIKDAIQQRLRTAVLAPTRVVA---AEMAEALR---GL 73

Query: 94  KVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDE-----AD 148
            V            QR  Q    V V     +   L   +  P+Y  +FV+DE       
Sbjct: 74  PV-----RYQTSAVQREHQGNEIVDVMCHATLTHRLMSPNRVPNY-NLFVMDEAHFTDPA 127

Query: 149 EMLSRGFKDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEG 208
            + +RG+     ++ +     +     +AT P             P       D    + 
Sbjct: 128 SIAARGYIATKVELGEAAAIFM-----TATPPGTTDPF-------PDSNAPIHDL---QD 172

Query: 209 IKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGD 268
                      EW  E              V FV + +  + +   ++     V   +  
Sbjct: 173 EIPDRAWSSGYEWITEYAGKT---------VWFVASVKMGNEIAMCLQRAGKKVIQLNRK 223

Query: 269 MDQNTRDIIMREFRSGSSRVLITTDLLARG--IDV-------QQVSLVINYD-------L 312
                      + ++G    +ITTD+   G            + V   I  +        
Sbjct: 224 SYDT----EYPKCKNGDWDFVITTDISEMGANFGASRVIDCRKSVKPTILEEGEGRVILG 279

Query: 313 PTQPENYLHRIGRSGRFGR 331
              P        R GR GR
Sbjct: 280 NPSPITSASAAQRRGRVGR 298

>1gku_B Reverse gyrase, TOP-RG; topoisomerase, DNA supercoiling, archaea, helicase; 2.7A {Archaeoglobus fulgidus} SCOP: c.37.1.16 c.37.1.16 e.10.1.1 PDB: 1gl9_B* Length = 1054

 Score = 42.4 bits (100), Expect = 2e-04
 Identities = 61/290 (21%), Positives = 105/290 (36%), Gaps = 58/290 (20%)

Query: 40  AQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACV 99
           A +G GKT +F  G+   L   L   +  V+ PT  L  Q  + +R   +  GV     +
Sbjct: 78  APTGVGKT-SF--GLAMSLFLALKGKRCYVIFPTSLLVIQAAETIRKYAEKAGVGTENLI 134

Query: 100 ----GGTSVREDQRILQA--GVHVVVGTPG---RVFDMLRRQSLRPDYIKMFVLDEADEM 150
               G    RE +  +Q      +V+ T     + +  L           +FV D+ D +
Sbjct: 135 GYYHGRIPKREKENFMQNLRNFKIVITTTQFLSKHYRELGHFDF------IFV-DDVDAI 187

Query: 151 L--SR---------GFKDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILV 199
           L  S+         GF   +     +  A+  + V +AT              K  +  +
Sbjct: 188 LKASKNVDKLLHLLGFHYDLKTKSWVGEARGCLMVSTAT------------AKKGKKAEL 235

Query: 200 KRDELTLE-GIKQFYV-NVE---KEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDK 254
            R  L  + G  +  V NVE     +  + TL  + E L  T  +I+  T  + + + + 
Sbjct: 236 FRQLLNFDIGSSRITVRNVEDVAVNDESISTLSSILEKLG-TGGIIYARTGEEAEEIYES 294

Query: 255 MRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITT----DLLARGID 300
           ++++      T        +     +F  G    LI T      L RG+D
Sbjct: 295 LKNKFRIGIVTAT------KKGDYEKFVEGEIDHLIGTAHYYGTLVRGLD 338

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	369
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	100.0
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	100.0
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	100.0
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	100.0
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	100.0
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	100.0
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	100.0
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	100.0
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	100.0
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	100.0
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	100.0
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	100.0
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	100.0
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	100.0
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	100.0
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	100.0
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	100.0
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	100.0
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	100.0
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	100.0
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	100.0
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	100.0
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	100.0
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	100.0
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	100.0
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	100.0
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	100.0
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	100.0
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	100.0
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	100.0
4gl2_A	699	Interferon-induced helicase C domain-containing P;	100.0
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	100.0
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	100.0
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	100.0
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	100.0
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	100.0
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	100.0
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	100.0
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	100.0
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	100.0
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	100.0
3h1t_A	590	Type I site-specific restriction-modification syst	100.0
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	100.0
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	100.0
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	100.0
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	100.0
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	100.0
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	100.0
1yks_A	440	Genome polyprotein [contains: flavivirin protease	100.0
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	100.0
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	100.0
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	100.0
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	100.0
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	100.0
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	100.0
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	100.0
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	100.0
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	100.0
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	100.0
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	100.0
3bor_A	237	Human initiation factor 4A-II; translation initiat	100.0
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	100.0
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	100.0
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	100.0
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	100.0
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	100.0
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	100.0
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	100.0
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	100.0
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	100.0
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	100.0
3jux_A	822	Protein translocase subunit SECA; protein transloc	100.0
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	100.0
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	99.96
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	99.96
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	99.96
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	99.95
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	99.95
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	99.95
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	99.95
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	99.95
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	99.95
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	99.94
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	99.93
3b6e_A	216	Interferon-induced helicase C domain-containing P;	99.93
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	99.87
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	99.92
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	99.9
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	99.9
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	99.87
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	99.87
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	99.86
1z5z_A	271	Helicase of the SNF2/RAD54 family; hydrolase, reco	99.79
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	98.91
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	98.74
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	98.72
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	98.68
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	98.65
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	98.64
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	98.57
3lfu_A	647	DNA helicase II; SF1 helicase, ATP-binding, DNA da	98.51
3hgt_A	328	HDA1 complex subunit 3; RECA-like domain, SWI2/SNF	98.25
2o0j_A	385	Terminase, DNA packaging protein GP17; nucleotide-	97.85
3cpe_A	592	Terminase, DNA packaging protein GP17; large termi	97.76
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	97.67
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	97.66
1uaa_A	673	REP helicase, protein (ATP-dependent DNA helicase	97.64
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	97.64
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	97.62
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	97.6
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	97.59
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	97.52
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	97.51
1pjr_A	724	PCRA; DNA repair, DNA replication, SOS response, h	97.49
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	97.45
2orv_A	234	Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2	97.4
3u4q_A	1232	ATP-dependent helicase/nuclease subunit A; helicas	97.34
2chg_A	226	Replication factor C small subunit; DNA-binding pr	97.26
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	97.24
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	97.16
3co5_A	143	Putative two-component system transcriptional RES	97.16
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	97.15
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	97.14
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	97.14
3e2i_A	219	Thymidine kinase; Zn-binding, ATP-binding, DNA syn	97.13
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	97.12
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	97.09
2zpa_A	671	Uncharacterized protein YPFI; RNA modification enz	96.97
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	96.9
3bos_A	242	Putative DNA replication factor; P-loop containing	96.89
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	96.86
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	96.82
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	96.68
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	96.68
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	96.65
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	96.55
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	96.49
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	96.49
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	96.48
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	96.42
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	96.39
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	96.33
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	96.3
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	96.26
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	96.14
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	96.1
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	96.1
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	96.09
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	96.05
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	96.01
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	95.96
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	95.94
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	95.94
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	95.91
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	95.88
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	95.88
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	95.76
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	95.68
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	95.64
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	95.58
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	95.55
2chq_A	319	Replication factor C small subunit; DNA-binding pr	95.47
3pvs_A	447	Replication-associated recombination protein A; ma	95.45
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	95.45
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	95.41
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	95.3
3hjh_A	483	Transcription-repair-coupling factor; MFD, mutatio	95.29
2r6a_A	454	DNAB helicase, replicative helicase; replication,	95.29
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	95.27
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	95.21
3io5_A	333	Recombination and repair protein; storage dimer, i	94.95
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	94.88
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	94.77
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	94.5
2qgz_A	308	Helicase loader, putative primosome component; str	93.93
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	93.92
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	93.87
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	93.75
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	93.45
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	93.31
2fna_A	357	Conserved hypothetical protein; structural genomic	93.31
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	93.06
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	91.97
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	91.97
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	91.57
1w36_B	1180	RECB, exodeoxyribonuclease V beta chain; recombina	91.54
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	91.5
3u4q_B	1166	ATP-dependent helicase/deoxyribonuclease subunit;	91.46
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	91.33
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	91.26
1u94_A	356	RECA protein, recombinase A; homologous recombinat	91.26
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	91.19
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	91.02
2z43_A	324	DNA repair and recombination protein RADA; archaea	90.98
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	90.94
1e9r_A	437	Conjugal transfer protein TRWB; coupling protein,	90.77
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	90.77
1sky_E	473	F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alp	90.72
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	90.66
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	90.61
2r2a_A	199	Uncharacterized protein; zonular occludens toxin,	90.57
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	90.57
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	90.41
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	90.38
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	90.37
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	90.37
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	90.33
1tue_A	212	Replication protein E1; helicase, replication, E1E	90.32
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	90.31
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	90.14
1xp8_A	366	RECA protein, recombinase A; recombination, radior	90.09
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	90.07
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	90.02
4ag6_A	392	VIRB4 ATPase, type IV secretory pathway VIRB4 comp	89.99
2cvh_A	220	DNA repair and recombination protein RADB; filamen	89.98
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	89.98
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	89.85
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	89.85
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	89.83
2l82_A	162	Designed protein OR32; structural genomics, northe	89.78
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	89.71
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	89.53
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	89.41
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	89.33
2r44_A	331	Uncharacterized protein; putative ATPase, structur	89.12
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	89.0
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	88.96
1p9r_A	418	General secretion pathway protein E; bacterial typ	88.95
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	88.68
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	88.68
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	88.6
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	88.51
2eyu_A	261	Twitching motility protein PILT; pilus retraction	88.48
2ewv_A	372	Twitching motility protein PILT; pilus retraction	88.35
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	88.35
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	88.35
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	88.33
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	88.16
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	88.06
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	87.94
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	87.88
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	87.85
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	87.71
2ius_A	512	DNA translocase FTSK; nucleotide-binding, chromoso	87.58
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	87.56
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	87.52
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	87.5
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	87.48
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	87.37
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	87.32
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	87.31
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	87.29
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	87.27
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	87.22
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	87.19
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	87.05
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	87.02
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	87.0
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	86.95
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	86.87
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	86.83
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	86.7
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	86.58
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	86.57
2l8b_A	189	Protein TRAI, DNA helicase I; RECD, hydrolase; NMR	86.53
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	86.49
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	86.48
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	86.31
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	86.25
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	86.19
1c9k_A	180	COBU, adenosylcobinamide kinase; alpha/beta struct	86.15
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	86.14
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	86.07
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	86.0
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	85.97
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	85.95
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	85.91
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	85.87
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	85.85
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	85.84
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	85.54
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	85.35
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	85.35
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	85.31
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	85.27
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	85.23
2iut_A	574	DNA translocase FTSK; nucleotide-binding, chromoso	85.22
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	85.18
3bs4_A	260	Uncharacterized protein PH0321; structural genomic	85.1
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	85.06
3umf_A	217	Adenylate kinase; rossmann fold, transferase; 2.05	85.01
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	84.96
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	84.93
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	84.84
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	84.8
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	84.8
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	84.79
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	84.75
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	84.43
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	84.42
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	84.41
3ice_A	422	Transcription termination factor RHO; transcriptio	84.29
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	84.19
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	84.1
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	83.98
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	83.97
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	83.88
1via_A	175	Shikimate kinase; structural genomics, transferase	83.85
3sr0_A	206	Adenylate kinase; phosphoryl transfer analogue, AL	83.59
3l0o_A	427	Transcription termination factor RHO; helicase, RH	83.49
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	83.19
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	83.03
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	82.96
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	82.86
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	82.84
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	82.82
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	82.79
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	82.77
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	82.71
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	82.63
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	82.57
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	82.57
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	82.5
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	82.49
2xxa_A	433	Signal recognition particle protein; protein trans	82.47
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	82.41
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	82.34
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	82.32
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	82.31
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	82.25
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	82.21
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	82.21
3eph_A	409	TRNA isopentenyltransferase; transferase, alternat	82.17
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	82.08
3tqf_A	181	HPR(Ser) kinase; transferase, hydrolase; 2.80A {Co	81.93
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	81.89
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	81.75
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	81.7
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	81.64
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	81.63
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	81.53
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	81.53
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	81.41
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	81.35
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	81.35
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	81.3
3nwn_A	359	Kinesin-like protein KIF9; motor domain, ADP, stru	81.22
4a74_A	231	DNA repair and recombination protein RADA; hydrola	81.2
2vli_A	183	Antibiotic resistance protein; transferase, tunica	81.08
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	80.94
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	80.86
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	80.69
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	80.65
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	80.64
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	80.57
1f9v_A	347	Kinesin-like protein KAR3; kinesin-related protein	80.54
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	80.53
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	80.51
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	80.37
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	80.18
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	80.11
3bor_A	237	Human initiation factor 4A-II; translation initiat	80.06
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	80.02

>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation, rRNA processing, mRNA splicing, mRNA transport; HET: ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B 2zu6_A

Probab=100.00  E-value=1.3e-61  Score=435.45  Aligned_cols=369  Identities=68%  Similarity=1.077  Sum_probs=342.5

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQI   80 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~   80 (369)
                      ++|++.+.++|.++||..|+|+|+++++.+.+++++++.+|||+|||++++++++..+.....+.++||++|+++|+.|+
T Consensus        42 ~~l~~~l~~~l~~~g~~~~~~~Q~~ai~~i~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~Pt~~L~~q~  121 (410)
T 2j0s_A           42 MGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQI  121 (410)
T ss_dssp             GCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTTSCSCCEEEECSSHHHHHHH
T ss_pred             cCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCCCchHHHHHHHHHHHhhccCCceEEEEcCcHHHHHHH
Confidence            57999999999999999999999999999999999999999999999999999998876555556999999999999999


Q ss_pred             HHHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHH
Q 017573           81 EKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIY  160 (369)
Q Consensus        81 ~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~  160 (369)
                      .+.+.++....++.+....++.....+......+++|+|+||+.+...+.........++++|+||+|++.+.++...+.
T Consensus       122 ~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~ivv~Tp~~l~~~l~~~~~~~~~~~~vViDEah~~~~~~~~~~~~  201 (410)
T 2j0s_A          122 QKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIY  201 (410)
T ss_dssp             HHHHHHHTTTTTCCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHTSTTTHHHHH
T ss_pred             HHHHHHHhccCCeEEEEEECCCCHHHHHHHhhcCCCEEEcCHHHHHHHHHhCCccHhheeEEEEccHHHHHhhhhHHHHH
Confidence            99999998888899999999888777766666778999999999999999888888889999999999999999999999


Q ss_pred             HHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHHHhccCCCeEE
Q 017573          161 DIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVI  240 (369)
Q Consensus       161 ~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lv  240 (369)
                      .+...+++..|++++|||++....+....++..+..+...........+.+.+........+...+..++.....+++||
T Consensus       202 ~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lV  281 (410)
T 2j0s_A          202 DVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVI  281 (410)
T ss_dssp             HHHTTSCTTCEEEEEESCCCHHHHTTGGGTCSSCEEECCCGGGCSCTTEEEEEEEESSTTHHHHHHHHHHHHHTSSEEEE
T ss_pred             HHHHhCccCceEEEEEcCCCHHHHHHHHHHcCCCEEEEecCccccCCCceEEEEEeCcHHhHHHHHHHHHHhcCCCcEEE
Confidence            99999999999999999999888788888888888887777777777888888888877778888999988888889999


Q ss_pred             EeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCCCCccchh
Q 017573          241 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYL  320 (369)
Q Consensus       241 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~  320 (369)
                      ||++.+.++.+++.|...+..+..+||+++..+|.++++.|++|+.+|||+|+++++|+|+|++++||++++|++...|.
T Consensus       282 f~~~~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~v~~Vi~~~~p~s~~~~~  361 (410)
T 2j0s_A          282 FCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYI  361 (410)
T ss_dssp             ECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHHTSSCEEEECGGGSSSCCCTTEEEEEESSCCSSHHHHH
T ss_pred             EEcCHHHHHHHHHHHHhCCCceEEeeCCCCHHHHHHHHHHHHCCCCCEEEECChhhCcCCcccCCEEEEECCCCCHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhcccccCCCceeEEEEeccccHHHHHHHHHHhccccccCCcchhhcC
Q 017573          321 HRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPSNVADLL  369 (369)
Q Consensus       321 Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  369 (369)
                      ||+||+||.|++|.+++++++.+...++.++++++..++++|.++.++|
T Consensus       362 Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~  410 (410)
T 2j0s_A          362 HRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVADLI  410 (410)
T ss_dssp             HHHTTSSGGGCCEEEEEEEEGGGHHHHHHHHHHTTCCCEECCSCCTTTC
T ss_pred             HhcccccCCCCceEEEEEecHHHHHHHHHHHHHhCCCceecccchhhcC
Confidence            9999999999999999999999999999999999999999999888765

>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=9.5e-61  Score=430.44  Aligned_cols=366  Identities=32%  Similarity=0.511  Sum_probs=329.8

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccC-----CCccEEEEcCCHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGL-----VQCQALVLAPTRE   75 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~-----~~~~~liv~P~~~   75 (369)
                      ++|++.+.++|.++||..|+|+|+++++.+.+++++++++|||+|||++++++++..+....     .++++||++|+++
T Consensus        61 ~~l~~~l~~~l~~~g~~~pt~iQ~~ai~~i~~g~d~i~~a~TGsGKT~a~~lpil~~l~~~~~~~~~~~~~~lil~Ptre  140 (434)
T 2db3_A           61 ADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPILSKLLEDPHELELGRPQVVIVSPTRE  140 (434)
T ss_dssp             SCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHSCCCCCTTCCSEEEECSSHH
T ss_pred             cCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEECCCCCCchHHHHHHHHHHHHhcccccccCCccEEEEecCHH
Confidence            58999999999999999999999999999999999999999999999999999998875432     2458999999999


Q ss_pred             HHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCc
Q 017573           76 LAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGF  155 (369)
Q Consensus        76 l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~  155 (369)
                      |+.|+.+.++++....++++..++|+.....+...+..+++|+|+||+++..++.+......+++++|+||||++.+.++
T Consensus       141 La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Ivv~Tp~~l~~~l~~~~~~l~~~~~lVlDEah~~~~~gf  220 (434)
T 2db3_A          141 LAIQIFNEARKFAFESYLKIGIVYGGTSFRHQNECITRGCHVVIATPGRLLDFVDRTFITFEDTRFVVLDEADRMLDMGF  220 (434)
T ss_dssp             HHHHHHHHHHHHTTTSSCCCCEECTTSCHHHHHHHHTTCCSEEEECHHHHHHHHHTTSCCCTTCCEEEEETHHHHTSTTT
T ss_pred             HHHHHHHHHHHHhccCCcEEEEEECCCCHHHHHHHhhcCCCEEEEChHHHHHHHHhCCcccccCCeEEEccHhhhhccCc
Confidence            99999999999988888889899999887777777778899999999999999998888888999999999999999999


Q ss_pred             HHHHHHHHhhC--CccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHHHhc
Q 017573          156 KDQIYDIFQLL--PAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETL  233 (369)
Q Consensus       156 ~~~~~~~~~~~--~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  233 (369)
                      ...+..++..+  ++..|++++|||++.....+...++..+..+...........+.+.+..... ..+...+.+++...
T Consensus       221 ~~~~~~i~~~~~~~~~~q~l~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~i~~~~~~~~~-~~k~~~l~~~l~~~  299 (434)
T 2db3_A          221 SEDMRRIMTHVTMRPEHQTLMFSATFPEEIQRMAGEFLKNYVFVAIGIVGGACSDVKQTIYEVNK-YAKRSKLIEILSEQ  299 (434)
T ss_dssp             HHHHHHHHHCTTSCSSCEEEEEESCCCHHHHHHHHTTCSSCEEEEESSTTCCCTTEEEEEEECCG-GGHHHHHHHHHHHC
T ss_pred             HHHHHHHHHhcCCCCCceEEEEeccCCHHHHHHHHHhccCCEEEEeccccccccccceEEEEeCc-HHHHHHHHHHHHhC
Confidence            99999998875  5688999999999999999999999988888777666666677777766654 34667777777766


Q ss_pred             cCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCC
Q 017573          234 AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLP  313 (369)
Q Consensus       234 ~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~  313 (369)
                      .. ++||||++++.++.+++.|.+.+..+..+||+++..+|.++++.|++|+.+|||||+++++|+|+|++++||++++|
T Consensus       300 ~~-~~lVF~~t~~~a~~l~~~L~~~~~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT~v~~rGlDi~~v~~VI~~d~p  378 (434)
T 2db3_A          300 AD-GTIVFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATSVASRGLDIKNIKHVINYDMP  378 (434)
T ss_dssp             CT-TEEEECSSHHHHHHHHHHHHHTTCCEEEESTTSCHHHHHHHHHHHHTSSCSEEEECGGGTSSCCCTTCCEEEESSCC
T ss_pred             CC-CEEEEEeCcHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHHHcCCCcEEEEchhhhCCCCcccCCEEEEECCC
Confidence            54 59999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCccchhhhhcccccCCCceeEEEEec-cccHHHHHHHHHHhccccccCCcchhhc
Q 017573          314 TQPENYLHRIGRSGRFGRKGVAINFVT-RDDERMLFDIQKFYNVVIEELPSNVADL  368 (369)
Q Consensus       314 ~~~~~~~Q~~GR~~R~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~  368 (369)
                      .+..+|.||+||+||.|+.|.+++|++ ..+......+.+.++...+++|++|.++
T Consensus       379 ~~~~~y~qriGR~gR~g~~G~a~~~~~~~~~~~~~~~l~~~l~~~~~~vp~~l~~~  434 (434)
T 2db3_A          379 SKIDDYVHRIGRTGRVGNNGRATSFFDPEKDRAIAADLVKILEGSGQTVPDFLRTC  434 (434)
T ss_dssp             SSHHHHHHHHTTSSCTTCCEEEEEEECTTTCGGGHHHHHHHHHHTTCCCCGGGC--
T ss_pred             CCHHHHHHHhcccccCCCCCEEEEEEeccccHHHHHHHHHHHHHcCCCCCHHHHhC
Confidence            999999999999999999999999999 4578888999999999999999998764

>3eiq_A Eukaryotic initiation factor 4A-I; PDCD4, anti-oncogene, apoptosis, cell cycle, nucleus, phosph RNA-binding, ATP-binding, helicase, hydrolase; 3.50A {Homo sapiens}

Probab=100.00  E-value=2.4e-60  Score=428.01  Aligned_cols=369  Identities=75%  Similarity=1.158  Sum_probs=323.3

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQI   80 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~   80 (369)
                      +++++.+.+.|.++|+..|+++|+++++.+.+++++++.+|||+|||+++++++++.+.....+.+++|++|+++|+.|+
T Consensus        45 ~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~  124 (414)
T 3eiq_A           45 MNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQQI  124 (414)
T ss_dssp             GCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEECCCSCSSSHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHH
T ss_pred             CCCCHHHHHHHHHcCCCCCCHHHHHHhHHHhCCCCEEEECCCCCcccHHHHHHHHHHHhhcCCceeEEEEeChHHHHHHH
Confidence            47899999999999999999999999999999999999999999999999999998887665566899999999999999


Q ss_pred             HHHHHHhccccCcEEEEEECCcchHHHHHHHc-cCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHH
Q 017573           81 EKVMRALGDYLGVKVHACVGGTSVREDQRILQ-AGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQI  159 (369)
Q Consensus        81 ~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~-~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~  159 (369)
                      .+.+.++....+..+....++........... ..++|+|+||+.+...+.........++++|+||+|++.+.++...+
T Consensus       125 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~l~~~~~~~~~~~~vViDEah~~~~~~~~~~~  204 (414)
T 3eiq_A          125 QKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQI  204 (414)
T ss_dssp             HHHHHHHGGGSCCCEEECCCCTTHHHHHHHHTTTCCSEEEECHHHHHHHHHHTSSCSTTCCEEEECSHHHHHHTTTHHHH
T ss_pred             HHHHHHHhcccCceEEEEECCcchHHHHHHHhcCCCCEEEECHHHHHHHHHcCCcccccCcEEEEECHHHhhccCcHHHH
Confidence            99999998888888888888877655544443 67899999999999999988888888999999999999999999999


Q ss_pred             HHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHHHhccCCCeE
Q 017573          160 YDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSV  239 (369)
Q Consensus       160 ~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~l  239 (369)
                      ..++..+++..+++++|||++.+.......++..+..+...........+.+.+........+...+..++.....+++|
T Consensus       205 ~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~l  284 (414)
T 3eiq_A          205 YDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLCDLYETLTITQAV  284 (414)
T ss_dssp             HHHHTTSCTTCEEEEECSCCCHHHHHHHTTTCSSCEEECCCCCCCCTTSCCEEEEECSSSTTHHHHHHHHHHSSCCSSCE
T ss_pred             HHHHHhCCCCCeEEEEEEecCHHHHHHHHHHcCCCEEEEecCCccCCCCceEEEEEeChHHhHHHHHHHHHHhCCCCcEE
Confidence            99999999999999999999999888889999999888887777788888888888888888999999999988889999


Q ss_pred             EEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCCCCccch
Q 017573          240 IFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENY  319 (369)
Q Consensus       240 v~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~  319 (369)
                      |||++++.++.+++.|...+..+..+||+++..+|.++++.|++|+.+|||+|+++++|+|+|++++||++++|++...|
T Consensus       285 vf~~~~~~~~~l~~~l~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidip~v~~Vi~~~~p~s~~~~  364 (414)
T 3eiq_A          285 IFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENY  364 (414)
T ss_dssp             EECSCHHHHHHHHHHHHTTTCCCEEC---CHHHHHHHHHHHHSCC---CEEECSSCC--CCGGGCSCEEESSCCSSTHHH
T ss_pred             EEeCCHHHHHHHHHHHHhcCCeEEEecCCCCHHHHHHHHHHHHcCCCcEEEECCccccCCCccCCCEEEEeCCCCCHHHh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhcccccCCCceeEEEEeccccHHHHHHHHHHhccccccCCcchhhcC
Q 017573          320 LHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPSNVADLL  369 (369)
Q Consensus       320 ~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  369 (369)
                      .||+||+||.|++|.+++++++.+...++.+.++++..+++++.++.++|
T Consensus       365 ~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  414 (414)
T 3eiq_A          365 IHRIGRGGRFGRKGVAINMVTEEDKRTLRDIETFYNTSIEEMPLNVADLI  414 (414)
T ss_dssp             HHHSCCC-------CEEEEECSTHHHHHHHHHHHTTCCCEECCC------
T ss_pred             hhhcCcccCCCCCceEEEEEcHHHHHHHHHHHHHHcCCccccChhhhhcC
Confidence            99999999999999999999999999999999999999999999998876

>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding, RNA binding protein; 2.10A {Saccharomyces cerevisiae} SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A

Probab=100.00  E-value=1.6e-58  Score=414.09  Aligned_cols=365  Identities=42%  Similarity=0.683  Sum_probs=327.6

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQI   80 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~   80 (369)
                      ++|++.+.++|.++||.+|+|+|+++++.+.+++++++.+|||+|||++++++++..+.....+.+++|++|+++|+.|+
T Consensus        26 ~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~li~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~  105 (400)
T 1s2m_A           26 FYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVPTRELALQT  105 (400)
T ss_dssp             GCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHH
T ss_pred             cCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEECCCCcHHHHHHHHHHHHHHhhccCCccEEEEcCCHHHHHHH
Confidence            58999999999999999999999999999999999999999999999999999998877655556899999999999999


Q ss_pred             HHHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHH
Q 017573           81 EKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIY  160 (369)
Q Consensus        81 ~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~  160 (369)
                      .+.+.++....+..+....++.....+.......++|+|+||+.+...+........+++++|+||+|++.+..+...+.
T Consensus       106 ~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~T~~~l~~~~~~~~~~~~~~~~vIiDEaH~~~~~~~~~~~~  185 (400)
T 1s2m_A          106 SQVVRTLGKHCGISCMVTTGGTNLRDDILRLNETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSRDFKTIIE  185 (400)
T ss_dssp             HHHHHHHTTTTTCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEEESHHHHSSHHHHHHHH
T ss_pred             HHHHHHHhcccCceEEEEeCCcchHHHHHHhcCCCCEEEEchHHHHHHHHhCCcccccCCEEEEeCchHhhhhchHHHHH
Confidence            99999998888889999888887666655566788999999999999888877778889999999999998888888888


Q ss_pred             HHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHHHhccCCCeEE
Q 017573          161 DIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVI  240 (369)
Q Consensus       161 ~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lv  240 (369)
                      .+...+++..+++++|||++..........+..+..+..... .....+..++..... ..+...+..++.....+++||
T Consensus       186 ~i~~~~~~~~~~i~lSAT~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~-~~k~~~l~~~~~~~~~~~~lV  263 (400)
T 1s2m_A          186 QILSFLPPTHQSLLFSATFPLTVKEFMVKHLHKPYEINLMEE-LTLKGITQYYAFVEE-RQKLHCLNTLFSKLQINQAII  263 (400)
T ss_dssp             HHHTTSCSSCEEEEEESCCCHHHHHHHHHHCSSCEEESCCSS-CBCTTEEEEEEECCG-GGHHHHHHHHHHHSCCSEEEE
T ss_pred             HHHHhCCcCceEEEEEecCCHHHHHHHHHHcCCCeEEEeccc-cccCCceeEEEEech-hhHHHHHHHHHhhcCCCcEEE
Confidence            999999889999999999998888888888888766554332 334455555554443 457778888888888889999


Q ss_pred             EeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCCCCccchh
Q 017573          241 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYL  320 (369)
Q Consensus       241 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~  320 (369)
                      ||++.+.++.+++.|...+..+..+||+++.++|.++++.|++|+.+|||+|+++++|+|+|++++||++++|++...|.
T Consensus       264 f~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vLv~T~~~~~Gidip~~~~Vi~~~~p~s~~~~~  343 (400)
T 1s2m_A          264 FCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYL  343 (400)
T ss_dssp             ECSSHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESSCSSSSCCCTTEEEEEESSCCSSHHHHH
T ss_pred             EEecHHHHHHHHHHHHhcCCCeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCccccCCCccCCCEEEEeCCCCCHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhcccccCCCceeEEEEeccccHHHHHHHHHHhccccccCCcchhh
Q 017573          321 HRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPSNVAD  367 (369)
Q Consensus       321 Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  367 (369)
                      |++||+||.|+.|.+++++++.+...++.+++.++..+++++.++.+
T Consensus       344 Qr~GR~gR~g~~g~~~~l~~~~~~~~~~~i~~~~~~~~~~~~~~~~~  390 (400)
T 1s2m_A          344 HRIGRSGRFGHLGLAINLINWNDRFNLYKIEQELGTEIAAIPATIDK  390 (400)
T ss_dssp             HHHCBSSCTTCCEEEEEEECGGGHHHHHHHHHHHTCCCEECCSSCCG
T ss_pred             HhcchhcCCCCCceEEEEeccchHHHHHHHHHHhCCCcccccccccc
Confidence            99999999999999999999999999999999999999999987754

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=100.00  E-value=9.9e-59  Score=417.78  Aligned_cols=367  Identities=35%  Similarity=0.519  Sum_probs=323.4

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccC------------------
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGL------------------   62 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~------------------   62 (369)
                      ++|++.+.++|..+||..|+|+|+++++.+.+++++++.+|||+|||++++++++..+....                  
T Consensus        20 ~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   99 (417)
T 2i4i_A           20 VEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYSDGPGEALRAMKENGRYGRRK   99 (417)
T ss_dssp             SCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHHCCCHHHHHHHHCBTTBSCS
T ss_pred             CCCCHHHHHHHHHCCCCCCCHHHHHHHHHHccCCCEEEEcCCCCHHHHHHHHHHHHHHHhccccchhhcccccccccccc
Confidence            58999999999999999999999999999999999999999999999999999988765332                  


Q ss_pred             CCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEE
Q 017573           63 VQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMF  142 (369)
Q Consensus        63 ~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~v  142 (369)
                      ..++++|++|+++|+.|+.+.+.++....++++..+.|+.........+..+++|+|+||+.|...+.........++++
T Consensus       100 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~~~~~~i  179 (417)
T 2i4i_A          100 QYPISLVLAPTRELAVQIYEEARKFSYRSRVRPCVVYGGADIGQQIRDLERGCHLLVATPGRLVDMMERGKIGLDFCKYL  179 (417)
T ss_dssp             BCCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCHHHHHHHHTTCCSEEEECHHHHHHHHHTTSBCCTTCCEE
T ss_pred             CCccEEEECCcHHHHHHHHHHHHHHhCcCCceEEEEECCCCHHHHHHHhhCCCCEEEEChHHHHHHHHcCCcChhhCcEE
Confidence            12479999999999999999999998878889999999888777666667788999999999999998888888889999


Q ss_pred             EEechhHhhccCcHHHHHHHHhh--CCc--cCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccc
Q 017573          143 VLDEADEMLSRGFKDQIYDIFQL--LPA--KVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEK  218 (369)
Q Consensus       143 iiDE~H~~~~~~~~~~~~~~~~~--~~~--~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  218 (369)
                      |+||+|++.+.++...+..+...  ++.  ..+++++|||++.........++..+..+...........+...+.....
T Consensus       180 ViDEah~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~  259 (417)
T 2i4i_A          180 VLDEADRMLDMGFEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGRVGSTSENITQKVVWVEE  259 (417)
T ss_dssp             EESSHHHHHHTTCHHHHHHHHTSSSCCCBTTBEEEEEESCCCHHHHHHHHHHCSSCEEEEEC----CCSSEEEEEEECCG
T ss_pred             EEEChhHhhccCcHHHHHHHHHhccCCCcCCcEEEEEEEeCCHHHHHHHHHHcCCCEEEEeCCCCCCccCceEEEEEecc
Confidence            99999999999889999888874  332  57899999999988888888889888877776666666667766665544


Q ss_pred             hhhhHHHHHHHHHhc-cCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcC
Q 017573          219 EEWKLETLCDLYETL-AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLAR  297 (369)
Q Consensus       219 ~~~~~~~l~~~~~~~-~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~  297 (369)
                       ..+...+.+++... ..+++||||++++.++.+++.|.+.+..+..+||+++.++|.++++.|++|+.+|||+|+++++
T Consensus       260 -~~~~~~l~~~l~~~~~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlvaT~~~~~  338 (417)
T 2i4i_A          260 -SDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAAR  338 (417)
T ss_dssp             -GGHHHHHHHHHHTCCTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHHTSSCEEEECHHHHT
T ss_pred             -HhHHHHHHHHHHhcCCCCeEEEEECCHHHHHHHHHHHHHCCCCeeEecCCCCHHHHHHHHHHHHcCCCCEEEECChhhc
Confidence             45677777888766 4578999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCcEEEEecCCCCccchhhhhcccccCCCceeEEEEeccccHHHHHHHHHHhccccccCCcchhhc
Q 017573          298 GIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPSNVADL  368 (369)
Q Consensus       298 G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  368 (369)
                      |+|+|++++||++++|++...|.||+||+||.|+.|.+++++++.+...++.+.+.++....++++++.++
T Consensus       339 Gidip~v~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~~  409 (417)
T 2i4i_A          339 GLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINITKDLLDLLVEAKQEVPSWLENM  409 (417)
T ss_dssp             TSCCCCEEEEEESSCCSSHHHHHHHHTTBCC--CCEEEEEEECGGGGGGHHHHHHHHHHTTCCCCHHHHHH
T ss_pred             CCCcccCCEEEEEcCCCCHHHHHHhcCccccCCCCceEEEEEccccHHHHHHHHHHHHHhcCcCCHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999887654

>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 1xtj_A* 1xtk_A

Probab=100.00  E-value=7e-58  Score=408.87  Aligned_cols=364  Identities=40%  Similarity=0.666  Sum_probs=320.9

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQI   80 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~   80 (369)
                      ++|++.+.+.|.++|+.+|+|+|+++++.+.+++++++.+|||+|||++++++++..+.....+.+++|++|+++|+.|+
T Consensus        13 ~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~P~~~L~~q~   92 (391)
T 1xti_A           13 FLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQI   92 (391)
T ss_dssp             GCCCHHHHHHHHHHSCCSCCHHHHHHHHHHTTTCCEEEECSSCSSHHHHHHHHHHHHCCCCTTCCCEEEECSCHHHHHHH
T ss_pred             cCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHHHHHHHhhcccCCCeeEEEECCCHHHHHHH
Confidence            57999999999999999999999999999999999999999999999999999998877655556899999999999999


Q ss_pred             HHHHHHhcccc-CcEEEEEECCcchHHHHHHHc-cCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhc-cCcHH
Q 017573           81 EKVMRALGDYL-GVKVHACVGGTSVREDQRILQ-AGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLS-RGFKD  157 (369)
Q Consensus        81 ~~~~~~~~~~~-~~~v~~~~~~~~~~~~~~~~~-~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~-~~~~~  157 (369)
                      .+.+.++.... ++++..+.|+.........+. ..++|+|+||+.+...+.........++++|+||+|++.+ .++..
T Consensus        93 ~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~iiv~T~~~l~~~~~~~~~~~~~~~~vViDEaH~~~~~~~~~~  172 (391)
T 1xti_A           93 SKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRR  172 (391)
T ss_dssp             HHHHHHHTTTCTTCCEEEECTTSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTTSSCCTTCSEEEECSHHHHTSSHHHHH
T ss_pred             HHHHHHHHhhCCCeEEEEEeCCCCHHHHHHHHhcCCCCEEEECHHHHHHHHHcCCccccccCEEEEeCHHHHhhccchHH
Confidence            99999987765 788888888887655544443 4579999999999999988888888899999999999976 36677


Q ss_pred             HHHHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCcc-ccccceeEEEEEccchhhhHHHHHHHHHhccCC
Q 017573          158 QIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDE-LTLEGIKQFYVNVEKEEWKLETLCDLYETLAIT  236 (369)
Q Consensus       158 ~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  236 (369)
                      .+..++...++..+++++|||++.........++..+..+...... .....+...+.... ...+...+..++.....+
T Consensus       173 ~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~l~~~l~~~~~~  251 (391)
T 1xti_A          173 DVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLK-DNEKNRKLFDLLDVLEFN  251 (391)
T ss_dssp             HHHHHHHTSCSSSEEEEEESSCCSTHHHHHHHHCSSCEEEECCCCCCCCCTTCEEEEEECC-GGGHHHHHHHHHHHSCCS
T ss_pred             HHHHHHhhCCCCceEEEEEeeCCHHHHHHHHHHcCCCeEEEecCccccCcccceEEEEEcC-chhHHHHHHHHHHhcCCC
Confidence            8888888888899999999999998888888888888777655433 33445555555544 345778888888888888


Q ss_pred             CeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCCCCc
Q 017573          237 QSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP  316 (369)
Q Consensus       237 k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~~~  316 (369)
                      ++||||++.+.++.+++.|...+..+..+||+++.++|.++++.|++|+.+|||+|+++++|+|+|++++||++++|++.
T Consensus       252 ~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gidi~~~~~Vi~~~~p~s~  331 (391)
T 1xti_A          252 QVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDS  331 (391)
T ss_dssp             EEEEECSCHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTCCSEEEESCCCSSCBCCTTEEEEEESSCCSSH
T ss_pred             cEEEEeCcHHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCcEEEECChhhcCCCcccCCEEEEeCCCCCH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cchhhhhcccccCCCceeEEEEeccc-cHHHHHHHHHHhccccccCCcch
Q 017573          317 ENYLHRIGRSGRFGRKGVAINFVTRD-DERMLFDIQKFYNVVIEELPSNV  365 (369)
Q Consensus       317 ~~~~Q~~GR~~R~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~  365 (369)
                      ..|.|++||+||.|+.|.+++++++. +.+.++.+.+.++..+++++.++
T Consensus       332 ~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  381 (391)
T 1xti_A          332 DTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEI  381 (391)
T ss_dssp             HHHHHHHCBCSSSCCCCEEEEEECSHHHHHHHHHHHHHTTCCCEECCSCC
T ss_pred             HHHHHhcccccCCCCceEEEEEEcccchHHHHHHHHHHhcCChhhCCccc
Confidence            99999999999999999999999876 55778999999999999988765

>1fuu_A Yeast initiation factor 4A; IF4A, helicase, DEAD-box protein, translation; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 2vso_A* 2vsx_A*

Probab=100.00  E-value=4.8e-60  Score=423.31  Aligned_cols=368  Identities=65%  Similarity=0.999  Sum_probs=180.3

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQI   80 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~   80 (369)
                      ++|++.+.+.|.++|+.+|+|+|+++++.+.+++++++.+|||+|||++++++++..+.....+++++|++|+++|+.|+
T Consensus        26 ~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~P~~~L~~q~  105 (394)
T 1fuu_A           26 MELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQI  105 (394)
T ss_dssp             GCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCCEEECCCSSHHHHHHHHHHHHHHCCTTCCSCCEEEECSSHHHHHHH
T ss_pred             cCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhhccCCCCCEEEEcCCHHHHHHH
Confidence            58999999999999999999999999999999999999999999999999999998877665666999999999999999


Q ss_pred             HHHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHH
Q 017573           81 EKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIY  160 (369)
Q Consensus        81 ~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~  160 (369)
                      .+.+.++....+..+....|+........... +++|+|+||+.+...+........+++++|+||+|.+.+.++...+.
T Consensus       106 ~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~-~~~i~v~T~~~l~~~~~~~~~~~~~~~~vIiDEah~~~~~~~~~~~~  184 (394)
T 1fuu_A          106 QKVVMALAFHMDIKVHACIGGTSFVEDAEGLR-DAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIY  184 (394)
T ss_dssp             HHHHHHHTTTSCCCEEEECSSCCHHHHHHHHH-HCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHHHTTCHHHHH
T ss_pred             HHHHHHHhccCCeeEEEEeCCCchHHHHhhcC-CCCEEEECHHHHHHHHHhCCcchhhCcEEEEEChHHhhCCCcHHHHH
Confidence            99999998888889999888887655544433 57999999999999998887778889999999999999888999999


Q ss_pred             HHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHHHhccCCCeEE
Q 017573          161 DIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVI  240 (369)
Q Consensus       161 ~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lv  240 (369)
                      .+...+++..+++++|||++.........++..+..+...........+...+........+...+..++.....+++||
T Consensus       185 ~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~lV  264 (394)
T 1fuu_A          185 QIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKDELTLEGIKQFYVNVEEEEYKYECLTDLYDSISVTQAVI  264 (394)
T ss_dssp             HHHHHSCTTCEEEEECSSCCHHHHHHHHHHCCSCEEEEECC---------------------------------------
T ss_pred             HHHHhCCCCceEEEEEEecCHHHHHHHHHhcCCCeEEEecCccccCCCceEEEEEcCchhhHHHHHHHHHhcCCCCcEEE
Confidence            99999999999999999999888888888999888887777666666666666666665556777777777777789999


Q ss_pred             EeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCCCCccchh
Q 017573          241 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYL  320 (369)
Q Consensus       241 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~  320 (369)
                      ||+++++++.+++.|++.+..+..+||+++.++|.++++.|++|+.+|||+|+++++|+|+|++++||++++|++...|.
T Consensus       265 f~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gldi~~~~~Vi~~~~p~s~~~~~  344 (394)
T 1fuu_A          265 FCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYI  344 (394)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             EECCHHHHHHHHHHHHHcCCeEEEeeCCCCHHHHHHHHHHHHCCCCcEEEECChhhcCCCcccCCEEEEeCCCCCHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhcccccCCCceeEEEEeccccHHHHHHHHHHhccccccCCcchhhcC
Q 017573          321 HRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPSNVADLL  369 (369)
Q Consensus       321 Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  369 (369)
                      |++||+||.|++|.+++++++.+...++.++++++..+++++.++.++|
T Consensus       345 Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~  393 (394)
T 1fuu_A          345 HRIGRGGRFGRKGVAINFVTNEDVGAMRELEKFYSTQIEELPSDIATLL  393 (394)
T ss_dssp             -------------------------------------------------
T ss_pred             HHcCcccCCCCCceEEEEEchhHHHHHHHHHHHhCCcccccCcchhhhc
Confidence            9999999999999999999999999999999999999999998887664

>3pey_A ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, ATPase, helicase, mRNA-export, nuclear pore, hydrolase-RNA complex; HET: ADP; 1.40A {Saccharomyces cerevisiae} PDB: 3pew_A* 3pex_A* 3pez_A* 3rrm_A* 3rrn_A* 2kbe_A 3gfp_A 2kbf_A 3pev_A* 3peu_A*

Probab=100.00  E-value=9e-57  Score=402.31  Aligned_cols=358  Identities=41%  Similarity=0.714  Sum_probs=321.5

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccC--CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKG--LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQ   78 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~--~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~   78 (369)
                      +||++.+.++|.++|+.+|+|+|.++++.+.++  +++++.+|||+|||++++++++..+.....+++++|++|+++|+.
T Consensus        10 ~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~   89 (395)
T 3pey_A           10 LGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRVNPEDASPQAICLAPSRELAR   89 (395)
T ss_dssp             SCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHCSSCCCEEEECCTTSCHHHHHHHHHHHHCCTTCCSCCEEEECSSHHHHH
T ss_pred             CCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCcHHHHHHHHHHHHhccCCCCccEEEECCCHHHHH
Confidence            689999999999999999999999999999988  999999999999999999999988876656669999999999999


Q ss_pred             HHHHHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhc-cCcHH
Q 017573           79 QIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLS-RGFKD  157 (369)
Q Consensus        79 q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~-~~~~~  157 (369)
                      |+.+.+.++....+..+....++......    ..+++|+|+||+.+...+.+......+++++|+||+|++.+ ..+..
T Consensus        90 q~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~iiv~T~~~l~~~~~~~~~~~~~~~~iIiDEah~~~~~~~~~~  165 (395)
T 3pey_A           90 QTLEVVQEMGKFTKITSQLIVPDSFEKNK----QINAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGD  165 (395)
T ss_dssp             HHHHHHHHHTTTSCCCEEEESTTSSCTTS----CBCCSEEEECHHHHHHHHHTTCBCCTTCCEEEEETHHHHHHSTTHHH
T ss_pred             HHHHHHHHHhcccCeeEEEEecCchhhhc----cCCCCEEEEcHHHHHHHHHcCCcccccCCEEEEEChhhhcCccccHH
Confidence            99999999988778888777766542221    34689999999999999988888888899999999999887 66778


Q ss_pred             HHHHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHHHhccCCC
Q 017573          158 QIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQ  237 (369)
Q Consensus       158 ~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k  237 (369)
                      .+..+...+++..+++++|||++.........++..+..+...........+...+........+...+..++.....++
T Consensus       166 ~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  245 (395)
T 3pey_A          166 QCIRVKRFLPKDTQLVLFSATFADAVRQYAKKIVPNANTLELQTNEVNVDAIKQLYMDCKNEADKFDVLTELYGLMTIGS  245 (395)
T ss_dssp             HHHHHHHTSCTTCEEEEEESCCCHHHHHHHHHHSCSCEEECCCGGGCSCTTEEEEEEECSSHHHHHHHHHHHHTTTTSSE
T ss_pred             HHHHHHHhCCCCcEEEEEEecCCHHHHHHHHHhCCCCeEEEccccccccccccEEEEEcCchHHHHHHHHHHHHhccCCC
Confidence            88888899988999999999999888888889988888887777777777888888888777788888888888888889


Q ss_pred             eEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCCC---
Q 017573          238 SVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPT---  314 (369)
Q Consensus       238 ~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~---  314 (369)
                      +||||++++.++.+++.|+..+..+..+||+++.++|.++++.|++|+.+|||+|+++++|+|+|++++||+++.|+   
T Consensus       246 ~lvf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidip~~~~Vi~~~~p~~~~  325 (395)
T 3pey_A          246 SIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLAN  325 (395)
T ss_dssp             EEEECSCHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHTTSCCEEEECGGGSSSCCCTTEEEEEESSCCBCTT
T ss_pred             EEEEeCCHHHHHHHHHHHHhcCCcEEEeCCCCCHHHHHHHHHHHHCCCCCEEEECChhhcCCCcccCCEEEEcCCCCCCc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999998   


Q ss_pred             ---CccchhhhhcccccCCCceeEEEEeccc-cHHHHHHHHHHhc-cccccCC
Q 017573          315 ---QPENYLHRIGRSGRFGRKGVAINFVTRD-DERMLFDIQKFYN-VVIEELP  362 (369)
Q Consensus       315 ---~~~~~~Q~~GR~~R~~~~~~~~~~~~~~-~~~~~~~~~~~~~-~~~~~~~  362 (369)
                         +...|.|++||+||.|++|.+++++++. +...++.+.+++. ..+.+++
T Consensus       326 ~~~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~  378 (395)
T 3pey_A          326 GQADPATYIHRIGRTGRFGRKGVAISFVHDKNSFNILSAIQKYFGDIEMTRVP  378 (395)
T ss_dssp             SSBCHHHHHHHHTTSSCTTCCEEEEEEECSHHHHHHHHHHHHHTTSCCCEECC
T ss_pred             CCCCHHHhhHhccccccCCCCceEEEEEechHHHHHHHHHHHHhCCceeecCC
Confidence               8999999999999999999999999864 5667788888887 6666665

>3fht_A ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box helicase, RNA dependent ATPase, mRNA export, nucleocytoplasmic transport, NUP214, CAN; HET: ANP; 2.20A {Homo sapiens} PDB: 3ews_A* 3g0h_A* 3fhc_B

Probab=100.00  E-value=3e-56  Score=401.08  Aligned_cols=361  Identities=40%  Similarity=0.689  Sum_probs=320.1

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccC--CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKG--LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQ   78 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~--~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~   78 (369)
                      ++|++.+.++|.++|+..|+++|.++++.+.++  +++++.+|||+|||++++++++..+.....+++++|++|+++|+.
T Consensus        30 ~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~  109 (412)
T 3fht_A           30 LRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELAL  109 (412)
T ss_dssp             GTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHSSSCCCEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHH
T ss_pred             CCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCchHHHHHHHHHHHHhhhcCCCCCEEEECCCHHHHH
Confidence            589999999999999999999999999999987  999999999999999999999988877666668999999999999


Q ss_pred             HHHHHHHHhcccc-CcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHc-CCCCCCCccEEEEechhHhhc-cCc
Q 017573           79 QIEKVMRALGDYL-GVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRR-QSLRPDYIKMFVLDEADEMLS-RGF  155 (369)
Q Consensus        79 q~~~~~~~~~~~~-~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~-~~~~~~~~~~viiDE~H~~~~-~~~  155 (369)
                      |+.+.+.++.... +..+....++......   ....++|+|+||+.+...+.. ......+++++|+||+|++.+ ..+
T Consensus       110 q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~ivv~T~~~l~~~~~~~~~~~~~~~~~iViDEah~~~~~~~~  186 (412)
T 3fht_A          110 QTGKVIEQMGKFYPELKLAYAVRGNKLERG---QKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGH  186 (412)
T ss_dssp             HHHHHHHHHTTTSTTCCEEEECTTCCCCTT---CCCCCSEEEECHHHHHHHHTTSCSSCGGGCCEEEEETHHHHHSTTTT
T ss_pred             HHHHHHHHHHhhcccceEEEeecCcchhhh---hcCCCCEEEECchHHHHHHHhcCCcChhhCcEEEEeCHHHHhhcCCc
Confidence            9999999987654 5667766666553322   134579999999999988865 445567799999999999886 677


Q ss_pred             HHHHHHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHHHhccC
Q 017573          156 KDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAI  235 (369)
Q Consensus       156 ~~~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  235 (369)
                      ......+...+++..+++++|||++.........++..+..+...........+.+.+........+...+..++.....
T Consensus       187 ~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  266 (412)
T 3fht_A          187 QDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVLCSSRDEKFQALCNLYGAITI  266 (412)
T ss_dssp             HHHHHHHHHTSCTTCEEEEEESCCCHHHHHHHHHHSSSCEEECCCGGGSSCTTEEEEEEECSSHHHHHHHHHHHHHHHSS
T ss_pred             HHHHHHHHhhCCCCceEEEEEeecCHHHHHHHHHhcCCCeEEeeccccccccCceEEEEEcCChHHHHHHHHHHHhhcCC
Confidence            88888888999999999999999999988999999999988888777777888888888888878888999999988888


Q ss_pred             CCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCCC-
Q 017573          236 TQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPT-  314 (369)
Q Consensus       236 ~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~-  314 (369)
                      +++||||++.+.++.+++.|.+.+..+..+||+++..+|.++++.|++|+.+|||+|+++++|+|+|++++||+++.|+ 
T Consensus       267 ~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidip~~~~Vi~~~~p~~  346 (412)
T 3fht_A          267 AQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVD  346 (412)
T ss_dssp             SEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHTTSCSEEEECGGGTSSCCCTTEEEEEESSCCBC
T ss_pred             CCEEEEeCCHHHHHHHHHHHHhCCCeEEEecCCCCHHHHHHHHHHHHCCCCcEEEEcCccccCCCccCCCEEEEECCCCC
Confidence            8999999999999999999999999999999999999999999999999999999999999999999999999999995 


Q ss_pred             -----CccchhhhhcccccCCCceeEEEEecccc-HHHHHHHHHHhccccccCCcc
Q 017573          315 -----QPENYLHRIGRSGRFGRKGVAINFVTRDD-ERMLFDIQKFYNVVIEELPSN  364 (369)
Q Consensus       315 -----~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~  364 (369)
                           +...|.||+||+||.|+.|.+++++++.+ ...++.+++.++..+++++.+
T Consensus       347 ~~~~~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~  402 (412)
T 3fht_A          347 KDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHSMNILNRIQEHFNKKIERLDTD  402 (412)
T ss_dssp             SSSSBCHHHHHHHHTTSSCTTCCEEEEEEECSHHHHHHHHHHHHHHTCCCEEC---
T ss_pred             CCCCcchheeecccCcccCCCCCceEEEEEcChhhHHHHHHHHHHHCCccccCCCc
Confidence                 55799999999999999999999998764 888899999999998887643

>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein, ATPase, RNA binding protein; 3.00A {Methanocaldococcus jannaschii} SCOP: c.37.1.19 c.37.1.19

Probab=100.00  E-value=1.1e-55  Score=391.33  Aligned_cols=354  Identities=36%  Similarity=0.626  Sum_probs=311.3

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccC-CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKG-LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQ   79 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~-~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q   79 (369)
                      ++|++.+.+.|+++|+.+|+|+|+++++.+.++ +++++.+|||+|||++++.+++..+... .+.+++|++|+++|+.|
T Consensus        11 ~~l~~~~~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~~l~~~~TGsGKT~~~~~~~~~~~~~~-~~~~~lil~P~~~L~~q   89 (367)
T 1hv8_A           11 LNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNEN-NGIEAIILTPTRELAIQ   89 (367)
T ss_dssp             SSCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCSS-SSCCEEEECSCHHHHHH
T ss_pred             cCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCEEEECCCCChHHHHHHHHHHHHhccc-CCCcEEEEcCCHHHHHH
Confidence            589999999999999999999999999999988 7999999999999999999888776553 33489999999999999


Q ss_pred             HHHHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHH
Q 017573           80 IEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQI  159 (369)
Q Consensus        80 ~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~  159 (369)
                      +.+.+.++....+..+....++........... .++|+|+||+.+...+.........++++|+||+|.+.+.++...+
T Consensus        90 ~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~-~~~iiv~T~~~l~~~~~~~~~~~~~~~~iIiDEah~~~~~~~~~~~  168 (367)
T 1hv8_A           90 VADEIESLKGNKNLKIAKIYGGKAIYPQIKALK-NANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEMLNMGFIKDV  168 (367)
T ss_dssp             HHHHHHHHHCSSCCCEEEECTTSCHHHHHHHHH-TCSEEEECHHHHHHHHHTTCSCTTSCCEEEEETHHHHHTTTTHHHH
T ss_pred             HHHHHHHHhCCCCceEEEEECCcchHHHHhhcC-CCCEEEecHHHHHHHHHcCCcccccCCEEEEeCchHhhhhchHHHH
Confidence            999999998877888888888887655544443 5799999999999999888777888999999999999998888999


Q ss_pred             HHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHHHhccCCCeE
Q 017573          160 YDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSV  239 (369)
Q Consensus       160 ~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~l  239 (369)
                      ..+...+++..+++++|||++.........++..+........    ..+...+..... ..+...+..++. ....++|
T Consensus       169 ~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~-~~~~~~l~~~l~-~~~~~~l  242 (367)
T 1hv8_A          169 EKILNACNKDKRILLFSATMPREILNLAKKYMGDYSFIKAKIN----ANIEQSYVEVNE-NERFEALCRLLK-NKEFYGL  242 (367)
T ss_dssp             HHHHHTSCSSCEEEEECSSCCHHHHHHHHHHCCSEEEEECCSS----SSSEEEEEECCG-GGHHHHHHHHHC-STTCCEE
T ss_pred             HHHHHhCCCCceEEEEeeccCHHHHHHHHHHcCCCeEEEecCC----CCceEEEEEeCh-HHHHHHHHHHHh-cCCCcEE
Confidence            9999999889999999999998888888888776655443222    244455554443 446666766665 4557999


Q ss_pred             EEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCCCCccch
Q 017573          240 IFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENY  319 (369)
Q Consensus       240 v~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~  319 (369)
                      |||++.+.++.+++.|++.+..+..+||+++.++|.++++.|++|+.+|||+|+++++|+|+|++++||++++|++..+|
T Consensus       243 vf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gid~~~~~~Vi~~~~~~s~~~~  322 (367)
T 1hv8_A          243 VFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVMSRGIDVNDLNCVINYHLPQNPESY  322 (367)
T ss_dssp             EECSSHHHHHHHHHHHHHTTCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECTTHHHHCCCSCCSEEEESSCCSCHHHH
T ss_pred             EEECCHHHHHHHHHHHHhcCCCeEEeeCCCCHHHHHHHHHHHHcCCCeEEEECChhhcCCCcccCCEEEEecCCCCHHHh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhcccccCCCceeEEEEeccccHHHHHHHHHHhccccccCC
Q 017573          320 LHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELP  362 (369)
Q Consensus       320 ~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  362 (369)
                      .|++||++|.|++|.+++++++.+...++.+.+.++..+++++
T Consensus       323 ~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~  365 (367)
T 1hv8_A          323 MHRIGRTGRAGKKGKAISIINRREYKKLRYIERAMKLKIKKLK  365 (367)
T ss_dssp             HHHSTTTCCSSSCCEEEEEECTTSHHHHHHHHHHHTCCCCCBC
T ss_pred             hhcccccccCCCccEEEEEEcHHHHHHHHHHHHHhCCCCceec
Confidence            9999999999999999999999999999999999999888764

>2z0m_A 337AA long hypothetical ATP-dependent RNA helicase DEAD; ATP-binding, hydrolase, nucleotide-binding, RNA binding protein, structural genomics; 1.90A {Sulfolobus tokodaii}

Probab=100.00  E-value=6.9e-54  Score=375.44  Aligned_cols=335  Identities=31%  Similarity=0.542  Sum_probs=287.9

Q ss_pred             CCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHH
Q 017573            3 LQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEK   82 (369)
Q Consensus         3 l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~   82 (369)
                      |++.|.+.|+++|+..|+|+|+++++.+.+++++++.+|||+|||++++++++..      +.+++|++|+++|+.|+.+
T Consensus         1 l~~~i~~~l~~~g~~~l~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~------~~~~liv~P~~~L~~q~~~   74 (337)
T 2z0m_A            1 MNEKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILEL------GMKSLVVTPTRELTRQVAS   74 (337)
T ss_dssp             CCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHH------TCCEEEECSSHHHHHHHHH
T ss_pred             CCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEEcCCCCcHHHHHHHHHHhh------cCCEEEEeCCHHHHHHHHH
Confidence            6899999999999999999999999999999999999999999999998887763      2389999999999999999


Q ss_pred             HHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHH
Q 017573           83 VMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDI  162 (369)
Q Consensus        83 ~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~  162 (369)
                      .+.++....+..+....++........... .++|+|+||+.+...+.........++++|+||+|.+.++++...+..+
T Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~i~v~T~~~l~~~~~~~~~~~~~~~~iViDEah~~~~~~~~~~~~~~  153 (337)
T 2z0m_A           75 HIRDIGRYMDTKVAEVYGGMPYKAQINRVR-NADIVVATPGRLLDLWSKGVIDLSSFEIVIIDEADLMFEMGFIDDIKII  153 (337)
T ss_dssp             HHHHHTTTSCCCEEEECTTSCHHHHHHHHT-TCSEEEECHHHHHHHHHTTSCCGGGCSEEEEESHHHHHHTTCHHHHHHH
T ss_pred             HHHHHhhhcCCcEEEEECCcchHHHHhhcC-CCCEEEECHHHHHHHHHcCCcchhhCcEEEEEChHHhhccccHHHHHHH
Confidence            999998877888988888887665544443 4899999999999988887777788999999999999999999999999


Q ss_pred             HhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHHHhccCCCeEEEe
Q 017573          163 FQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFV  242 (369)
Q Consensus       163 ~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lv~~  242 (369)
                      +...+...+++++|||++.........++..+..+...   .....+...+.......   ......+.....+++||||
T Consensus       154 ~~~~~~~~~~~~~SAT~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~lvf~  227 (337)
T 2z0m_A          154 LAQTSNRKITGLFSATIPEEIRKVVKDFITNYEEIEAC---IGLANVEHKFVHVKDDW---RSKVQALRENKDKGVIVFV  227 (337)
T ss_dssp             HHHCTTCSEEEEEESCCCHHHHHHHHHHSCSCEEEECS---GGGGGEEEEEEECSSSS---HHHHHHHHTCCCSSEEEEC
T ss_pred             HhhCCcccEEEEEeCcCCHHHHHHHHHhcCCceeeecc---cccCCceEEEEEeChHH---HHHHHHHHhCCCCcEEEEE
Confidence            99999899999999999998888888888777655332   33344555555444322   2222455556778999999


Q ss_pred             CCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCCCCccchhhh
Q 017573          243 NTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHR  322 (369)
Q Consensus       243 ~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~  322 (369)
                      ++.++++.+++.|.    ++..+||+++..+|.++++.|++|+.+|||+|+++++|+|+|++++||++++|++...|.|+
T Consensus       228 ~~~~~~~~l~~~l~----~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gid~~~~~~Vi~~~~~~s~~~~~Q~  303 (337)
T 2z0m_A          228 RTRNRVAKLVRLFD----NAIELRGDLPQSVRNRNIDAFREGEYDMLITTDVASRGLDIPLVEKVINFDAPQDLRTYIHR  303 (337)
T ss_dssp             SCHHHHHHHHTTCT----TEEEECTTSCHHHHHHHHHHHHTTSCSEEEECHHHHTTCCCCCBSEEEESSCCSSHHHHHHH
T ss_pred             cCHHHHHHHHHHhh----hhhhhcCCCCHHHHHHHHHHHHcCCCcEEEEcCccccCCCccCCCEEEEecCCCCHHHhhHh
Confidence            99999999999886    57899999999999999999999999999999999999999999999999999999999999


Q ss_pred             hcccccCCCceeEEEEeccccHHHHHHHHHHhc
Q 017573          323 IGRSGRFGRKGVAINFVTRDDERMLFDIQKFYN  355 (369)
Q Consensus       323 ~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~  355 (369)
                      +||+||.|++|.+++++. .+...++.+.+.++
T Consensus       304 ~GR~gR~g~~g~~~~~~~-~~~~~~~~i~~~~~  335 (337)
T 2z0m_A          304 IGRTGRMGRKGEAITFIL-NEYWLEKEVKKVSQ  335 (337)
T ss_dssp             HTTBCGGGCCEEEEEEES-SCHHHHHHHC----
T ss_pred             cCccccCCCCceEEEEEe-CcHHHHHHHHHHhc
Confidence            999999999999999999 88888888877664

>3fmp_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 3.19A {Homo sapiens}

Probab=100.00  E-value=1.2e-55  Score=403.58  Aligned_cols=361  Identities=40%  Similarity=0.689  Sum_probs=168.5

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccC--CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKG--LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQ   78 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~--~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~   78 (369)
                      ++|++.+.++|.++||..|+++|.++++.+..+  +++++++|||+|||++++++++..+..+...+++||++|+++|+.
T Consensus        97 ~~l~~~l~~~l~~~g~~~p~~~Q~~ai~~il~~~~~~~l~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~  176 (479)
T 3fmp_B           97 LRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELAL  176 (479)
T ss_dssp             GTCCHHHHHHHHHTTCCSCCHHHHHHHHHHTSBSCCEEEEECCSSSSHHHHHHHHHHTTCCTTSCSCCEEEECSSHHHHH
T ss_pred             cCCCHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCcEEEEcCCCCchhHHHHHHHHHHHhhcCCCCcEEEEeChHHHHH
Confidence            479999999999999999999999999999987  999999999999999999999998887766668999999999999


Q ss_pred             HHHHHHHHhcccc-CcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHc-CCCCCCCccEEEEechhHhhc-cCc
Q 017573           79 QIEKVMRALGDYL-GVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRR-QSLRPDYIKMFVLDEADEMLS-RGF  155 (369)
Q Consensus        79 q~~~~~~~~~~~~-~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~-~~~~~~~~~~viiDE~H~~~~-~~~  155 (369)
                      |+.+.+.++.... ++.+....++......   ....++|+|+||+.+..++.+ ..+...+++++|+||+|++.+ ..+
T Consensus       177 Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~~~iViDEah~~~~~~~~  253 (479)
T 3fmp_B          177 QTGKVIEQMGKFYPELKLAYAVRGNKLERG---QKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGH  253 (479)
T ss_dssp             HHHHHHHHHHTTSTTCCEEEESTTCCCCTT---CCCCCSEEEECHHHHHHHHTTSCCCCGGGCCEEEECCHHHHHTSTTH
T ss_pred             HHHHHHHHHHhhCCCceEEEEeCCcccccc---ccCCCCEEEECchHHHHHHHhcCCcCcccCCEEEEECHHHHhhcCCc
Confidence            9999998876643 4566666665543222   133578999999999988865 345567899999999999986 577


Q ss_pred             HHHHHHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHHHhccC
Q 017573          156 KDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAI  235 (369)
Q Consensus       156 ~~~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  235 (369)
                      ......+...++...|++++|||++.........++..+..+...........+.+.+........+...+..++.....
T Consensus       254 ~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  333 (479)
T 3fmp_B          254 QDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVLCSSRDEKFQALCNLYGAITI  333 (479)
T ss_dssp             HHHHHHHHTTSCTTSEEEEEESCCCHHHHHHHHHHSSSEEEEEEC-----------------------------------
T ss_pred             HHHHHHHHhhCCccceEEEEeCCCCHHHHHHHHHHcCCCeEEeccccccCcCCceEEEEEeCCHHHHHHHHHHHHhhccC
Confidence            78888888889999999999999999888899999999888887777667777777777777666677788888877777


Q ss_pred             CCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCCC-
Q 017573          236 TQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPT-  314 (369)
Q Consensus       236 ~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~-  314 (369)
                      +++||||++.+.++.+++.|...+..+..+||+++..+|..+++.|++|+.+|||+|+++++|+|+|++++||++++|. 
T Consensus       334 ~~~lvF~~s~~~~~~l~~~L~~~~~~v~~lh~~~~~~~R~~~~~~f~~g~~~iLv~T~~~~~GlDip~v~~VI~~d~p~~  413 (479)
T 3fmp_B          334 AQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVD  413 (479)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             CceEEEeCcHHHHHHHHHHHHhCCccEEEecCCCCHHHHHHHHHHHHcCCCcEEEEccccccCCccccCCEEEEecCCCC
Confidence            8999999999999999999999999999999999999999999999999999999999999999999999999999995 


Q ss_pred             -----CccchhhhhcccccCCCceeEEEEecccc-HHHHHHHHHHhccccccCCcc
Q 017573          315 -----QPENYLHRIGRSGRFGRKGVAINFVTRDD-ERMLFDIQKFYNVVIEELPSN  364 (369)
Q Consensus       315 -----~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~  364 (369)
                           +...|.||+||+||.|+.|.+++++++.+ ...++.+.+.++..+.++..+
T Consensus       414 ~~~~~s~~~~~Qr~GRagR~g~~G~~i~~~~~~~~~~~~~~i~~~~~~~~~~l~~~  469 (479)
T 3fmp_B          414 KDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHSMNILNRIQEHFNKKIERLDTD  469 (479)
T ss_dssp             --------------------------------------------------------
T ss_pred             CccCCCHHHHHHHhcccccCCCCceEEEEEcCcchHHHHHHHHHHhCCCceECCCc
Confidence                 56799999999999999999999998765 788888999998888776643

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=100.00  E-value=3.6e-53  Score=394.93  Aligned_cols=358  Identities=30%  Similarity=0.469  Sum_probs=294.6

Q ss_pred             CCCHHHHHHHHhCCCCCCcHhhhhhhhccc--cCCcEEEEcCCCChhhHHHHHHHHHhhhccC----CCccEEEEcCCHH
Q 017573            2 GLQENLLRGIYAYGFEKPSAIQQRGIVPFC--KGLDVIQQAQSGTGKTATFCSGILQQLDYGL----VQCQALVLAPTRE   75 (369)
Q Consensus         2 ~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~--~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~----~~~~~liv~P~~~   75 (369)
                      .|++++.++|..+||.+|+|+|.++++.++  +++++++.+|||+|||++++++++..+....    .++++||++|+++
T Consensus        27 ~l~~~l~~~l~~~g~~~~~~~Q~~~i~~il~~~~~dvlv~apTGsGKTl~~~lpil~~l~~~~~~~~~~~~~lvl~Ptr~  106 (579)
T 3sqw_A           27 VLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRD  106 (579)
T ss_dssp             SSCHHHHHHHHTTTCSSCCHHHHHHHHHHHCSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTSSTTSCCEEEECSSHH
T ss_pred             CCCHHHHHHHHHCCCCCCCHHHHHHHHHHHccCCCeEEEEcCCCcHHHHHHHHHHHHHHHhccccccCCCeEEEEcchHH
Confidence            389999999999999999999999999999  7789999999999999999999998876542    2348999999999


Q ss_pred             HHHHHHHHHHHhcc----ccCcEEEEEECCcchHHHHHHH-ccCCcEEEeccHHHHHHHHcC-CCCCCCccEEEEechhH
Q 017573           76 LAQQIEKVMRALGD----YLGVKVHACVGGTSVREDQRIL-QAGVHVVVGTPGRVFDMLRRQ-SLRPDYIKMFVLDEADE  149 (369)
Q Consensus        76 l~~q~~~~~~~~~~----~~~~~v~~~~~~~~~~~~~~~~-~~~~~iiv~t~~~l~~~~~~~-~~~~~~~~~viiDE~H~  149 (369)
                      |+.|+.+.+.++..    .....+....++.........+ ..+++|+|+||+.+..++... ......++++|+||||+
T Consensus       107 La~Q~~~~~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~~~~~lViDEah~  186 (579)
T 3sqw_A          107 LALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADR  186 (579)
T ss_dssp             HHHHHHHHHHHHHHHCGGGTTSCEEEECTTSCHHHHHHHHHHHCCSEEEECHHHHHHHHHHHHHHHCTTCCEEEEETHHH
T ss_pred             HHHHHHHHHHHHHhhcccccceEEEEEECCccHHHHHHHHhcCCCCEEEECHHHHHHHHHhccccccccCCEEEEEChHH
Confidence            99999999998753    2245677777777655444333 457899999999998877654 33456689999999999


Q ss_pred             hhccCcHHHHHHHHhhCCc-------cCcEEEEEeeCChhHHHHHHHhcCCCEEEEecC----ccccccceeEEEEEccc
Q 017573          150 MLSRGFKDQIYDIFQLLPA-------KVQVGVFSATMPPEALEITRKFMNKPVRILVKR----DELTLEGIKQFYVNVEK  218 (369)
Q Consensus       150 ~~~~~~~~~~~~~~~~~~~-------~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~  218 (369)
                      +.++++...+..+...++.       ..+++++|||+++........++..+..+....    .......+...+.....
T Consensus       187 l~~~gf~~~~~~i~~~l~~~~~~~~~~~~~l~~SAT~~~~v~~~~~~~l~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~  266 (579)
T 3sqw_A          187 LLEIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEK  266 (579)
T ss_dssp             HTSTTTHHHHHHHHHHHHHHCSSCTTCCEEEEEESSCCTHHHHHTTTTCCSSEEEEEESSCSSSCSSCTTEEEEEEEESS
T ss_pred             hhcCCCHHHHHHHHHHhhhhhcccccCceEEEEeccCChHHHHHHHHHcCCCceEEEeecCccccccccccceEEEEecc
Confidence            9999888888877766532       668999999999888888888888776655432    22223344444444443


Q ss_pred             hh-hh---HHHHHHHHHh-ccCCCeEEEeCCHhhHHHHHHHHhhC---CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEE
Q 017573          219 EE-WK---LETLCDLYET-LAITQSVIFVNTRRKVDWLTDKMRSR---DHTVSATHGDMDQNTRDIIMREFRSGSSRVLI  290 (369)
Q Consensus       219 ~~-~~---~~~l~~~~~~-~~~~k~lv~~~~~~~~~~~~~~l~~~---~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli  290 (369)
                      .. ..   ...+...+.. ....++||||++++.++.+++.|...   +..+..+||+++..+|.++++.|++|+.+|||
T Consensus       267 ~~~~~~~~~~~l~~~~~~~~~~~~~iVF~~t~~~~~~l~~~L~~~~~~~~~v~~~hg~~~~~~R~~~~~~F~~g~~~vLV  346 (579)
T 3sqw_A          267 FANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILV  346 (579)
T ss_dssp             TTHHHHHHHHHHHHHHHHTTTCCEEEEECSSHHHHHHHHHHHHHHHTTTSCEEEESTTSCHHHHHHHHHHHHHCSSEEEE
T ss_pred             hhhhHHHHHHHHHHHHhhcCCCCcEEEECCcHHHHHHHHHHHHHhhcCCCcEEEecCCCCHHHHHHHHHHhhcCCCeEEE
Confidence            22 22   2233333333 45679999999999999999999876   88999999999999999999999999999999


Q ss_pred             EecCCcCCCCCCCCcEEEEecCCCCccchhhhhcccccCCCceeEEEEeccccHHHHHHHHHHhccccc
Q 017573          291 TTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIE  359 (369)
Q Consensus       291 ~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  359 (369)
                      ||+++++|+|+|++++||++++|.+...|.|++||+||.|+.|.+++++.+.+...++.+.+.....+.
T Consensus       347 aT~~~~~GiDip~v~~VI~~~~p~s~~~y~Qr~GRagR~g~~g~~i~~~~~~e~~~~~~l~~~~~~~~~  415 (579)
T 3sqw_A          347 CTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRELEDAKNIVIA  415 (579)
T ss_dssp             ECGGGTSSCCCTTCCEEEEESCCSSTTHHHHHHTTSSCTTCCEEEEEEEEGGGHHHHHHHHHHHCCCCC
T ss_pred             EcchhhcCCCcccCCEEEEcCCCCCHHHhhhhccccccCCCCceEEEEEcccHHHHHHHHHHHhCCCcc
Confidence            999999999999999999999999999999999999999999999999999999999999988776654

>3i5x_A ATP-dependent RNA helicase MSS116; protein-RNA complex, RNA helicase, DEAD-BOX, ATP-binding, HE hydrolase, mitochondrion; HET: ANP; 1.90A {Saccharomyces cerevisiae} PDB: 3i5y_A* 3i61_A* 3i62_A* 3sqx_A* 4db2_A 4db4_A

Probab=100.00  E-value=1.8e-52  Score=390.24  Aligned_cols=358  Identities=30%  Similarity=0.459  Sum_probs=292.8

Q ss_pred             CCCHHHHHHHHhCCCCCCcHhhhhhhhccc--cCCcEEEEcCCCChhhHHHHHHHHHhhhccC----CCccEEEEcCCHH
Q 017573            2 GLQENLLRGIYAYGFEKPSAIQQRGIVPFC--KGLDVIQQAQSGTGKTATFCSGILQQLDYGL----VQCQALVLAPTRE   75 (369)
Q Consensus         2 ~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~--~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~----~~~~~liv~P~~~   75 (369)
                      .|++.+.+.|..+||.+|+|+|.++++.++  +++++++++|||+|||++++++++..+....    .++++||++|+++
T Consensus        78 ~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~l~~~~~~~lv~apTGsGKTl~~~lpil~~l~~~~~~~~~~~~~lil~Ptr~  157 (563)
T 3i5x_A           78 VLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRD  157 (563)
T ss_dssp             SSCHHHHHHHHTTCCSSCCHHHHHHHHHHHSSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTSSTTSCCEEEECSSHH
T ss_pred             CCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCCCccHHHHHHHHHHHHhccccccCCeeEEEEcCcHH
Confidence            389999999999999999999999999999  6789999999999999999999998876543    2348999999999


Q ss_pred             HHHHHHHHHHHhccc----cCcEEEEEECCcchHHHHHH-HccCCcEEEeccHHHHHHHHcC-CCCCCCccEEEEechhH
Q 017573           76 LAQQIEKVMRALGDY----LGVKVHACVGGTSVREDQRI-LQAGVHVVVGTPGRVFDMLRRQ-SLRPDYIKMFVLDEADE  149 (369)
Q Consensus        76 l~~q~~~~~~~~~~~----~~~~v~~~~~~~~~~~~~~~-~~~~~~iiv~t~~~l~~~~~~~-~~~~~~~~~viiDE~H~  149 (369)
                      |+.|+.+.+.++...    ....+....++......... ...+++|+|+||+.+..++.+. ......++++|+||||+
T Consensus       158 La~Q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~l~~~~~~~~~~~~~lViDEah~  237 (563)
T 3i5x_A          158 LALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADR  237 (563)
T ss_dssp             HHHHHHHHHHHHHHHCGGGTTSCEEEECTTSCHHHHHHHHHHHCCSEEEECHHHHHHHHHHHHHHHCTTCCEEEEETHHH
T ss_pred             HHHHHHHHHHHHHhhccccCceeEEEEECCcCHHHHHHHHhcCCCCEEEECcHHHHHHHHhccccccccceEEEEeCHHH
Confidence            999999999986432    24557777777765444333 3457899999999998877654 23456689999999999


Q ss_pred             hhccCcHHHHHHHHhhCC-------ccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCc----cccccceeEEEEEccc
Q 017573          150 MLSRGFKDQIYDIFQLLP-------AKVQVGVFSATMPPEALEITRKFMNKPVRILVKRD----ELTLEGIKQFYVNVEK  218 (369)
Q Consensus       150 ~~~~~~~~~~~~~~~~~~-------~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~  218 (369)
                      +.++++...+..+...++       +..|++++|||++.....+...++..+........    ......+...+.....
T Consensus       238 l~~~~f~~~~~~i~~~l~~~~~~~~~~~~~l~~SAT~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  317 (563)
T 3i5x_A          238 LLEIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEK  317 (563)
T ss_dssp             HTSTTTHHHHHHHHHHHHHHCSSCTTCCEEEEEESSCCTHHHHHTTTTCCSSEEEEEESSCSSSCSSCTTEEEEEEEESS
T ss_pred             HhccchHHHHHHHHHhhhhccccCccCceEEEEEccCCHHHHHHHHHhcCCCceEEEeccCCCCccccccCceEEEECch
Confidence            999988888887766653       36789999999998888888888887765554321    2223344444444433


Q ss_pred             hhhh----HHHHHHHHHh-ccCCCeEEEeCCHhhHHHHHHHHhhC---CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEE
Q 017573          219 EEWK----LETLCDLYET-LAITQSVIFVNTRRKVDWLTDKMRSR---DHTVSATHGDMDQNTRDIIMREFRSGSSRVLI  290 (369)
Q Consensus       219 ~~~~----~~~l~~~~~~-~~~~k~lv~~~~~~~~~~~~~~l~~~---~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli  290 (369)
                      ....    ...+...+.. ....++||||++++.++.+++.|.+.   +..+..+||+++..+|..+++.|++|+.+|||
T Consensus       318 ~~~~~~~~~~~l~~~~~~~~~~~~~iVF~~s~~~~~~l~~~L~~~~~~~~~v~~~h~~~~~~~R~~~~~~f~~g~~~vLv  397 (563)
T 3i5x_A          318 FANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILV  397 (563)
T ss_dssp             TTHHHHHHHHHHHHHHHHTTTCCEEEEECSCHHHHHHHHHHHHHHHTTTSCEEEESTTSCHHHHHHHHHHHHHCSSEEEE
T ss_pred             hHhhHHHHHHHHHHHHhhcCCCCcEEEEcCcHHHHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcCCCCEEE
Confidence            2222    2223333332 45679999999999999999999876   88999999999999999999999999999999


Q ss_pred             EecCCcCCCCCCCCcEEEEecCCCCccchhhhhcccccCCCceeEEEEeccccHHHHHHHHHHhccccc
Q 017573          291 TTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIE  359 (369)
Q Consensus       291 ~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  359 (369)
                      ||+++++|+|+|++++||++++|.+...|.|++||+||.|+.|.+++++.+.+...++.+.+..+..+.
T Consensus       398 aT~~~~~GiDip~v~~VI~~~~p~s~~~y~Qr~GRagR~g~~g~~i~~~~~~e~~~~~~l~~~~~~~~~  466 (563)
T 3i5x_A          398 CTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRELEDAKNIVIA  466 (563)
T ss_dssp             ECGGGTSSCCCTTCCEEEEESCCSSTTHHHHHHTTSSCTTCCEEEEEEEEGGGHHHHHHHHHHHCCCCC
T ss_pred             EcchhhcCCCcccCCEEEEECCCCchhhhhhhcCccccCCCCceEEEEEchhHHHHHHHHHHHhCCCcc
Confidence            999999999999999999999999999999999999999999999999999999999999988776554

>2v1x_A ATP-dependent DNA helicase Q1; DNA strand annealing, mismatch repair, nucleotide-binding, DNA-binding, polymorphism, nuclear protein, ATPase; HET: ADP; 2.00A {Homo sapiens} PDB: 2wwy_A*

Probab=100.00  E-value=3.6e-51  Score=377.93  Aligned_cols=337  Identities=16%  Similarity=0.212  Sum_probs=269.1

Q ss_pred             CCCCHHHHHHHHh-CCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHH
Q 017573            1 MGLQENLLRGIYA-YGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQ   79 (369)
Q Consensus         1 ~~l~~~i~~~l~~-~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q   79 (369)
                      +++++.+...|++ ||+..|||+|.++++.+++++++++.+|||+|||++++++++..      .+.+|||+|+++|+.|
T Consensus        26 ~~l~~~l~~~L~~~fg~~~~rp~Q~~~i~~il~g~d~lv~~pTGsGKTl~~~lpal~~------~g~~lVisP~~~L~~q   99 (591)
T 2v1x_A           26 FPWSGKVKDILQNVFKLEKFRPLQLETINVTMAGKEVFLVMPTGGGKSLCYQLPALCS------DGFTLVICPLISLMED   99 (591)
T ss_dssp             STTHHHHHHHHHHTSCCCSCCTTHHHHHHHHHTTCCEEEECCTTSCTTHHHHHHHHTS------SSEEEEECSCHHHHHH
T ss_pred             CCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEEECCCChHHHHHHHHHHHc------CCcEEEEeCHHHHHHH
Confidence            5788999999987 89999999999999999999999999999999999999888752      2389999999999999


Q ss_pred             HHHHHHHhccccCcEEEEEECCcchHHHHHH------HccCCcEEEeccHHHH------HHHHcCCCCCCCccEEEEech
Q 017573           80 IEKVMRALGDYLGVKVHACVGGTSVREDQRI------LQAGVHVVVGTPGRVF------DMLRRQSLRPDYIKMFVLDEA  147 (369)
Q Consensus        80 ~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~------~~~~~~iiv~t~~~l~------~~~~~~~~~~~~~~~viiDE~  147 (369)
                      +.+.+.++    ++.+..++++.........      ....++|+++||+++.      ..+.. ......++++|+|||
T Consensus       100 ~~~~l~~~----gi~~~~l~~~~~~~~~~~~~~~l~~~~~~~~Ilv~Tpe~L~~~~~~~~~l~~-~~~~~~i~~iViDEA  174 (591)
T 2v1x_A          100 QLMVLKQL----GISATMLNASSSKEHVKWVHAEMVNKNSELKLIYVTPEKIAKSKMFMSRLEK-AYEARRFTRIAVDEV  174 (591)
T ss_dssp             HHHHHHHH----TCCEEECCSSCCHHHHHHHHHHHHCTTCCCCEEEECHHHHHSCHHHHHHHHH-HHHTTCEEEEEEETG
T ss_pred             HHHHHHhc----CCcEEEEeCCCCHHHHHHHHHHhhcccCCCCEEEEChhHhhccHHHHHHHHh-hhhccCCcEEEEECc
Confidence            99999987    6778888888765544332      2457899999999874      22222 233456899999999


Q ss_pred             hHhhccC--cHHHHH---HHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEcc-chhh
Q 017573          148 DEMLSRG--FKDQIY---DIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVE-KEEW  221 (369)
Q Consensus       148 H~~~~~~--~~~~~~---~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~  221 (369)
                      |.+..++  |...+.   .+...+ +..+++++|||+++.....+..++..+....... ....+.+........ ....
T Consensus       175 H~is~~g~dfr~~~~~l~~l~~~~-~~~~ii~lSAT~~~~v~~~i~~~l~~~~~~~~~~-~~~r~nl~~~v~~~~~~~~~  252 (591)
T 2v1x_A          175 HCCSQWGHDFRPDYKALGILKRQF-PNASLIGLTATATNHVLTDAQKILCIEKCFTFTA-SFNRPNLYYEVRQKPSNTED  252 (591)
T ss_dssp             GGGSTTCTTCCGGGGGGGHHHHHC-TTSEEEEEESSCCHHHHHHHHHHTTCCSCEEEEC-CCCCTTEEEEEEECCSSHHH
T ss_pred             ccccccccccHHHHHHHHHHHHhC-CCCcEEEEecCCCHHHHHHHHHHhCCCCcEEEec-CCCCcccEEEEEeCCCcHHH
Confidence            9998765  443333   233333 4688999999999887777766665442222211 222333333333222 2234


Q ss_pred             hHHHHHHHHHh-ccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCC
Q 017573          222 KLETLCDLYET-LAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID  300 (369)
Q Consensus       222 ~~~~l~~~~~~-~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d  300 (369)
                      ....+.+++.. ...+++||||++++.++.+++.|...+..+..+||+++.++|.++++.|.+|+.+|||+|+++++|+|
T Consensus       253 ~~~~l~~~l~~~~~~~~~IVf~~sr~~~e~la~~L~~~g~~~~~~h~~l~~~~R~~~~~~F~~g~~~VlVAT~a~~~GID  332 (591)
T 2v1x_A          253 FIEDIVKLINGRYKGQSGIIYCFSQKDSEQVTVSLQNLGIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATVAFGMGID  332 (591)
T ss_dssp             HHHHHHHHHTTTTTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEECTTSCTTCC
T ss_pred             HHHHHHHHHHHhccCCCeEEEeCcHHHHHHHHHHHHHCCCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEechhhcCCC
Confidence            55666666653 36679999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCcEEEEecCCCCccchhhhhcccccCCCceeEEEEeccccHHHHHHH
Q 017573          301 VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDI  350 (369)
Q Consensus       301 ~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~  350 (369)
                      +|++++||++++|.|...|.|++||+||.|++|.+++++.+.|...+..+
T Consensus       333 ~p~V~~VI~~~~p~s~~~y~Qr~GRaGR~G~~g~~i~l~~~~D~~~~~~~  382 (591)
T 2v1x_A          333 KPDVRFVIHHSMSKSMENYYQESGRAGRDDMKADCILYYGFGDIFRISSM  382 (591)
T ss_dssp             CSCEEEEEESSCCSSHHHHHHHHTTSCTTSSCEEEEEEECHHHHHHHHHH
T ss_pred             cccccEEEEeCCCCCHHHHHHHhccCCcCCCCceEEEEEChHHHHHHHHH
Confidence            99999999999999999999999999999999999999998876655444

>1oyw_A RECQ helicase, ATP-dependent DNA helicase; winged helix, helix-turn-helix, ATP binding, Zn(2+) binding, hydrolase; 1.80A {Escherichia coli} SCOP: a.4.5.43 c.37.1.19 c.37.1.19 PDB: 1oyy_A*

Probab=100.00  E-value=1.9e-50  Score=369.71  Aligned_cols=335  Identities=19%  Similarity=0.271  Sum_probs=269.0

Q ss_pred             CCCCHHHHHHHHh-CCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHH
Q 017573            1 MGLQENLLRGIYA-YGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQ   79 (369)
Q Consensus         1 ~~l~~~i~~~l~~-~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q   79 (369)
                      ++|++.+.+.|++ ||+..|+|+|.++++.+.+++++++.+|||+|||++++++++..   .   +.++||+|+++|+.|
T Consensus         7 l~L~~~~~~~l~~~~g~~~~r~~Q~~~i~~il~g~d~lv~apTGsGKTl~~~lp~l~~---~---g~~lvi~P~~aL~~q   80 (523)
T 1oyw_A            7 LNLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLL---N---GLTVVVSPLISLMKD   80 (523)
T ss_dssp             SSHHHHHHHHHHHTTCCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHS---S---SEEEEECSCHHHHHH
T ss_pred             CCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEECCCCcHHHHHHHHHHHHh---C---CCEEEECChHHHHHH
Confidence            5789999999988 99999999999999999999999999999999999998887743   1   279999999999999


Q ss_pred             HHHHHHHhccccCcEEEEEECCcchHHHH----HHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccC-
Q 017573           80 IEKVMRALGDYLGVKVHACVGGTSVREDQ----RILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRG-  154 (369)
Q Consensus        80 ~~~~~~~~~~~~~~~v~~~~~~~~~~~~~----~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~-  154 (369)
                      +.+.+.++    ++.+..++++.......    ....+..+|+++||+++........+...+++++|+||+|.+.+++ 
T Consensus        81 ~~~~l~~~----gi~~~~l~~~~~~~~~~~~~~~~~~~~~~ilv~Tpe~l~~~~~~~~l~~~~~~~vViDEaH~i~~~g~  156 (523)
T 1oyw_A           81 QVDQLQAN----GVAAACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDNFLEHLAHWNPVLLAVDEAHCISQWGH  156 (523)
T ss_dssp             HHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHHTCCSEEEECHHHHTSTTHHHHHTTSCEEEEEESSGGGGCTTSS
T ss_pred             HHHHHHHc----CCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhChHHHHHHhhCCCCEEEEeCccccCcCCC
Confidence            99999886    67777888776654432    2334678999999999853222112233568999999999998765 


Q ss_pred             -cHHHH---HHHHhhCCccCcEEEEEeeCChhHHHHHHHhc--CCCEEEEecCccccccceeEEEEEccchhhhHHHHHH
Q 017573          155 -FKDQI---YDIFQLLPAKVQVGVFSATMPPEALEITRKFM--NKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCD  228 (369)
Q Consensus       155 -~~~~~---~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  228 (369)
                       +...+   ..+...++ ..+++++|||+++.....+...+  ..+.....   ....+++.....   ....+.+.+.+
T Consensus       157 ~fr~~~~~l~~l~~~~~-~~~~i~lSAT~~~~~~~~i~~~l~~~~~~~~~~---~~~r~~l~~~v~---~~~~~~~~l~~  229 (523)
T 1oyw_A          157 DFRPEYAALGQLRQRFP-TLPFMALTATADDTTRQDIVRLLGLNDPLIQIS---SFDRPNIRYMLM---EKFKPLDQLMR  229 (523)
T ss_dssp             CCCHHHHGGGGHHHHCT-TSCEEEEESCCCHHHHHHHHHHHTCCSCEEEEC---CCCCTTEEEEEE---ECSSHHHHHHH
T ss_pred             ccHHHHHHHHHHHHhCC-CCCEEEEeCCCCHHHHHHHHHHhCCCCCeEEeC---CCCCCceEEEEE---eCCCHHHHHHH
Confidence             43333   33444554 57899999999987655444433  33433322   122233332222   22345677778


Q ss_pred             HHHhccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEE
Q 017573          229 LYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVI  308 (369)
Q Consensus       229 ~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi  308 (369)
                      ++....++++||||++++.++.+++.|...+..+..+||+++.++|.++++.|.+|+.+|||||+++++|+|+|++++||
T Consensus       230 ~l~~~~~~~~IVf~~sr~~~e~l~~~L~~~g~~~~~~h~~l~~~~R~~~~~~f~~g~~~vlVaT~a~~~GiD~p~v~~VI  309 (523)
T 1oyw_A          230 YVQEQRGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMGINKPNVRFVV  309 (523)
T ss_dssp             HHHHTTTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECTTSCTTTCCTTCCEEE
T ss_pred             HHHhcCCCcEEEEeCCHHHHHHHHHHHHHCCCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEechhhCCCCccCccEEE
Confidence            88777778999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EecCCCCccchhhhhcccccCCCceeEEEEeccccHHHHHHHHH
Q 017573          309 NYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQK  352 (369)
Q Consensus       309 ~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~  352 (369)
                      +++.|+|...|.|++||+||.|++|.+++++++.|...++.+.+
T Consensus       310 ~~~~p~s~~~y~Qr~GRaGR~g~~~~~~l~~~~~d~~~~~~~~~  353 (523)
T 1oyw_A          310 HFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLRRCLE  353 (523)
T ss_dssp             ESSCCSSHHHHHHHHTTSCTTSSCEEEEEEECHHHHHHHHHHHH
T ss_pred             EECCCCCHHHHHHHhccccCCCCCceEEEEeCHHHHHHHHHHHh
Confidence            99999999999999999999999999999999888776655443

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=100.00  E-value=9.2e-49  Score=351.84  Aligned_cols=326  Identities=21%  Similarity=0.263  Sum_probs=257.6

Q ss_pred             HHHHHHHh-CCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHH
Q 017573            6 NLLRGIYA-YGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVM   84 (369)
Q Consensus         6 ~i~~~l~~-~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~   84 (369)
                      ++.+.+++ +++ +|+|+|.++++.+.+++++++.+|||+|||++++++++.....   +++++|++|+++|+.|+.+.+
T Consensus         9 ~~~~~l~~~~~~-~~~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~l~~~~~~~~~---~~~~lil~Pt~~L~~q~~~~~   84 (414)
T 3oiy_A            9 DFRSFFKKKFGK-DLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLARK---GKKSALVFPTVTLVKQTLERL   84 (414)
T ss_dssp             HHHHHHHHHHSS-CCCHHHHHHHHHHTTTCCEECCSCSSSSHHHHHHHHHHHHHTT---TCCEEEEESSHHHHHHHHHHH
T ss_pred             HHHHHHHHhcCC-CCCHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHhcC---CCEEEEEECCHHHHHHHHHHH
Confidence            45555654 566 8999999999999999999999999999999888887776633   338999999999999999999


Q ss_pred             HHhccccCcEEEEEECCcchHH---HHHHH-ccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhc--------
Q 017573           85 RALGDYLGVKVHACVGGTSVRE---DQRIL-QAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLS--------  152 (369)
Q Consensus        85 ~~~~~~~~~~v~~~~~~~~~~~---~~~~~-~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~--------  152 (369)
                      .++.. .++++..++|+.....   ....+ .++++|+|+||+.+...+..  .....++++|+||+|.+..        
T Consensus        85 ~~~~~-~~~~v~~~~g~~~~~~~~~~~~~l~~~~~~Iiv~Tp~~l~~~l~~--~~~~~~~~iViDEaH~~~~~~~~~d~~  161 (414)
T 3oiy_A           85 QKLAD-EKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREK--LSQKRFDFVFVDDVDAVLKASRNIDTL  161 (414)
T ss_dssp             HHHCC-SSCCEEECCTTSCHHHHHHHHHHHHHTCCSEEEEEHHHHHHCHHH--HTTCCCSEEEESCHHHHHHCHHHHHHH
T ss_pred             HHHcc-CCceEEEEECCCChhhHHHHHHHhhcCCCCEEEECHHHHHHHHHH--hccccccEEEEeChHhhhhccchhhhH
Confidence            99877 7889999999887632   22333 34589999999999877765  4556789999999998764        


Q ss_pred             ---cCcHHH-HHHHHhhCC-----------ccCcEEEEEeeC-ChhHH-HHHHHhcCCCEEEEecCccccccceeEEEEE
Q 017573          153 ---RGFKDQ-IYDIFQLLP-----------AKVQVGVFSATM-PPEAL-EITRKFMNKPVRILVKRDELTLEGIKQFYVN  215 (369)
Q Consensus       153 ---~~~~~~-~~~~~~~~~-----------~~~~~i~~saT~-~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  215 (369)
                         .++... +..++..++           +..|++++|||+ +.... .....+..    +...........+.+.+..
T Consensus       162 l~~~~~~~~~~~~i~~~~~~~~~~~~l~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~----~~~~~~~~~~~~i~~~~~~  237 (414)
T 3oiy_A          162 LMMVGIPEEIIRKAFSTIKQGKIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLLN----FTVGRLVSVARNITHVRIS  237 (414)
T ss_dssp             HHHTTCCHHHHHHHHHHHHHTCCCCCCTTCCCCEEEESSCCSSCCSSTTHHHHHHHS----CCSSCCCCCCCSEEEEEES
T ss_pred             HhhcCCcHHHHHHHHHhcccchhhhhcccCCCceEEEEecCCCcchhHHHHHHHhhc----cCcCccccccccchheeec
Confidence               445555 666776665           778999999994 43322 22333332    1122233334455555554


Q ss_pred             ccchhhhHHHHHHHHHhccCCCeEEEeCCHhhHHHHHHHHhhCCCeeE-EecCCCCHHHHHHHHHHHhcCCCcEEEE---
Q 017573          216 VEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVS-ATHGDMDQNTRDIIMREFRSGSSRVLIT---  291 (369)
Q Consensus       216 ~~~~~~~~~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~-~~~~~~~~~~r~~~~~~f~~~~~~vli~---  291 (369)
                      ..    +.+.+..++.. .++++||||++++.++.+++.|...+..+. .+||+    +|.  ++.|++|+.+|||+   
T Consensus       238 ~~----~~~~l~~~l~~-~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~h~~----~r~--~~~f~~g~~~vLvat~s  306 (414)
T 3oiy_A          238 SR----SKEKLVELLEI-FRDGILIFAQTEEEGKELYEYLKRFKFNVGETWSEF----EKN--FEDFKVGKINILIGVQA  306 (414)
T ss_dssp             SC----CHHHHHHHHHH-HCSSEEEEESSHHHHHHHHHHHHHTTCCEEESSSCH----HHH--HHHHHTTSCSEEEEECC
T ss_pred             cC----HHHHHHHHHHH-cCCCEEEEECCHHHHHHHHHHHHHcCCceehhhcCc----chH--HHHHhCCCCeEEEEecC
Confidence            42    44556666665 348999999999999999999999999998 88884    333  99999999999999   


Q ss_pred             -ecCCcCCCCCCC-CcEEEEecCC--CCccchhhhhcccccCC----CceeEEEEeccccHHHHHHHHHHhc
Q 017573          292 -TDLLARGIDVQQ-VSLVINYDLP--TQPENYLHRIGRSGRFG----RKGVAINFVTRDDERMLFDIQKFYN  355 (369)
Q Consensus       292 -t~~~~~G~d~~~-~~~vi~~~~~--~~~~~~~Q~~GR~~R~~----~~~~~~~~~~~~~~~~~~~~~~~~~  355 (369)
                       |+++++|+|+|+ +++||+++.|  .+...|.|++||+||.|    +.|.+++++  .+...++.+.+.++
T Consensus       307 ~T~~~~~GiDip~~v~~VI~~~~p~~~~~~~y~qr~GR~gR~g~~~~~~g~~i~~~--~~~~~~~~l~~~~~  376 (414)
T 3oiy_A          307 YYGKLTRGVDLPERIKYVIFWGTPSGPDVYTYIQASGRSSRILNGVLVKGVSVIFE--EDEEIFESLKTRLL  376 (414)
T ss_dssp             TTCCCCCCCCCTTTCCEEEEESCCTTTCHHHHHHHHGGGCCEETTEECCEEEEEEC--CCHHHHHHHHHHHH
T ss_pred             cCchhhccCccccccCEEEEECCCCCCCHHHHHHHhCccccCCCCCCcceEEEEEE--ccHHHHHHHHHHhc
Confidence             999999999999 9999999999  99999999999999987    479999998  77788888888887

>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=100.00  E-value=6.8e-47  Score=361.01  Aligned_cols=348  Identities=20%  Similarity=0.259  Sum_probs=269.0

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhc-cccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVP-FCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQ   79 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~-~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q   79 (369)
                      +|||+++.+.++++|+.+|+++|.++++. +.+++++++++|||+|||+++.+++++.+...  +.+++|++|+++|+.|
T Consensus         6 l~l~~~~~~~l~~~g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~--~~~~l~i~P~raLa~q   83 (720)
T 2zj8_A            6 LRVDERIKSTLKERGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRILTQ--GGKAVYIVPLKALAEE   83 (720)
T ss_dssp             CCSCHHHHHHHHHTTCCBCCHHHHHHHTTTGGGTCEEEEECCGGGCHHHHHHHHHHHHHHHH--CSEEEEECSSGGGHHH
T ss_pred             cCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCcEEEEcCCccHHHHHHHHHHHHHHHhC--CCEEEEEcCcHHHHHH
Confidence            68999999999999999999999999998 88899999999999999999999998777532  2389999999999999


Q ss_pred             HHHHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHH
Q 017573           80 IEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQI  159 (369)
Q Consensus        80 ~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~  159 (369)
                      +.+.++++. ..+.++...+|+......   ...+++|+|+||+++...+........++++||+||+|.+.+......+
T Consensus        84 ~~~~~~~l~-~~g~~v~~~~G~~~~~~~---~~~~~~Iiv~Tpe~l~~~~~~~~~~l~~~~~vIiDE~H~l~~~~r~~~~  159 (720)
T 2zj8_A           84 KFQEFQDWE-KIGLRVAMATGDYDSKDE---WLGKYDIIIATAEKFDSLLRHGSSWIKDVKILVADEIHLIGSRDRGATL  159 (720)
T ss_dssp             HHHHTGGGG-GGTCCEEEECSCSSCCCG---GGGGCSEEEECHHHHHHHHHHTCTTGGGEEEEEEETGGGGGCTTTHHHH
T ss_pred             HHHHHHHHH-hcCCEEEEecCCCCcccc---ccCCCCEEEECHHHHHHHHHcChhhhhcCCEEEEECCcccCCCcccHHH
Confidence            999996554 348889888887654332   1246899999999999888886665778999999999999877777888


Q ss_pred             HHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEE------Ecc----chhhhHHHHHHH
Q 017573          160 YDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYV------NVE----KEEWKLETLCDL  229 (369)
Q Consensus       160 ~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~----~~~~~~~~l~~~  229 (369)
                      ..++..+++..+++++|||++. ..++. .++.... +...   ..+..+...+.      ...    ........+.+.
T Consensus       160 ~~ll~~l~~~~~ii~lSATl~n-~~~~~-~~l~~~~-~~~~---~rp~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  233 (720)
T 2zj8_A          160 EVILAHMLGKAQIIGLSATIGN-PEELA-EWLNAEL-IVSD---WRPVKLRRGVFYQGFVTWEDGSIDRFSSWEELVYDA  233 (720)
T ss_dssp             HHHHHHHBTTBEEEEEECCCSC-HHHHH-HHTTEEE-EECC---CCSSEEEEEEEETTEEEETTSCEEECSSTTHHHHHH
T ss_pred             HHHHHHhhcCCeEEEEcCCcCC-HHHHH-HHhCCcc-cCCC---CCCCcceEEEEeCCeeeccccchhhhhHHHHHHHHH
Confidence            8888777668899999999963 33343 3443221 1111   11111111111      111    022334445544


Q ss_pred             HHhccCCCeEEEeCCHhhHHHHHHHHhhCC---------------------------------CeeEEecCCCCHHHHHH
Q 017573          230 YETLAITQSVIFVNTRRKVDWLTDKMRSRD---------------------------------HTVSATHGDMDQNTRDI  276 (369)
Q Consensus       230 ~~~~~~~k~lv~~~~~~~~~~~~~~l~~~~---------------------------------~~~~~~~~~~~~~~r~~  276 (369)
                      +.  +++++||||+++++++.+++.|.+..                                 ..+..+||+++.++|..
T Consensus       234 ~~--~~~~~LVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~l~~~~~~~v~~~h~~l~~~~R~~  311 (720)
T 2zj8_A          234 IR--KKKGALIFVNMRRKAERVALELSKKVKSLLTKPEIRALNELADSLEENPTNEKLAKAIRGGVAFHHAGLGRDERVL  311 (720)
T ss_dssp             HH--TTCCEEEECSCHHHHHHHHHHHHHHHGGGSCHHHHHHHHHHHHTSCSCHHHHHHHHHHTTTEEEECTTSCHHHHHH
T ss_pred             Hh--CCCCEEEEecCHHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHhcccchHHHHHHHhcCeeeecCCCCHHHHHH
Confidence            43  35799999999999999999887531                                 24899999999999999


Q ss_pred             HHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEE----ec----CCCCccchhhhhcccccCC--CceeEEEEeccccHHH
Q 017573          277 IMREFRSGSSRVLITTDLLARGIDVQQVSLVIN----YD----LPTQPENYLHRIGRSGRFG--RKGVAINFVTRDDERM  346 (369)
Q Consensus       277 ~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~----~~----~~~~~~~~~Q~~GR~~R~~--~~~~~~~~~~~~~~~~  346 (369)
                      +++.|.+|..+|||||+++++|+|+|++++||.    ++    .|.+..+|.||+||+||.|  ..|.|++++++.+.. 
T Consensus       312 v~~~f~~g~~~vlvaT~~l~~Gvdip~~~~VI~~~~~yd~~g~~~~s~~~~~Qr~GRaGR~g~~~~G~~~~l~~~~~~~-  390 (720)
T 2zj8_A          312 VEENFRKGIIKAVVATPTLSAGINTPAFRVIIRDIWRYSDFGMERIPIIEVHQMLGRAGRPKYDEVGEGIIVSTSDDPR-  390 (720)
T ss_dssp             HHHHHHTTSSCEEEECSTTGGGCCCCBSEEEECCSEECCSSSCEECCHHHHHHHHTTBCCTTTCSEEEEEEECSSSCHH-
T ss_pred             HHHHHHCCCCeEEEECcHhhccCCCCceEEEEcCCeeecCCCCccCCHHHHHHHHhhcCCCCCCCCceEEEEecCccHH-
Confidence            999999999999999999999999999999987    44    4788999999999999988  468999999988733 


Q ss_pred             HHHHHHHhccccccCCcc
Q 017573          347 LFDIQKFYNVVIEELPSN  364 (369)
Q Consensus       347 ~~~~~~~~~~~~~~~~~~  364 (369)
                       ..+.+++....++++..
T Consensus       391 -~~~~~~~~~~~~~i~s~  407 (720)
T 2zj8_A          391 -EVMNHYIFGKPEKLFSQ  407 (720)
T ss_dssp             -HHHHHHTTSCCCCCCCC
T ss_pred             -HHHHHHhcCCCCCcEee
Confidence             23445555555555433

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=100.00  E-value=1.1e-47  Score=366.92  Aligned_cols=354  Identities=22%  Similarity=0.259  Sum_probs=228.6

Q ss_pred             HHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCC--CccEEEEcCCHHHHHHHHHHH
Q 017573            7 LLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLV--QCQALVLAPTRELAQQIEKVM   84 (369)
Q Consensus         7 i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~--~~~~liv~P~~~l~~q~~~~~   84 (369)
                      +..+|..+|+.+||++|.++++.+.+++++++++|||+|||+++++++++.+.....  +++++|++|+++|+.||.+.+
T Consensus         2 ~~~~l~~~g~~~lr~~Q~~~i~~~l~g~~~iv~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~lvl~Pt~~L~~Q~~~~~   81 (696)
T 2ykg_A            2 EVSDTNLYSPFKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQIPVYEQNKSVF   81 (696)
T ss_dssp             -----CTTC--CCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHSCTTCCCCEEEECSSHHHHHHHHHHH
T ss_pred             CCCcccccCCCCccHHHHHHHHHHHcCCCEEEEcCCCchHHHHHHHHHHHHHHhCccCCCCeEEEEECCHHHHHHHHHHH
Confidence            356788999999999999999999999999999999999999999999987765432  248999999999999999999


Q ss_pred             HHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCC-CCCCccEEEEechhHhhccCcHHHH-HHH
Q 017573           85 RALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSL-RPDYIKMFVLDEADEMLSRGFKDQI-YDI  162 (369)
Q Consensus        85 ~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~-~~~~~~~viiDE~H~~~~~~~~~~~-~~~  162 (369)
                      .++....++++..++|+............+++|+|+||+.+...+..... ....++++|+||||++.+......+ ...
T Consensus        82 ~~~~~~~~~~v~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~L~~~l~~~~~~~l~~~~~vViDEaH~~~~~~~~~~i~~~~  161 (696)
T 2ykg_A           82 SKYFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTIPSLSIFTLMIFDECHNTSKQHPYNMIMFNY  161 (696)
T ss_dssp             HHHTTTTTCCEEEECSSSCSSSCHHHHHHTCSEEEECHHHHHHHHHTTSSCCGGGCSEEEEETGGGCSTTCHHHHHHHHH
T ss_pred             HHHhccCCceEEEEeCCccccccHHHhccCCCEEEECHHHHHHHHhcCcccccccccEEEEeCCCcccCcccHHHHHHHH
Confidence            99988778899999988765444444445689999999999999988766 6778999999999998755422222 222


Q ss_pred             Hhh-----CCccCcEEEEEeeCC-------hhHHHHHHHh----------------------cCCCEEEEecCccccc--
Q 017573          163 FQL-----LPAKVQVGVFSATMP-------PEALEITRKF----------------------MNKPVRILVKRDELTL--  206 (369)
Q Consensus       163 ~~~-----~~~~~~~i~~saT~~-------~~~~~~~~~~----------------------~~~~~~~~~~~~~~~~--  206 (369)
                      +..     .++..++++|||||.       .+....+...                      ...|............  
T Consensus       162 l~~~~~~~~~~~~~il~LTATp~~~~~~~~~~~~~~i~~~~~~l~~~~~~~~~~~~~~l~~~~~~p~~~~~~~~~~~~~~  241 (696)
T 2ykg_A          162 LDQKLGGSSGPLPQVIGLTASVGVGDAKTTDEALDYICKLCASLDASVIATVKHNLEELEQVVYKPQKFFRKVESRISDK  241 (696)
T ss_dssp             HHHHHTTCCSCCCEEEEEESCCCCSSCCSHHHHHHHHHHHHHHTTCCEEECCCTTHHHHHHHSCCCEEEEEECCCCSCCH
T ss_pred             HHHhhcccCCCCCeEEEEeCccccCccccHHHHHHHHHHHHHhcCCceEeecccchHHHHhhcCCCceeEEecCcccCCh
Confidence            221     245789999999997       2222211111                      1112111100000000  


Q ss_pred             --------------------------------------------------------------------------------
Q 017573          207 --------------------------------------------------------------------------------  206 (369)
Q Consensus       207 --------------------------------------------------------------------------------  206 (369)
                                                                                                      
T Consensus       242 fs~~~~~l~~~i~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~  321 (696)
T 2ykg_A          242 FKYIIAQLMRDTESLAKRICKDLENLSQIQNREFGTQKYEQWIVTVQKACMVFQMPDKDEESRICKALFLYTSHLRKYND  321 (696)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSTTGGGSSSCCSCCSSSHHHHHHHHHHHHTSCC------CCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhhccccccccchhHHHHHHHHHHHHHHhhcccchhhhHHHHHHHHHHHHHHHHhH
Confidence                                                                                            


Q ss_pred             -----------------------------cceeEEEE---------------EccchhhhHHHHHHHHHhc----cCCCe
Q 017573          207 -----------------------------EGIKQFYV---------------NVEKEEWKLETLCDLYETL----AITQS  238 (369)
Q Consensus       207 -----------------------------~~~~~~~~---------------~~~~~~~~~~~l~~~~~~~----~~~k~  238 (369)
                                                   ..+.+.+.               .......+...+..++...    +++++
T Consensus       322 ~~~i~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~k~~~L~~ll~~~~~~~~~~~~  401 (696)
T 2ykg_A          322 ALIISEHARMKDALDYLKDFFSNVRAAGFDEIEQDLTQRFEEKLQELESVSRDPSNENPKLEDLCFILQEEYHLNPETIT  401 (696)
T ss_dssp             HHHHHHHSCHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHTTHHHHHHHHHCGGGCCHHHHHHHHHHHHHHTTCTTCCE
T ss_pred             HHhccchhhHHHHHHHHHHHHHHHhhcccchHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhccCCCCcE
Confidence                                         00000000               0001233556666666654    56799


Q ss_pred             EEEeCCHhhHHHHHHHHhhCC----CeeEEe--------cCCCCHHHHHHHHHHHhc-CCCcEEEEecCCcCCCCCCCCc
Q 017573          239 VIFVNTRRKVDWLTDKMRSRD----HTVSAT--------HGDMDQNTRDIIMREFRS-GSSRVLITTDLLARGIDVQQVS  305 (369)
Q Consensus       239 lv~~~~~~~~~~~~~~l~~~~----~~~~~~--------~~~~~~~~r~~~~~~f~~-~~~~vli~t~~~~~G~d~~~~~  305 (369)
                      ||||++++.++.+++.|...+    .++..+        |++++.++|.++++.|++ |+.+|||+|+++++|+|+|+++
T Consensus       402 IIF~~~~~~~~~l~~~L~~~~~~~~~~~~~l~G~~~~~~h~~~~~~eR~~v~~~F~~~g~~~vLVaT~v~~~GiDip~v~  481 (696)
T 2ykg_A          402 ILFVKTRALVDALKNWIEGNPKLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAFKASGDHNILIATSVADEGIDIAQCN  481 (696)
T ss_dssp             EEECSCHHHHHHHHHHHHHCTTCCSCCEEC-----------------------------CCSCSEEEESSCCC---CCCS
T ss_pred             EEEeCcHHHHHHHHHHHHhCCCccccceeEEEccCCCccccCCCHHHHHHHHHHHHhcCCccEEEEechhhcCCcCccCC
Confidence            999999999999999999987    788888        459999999999999998 9999999999999999999999


Q ss_pred             EEEEecCCCCccchhhhhcccccCCCceeEEEEeccccHHHHHHH----HHHhccccccCC
Q 017573          306 LVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDI----QKFYNVVIEELP  362 (369)
Q Consensus       306 ~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~  362 (369)
                      +||++++|++...|.||+|| ||. +.|.++++++..+....+.+    +++++..+.+++
T Consensus       482 ~VI~~d~p~s~~~~~Qr~GR-GR~-~~g~~~~l~~~~~~~~~~~~~~~~e~~~~~~~~~~~  540 (696)
T 2ykg_A          482 LVILYEYVGNVIKMIQTRGR-GRA-RGSKCFLLTSNAGVIEKEQINMYKEKMMNDSILRLQ  540 (696)
T ss_dssp             EEEEESCC--CCCC-----------CCCEEEEEESCHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             EEEEeCCCCCHHHHHHhhcc-CcC-CCceEEEEecCCCHHHHHHHHHHHHHHHHHHHHHhh
Confidence            99999999999999999999 998 78999999998877655555    445555444443

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=100.00  E-value=4.7e-46  Score=355.46  Aligned_cols=347  Identities=19%  Similarity=0.251  Sum_probs=261.8

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhc-cccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVP-FCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQ   79 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~-~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q   79 (369)
                      +|||+++.+.++.+||.+|+++|.++++. +.+++++++++|||+|||+++.+++++.+...  +.+++|++|+++|+.|
T Consensus        13 l~l~~~~~~~l~~~g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~--~~~il~i~P~r~La~q   90 (715)
T 2va8_A           13 LKLPSNVIEIIKKRGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGIISFLLKN--GGKAIYVTPLRALTNE   90 (715)
T ss_dssp             SSSCHHHHHHHHTTSCCBCCHHHHHHHHTTTTTTCCEEEECCTTSCHHHHHHHHHHHHHHHS--CSEEEEECSCHHHHHH
T ss_pred             cCCCHHHHHHHHhCCCCCCCHHHHHHHHHHhcCCCcEEEEcCCCCcHHHHHHHHHHHHHHHC--CCeEEEEeCcHHHHHH
Confidence            58999999999999999999999999999 77899999999999999999999998876532  2389999999999999


Q ss_pred             HHHHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHH
Q 017573           80 IEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQI  159 (369)
Q Consensus        80 ~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~  159 (369)
                      +.+.++.+ ...+.++....|+......  . ..+++|+|+||+.+...+.......+++++||+||+|.+.+..+...+
T Consensus        91 ~~~~~~~~-~~~g~~v~~~~G~~~~~~~--~-~~~~~Iiv~Tpe~l~~~~~~~~~~l~~~~~vIiDE~H~l~~~~~~~~l  166 (715)
T 2va8_A           91 KYLTFKDW-ELIGFKVAMTSGDYDTDDA--W-LKNYDIIITTYEKLDSLWRHRPEWLNEVNYFVLDELHYLNDPERGPVV  166 (715)
T ss_dssp             HHHHHGGG-GGGTCCEEECCSCSSSCCG--G-GGGCSEEEECHHHHHHHHHHCCGGGGGEEEEEECSGGGGGCTTTHHHH
T ss_pred             HHHHHHHh-hcCCCEEEEEeCCCCCchh--h-cCCCCEEEEcHHHHHHHHhCChhHhhccCEEEEechhhcCCcccchHH
Confidence            99999644 3447888888887654332  1 236899999999999988886655778999999999998876777777


Q ss_pred             HHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEE-----------EEccc--------hh
Q 017573          160 YDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFY-----------VNVEK--------EE  220 (369)
Q Consensus       160 ~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----------~~~~~--------~~  220 (369)
                      ..+...++ ..+++++|||++. ..++.. ++..+.. .....   +..+...+           .....        ..
T Consensus       167 ~~i~~~~~-~~~ii~lSATl~n-~~~~~~-~l~~~~~-~~~~r---~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  239 (715)
T 2va8_A          167 ESVTIRAK-RRNLLALSATISN-YKQIAK-WLGAEPV-ATNWR---PVPLIEGVIYPERKKKEYNVIFKDNTTKKVHGDD  239 (715)
T ss_dssp             HHHHHHHH-TSEEEEEESCCTT-HHHHHH-HHTCEEE-ECCCC---SSCEEEEEEEECSSTTEEEEEETTSCEEEEESSS
T ss_pred             HHHHHhcc-cCcEEEEcCCCCC-HHHHHH-HhCCCcc-CCCCC---CCCceEEEEecCCcccceeeecCcchhhhcccch
Confidence            77776665 7889999999963 334443 4443221 11111   11111110           00110        12


Q ss_pred             hhHHHHHHHHHhccCCCeEEEeCCHhhHHHHHHHHhhCC------------------------------------CeeEE
Q 017573          221 WKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRD------------------------------------HTVSA  264 (369)
Q Consensus       221 ~~~~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~~------------------------------------~~~~~  264 (369)
                      .....+.+.+.  .++++||||+++++++.+++.|.+..                                    ..+..
T Consensus       240 ~~~~~~~~~~~--~~~~~LVF~~s~~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~l~~~~~~~v~~  317 (715)
T 2va8_A          240 AIIAYTLDSLS--KNGQVLVFRNSRKMAESTALKIANYMNFVSLDENALSEILKQLDDIEEGGSDEKELLKSLISKGVAY  317 (715)
T ss_dssp             HHHHHHHHHHT--TTCCEEEECSSHHHHHHHHHHHHHTTTSSCCCHHHHHHHHHHHHTCCSSCHHHHHHHHHHHTTTEEE
T ss_pred             HHHHHHHHHHh--cCCCEEEEECCHHHHHHHHHHHHHHHhhccCChHHHHHHHHHHHHhhhccccccHHHHHHHhcCEEE
Confidence            33444444443  45799999999999999999998642                                    24899


Q ss_pred             ecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEE----ec-------CCCCccchhhhhcccccCC--C
Q 017573          265 THGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVIN----YD-------LPTQPENYLHRIGRSGRFG--R  331 (369)
Q Consensus       265 ~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~----~~-------~~~~~~~~~Q~~GR~~R~~--~  331 (369)
                      +||+++.++|..+++.|.+|..+|||||+++++|+|+|++++||.    ++       .|.|..+|.||+||+||.|  .
T Consensus       318 ~h~~l~~~~r~~v~~~f~~g~~~vlvaT~~l~~Gidip~~~~VI~~~~~~d~~~~~~~~~~s~~~~~Qr~GRaGR~g~~~  397 (715)
T 2va8_A          318 HHAGLSKALRDLIEEGFRQRKIKVIVATPTLAAGVNLPARTVIIGDIYRFNKKIAGYYDEIPIMEYKQMSGRAGRPGFDQ  397 (715)
T ss_dssp             ECTTSCHHHHHHHHHHHHTTCSCEEEECGGGGGSSCCCBSEEEECCC--------------CHHHHHHHHTTBCCTTTCS
T ss_pred             ECCCCCHHHHHHHHHHHHcCCCeEEEEChHHhcccCCCceEEEEeCCeeccccCCCCCCcCCHHHHHHHhhhcCCCCCCC
Confidence            999999999999999999999999999999999999999999998    77       7889999999999999987  4


Q ss_pred             ceeEEEEeccccHHHHHHHHHHhccccccCCc
Q 017573          332 KGVAINFVTRDDERMLFDIQKFYNVVIEELPS  363 (369)
Q Consensus       332 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  363 (369)
                      .|.|++++++.+. ....+.+++....+.++.
T Consensus       398 ~G~~~~l~~~~~~-~~~~~~~~l~~~~e~~~s  428 (715)
T 2va8_A          398 IGESIVVVRDKED-VDRVFKKYVLSDVEPIES  428 (715)
T ss_dssp             CEEEEEECSCGGG-HHHHHHHTTSSCCCCCCC
T ss_pred             CceEEEEeCCchH-HHHHHHHHHcCCCCCcee
Confidence            6999999887764 112233454444444443

>4a2p_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.00A {Anas platyrhynchos} PDB: 4a36_A*

Probab=100.00  E-value=2.2e-47  Score=356.28  Aligned_cols=333  Identities=17%  Similarity=0.196  Sum_probs=200.8

Q ss_pred             CCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCC--CccEEEEcCCHHHHHHHHHHHHHhcccc
Q 017573           14 YGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLV--QCQALVLAPTRELAQQIEKVMRALGDYL   91 (369)
Q Consensus        14 ~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~--~~~~liv~P~~~l~~q~~~~~~~~~~~~   91 (369)
                      ++..+|||+|.++++.+..++++++.+|||+|||+++++++++.+.....  ++++||++|+++|+.||.+.+.++....
T Consensus         3 ~~~~~~~~~Q~~~i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~   82 (556)
T 4a2p_A            3 METKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFERQ   82 (556)
T ss_dssp             -----CCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHGGG
T ss_pred             CCCCCCCHHHHHHHHHHHcCCCEEEEcCCCChHHHHHHHHHHHHHHhCcccCCCeEEEEeCCHHHHHHHHHHHHHHhccc
Confidence            34568999999999999999999999999999999999999988766432  4489999999999999999999998888


Q ss_pred             CcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCC-CCCCccEEEEechhHhhccCcHHHHH-HHHhh----
Q 017573           92 GVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSL-RPDYIKMFVLDEADEMLSRGFKDQIY-DIFQL----  165 (369)
Q Consensus        92 ~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~-~~~~~~~viiDE~H~~~~~~~~~~~~-~~~~~----  165 (369)
                      ++++..++|+............+++|+|+||+.+...+..... ....++++|+||||++.+.+....+. ..+..    
T Consensus        83 ~~~~~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~~vViDEah~~~~~~~~~~~~~~~~~~~~~~  162 (556)
T 4a2p_A           83 GYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQKFNS  162 (556)
T ss_dssp             TCCEEECCCC-----CHHHHHHHCSEEEECHHHHHHHHHSSSCCCSTTCSEEEEETGGGCSTTSHHHHHHHHHHHHHHCC
T ss_pred             CceEEEEeCCCCcchhHHHhhCCCCEEEECHHHHHHHHHhCcccccccCCEEEEECCcccCCcchHHHHHHHHHHhhhcc
Confidence            8999999988865554444455689999999999999988777 67889999999999998766433332 22211    


Q ss_pred             CCccCcEEEEEeeCChh-----------HHHHHHHh------------------cCCCEEEEecCccccccc--------
Q 017573          166 LPAKVQVGVFSATMPPE-----------ALEITRKF------------------MNKPVRILVKRDELTLEG--------  208 (369)
Q Consensus       166 ~~~~~~~i~~saT~~~~-----------~~~~~~~~------------------~~~~~~~~~~~~~~~~~~--------  208 (369)
                      ..+..+++++||||...           ...+...+                  ...+..............        
T Consensus       163 ~~~~~~~l~lSAT~~~~~~~~~~~~~~~i~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  242 (556)
T 4a2p_A          163 ASQLPQILGLTASVGVGNAKNIEETIEHICSLCSYLDIQAISTVRENIQELQRFMNKPEIDVRLVKRRIHNPFAAIISNL  242 (556)
T ss_dssp             ---CCEEEEEESCCCCTTCSSHHHHHHHHHHHHHHHTCSEEECCCTTHHHHHHHTCCCCEEEEECCCCSCCHHHHHHHHH
T ss_pred             cCCCCeEEEEeCCcccCchhhHHHHHHHHHHHHHhcCCeEecchhcchHHHHhcCCCCceEEEEcCCCcCChHHHHHHHH
Confidence            13567899999999531           11111111                  111111110000000000        


Q ss_pred             -------------eeEEEE-------------------------------------------------------------
Q 017573          209 -------------IKQFYV-------------------------------------------------------------  214 (369)
Q Consensus       209 -------------~~~~~~-------------------------------------------------------------  214 (369)
                                   ......                                                             
T Consensus       243 ~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~  322 (556)
T 4a2p_A          243 MSETEALMRTIYSVDTLSQNSKKDFGTQNYEHWIVVTQRKCRLLQLEDKEEESRICRALFICTEHLRKYNDALIISEDAR  322 (556)
T ss_dssp             HHHHHHHHHHHCC---------CCCSSHHHHHHHHHHHHHHHHC---CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHhhhhhhhcccccccchhhHHHHHHHHHHHHHhhcccccchhHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence                         000000                                                             


Q ss_pred             -------------------------------------------EccchhhhHHHHHHHHHh----ccCCCeEEEeCCHhh
Q 017573          215 -------------------------------------------NVEKEEWKLETLCDLYET----LAITQSVIFVNTRRK  247 (369)
Q Consensus       215 -------------------------------------------~~~~~~~~~~~l~~~~~~----~~~~k~lv~~~~~~~  247 (369)
                                                                 .......+...+.+++..    ..+.++||||++++.
T Consensus       323 ~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~K~~~L~~~l~~~~~~~~~~k~lVF~~~~~~  402 (556)
T 4a2p_A          323 IIDALSYLTEFFTNVKNGPYTELEQHLTAKFQEKEPELIALSKDETNENPKLEELVCILDDAYRYNPQTRTLLFAKTRAL  402 (556)
T ss_dssp             HHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHTTHHHHHHHHHCSSSCCHHHHHHHHHHHHHHHHCTTCCEEEEESSHHH
T ss_pred             HHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHhhHHHHhhhhccCCCCCChHHHHHHHHHHHHhcCCCCceEEEEEccHHH
Confidence                                                       000012244444555543    456799999999999


Q ss_pred             HHHHHHHHhhC------------CCeeEEecCCCCHHHHHHHHHHHhc-CCCcEEEEecCCcCCCCCCCCcEEEEecCCC
Q 017573          248 VDWLTDKMRSR------------DHTVSATHGDMDQNTRDIIMREFRS-GSSRVLITTDLLARGIDVQQVSLVINYDLPT  314 (369)
Q Consensus       248 ~~~~~~~l~~~------------~~~~~~~~~~~~~~~r~~~~~~f~~-~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~  314 (369)
                      ++.+++.|...            |.....+||+++.++|.++++.|++ |+.+|||+|+++++|+|+|++++||++++|+
T Consensus       403 ~~~l~~~L~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~R~~~~~~F~~~g~~~vLvaT~~~~~GiDip~v~~VI~~d~p~  482 (556)
T 4a2p_A          403 VSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSG  482 (556)
T ss_dssp             HHHHHHHHTTCSGGGSCCEEC------------------------------CCEEEEEC-----------CEEEEETCCS
T ss_pred             HHHHHHHHHhCCCcceeeeeEEEccCCcccccccCHHHHHHHHHHhcccCceEEEEEcCchhcCCCchhCCEEEEeCCCC
Confidence            99999999876            4455566778999999999999999 9999999999999999999999999999999


Q ss_pred             CccchhhhhcccccCCCceeEEEEeccccHHHHH
Q 017573          315 QPENYLHRIGRSGRFGRKGVAINFVTRDDERMLF  348 (369)
Q Consensus       315 ~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~  348 (369)
                      |+..|.||+|| ||. +.|.++++++..+.+...
T Consensus       483 s~~~~~Qr~GR-gR~-~~g~~~~l~~~~~~~~~~  514 (556)
T 4a2p_A          483 NVTKMIQVRGR-GRA-AGSKCILVTSKTEVVENE  514 (556)
T ss_dssp             CHHHHHHC----------CCEEEEESCHHHHHHH
T ss_pred             CHHHHHHhcCC-CCC-CCceEEEEEeCcchHHHH
Confidence            99999999999 998 889999999987665443

>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=100.00  E-value=1.1e-45  Score=339.94  Aligned_cols=325  Identities=20%  Similarity=0.228  Sum_probs=249.9

Q ss_pred             CCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEE
Q 017573           18 KPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHA   97 (369)
Q Consensus        18 ~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~   97 (369)
                      +|+|+|.++++.+.++ ++++.+|||+|||++++.++...+.  ..+.++||++|+++|+.||.+++.++....+..+..
T Consensus         9 ~l~~~Q~~~i~~~~~~-~~ll~~~tG~GKT~~~~~~~~~~~~--~~~~~~liv~P~~~L~~q~~~~~~~~~~~~~~~v~~   85 (494)
T 1wp9_A            9 QPRIYQEVIYAKCKET-NCLIVLPTGLGKTLIAMMIAEYRLT--KYGGKVLMLAPTKPLVLQHAESFRRLFNLPPEKIVA   85 (494)
T ss_dssp             CCCHHHHHHHHHGGGS-CEEEECCTTSCHHHHHHHHHHHHHH--HSCSCEEEECSSHHHHHHHHHHHHHHBCSCGGGEEE
T ss_pred             CccHHHHHHHHHHhhC-CEEEEcCCCCCHHHHHHHHHHHHHh--cCCCeEEEEECCHHHHHHHHHHHHHHhCcchhheEE
Confidence            7999999999999999 9999999999999999988887765  223389999999999999999999987544557888


Q ss_pred             EECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEEe
Q 017573           98 CVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSA  177 (369)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~sa  177 (369)
                      ++|+......... ...++|+|+||+.+...+.........+++||+||||++.+......+...+....+..+++++||
T Consensus        86 ~~g~~~~~~~~~~-~~~~~ivv~T~~~l~~~~~~~~~~~~~~~~vIiDEaH~~~~~~~~~~~~~~~~~~~~~~~~l~lTa  164 (494)
T 1wp9_A           86 LTGEKSPEERSKA-WARAKVIVATPQTIENDLLAGRISLEDVSLIVFDEAHRAVGNYAYVFIAREYKRQAKNPLVIGLTA  164 (494)
T ss_dssp             ECSCSCHHHHHHH-HHHCSEEEECHHHHHHHHHTTSCCTTSCSEEEEETGGGCSTTCHHHHHHHHHHHHCSSCCEEEEES
T ss_pred             eeCCcchhhhhhh-ccCCCEEEecHHHHHHHHhcCCcchhhceEEEEECCcccCCCCcHHHHHHHHHhcCCCCeEEEEec
Confidence            8888775544333 235799999999999988887777888999999999998765445555555555566788999999


Q ss_pred             eCChhH---HHHHHHhcCCCEEEEecCccc-----cccceeEEEEEc---------------------------------
Q 017573          178 TMPPEA---LEITRKFMNKPVRILVKRDEL-----TLEGIKQFYVNV---------------------------------  216 (369)
Q Consensus       178 T~~~~~---~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~---------------------------------  216 (369)
                      ||..+.   ..+...+..............     ............                                 
T Consensus       165 Tp~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  244 (494)
T 1wp9_A          165 SPGSTPEKIMEVINNLGIEHIEYRSENSPDVRPYVKGIRFEWVRVDLPEIYKEVRKLLREMLRDALKPLAETGLLESSSP  244 (494)
T ss_dssp             CSCSSHHHHHHHHHHTTCCEEEECCTTSTTTGGGCCCCCEEEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHTSSSCCCT
T ss_pred             CCCCCcHHHHHHHHhcChheeeccCCCcHHHHHhcCCCceeEEecCCcHHHHHHHHHHHHHHHHHHHHHHHhccccccCC
Confidence            997432   223332222211111110000     000000000000                                 


Q ss_pred             --------------------------------------------------------------------------------
Q 017573          217 --------------------------------------------------------------------------------  216 (369)
Q Consensus       217 --------------------------------------------------------------------------------  216 (369)
                                                                                                      
T Consensus       245 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~  324 (494)
T 1wp9_A          245 DIPKKEVLRAGQIINEEMAKGNHDLRGLLLYHAMALKLHHAIELLETQGLSALRAYIKKLYEEAKAGSTKASKEIFSDKR  324 (494)
T ss_dssp             TSCHHHHHHHHHHHHHHHTTTCCSTTTHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTTCCHHHHHHHTSHH
T ss_pred             CcchhHHHHHHHHHHHHhhccccchhhHHHHHHHHHHHHHHHHHHHhhcHHHHHHHHHHHHHhhccccchhhhhhhhhHH
Confidence                                                                                            


Q ss_pred             --------------cchhhhHHHHHHHHHh----ccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecC--------CCC
Q 017573          217 --------------EKEEWKLETLCDLYET----LAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHG--------DMD  270 (369)
Q Consensus       217 --------------~~~~~~~~~l~~~~~~----~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~--------~~~  270 (369)
                                    .....+...+.+++..    ..+.++||||++.+.++.+++.|...+..+..+||        +++
T Consensus       325 ~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~~~~~~  404 (494)
T 1wp9_A          325 MKKAISLLVQAKEIGLDHPKMDKLKEIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLS  404 (494)
T ss_dssp             HHHHHHHHHHHHHHTCSCHHHHHHHHHHHHHHHHCTTCCEEEECSCHHHHHHHHHHHHHTTCCEEEECCSSCC-------
T ss_pred             HHHHHHHHHHHHhcCCCChHHHHHHHHHHHHhccCCCCeEEEEEccHHHHHHHHHHHHHcCCCcEEEeccccccccccCC
Confidence                          0122244555556655    46789999999999999999999999999999999        999


Q ss_pred             HHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCCCCccchhhhhcccccCCCceeEEEEeccccHHHH
Q 017573          271 QNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERML  347 (369)
Q Consensus       271 ~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~  347 (369)
                      .++|.++++.|++|+.+|||+|+++++|+|+|.+++||++++|+++..|.|++||+||.|+ |.++.++++.+.+..
T Consensus       405 ~~~r~~~~~~F~~~~~~vLv~T~~~~~Gldl~~~~~Vi~~d~~~~~~~~~Qr~GR~~R~g~-g~~~~l~~~~t~ee~  480 (494)
T 1wp9_A          405 QREQKLILDEFARGEFNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRHMP-GRVIILMAKGTRDEA  480 (494)
T ss_dssp             CCHHHHHHHHHHHTSCSEEEECGGGGGGGGSTTCCEEEESSCCHHHHHHHHHHTTSCSCCC-SEEEEEEETTSHHHH
T ss_pred             HHHHHHHHHHHhcCCceEEEECCccccCCCchhCCEEEEeCCCCCHHHHHHHHhhccCCCC-ceEEEEEecCCHHHH
Confidence            9999999999999999999999999999999999999999999999999999999999998 999999998876543

>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=100.00  E-value=1.1e-46  Score=358.48  Aligned_cols=327  Identities=18%  Similarity=0.252  Sum_probs=253.2

Q ss_pred             CCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHH
Q 017573            3 LQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEK   82 (369)
Q Consensus         3 l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~   82 (369)
                      ||+.+.+.++++||.+|+++|.++++.+.+++++++++|||+|||+++.+++++.+..+   ++++|++|+++|+.|+.+
T Consensus        10 l~~~~~~~l~~~g~~~l~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~~l~il~~~~~~---~~~l~i~P~r~La~q~~~   86 (702)
T 2p6r_A           10 ISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKG---GKSLYVVPLRALAGEKYE   86 (702)
T ss_dssp             HHHHHHHHHHCC---CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHHTT---CCEEEEESSHHHHHHHHH
T ss_pred             cCHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCcEEEEcCCccHHHHHHHHHHHHHHHhC---CcEEEEeCcHHHHHHHHH
Confidence            88999999999999999999999999999999999999999999999999999877643   389999999999999999


Q ss_pred             HHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHH
Q 017573           83 VMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDI  162 (369)
Q Consensus        83 ~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~  162 (369)
                      .++++. ..+.++....|+......   ...+++|+|+||+++...+.+.....+.+++||+||+|.+.+......+..+
T Consensus        87 ~~~~~~-~~g~~v~~~~G~~~~~~~---~~~~~~Iiv~Tpe~l~~~l~~~~~~l~~~~~vIiDE~H~l~~~~r~~~~~~l  162 (702)
T 2p6r_A           87 SFKKWE-KIGLRIGISTGDYESRDE---HLGDCDIIVTTSEKADSLIRNRASWIKAVSCLVVDEIHLLDSEKRGATLEIL  162 (702)
T ss_dssp             HHTTTT-TTTCCEEEECSSCBCCSS---CSTTCSEEEEEHHHHHHHHHTTCSGGGGCCEEEETTGGGGGCTTTHHHHHHH
T ss_pred             HHHHHH-hcCCEEEEEeCCCCcchh---hccCCCEEEECHHHHHHHHHcChhHHhhcCEEEEeeeeecCCCCcccHHHHH
Confidence            996543 447888888887654332   1236899999999999988886665778999999999998876666666555


Q ss_pred             HhhC---CccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEE--------EEcc----chhhhHHHHH
Q 017573          163 FQLL---PAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFY--------VNVE----KEEWKLETLC  227 (369)
Q Consensus       163 ~~~~---~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------~~~~----~~~~~~~~l~  227 (369)
                      +..+   .+..+++++|||++. ..++. .++..+.. .....   +..+...+        ....    ........+.
T Consensus       163 l~~l~~~~~~~~ii~lSATl~n-~~~~~-~~l~~~~~-~~~~r---~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  236 (702)
T 2p6r_A          163 VTKMRRMNKALRVIGLSATAPN-VTEIA-EWLDADYY-VSDWR---PVPLVEGVLCEGTLELFDGAFSTSRRVKFEELVE  236 (702)
T ss_dssp             HHHHHHHCTTCEEEEEECCCTT-HHHHH-HHTTCEEE-ECCCC---SSCEEEEEECSSEEEEEETTEEEEEECCHHHHHH
T ss_pred             HHHHHhcCcCceEEEECCCcCC-HHHHH-HHhCCCcc-cCCCC---CccceEEEeeCCeeeccCcchhhhhhhhHHHHHH
Confidence            5444   568899999999973 33444 44443321 11111   11111111        1100    0011444455


Q ss_pred             HHHHhccCCCeEEEeCCHhhHHHHHHHHhhC------------------------------CCeeEEecCCCCHHHHHHH
Q 017573          228 DLYETLAITQSVIFVNTRRKVDWLTDKMRSR------------------------------DHTVSATHGDMDQNTRDII  277 (369)
Q Consensus       228 ~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~------------------------------~~~~~~~~~~~~~~~r~~~  277 (369)
                      +.+.  .++++||||+++++++.+++.|...                              +..+..+||+++.++|..+
T Consensus       237 ~~~~--~~~~~LVF~~s~~~~~~~a~~L~~~~~~~~~~~~~~~~i~~~~~~~~~~~l~~~~~~~v~~~h~~l~~~~R~~v  314 (702)
T 2p6r_A          237 ECVA--ENGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLNGQRRVV  314 (702)
T ss_dssp             HHHH--TTCCEEEECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECTTSCHHHHHHH
T ss_pred             HHHh--cCCCEEEEcCCHHHHHHHHHHHHHHHHhhcChHHHHHHHHhhccccccHHHHHHHhcCeEEecCCCCHHHHHHH
Confidence            4443  4679999999999999999888653                              1357889999999999999


Q ss_pred             HHHHhcCCCcEEEEecCCcCCCCCCCCcEEEE----ec---CCCCccchhhhhcccccCC--CceeEEEEeccccH
Q 017573          278 MREFRSGSSRVLITTDLLARGIDVQQVSLVIN----YD---LPTQPENYLHRIGRSGRFG--RKGVAINFVTRDDE  344 (369)
Q Consensus       278 ~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~----~~---~~~~~~~~~Q~~GR~~R~~--~~~~~~~~~~~~~~  344 (369)
                      ++.|.+|..+|||||+++++|+|+|++++||.    ++   .|.+..+|.||+||+||.|  ..|.|++++++.+.
T Consensus       315 ~~~f~~g~~~vlvaT~~l~~Gidip~~~~VI~~~~~yd~~~~~~s~~~~~Qr~GRaGR~g~~~~G~~~~l~~~~~~  390 (702)
T 2p6r_A          315 EDAFRRGNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIVGKRDR  390 (702)
T ss_dssp             HHHHHTTSCCEEEECSTTTSSSCCCBSEEEECCSEEESSSEEECCHHHHHHHHTTBSCTTTCSCEEEEEECCGGGH
T ss_pred             HHHHHCCCCeEEEECcHHhccCCCCceEEEEcCceeeCCCCCcCCHHHHHHHhhhcCCCCCCCCceEEEEecCccH
Confidence            99999999999999999999999999999987    44   6788999999999999988  47999999998773

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=100.00  E-value=4.4e-46  Score=347.52  Aligned_cols=332  Identities=20%  Similarity=0.215  Sum_probs=228.8

Q ss_pred             CCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCC--CccEEEEcCCHHHHHHHHHHHHHhccccCcE
Q 017573           17 EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLV--QCQALVLAPTRELAQQIEKVMRALGDYLGVK   94 (369)
Q Consensus        17 ~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~--~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~   94 (369)
                      .+|+|+|.++++.+.+++++++.+|||+|||++++++++..+.....  ++++||++|+++|+.||.+.+.++....+++
T Consensus         3 ~~~~~~Q~~~i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~   82 (555)
T 3tbk_A            3 LKPRNYQLELALPAKKGKNTIICAPTGCGKTFVSLLICEHHLKKFPCGQKGKVVFFANQIPVYEQQATVFSRYFERLGYN   82 (555)
T ss_dssp             CCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHHTTTCC
T ss_pred             CCCcHHHHHHHHHHhCCCCEEEEeCCCChHHHHHHHHHHHHHHhcccCCCCEEEEEeCCHHHHHHHHHHHHHHhccCCcE
Confidence            37999999999999999999999999999999999999988776432  4489999999999999999999998888899


Q ss_pred             EEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCC-CCCCccEEEEechhHhhccCcHHH-HHHHHhhC-----C
Q 017573           95 VHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSL-RPDYIKMFVLDEADEMLSRGFKDQ-IYDIFQLL-----P  167 (369)
Q Consensus        95 v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~-~~~~~~~viiDE~H~~~~~~~~~~-~~~~~~~~-----~  167 (369)
                      +..++|+............+++|+|+||+.+...+..... ....++++|+||||++.+...... +...+...     .
T Consensus        83 ~~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~~vViDEah~~~~~~~~~~~~~~~~~~~~~~~~~  162 (555)
T 3tbk_A           83 IASISGATSDSVSVQHIIEDNDIIILTPQILVNNLNNGAIPSLSVFTLMIFDECHNTSKNHPYNQIMFRYLDHKLGESRD  162 (555)
T ss_dssp             EEEECTTTGGGSCHHHHHHHCSEEEECHHHHHHHHHTSSSCCGGGCSEEEETTGGGCSTTCHHHHHHHHHHHHHTSSCCS
T ss_pred             EEEEcCCCcchhhHHHHhcCCCEEEECHHHHHHHHhcCcccccccCCEEEEECccccCCcchHHHHHHHHHHhhhccccC
Confidence            9999998876555444455689999999999999988776 677799999999999976643222 22332221     2


Q ss_pred             ccCcEEEEEeeCChhH-------HH---HHHHhcCCCEEEEecCc------cccccceeEEEEE----------------
Q 017573          168 AKVQVGVFSATMPPEA-------LE---ITRKFMNKPVRILVKRD------ELTLEGIKQFYVN----------------  215 (369)
Q Consensus       168 ~~~~~i~~saT~~~~~-------~~---~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~----------------  215 (369)
                      +..+++++||||....       ..   .....+...........      .............                
T Consensus       163 ~~~~~l~lSAT~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  242 (555)
T 3tbk_A          163 PLPQVVGLTASVGVGDAKTAEEAMQHICKLCAALDASVIATVRDNVAELEQVVYKPQKISRKVASRTSNTFKCIISQLMK  242 (555)
T ss_dssp             CCCEEEEEESCCCCTTCCSHHHHHHHHHHHHHHTTCSEEECCCSCHHHHHTTCCCCCEEEEECCCCSCCHHHHHHHHHHH
T ss_pred             CCCeEEEEecCcccCccccHHHHHHHHHHHHHhcCCeeeeccccCHHHHHhhcCCCceEEEEecCcccChHHHHHHHHHH
Confidence            4578999999995421       11   11112221111110000      0000000000000                


Q ss_pred             --------------------------------------------------------------------------------
Q 017573          216 --------------------------------------------------------------------------------  215 (369)
Q Consensus       216 --------------------------------------------------------------------------------  215 (369)
                                                                                                      
T Consensus       243 ~~~~~~~~~~~~l~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~  322 (555)
T 3tbk_A          243 ETEKLAKDVSEELGKLFQIQNREFGTQKYEQWIVGVHKACSVFQMADKEEESRVCKALFLYTSHLRKYNDALIISEDAQM  322 (555)
T ss_dssp             HHHHHHHTSCHHHHGGGGCCSCCSSSHHHHHHHHHHHHHHHTCCCSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCH
T ss_pred             HHHHHHHHHHHhhhhhhhcccccccchhhhHHHHHHHHHhhhhhccchhhHHHHHHHHHHHHHHHHHHHHHHhhhhhhhH
Confidence                                                                                            


Q ss_pred             -------------------------------------------ccchhhhHHHHHHHHHh----ccCCCeEEEeCCHhhH
Q 017573          216 -------------------------------------------VEKEEWKLETLCDLYET----LAITQSVIFVNTRRKV  248 (369)
Q Consensus       216 -------------------------------------------~~~~~~~~~~l~~~~~~----~~~~k~lv~~~~~~~~  248 (369)
                                                                 ......+...+.+++..    .+..++||||++++.+
T Consensus       323 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~k~lVF~~~~~~~  402 (555)
T 3tbk_A          323 TDALNYLKAFFHDVREAAFDETERELTRRFEEKLEELEKVSRDPSNENPKLRDLYLVLQEEYHLKPETKTILFVKTRALV  402 (555)
T ss_dssp             HHHHHHHHHHHHHHCC-----HHHHHHHHHHTTHHHHHHHHHCGGGCCHHHHHHHHHHHHHHHHCTTCCEEEECSSHHHH
T ss_pred             HHHHHHHHHHHHHHhhcccchHHHHHHHHHhhhhhhhhhhccCCCcCCHHHHHHHHHHHHHhccCCCceEEEEeCcHHHH
Confidence                                                       00012244444444443    3568999999999999


Q ss_pred             HHHHHHHhhCC------------CeeEEecCCCCHHHHHHHHHHHhc-CCCcEEEEecCCcCCCCCCCCcEEEEecCCCC
Q 017573          249 DWLTDKMRSRD------------HTVSATHGDMDQNTRDIIMREFRS-GSSRVLITTDLLARGIDVQQVSLVINYDLPTQ  315 (369)
Q Consensus       249 ~~~~~~l~~~~------------~~~~~~~~~~~~~~r~~~~~~f~~-~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~~  315 (369)
                      +.+++.|...+            .....+||+++.++|.++++.|++ |+++|||||+++++|+|+|++++||++++|+|
T Consensus       403 ~~l~~~L~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~R~~~~~~F~~~g~~~vLvaT~~~~~GlDlp~v~~VI~~d~p~s  482 (555)
T 3tbk_A          403 DALKKWIEENPALSFLKPGILTGRGRTNRATGMTLPAQKCVLEAFRASGDNNILIATSVADEGIDIAECNLVILYEYVGN  482 (555)
T ss_dssp             HHHHHHHHHCGGGTTCCEEECCC--------------------------CCSEEEECCCTTCCEETTSCSEEEEESCCSS
T ss_pred             HHHHHHHhhCcCcCceeeeEEEecCCcccccccCHHHHHHHHHHHhcCCCeeEEEEcchhhcCCccccCCEEEEeCCCCC
Confidence            99999998863            344455569999999999999999 99999999999999999999999999999999


Q ss_pred             ccchhhhhcccccCCCceeEEEEeccccHHHHHHH
Q 017573          316 PENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDI  350 (369)
Q Consensus       316 ~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~  350 (369)
                      +..|.||+|| ||. +.|.+++++++.+......+
T Consensus       483 ~~~~~Qr~GR-gR~-~~g~~~~l~~~~~~~~~~~~  515 (555)
T 3tbk_A          483 VIKMIQTRGR-GRA-RDSKCFLLTSSADVIEKEKA  515 (555)
T ss_dssp             CCCEECSSCC-CTT-TSCEEEEEESCHHHHHHHHH
T ss_pred             HHHHHHhcCc-CcC-CCceEEEEEcCCCHHHHHHH
Confidence            9999999999 898 88999999998877766655

>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=100.00  E-value=1.1e-45  Score=355.83  Aligned_cols=333  Identities=18%  Similarity=0.217  Sum_probs=207.9

Q ss_pred             hCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCC--CccEEEEcCCHHHHHHHHHHHHHhccc
Q 017573           13 AYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLV--QCQALVLAPTRELAQQIEKVMRALGDY   90 (369)
Q Consensus        13 ~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~--~~~~liv~P~~~l~~q~~~~~~~~~~~   90 (369)
                      .+|+..|+|+|.++++.+..++++++.+|||+|||++++++++..+.....  ++++||++|+++|+.||.+.+.++...
T Consensus       243 ~~g~~~l~~~Q~~~i~~~l~~~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~Lvl~Pt~~L~~Q~~~~~~~~~~~  322 (797)
T 4a2q_A          243 VYETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFER  322 (797)
T ss_dssp             -----CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHGG
T ss_pred             hcCCCCCCHHHHHHHHHHHhCCCEEEEeCCCChHHHHHHHHHHHHHHhccccCCCeEEEEeCCHHHHHHHHHHHHHhccc
Confidence            457889999999999999999999999999999999999999988776432  448999999999999999999999888


Q ss_pred             cCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCC-CCCCccEEEEechhHhhccCcHHHHH-HHHhh---
Q 017573           91 LGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSL-RPDYIKMFVLDEADEMLSRGFKDQIY-DIFQL---  165 (369)
Q Consensus        91 ~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~-~~~~~~~viiDE~H~~~~~~~~~~~~-~~~~~---  165 (369)
                      .++++..++|+............+++|+|+||+.+...+..... ....+++||+||||++.+......+. .+...   
T Consensus       323 ~~~~v~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~~~iViDEaH~~~~~~~~~~i~~~~~~~~~~  402 (797)
T 4a2q_A          323 QGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQKFN  402 (797)
T ss_dssp             GTCCEEEECCC-----CHHHHHHTCSEEEECHHHHHHHHHSSSCCCGGGCSEEEETTGGGCSTTSHHHHHHHHHHHHHHT
T ss_pred             CCceEEEEeCCcchhhhHHHhhCCCCEEEEchHHHHHHHHhccccccccCCEEEEECccccCCCccHHHHHHHHHHHhhc
Confidence            88999999998876655555556789999999999999887766 67779999999999987654333322 22222   


Q ss_pred             -CCccCcEEEEEeeCChh-----------HHHHHH------------------HhcCCCEEEEecCccccccc-------
Q 017573          166 -LPAKVQVGVFSATMPPE-----------ALEITR------------------KFMNKPVRILVKRDELTLEG-------  208 (369)
Q Consensus       166 -~~~~~~~i~~saT~~~~-----------~~~~~~------------------~~~~~~~~~~~~~~~~~~~~-------  208 (369)
                       ..+..+++++||||...           ...+..                  .++..+..............       
T Consensus       403 ~~~~~~~~l~lSATp~~~~~~~~~~~~~~i~~l~~~L~~~~i~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~  482 (797)
T 4a2q_A          403 SASQLPQILGLTASVGVGNAKNIEETIEHICSLCSYLDIQAISTVRENIQELQRFMNKPEIDVRLVKRRIHNPFAAIISN  482 (797)
T ss_dssp             TCCCCCEEEEEESCCCCTTCCSHHHHHHHHHHHHHHHTCSEEECCCTTHHHHHHHSCCCCCEEEECCCCSCCHHHHHHHH
T ss_pred             cCCCCCeEEEEcCCccccccccHHHHHHHHHHHHHhcCCcEEecccccHHHHHHhcCCCceEEEecCCCCCcHHHHHHHH
Confidence             14568899999999521           111111                  11111111110000000000       


Q ss_pred             -----------------eeEEE-EEc------------------------------------------------------
Q 017573          209 -----------------IKQFY-VNV------------------------------------------------------  216 (369)
Q Consensus       209 -----------------~~~~~-~~~------------------------------------------------------  216 (369)
                                       +.... ...                                                      
T Consensus       483 l~~~i~~~~~~~~~l~~l~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~  562 (797)
T 4a2q_A          483 LMSETEALMRTIYSVDTLSQNSKKDFGTQNYEHWIVVTQRKCRLLQLEDKEEESRICRALFICTEHLRKYNDALIISEDA  562 (797)
T ss_dssp             HHHHHHHHHHHC------------CCSSHHHHHHHHHHHHHHHHCCCSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHhhHHhhhhccccccchhHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHHHHHHHHHHHHhhhccc
Confidence                             00000 000                                                      


Q ss_pred             ----------------------------------------------cchhhhHHHHHHHHHh----ccCCCeEEEeCCHh
Q 017573          217 ----------------------------------------------EKEEWKLETLCDLYET----LAITQSVIFVNTRR  246 (369)
Q Consensus       217 ----------------------------------------------~~~~~~~~~l~~~~~~----~~~~k~lv~~~~~~  246 (369)
                                                                    .....+...+..++..    .++.++||||+++.
T Consensus       563 ~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~~~~~~~~K~~~L~~lL~~~~~~~~~~kvLIF~~~~~  642 (797)
T 4a2q_A          563 RIIDALSYLTEFFTNVKNGPYTELEQHLTAKFQEKEPELIALSKDETNENPKLEELVCILDDAYRYNPQTRTLLFAKTRA  642 (797)
T ss_dssp             CHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHTTHHHHHHHHHCTTCCCHHHHHHHHHHHHHHHHCSSCCEEEEESSHH
T ss_pred             cHHHHHHHHHHHHHHHhccCccHHHHHHHHHHHHHHHHHHHhhcCCCCCChHHHHHHHHHHHHhccCCCCeEEEEECcHH
Confidence                                                          0012244444455543    45689999999999


Q ss_pred             hHHHHHHHHhhC------------CCeeEEecCCCCHHHHHHHHHHHhc-CCCcEEEEecCCcCCCCCCCCcEEEEecCC
Q 017573          247 KVDWLTDKMRSR------------DHTVSATHGDMDQNTRDIIMREFRS-GSSRVLITTDLLARGIDVQQVSLVINYDLP  313 (369)
Q Consensus       247 ~~~~~~~~l~~~------------~~~~~~~~~~~~~~~r~~~~~~f~~-~~~~vli~t~~~~~G~d~~~~~~vi~~~~~  313 (369)
                      .++.+++.|+..            |.....+||+++..+|.++++.|++ |+++|||+|+++++|+|+|++++||++++|
T Consensus       643 ~~~~L~~~L~~~~~~~~~~~~~l~G~~~~~~hg~~~~~eR~~~l~~F~~~g~~~vLVaT~~~~~GIDlp~v~~VI~yd~p  722 (797)
T 4a2q_A          643 LVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYS  722 (797)
T ss_dssp             HHHHHHHHHHTCSTTCSCCCEEC----------------------------CCSEEEEECC-------CCCSEEEEESCC
T ss_pred             HHHHHHHHHHhCcccccccceEEEecCCcccCCCCCHHHHHHHHHHhhccCCceEEEEcCchhcCCCchhCCEEEEeCCC
Confidence            999999999874            4456677888999999999999999 999999999999999999999999999999


Q ss_pred             CCccchhhhhcccccCCCceeEEEEeccccHHHH
Q 017573          314 TQPENYLHRIGRSGRFGRKGVAINFVTRDDERML  347 (369)
Q Consensus       314 ~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~  347 (369)
                      +|+..|.||+|| ||. +.|.++++++..+....
T Consensus       723 ~s~~~~iQr~GR-GR~-~~g~~i~l~~~~~~ee~  754 (797)
T 4a2q_A          723 GNVTKMIQVRGR-GRA-AGSKCILVTSKTEVVEN  754 (797)
T ss_dssp             SCHHHHHTC---------CCCEEEEECCHHHHHH
T ss_pred             CCHHHHHHhcCC-CCC-CCceEEEEEeCCcHHHH
Confidence            999999999999 998 88999999988766443

>3l9o_A ATP-dependent RNA helicase DOB1; REC-A fold, winged-helix-turn-helix, antiparallel-coiled-COI domain, ATP-binding, helicase, hydrolase; 3.39A {Saccharomyces cerevisiae}

Probab=100.00  E-value=2e-45  Score=359.85  Aligned_cols=325  Identities=19%  Similarity=0.221  Sum_probs=251.5

Q ss_pred             CCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHH
Q 017573            3 LQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEK   82 (369)
Q Consensus         3 l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~   82 (369)
                      +++.+...+.......|+++|.++++.+..+++++++||||+|||+++.++++..+..+.   +++|++|+++|+.|+++
T Consensus       169 l~~~~~~~~~~~~~f~ltp~Q~~AI~~i~~g~dvLV~ApTGSGKTlva~l~i~~~l~~g~---rvlvl~PtraLa~Q~~~  245 (1108)
T 3l9o_A          169 IAEHKRVNEARTYPFTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKNKQ---RVIYTSPIKALSNQKYR  245 (1108)
T ss_dssp             TTTTCCCSCSSCCSSCCCHHHHHHHHHHTTTCCEEEECCSSSHHHHHHHHHHHHHHHTTC---EEEEEESSHHHHHHHHH
T ss_pred             CChhhhHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHHhcCC---eEEEEcCcHHHHHHHHH
Confidence            444444455555556899999999999999999999999999999999999998876544   89999999999999999


Q ss_pred             HHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHH
Q 017573           83 VMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDI  162 (369)
Q Consensus        83 ~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~  162 (369)
                      .+.++..    .+..++|+..       ...+++|+|+||+.|.+++.+......++++||+||+|++.+.++...+..+
T Consensus       246 ~l~~~~~----~VglltGd~~-------~~~~~~IlV~Tpe~L~~~L~~~~~~l~~l~lVVIDEaH~l~d~~rg~~~e~i  314 (1108)
T 3l9o_A          246 ELLAEFG----DVGLMTGDIT-------INPDAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMRDKERGVVWEET  314 (1108)
T ss_dssp             HHHHHTS----SEEEECSSCB-------CCCSCSEEEEEHHHHHHHHHHCSSHHHHEEEEEEETGGGTTSHHHHHHHHHH
T ss_pred             HHHHHhC----CccEEeCccc-------cCCCCCEEEeChHHHHHHHHcCccccccCCEEEEhhhhhccccchHHHHHHH
Confidence            9999765    5666777665       2346899999999999999887776777999999999999988888889999


Q ss_pred             HhhCCccCcEEEEEeeCChh--HHHHHHHhcCCCEEEEecCccccccceeEEEEEccc----------------------
Q 017573          163 FQLLPAKVQVGVFSATMPPE--ALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEK----------------------  218 (369)
Q Consensus       163 ~~~~~~~~~~i~~saT~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----------------------  218 (369)
                      +..+++..+++++|||++..  ...........+..+......  +..+..++.....                      
T Consensus       315 i~~l~~~~qvl~lSATipn~~e~a~~l~~~~~~~~~vi~~~~r--p~pl~~~~~~~~~~~~~~~vd~~~~~~~~~~~~~~  392 (1108)
T 3l9o_A          315 IILLPDKVRYVFLSATIPNAMEFAEWICKIHSQPCHIVYTNFR--PTPLQHYLFPAHGDGIYLVVDEKSTFREENFQKAM  392 (1108)
T ss_dssp             HHHSCTTSEEEEEECSCSSCHHHHHHHHHHTCSCEEEEEECCC--SSCEEEEEEETTSSCCEEEEETTTEECHHHHHHHH
T ss_pred             HHhcCCCceEEEEcCCCCCHHHHHHHHHhhcCCCeEEEecCCC--cccceEEEeecCCcceeeeeccccchhhhhHHHHH
Confidence            99999999999999998643  334444444444443332211  1111222211000                      


Q ss_pred             --------------------------------hhhhHHHHHHHHHhccCCCeEEEeCCHhhHHHHHHHHhhCCCe-----
Q 017573          219 --------------------------------EEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHT-----  261 (369)
Q Consensus       219 --------------------------------~~~~~~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~~~~-----  261 (369)
                                                      .......+...+.....+++||||+++..++.++..|...+..     
T Consensus       393 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~li~~l~~~~~~~vIVF~~sr~~~e~la~~L~~~~~~~~~e~  472 (1108)
T 3l9o_A          393 ASISNQIGDDPNSTDSRGKKGQTYKGGSAKGDAKGDIYKIVKMIWKKKYNPVIVFSFSKRDCEELALKMSKLDFNSDDEK  472 (1108)
T ss_dssp             TTC-----------------------------CHHHHHHHHHHHHHTTCCCEEEEESCHHHHHHHHHHTCSHHHHCC---
T ss_pred             HHHHhhhcccccccccccccccccccccccccchhHHHHHHHHHHhcCCCCEEEEeCcHHHHHHHHHHHHhccCCCHHHH
Confidence                                            0122233344444455679999999999999999998653221     


Q ss_pred             ----------------------------------eEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEE
Q 017573          262 ----------------------------------VSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLV  307 (369)
Q Consensus       262 ----------------------------------~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~v  307 (369)
                                                        +..+||++++.+|..+++.|.+|.++|||||+++++|+|+|.+++|
T Consensus       473 ~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~gV~~~Hg~l~~~~R~~v~~~F~~G~ikVLVAT~vla~GIDiP~v~~V  552 (1108)
T 3l9o_A          473 EALTKIFNNAIALLPETDRELPQIKHILPLLRRGIGIHHSGLLPILKEVIEILFQEGFLKVLFATETFSIGLNMPAKTVV  552 (1108)
T ss_dssp             -CHHHHGGGSCTHHHHHTTCCHHHHHHTHHHHHTEEEECSCSCHHHHHHHHHHHHHTCCCEEEEESCCCSCCCC--CEEE
T ss_pred             HHHHHHHHHHHhhcchhhhhhhhHHHHHHhhhcCeeeecCCCCHHHHHHHHHHHhCCCCeEEEECcHHhcCCCCCCceEE
Confidence                                              7899999999999999999999999999999999999999999999


Q ss_pred             EEecCCC--------CccchhhhhcccccCC--CceeEEEEecccc
Q 017573          308 INYDLPT--------QPENYLHRIGRSGRFG--RKGVAINFVTRDD  343 (369)
Q Consensus       308 i~~~~~~--------~~~~~~Q~~GR~~R~~--~~~~~~~~~~~~~  343 (369)
                      |.++.++        |..+|.||+||+||.|  ..|.+++++++..
T Consensus       553 I~~~~~~d~~~~r~iS~~eyiQr~GRAGR~G~d~~G~~ill~~~~~  598 (1108)
T 3l9o_A          553 FTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLDDRGIVIMMIDEKM  598 (1108)
T ss_dssp             ESCSEEESSSCEEECCHHHHHHHHHHSCCSSSCSSEEEEEEECCCC
T ss_pred             EecCcccCccccccCCHHHHHHhhcccCCCCCCCceEEEEEecCCc
Confidence            9766544        5556999999999999  6789998888763

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}

Probab=100.00  E-value=7.3e-44  Score=346.08  Aligned_cols=323  Identities=20%  Similarity=0.269  Sum_probs=253.1

Q ss_pred             HHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccc
Q 017573           11 IYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDY   90 (369)
Q Consensus        11 l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~   90 (369)
                      ...++| +|+++|.++++.+..++++++++|||+|||+++.++++..+..+.   +++|++|+++|+.|+.+.+.+++. 
T Consensus        80 ~~~~~f-~L~~~Q~eai~~l~~g~~vLV~apTGSGKTlva~lai~~~l~~g~---rvL~l~PtkaLa~Q~~~~l~~~~~-  154 (1010)
T 2xgj_A           80 ARTYPF-TLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKNKQ---RVIYTSPIKALSNQKYRELLAEFG-  154 (1010)
T ss_dssp             SCCCSS-CCCHHHHHHHHHHHHTCEEEEECCTTSCHHHHHHHHHHHHHHTTC---EEEEEESSHHHHHHHHHHHHHHHS-
T ss_pred             HHhCCC-CCCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHhccCC---eEEEECChHHHHHHHHHHHHHHhC-
Confidence            345677 599999999999999999999999999999999988888776543   899999999999999999998764 


Q ss_pred             cCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCccC
Q 017573           91 LGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKV  170 (369)
Q Consensus        91 ~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~  170 (369)
                         ++..++|+....       .+++|+|+||+.|..++.++......+++||+||+|.+.+..+...+..++..+++..
T Consensus       155 ---~vglltGd~~~~-------~~~~IvV~Tpe~L~~~L~~~~~~l~~l~lVViDEaH~l~d~~rg~~~e~il~~l~~~~  224 (1010)
T 2xgj_A          155 ---DVGLMTGDITIN-------PDAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMRDKERGVVWEETIILLPDKV  224 (1010)
T ss_dssp             ---CEEEECSSCEEC-------TTCSEEEEEHHHHHHHHHHTCTTGGGEEEEEEETGGGGGCTTTHHHHHHHHHHSCTTC
T ss_pred             ---CEEEEeCCCccC-------CCCCEEEEcHHHHHHHHHcCcchhhcCCEEEEechhhhcccchhHHHHHHHHhcCCCC
Confidence               566777776532       3579999999999998888777778899999999999998888888888999999999


Q ss_pred             cEEEEEeeCChhHH--HHHHHhcCCCEEEEecCccccccceeEEEEEcc---------ch--------------------
Q 017573          171 QVGVFSATMPPEAL--EITRKFMNKPVRILVKRDELTLEGIKQFYVNVE---------KE--------------------  219 (369)
Q Consensus       171 ~~i~~saT~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------~~--------------------  219 (369)
                      +++++|||++....  ..+......+..+.....  .+..+..++....         ..                    
T Consensus       225 ~il~LSATi~n~~e~a~~l~~~~~~~~~vi~~~~--rp~pl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  302 (1010)
T 2xgj_A          225 RYVFLSATIPNAMEFAEWICKIHSQPCHIVYTNF--RPTPLQHYLFPAHGDGIYLVVDEKSTFREENFQKAMASISNQIG  302 (1010)
T ss_dssp             EEEEEECCCTTHHHHHHHHHHHHTSCEEEEEECC--CSSCEEEEEEETTSSCCEEEECTTCCBCHHHHHHHHHTCC----
T ss_pred             eEEEEcCCCCCHHHHHHHHHhhcCCCeEEEecCC--CcccceEEEEecCCcceeeeeccccccchHHHHHHHHHHhhhhc
Confidence            99999999864321  222223344443332211  1112222222110         00                    


Q ss_pred             -------------------------hhhHHHHHHHHHhccCCCeEEEeCCHhhHHHHHHHHhhCCC--------------
Q 017573          220 -------------------------EWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDH--------------  260 (369)
Q Consensus       220 -------------------------~~~~~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~~~--------------  260 (369)
                                               ......+...+......++|||++++..++.+++.|...+.              
T Consensus       303 ~~~~~~~~~g~~~~~~k~~~~~~~~~~~l~~l~~~l~~~~~~~~IVF~~sr~~~e~la~~L~~~~~~~~~e~~~i~~~~~  382 (1010)
T 2xgj_A          303 DDPNSTDSRGKKGQTYKGGSAKGDAKGDIYKIVKMIWKKKYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEALTKIFN  382 (1010)
T ss_dssp             --------------------------CHHHHHHHHHHHHTCCSEEEEESSHHHHHHHHHTTTTSCCCCHHHHHHHHHHHH
T ss_pred             ccccccccccccccccccccccccchHHHHHHHHHHHhcCCCCEEEEECCHHHHHHHHHHHHhCCCCChHHHHHHHHHHH
Confidence                                     11222344444444556999999999999999999876433              


Q ss_pred             -------------------------eeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEE----ec
Q 017573          261 -------------------------TVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVIN----YD  311 (369)
Q Consensus       261 -------------------------~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~----~~  311 (369)
                                               .+..+||++++.+|..+++.|++|.++|||||+++++|+|+|.+++||.    ++
T Consensus       383 ~~~~~l~~~d~~l~~~~~l~~~l~~gI~~~Hggl~~~eR~~ve~~F~~G~ikVLVAT~~la~GIDiP~~~vVI~~~~kfd  462 (1010)
T 2xgj_A          383 NAIALLPETDRELPQIKHILPLLRRGIGIHHSGLLPILKEVIEILFQEGFLKVLFATETFSIGLNMPAKTVVFTSVRKWD  462 (1010)
T ss_dssp             HHHTTSCGGGTTCHHHHHHHHHHHHTEEEESTTSCHHHHHHHHHHHHTTCCSEEEEEGGGGGSTTCCBSEEEESCSEEEC
T ss_pred             HHHHhcchhhhcchhHHHHHHHHhCCeeEECCCCCHHHHHHHHHHHhcCCCcEEEEehHhhccCCCCCceEEEeCCcccC
Confidence                                     2789999999999999999999999999999999999999999999998    88


Q ss_pred             C----CCCccchhhhhcccccCCC--ceeEEEEeccc-cHHHHHHH
Q 017573          312 L----PTQPENYLHRIGRSGRFGR--KGVAINFVTRD-DERMLFDI  350 (369)
Q Consensus       312 ~----~~~~~~~~Q~~GR~~R~~~--~~~~~~~~~~~-~~~~~~~~  350 (369)
                      .    |.++.+|.|++||+||.|.  .|.+++++++. +...+..+
T Consensus       463 ~~~~rp~s~~~y~Qr~GRAGR~G~d~~G~vi~l~~~~~e~~~~~~l  508 (1010)
T 2xgj_A          463 GQQFRWVSGGEYIQMSGRAGRRGLDDRGIVIMMIDEKMEPQVAKGM  508 (1010)
T ss_dssp             SSCEEECCHHHHHHHHTTBCCTTTCSSEEEEEEECSCCCHHHHHHH
T ss_pred             CcCCccCCHHHHhHhhhhcccCCCCCceEEEEEECCCCCHHHHHHH
Confidence            7    7899999999999999986  49999999876 44444433

>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=100.00  E-value=1.8e-44  Score=350.77  Aligned_cols=333  Identities=18%  Similarity=0.215  Sum_probs=207.0

Q ss_pred             hCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCC--CccEEEEcCCHHHHHHHHHHHHHhccc
Q 017573           13 AYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLV--QCQALVLAPTRELAQQIEKVMRALGDY   90 (369)
Q Consensus        13 ~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~--~~~~liv~P~~~l~~q~~~~~~~~~~~   90 (369)
                      -.++.+|+++|.++++.+.+++++++.+|||+|||++++++++..+.....  ++++||++|+++|+.||.+.+.++...
T Consensus       243 l~~~~~~r~~Q~~ai~~il~g~~~ll~a~TGsGKTl~~~~~i~~~l~~~~~~~~~~vLvl~Pt~~L~~Q~~~~~~~~~~~  322 (936)
T 4a2w_A          243 VYETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFER  322 (936)
T ss_dssp             -----CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHTTTTTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHHT
T ss_pred             ccCCCCCCHHHHHHHHHHHcCCCEEEEeCCCchHHHHHHHHHHHHHHhccccCCCeEEEEeCCHHHHHHHHHHHHHHhcc
Confidence            346789999999999999999999999999999999999999888766431  448999999999999999999999887


Q ss_pred             cCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCC-CCCCccEEEEechhHhhccCcHHHH-HHHHhh---
Q 017573           91 LGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSL-RPDYIKMFVLDEADEMLSRGFKDQI-YDIFQL---  165 (369)
Q Consensus        91 ~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~-~~~~~~~viiDE~H~~~~~~~~~~~-~~~~~~---  165 (369)
                      .++++..++|+............+++|+|+||+.+...+..... ....++++|+||||++.+......+ ..+...   
T Consensus       323 ~~~~v~~~~G~~~~~~~~~~~~~~~~IvI~Tp~~L~~~l~~~~~~~l~~~~liViDEaH~~~~~~~~~~i~~~~~~~~~~  402 (936)
T 4a2w_A          323 QGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQKFN  402 (936)
T ss_dssp             TTCCEEEECCC-----CCHHHHHHCSEEEECHHHHHHHHHSSSCCCGGGCSEEEEETGGGCSTTCHHHHHHHHHHHHHHT
T ss_pred             cCceEEEEECCcchhhHHHHhccCCCEEEecHHHHHHHHHcCccccccCCCEEEEECccccCCCccHHHHHHHHHHHhhc
Confidence            78999999998865544334445689999999999999887766 5677999999999998765433222 222222   


Q ss_pred             -CCccCcEEEEEeeCChh-----------HHHHH------------------HHhcCCCEEEEecCccccccc-------
Q 017573          166 -LPAKVQVGVFSATMPPE-----------ALEIT------------------RKFMNKPVRILVKRDELTLEG-------  208 (369)
Q Consensus       166 -~~~~~~~i~~saT~~~~-----------~~~~~------------------~~~~~~~~~~~~~~~~~~~~~-------  208 (369)
                       ..+..+++++||||...           ...+.                  ..++..+..............       
T Consensus       403 ~~~~~~~~l~LSATp~~~~~~~l~~~~~~i~~L~~~L~~~~i~~~~~~~~~l~~~~~~p~~~~~~~~~~~~~~~~~~l~~  482 (936)
T 4a2w_A          403 SASQLPQILGLTASVGVGNAKNIEETIEHICSLCSYLDIQAISTVRENIQELQRFMNKPEIDVRLVKRRIHNPFAAIISN  482 (936)
T ss_dssp             TCSCCCEEEEEESCCCCTTCCSHHHHHHHHHHHHHHHTCSEEECCCSSHHHHHHHSCCCCEEEEECCCCSCCHHHHHHHH
T ss_pred             cCCCcCeEEEecCCcccccchhHHHHHHHHHHHHHhcCCceeecccccHHHHHHhccCCcceEEecccccCcHHHHHHHH
Confidence             14467899999999521           11111                  111122211111000000000       


Q ss_pred             -----------------eeEEEE-E-------------------------------------------------------
Q 017573          209 -----------------IKQFYV-N-------------------------------------------------------  215 (369)
Q Consensus       209 -----------------~~~~~~-~-------------------------------------------------------  215 (369)
                                       +..... .                                                       
T Consensus       483 l~~~i~~~~~~~l~~~~l~~~~~~~~g~~~y~~~l~~l~k~~~~~~l~~~~~~~~~~~~l~~~~~~l~~~~~al~i~~~~  562 (936)
T 4a2w_A          483 LMSETEALMRTIAYVDTLSQNSKKDFGTQNYEHWIVVTQRKCRLLQLEDKEEESRICRALFICTEHLRKYNDALIISEDA  562 (936)
T ss_dssp             HHHHHHHHHHHC------------CCSSHHHHHHHHHHHHHHHHCCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHhhhhhhhccccccchHHHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHHHHHHHHHHHHhhhcch
Confidence                             000000 0                                                       


Q ss_pred             ---------------------------------------------ccchhhhHHHHHHHHHh----ccCCCeEEEeCCHh
Q 017573          216 ---------------------------------------------VEKEEWKLETLCDLYET----LAITQSVIFVNTRR  246 (369)
Q Consensus       216 ---------------------------------------------~~~~~~~~~~l~~~~~~----~~~~k~lv~~~~~~  246 (369)
                                                                   ......+...+.+++..    ..+.++||||+++.
T Consensus       563 ~~~~~~~~l~~~~~~~~~~~~~~~e~~l~~~~~~~~~~l~~~~~~~~~~~~K~~~L~~lL~~~~~~~~~~rvLIF~~t~~  642 (936)
T 4a2w_A          563 RIIDALSYLTEFFTNVKNGPYTELEQHLTAKFQEKEPELIALSKDETNENPKLEELVCILDDAYRYNPQTRTLLFAKTRA  642 (936)
T ss_dssp             CHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHTSTTCCCHHHHHHHHHHHHTTTSCTTCCEEEEESSHH
T ss_pred             hHHHHHHHHHHHHHHHhhccCCHHHHHHHHHHHHHHHHHHHhhhccCCCCHHHHHHHHHHHHHhccCCCCeEEEEeCCHH
Confidence                                                         00012234444455544    34579999999999


Q ss_pred             hHHHHHHHHhhC------------CCeeEEecCCCCHHHHHHHHHHHhc-CCCcEEEEecCCcCCCCCCCCcEEEEecCC
Q 017573          247 KVDWLTDKMRSR------------DHTVSATHGDMDQNTRDIIMREFRS-GSSRVLITTDLLARGIDVQQVSLVINYDLP  313 (369)
Q Consensus       247 ~~~~~~~~l~~~------------~~~~~~~~~~~~~~~r~~~~~~f~~-~~~~vli~t~~~~~G~d~~~~~~vi~~~~~  313 (369)
                      .++.+++.|...            |.....+||+++..+|.++++.|++ |+++|||+|+++++|+|+|++++||++++|
T Consensus       643 ~ae~L~~~L~~~~~l~~ik~~~l~G~~~~~~hg~m~~~eR~~il~~Fr~~g~~~VLVaT~~~~eGIDlp~v~~VI~yD~p  722 (936)
T 4a2w_A          643 LVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYS  722 (936)
T ss_dssp             HHHHHHHHHHHCSTTSSCCCEEC----------------------------CCSEEEEECC------CCCCSEEEEESCC
T ss_pred             HHHHHHHHHhhCccccccceeEEecCCCcccCCCCCHHHHHHHHHHhhccCCeeEEEEeCchhcCCcchhCCEEEEeCCC
Confidence            999999999986            4556666888999999999999999 999999999999999999999999999999


Q ss_pred             CCccchhhhhcccccCCCceeEEEEeccccHHHH
Q 017573          314 TQPENYLHRIGRSGRFGRKGVAINFVTRDDERML  347 (369)
Q Consensus       314 ~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~  347 (369)
                      +|+..|.||+|| ||. +.|.++.+++..+.+..
T Consensus       723 ~s~~~~iQr~GR-GR~-~~g~vi~Li~~~t~ee~  754 (936)
T 4a2w_A          723 GNVTKMIQVRGR-GRA-AGSKCILVTSKTEVVEN  754 (936)
T ss_dssp             SCSHHHHCC---------CCCEEEEESCHHHHHH
T ss_pred             CCHHHHHHhcCC-CCC-CCCEEEEEEeCCCHHHH
Confidence            999999999999 998 78999999988765543

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=100.00  E-value=1.6e-43  Score=346.34  Aligned_cols=322  Identities=20%  Similarity=0.248  Sum_probs=252.8

Q ss_pred             HhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhcccc
Q 017573           12 YAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYL   91 (369)
Q Consensus        12 ~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~   91 (369)
                      ..+|| +|+++|.++++.+.++++++++||||+|||++++.+++..+..+   ++++|++|+++|+.|+.+.+.++. ..
T Consensus        73 ~~~gf-~pt~iQ~~ai~~il~g~dvlv~ApTGSGKTl~~l~~il~~~~~~---~~~Lil~PtreLa~Q~~~~l~~l~-~~  147 (1104)
T 4ddu_A           73 KKFGK-DLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLARKG---KKSALVFPTVTLVKQTLERLQKLA-DE  147 (1104)
T ss_dssp             HHSSS-CCCHHHHHHHHHHTTTCCEEECCSTTCCHHHHHHHHHHHHHTTT---CCEEEEESSHHHHHHHHHHHHTTS-CT
T ss_pred             HhcCC-CCCHHHHHHHHHHHcCCCEEEEeCCCCcHHHHHHHHHHHHHhcC---CeEEEEechHHHHHHHHHHHHHhh-CC
Confidence            34787 79999999999999999999999999999998888877776433   389999999999999999999977 66


Q ss_pred             CcEEEEEECCcch---HHHHHHHc-cCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhc-----------cCcH
Q 017573           92 GVKVHACVGGTSV---REDQRILQ-AGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLS-----------RGFK  156 (369)
Q Consensus        92 ~~~v~~~~~~~~~---~~~~~~~~-~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~-----------~~~~  156 (369)
                      ++++..++|+...   ......+. +.++|+|+||+.+.+++..  +...+++++|+||+|.+..           .++.
T Consensus       148 ~i~v~~l~Gg~~~~er~~~~~~l~~g~~~IlV~Tp~rL~~~l~~--l~~~~l~~lViDEaH~l~~~~r~~Dr~L~~~gf~  225 (1104)
T 4ddu_A          148 KVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREK--LSQKRFDFVFVDDVDAVLKASRNIDTLLMMVGIP  225 (1104)
T ss_dssp             TSCEEEECTTCCTTHHHHHHHHHHTSCCSEEEEEHHHHHHSHHH--HHTSCCSEEEESCHHHHTTSSHHHHHHHHTSSCC
T ss_pred             CCeEEEEeCCCCHHHHHHHHHHHhCCCCCEEEECHHHHHHHHHh--hcccCcCEEEEeCCCccccccccchhhhHhcCCC
Confidence            8899999998876   33333333 4589999999999877664  4556789999999997654           5555


Q ss_pred             HH-HHHHHhhCC-----------ccCcEEEEEeeCCh-hHH-HHHHHhcCCCEEEEecCccccccceeEEEEEccchhhh
Q 017573          157 DQ-IYDIFQLLP-----------AKVQVGVFSATMPP-EAL-EITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWK  222 (369)
Q Consensus       157 ~~-~~~~~~~~~-----------~~~~~i~~saT~~~-~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  222 (369)
                      .. +..++..++           +..|++++|||+.+ ... ......+.    +...........+.+.+....    +
T Consensus       226 ~~~i~~il~~l~~~~~~~~~~~~~~~q~ll~SAT~~p~~~~~~~~~~~l~----i~v~~~~~~~~~i~~~~~~~~----k  297 (1104)
T 4ddu_A          226 EEIIRKAFSTIKQGKIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLLN----FTVGRLVSVARNITHVRISSR----S  297 (1104)
T ss_dssp             HHHHHHHHHHHHHTSCCCCCSSCCCCEEEEECBSSCCCSSTTHHHHHHTC----CCCCBCCCCCCCEEEEEESCC----C
T ss_pred             HHHHHHHHHhcccchhhhhhccCCCceEEEEcCCCCcHHHHHHHhhccee----EEeccCCCCcCCceeEEEecC----H
Confidence            56 777777766           78899999999533 322 22333332    222333344555666665542    4


Q ss_pred             HHHHHHHHHhccCCCeEEEeCCHhhHHHHHHHHhhCCCeeE-EecCCCCHHHHHHHHHHHhcCCCcEEEE----ecCCcC
Q 017573          223 LETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVS-ATHGDMDQNTRDIIMREFRSGSSRVLIT----TDLLAR  297 (369)
Q Consensus       223 ~~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~-~~~~~~~~~~r~~~~~~f~~~~~~vli~----t~~~~~  297 (369)
                      ...+..++... ++++||||++++.++.+++.|...+..+. .+||+     |.+ ++.|++|+.+|||+    |+++++
T Consensus       298 ~~~L~~ll~~~-~~~~LVF~~s~~~a~~l~~~L~~~g~~~~~~lhg~-----rr~-l~~F~~G~~~VLVatas~Tdvlar  370 (1104)
T 4ddu_A          298 KEKLVELLEIF-RDGILIFAQTEEEGKELYEYLKRFKFNVGETWSEF-----EKN-FEDFKVGKINILIGVQAYYGKLTR  370 (1104)
T ss_dssp             HHHHHHHHHHH-CSSEEEEESSSHHHHHHHHHHHHTTCCEEESSSSH-----HHH-HHHHHHTSCSEEEEETTTHHHHCC
T ss_pred             HHHHHHHHHhc-CCCEEEEECcHHHHHHHHHHHHhCCCCeeeEecCc-----HHH-HHHHHCCCCCEEEEecCCCCeeEe
Confidence            45556666653 48999999999999999999999999998 99982     555 99999999999999    999999


Q ss_pred             CCCCCC-CcEEEEecCCC--------------------------------------------------------------
Q 017573          298 GIDVQQ-VSLVINYDLPT--------------------------------------------------------------  314 (369)
Q Consensus       298 G~d~~~-~~~vi~~~~~~--------------------------------------------------------------  314 (369)
                      |+|+|+ +++||++++|.                                                              
T Consensus       371 GIDip~~V~~VI~~d~P~~~~Sle~~~~~~~~~~~l~~l~~~~~~~~~~~~~~~~e~~~~~l~~~~~~~~i~~~~~~l~~  450 (1104)
T 4ddu_A          371 GVDLPERIKYVIFWGTPSMRFSLELDKAPRFVLARVLKEMGLIKAQENPDVEELRKIAKEHLTQKEFVEKVKEMFRGVVV  450 (1104)
T ss_dssp             SCCCTTTCCEEEEESCCEEEEECSSSSCCHHHHHHHHHHHSSCSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHCCSSEE
T ss_pred             cCcCCCCCCEEEEECCCCCCCCcccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccHHHHHHHhhccceEEe
Confidence            999999 99999999998                                                              


Q ss_pred             ----------CccchhhhhcccccCCCce--eEEEEeccccHHHHHHHHHHhc
Q 017573          315 ----------QPENYLHRIGRSGRFGRKG--VAINFVTRDDERMLFDIQKFYN  355 (369)
Q Consensus       315 ----------~~~~~~Q~~GR~~R~~~~~--~~~~~~~~~~~~~~~~~~~~~~  355 (369)
                                +..+|+||+||+||.|..|  ..+.+...+|.+.++.+.+.++
T Consensus       451 ~~~~~~~~~pd~~tYihr~GRtgR~~~gg~~~Glsi~~~~d~~~~~~l~~~~~  503 (1104)
T 4ddu_A          451 KDEDLELIIPDVYTYIQASGRSSRILNGVLVKGVSVIFEEDEEIFESLKTRLL  503 (1104)
T ss_dssp             ETTTTEEEEECHHHHHHHHHTTCCEETTEECCEEEEEECCCHHHHHHHHHHHH
T ss_pred             cCCeeEEEecChhhhhcccCchhcccCCCcccceEEEEEecHHHHHHHHHHHh
Confidence                      6668999999999975432  3343444488888888888876

>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=100.00  E-value=9e-44  Score=339.97  Aligned_cols=323  Identities=17%  Similarity=0.235  Sum_probs=220.7

Q ss_pred             CCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCC---CccEEEEcCCHHHHHHH-HHHHHHhccccC
Q 017573           17 EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLV---QCQALVLAPTRELAQQI-EKVMRALGDYLG   92 (369)
Q Consensus        17 ~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~---~~~~liv~P~~~l~~q~-~~~~~~~~~~~~   92 (369)
                      ..|+++|.++++.+.+++++++.+|||+|||++++++++..+..+..   ++++||++|+++|+.|| .+.+.++... +
T Consensus         6 ~~l~~~Q~~~i~~il~g~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~vlvl~P~~~L~~Q~~~~~l~~~~~~-~   84 (699)
T 4gl2_A            6 LQLRPYQMEVAQPALEGKNIIICLPTGCGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEFQPFLKK-W   84 (699)
T ss_dssp             -CCCHHHHHHHHHHHSSCCEEECCCTTSCHHHHHHHHHHHHHHHHHHHTCCCCBCCEESCSHHHHHHHHHTHHHHHTT-T
T ss_pred             CCccHHHHHHHHHHHhCCCEEEEcCCCCcHHHHHHHHHHHHHHhccccCCCCeEEEEECCHHHHHHHHHHHHHHHcCc-C
Confidence            48999999999999999999999999999999999999887765422   23899999999999999 9999998765 4


Q ss_pred             cEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHH------HcCCCCCCCccEEEEechhHhhccC-cHHHHHHHHhh
Q 017573           93 VKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDML------RRQSLRPDYIKMFVLDEADEMLSRG-FKDQIYDIFQL  165 (369)
Q Consensus        93 ~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~------~~~~~~~~~~~~viiDE~H~~~~~~-~~~~~~~~~~~  165 (369)
                      +++..++|+.............++|+|+||+.|...+      ....+....+++||+||||++.... +......+...
T Consensus        85 ~~v~~~~g~~~~~~~~~~~~~~~~Ilv~Tp~~L~~~l~~~~~~~~~~~~~~~~~lvViDEaH~~~~~~~~~~i~~~~l~~  164 (699)
T 4gl2_A           85 YRVIGLSGDTQLKISFPEVVKSCDIIISTAQILENSLLNLENGEDAGVQLSDFSLIIIDECHHTNKEAVYNNIMRHYLMQ  164 (699)
T ss_dssp             SCEEEEC----CCCCHHHHHHSCSEEEEEHHHHHHHTC--------CCCGGGCSEEEEESGGGCBTTBSSCSHHHHHHHH
T ss_pred             ceEEEEeCCcchhhHHHhhhcCCCEEEECHHHHHHHHhccccccccceecccCcEEEEECccccCccchHHHHHHHHHHh
Confidence            7888888887655444444567899999999999887      4445666779999999999875433 22222222211


Q ss_pred             -------------CCccCcEEEEEeeCChh-----------HHHHHHHhc------------------CCCEEEEecCcc
Q 017573          166 -------------LPAKVQVGVFSATMPPE-----------ALEITRKFM------------------NKPVRILVKRDE  203 (369)
Q Consensus       166 -------------~~~~~~~i~~saT~~~~-----------~~~~~~~~~------------------~~~~~~~~~~~~  203 (369)
                                   ..+..+++++||||...           ...+...+.                  ..|.........
T Consensus       165 ~~~~~~~~~~~~~~~~~~~il~lTATp~~~~~~~~~~~~~~i~~l~~~l~~~~i~~~~~~~~~l~~~~~~p~~~~~~~~~  244 (699)
T 4gl2_A          165 KLKNNRLKKENKPVIPLPQILGLTASPGVGGATKQAKAEEHILKLCANLDAFTIKTVKENLDQLKNQIQEPCKKFAIADA  244 (699)
T ss_dssp             HHHHHHHHC----CCCCCEEEEECSCCCCCSCCSHHHHHHHHHHHHHHHTCSCCCCCCTTHHHHHHHSCCCEEEEEEEC-
T ss_pred             hhcccccccccccCCCCCEEEEecccccccccccHHHHHHHHHHHHhhcCCCEEEeecCchHHHhhhcCCCceEEEEccc
Confidence                         11457899999999852           111111111                  111111100000


Q ss_pred             ccccc-----------------e---eE----------------------------------------------------
Q 017573          204 LTLEG-----------------I---KQ----------------------------------------------------  211 (369)
Q Consensus       204 ~~~~~-----------------~---~~----------------------------------------------------  211 (369)
                      .....                 +   ..                                                    
T Consensus       245 ~~~~~~~~~l~~l~~~i~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~  324 (699)
T 4gl2_A          245 TREDPFKEKLLEIMTRIQTYCQMSPMSDFGTQPYEQWAIQMEKKAAKEGNRKERVCAEHLRKYNEALQINDTIRMIDAYT  324 (699)
T ss_dssp             ----CHHHHHHHHHHHHHHHHTCCCCSCSSSHHHHHHHHHHHHHHHHHTCTTTHHHHHHHHHHHHHHHHHHHSCHHHHHH
T ss_pred             ccCChHHHHHHHHHHHHHHHhccCcchhccchHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            00000                 0   00                                                    


Q ss_pred             ----------------------EEEEccc-------------------------hhhhH----HHHHHHHHhcc-CCCeE
Q 017573          212 ----------------------FYVNVEK-------------------------EEWKL----ETLCDLYETLA-ITQSV  239 (369)
Q Consensus       212 ----------------------~~~~~~~-------------------------~~~~~----~~l~~~~~~~~-~~k~l  239 (369)
                                            .......                         ...+.    +.+...+...+ ++++|
T Consensus       325 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~~~~~~~~k~~~L~~~L~~~~~~~~~~~~~I  404 (699)
T 4gl2_A          325 HLETFYNEEKDKKFAVIEDDLKKPLKLDETDRFLMTLFFENNKMLKRLAENPEYENEKLTKLRNTIMEQYTRTEESARGI  404 (699)
T ss_dssp             HHHHHHHHHHHHHC------------CCHHHHHHHHHHHHHHHHHHHHHTCCC----CSSCSHHHHHHHHHHSSSCCCEE
T ss_pred             HHHHHHHHHHhhhccccccccccccccchhHHHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHhcCCCCCcEE
Confidence                                  0000000                         00011    11222222223 68999


Q ss_pred             EEeCCHhhHHHHHHHHhhC------CCeeEEecCC--------CCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCc
Q 017573          240 IFVNTRRKVDWLTDKMRSR------DHTVSATHGD--------MDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVS  305 (369)
Q Consensus       240 v~~~~~~~~~~~~~~l~~~------~~~~~~~~~~--------~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~  305 (369)
                      |||++++.++.+++.|...      +.++..+||+        ++..+|.++++.|++|+.+|||||+++++|+|+|+++
T Consensus       405 VF~~s~~~~~~l~~~L~~~~~l~~~g~~~~~lhg~~~~~~~~~~~~~eR~~~~~~F~~g~~~VLVaT~~~~~GIDip~v~  484 (699)
T 4gl2_A          405 IFTKTRQSAYALSQWITENEKFAEVGVKAHHLIGAGHSSEFKPMTQNEQKEVISKFRTGKINLLIATTVAEEGLDIKECN  484 (699)
T ss_dssp             EECSCHHHHHHHHHHHHSSCSCC-----CEECCCSCCCTTCCCCCHHHHHHHHHHHCC---CCSEEECSCCTTSCCCSCC
T ss_pred             EEECcHHHHHHHHHHHHhCccccccCcceEEEECCCCccCCCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCccccCC
Confidence            9999999999999999987      8999999999        9999999999999999999999999999999999999


Q ss_pred             EEEEecCCCCccchhhhhcccccCCCceeEEEEeccc
Q 017573          306 LVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRD  342 (369)
Q Consensus       306 ~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~  342 (369)
                      +||++++|+|+..|.|++||+||.|  +.++++....
T Consensus       485 ~VI~~d~p~s~~~~~Qr~GRArr~g--~~~~l~~~~~  519 (699)
T 4gl2_A          485 IVIRYGLVTNEIAMVQARGRARADE--STYVLVAHSG  519 (699)
T ss_dssp             CCEEESCCCCHHHHHHHHTTSCSSS--CEEEEEEESS
T ss_pred             EEEEeCCCCCHHHHHHHcCCCCCCC--ceEEEEEeCC
Confidence            9999999999999999999987654  4444444433

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=100.00  E-value=1.9e-42  Score=336.20  Aligned_cols=321  Identities=17%  Similarity=0.243  Sum_probs=247.5

Q ss_pred             hCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccC
Q 017573           13 AYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLG   92 (369)
Q Consensus        13 ~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~   92 (369)
                      .++| +|+++|.++++.+.+++++++.+|||+|||+++++++...+..+.   +++|++|+++|+.|+++.+.++..  +
T Consensus        35 ~~~f-~l~~~Q~~aI~~il~g~~vlv~apTGsGKTlv~~~~i~~~~~~g~---~vlvl~PtraLa~Q~~~~l~~~~~--~  108 (997)
T 4a4z_A           35 SWPF-ELDTFQKEAVYHLEQGDSVFVAAHTSAGKTVVAEYAIAMAHRNMT---KTIYTSPIKALSNQKFRDFKETFD--D  108 (997)
T ss_dssp             CCSS-CCCHHHHHHHHHHHTTCEEEEECCTTSCSHHHHHHHHHHHHHTTC---EEEEEESCGGGHHHHHHHHHTTC----
T ss_pred             hCCC-CCCHHHHHHHHHHHcCCCEEEEECCCCcHHHHHHHHHHHHHhcCC---eEEEEeCCHHHHHHHHHHHHHHcC--C
Confidence            3566 699999999999999999999999999999998888887665443   899999999999999999998654  5


Q ss_pred             cEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCccCcE
Q 017573           93 VKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQV  172 (369)
Q Consensus        93 ~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~  172 (369)
                      .++..++|+...       ..+++|+|+||+.|...+.........+++||+||+|.+.++++...+..++..+++..++
T Consensus       109 ~~v~~l~G~~~~-------~~~~~IlV~Tpe~L~~~l~~~~~~l~~l~lvViDEaH~l~d~~~g~~~e~ii~~l~~~v~i  181 (997)
T 4a4z_A          109 VNIGLITGDVQI-------NPDANCLIMTTEILRSMLYRGADLIRDVEFVIFDEVHYVNDQDRGVVWEEVIIMLPQHVKF  181 (997)
T ss_dssp             CCEEEECSSCEE-------CTTSSEEEEEHHHHHHHHHHTCSGGGGEEEEEECCTTCCCTTCTTCCHHHHHHHSCTTCEE
T ss_pred             CeEEEEeCCCcc-------CCCCCEEEECHHHHHHHHHhCchhhcCCCEEEEECcccccccchHHHHHHHHHhcccCCCE
Confidence            677888887652       2457999999999999888877777889999999999998888888888899999999999


Q ss_pred             EEEEeeCChhHHHHHHHhc---CCCEEEEecCccccccceeEEE------------------------------------
Q 017573          173 GVFSATMPPEALEITRKFM---NKPVRILVKRDELTLEGIKQFY------------------------------------  213 (369)
Q Consensus       173 i~~saT~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~------------------------------------  213 (369)
                      +++|||++.. .++..++.   ..+..+......  +..+...+                                    
T Consensus       182 IlLSAT~~n~-~ef~~~l~~~~~~~~~vi~~~~r--~~pl~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  258 (997)
T 4a4z_A          182 ILLSATVPNT-YEFANWIGRTKQKNIYVISTPKR--PVPLEINIWAKKELIPVINQNSEFLEANFRKHKEILNGESAKGA  258 (997)
T ss_dssp             EEEECCCTTH-HHHHHHHHHHHTCCEEEEECSSC--SSCEEEEEEETTEEEEEECTTCCBCHHHHHHHHHHHC-------
T ss_pred             EEEcCCCCCh-HHHHHHHhcccCCceEEEecCCC--CccceEEEecCCcchhcccchhhhhHHHHHHHHHHhhccccccc
Confidence            9999998643 23333322   122221111100  00011000                                    


Q ss_pred             --------------------------------------------------------EEccchhhhHHHHHHHHHhccCCC
Q 017573          214 --------------------------------------------------------VNVEKEEWKLETLCDLYETLAITQ  237 (369)
Q Consensus       214 --------------------------------------------------------~~~~~~~~~~~~l~~~~~~~~~~k  237 (369)
                                                                              ............+...+......+
T Consensus       259 ~~~~~~~~~~~~~~~~~~~~~~rg~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~~l~~~~~~~  338 (997)
T 4a4z_A          259 PSKTDNGRGGSTARGGRGGSNTRDGRGGRGNSTRGGANRGGSRGAGAIGSNKRKFFTQDGPSKKTWPEIVNYLRKRELLP  338 (997)
T ss_dssp             ----------------------------------------------------------CCCCTTHHHHHHHHHHHTTCCS
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccchhHHHHHHHHHHhCCCCC
Confidence                                                                    000112233556666677667789


Q ss_pred             eEEEeCCHhhHHHHHHHHhhCCC---------------------------------------eeEEecCCCCHHHHHHHH
Q 017573          238 SVIFVNTRRKVDWLTDKMRSRDH---------------------------------------TVSATHGDMDQNTRDIIM  278 (369)
Q Consensus       238 ~lv~~~~~~~~~~~~~~l~~~~~---------------------------------------~~~~~~~~~~~~~r~~~~  278 (369)
                      +||||++++.++.++..|...+.                                       .+..+||++++.+|..++
T Consensus       339 ~IVF~~sr~~~e~la~~L~~~~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~gi~~~H~gl~~~~R~~v~  418 (997)
T 4a4z_A          339 MVVFVFSKKRCEEYADWLEGINFCNNKEKSQIHMFIEKSITRLKKEDRDLPQILKTRSLLERGIAVHHGGLLPIVKELIE  418 (997)
T ss_dssp             EEEECSCHHHHHHHHHTTTTCCCCCHHHHHHHHHHHHHHHTTSCHHHHTCHHHHHHHHHHTTTEEEECTTSCHHHHHHHH
T ss_pred             EEEEECCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHhcchhhhcchhHHHHHHHhhcCeeeecCCCCHHHHHHHH
Confidence            99999999999999999977554                                       578999999999999999


Q ss_pred             HHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCCC---------CccchhhhhcccccCC--CceeEEEEec--cccHH
Q 017573          279 REFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPT---------QPENYLHRIGRSGRFG--RKGVAINFVT--RDDER  345 (369)
Q Consensus       279 ~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~---------~~~~~~Q~~GR~~R~~--~~~~~~~~~~--~~~~~  345 (369)
                      +.|.+|..+|||||+++++|+|+|+ ..||+.+.++         |..+|.|++||+||.|  ..|.+++++.  ..+..
T Consensus       419 ~~F~~G~~kVLvAT~~~a~GIDiP~-~~VVi~~~~k~dg~~~~~~s~~~y~Qr~GRAGR~G~~~~G~vi~l~~~~~~~~~  497 (997)
T 4a4z_A          419 ILFSKGFIKVLFATETFAMGLNLPT-RTVIFSSIRKHDGNGLRELTPGEFTQMAGRAGRRGLDSTGTVIVMAYNSPLSIA  497 (997)
T ss_dssp             HHHHTTCCSEEEECTHHHHSCCCCC-SEEEESCSEEEETTEEEECCHHHHHHHHGGGCCTTTCSSEEEEEECCSSCCCHH
T ss_pred             HHHHCCCCcEEEEchHhhCCCCCCC-ceEEEeccccccCccCCCCCHHHHhHHhcccccCCCCcceEEEEecCCCcchHH
Confidence            9999999999999999999999999 6666655554         8999999999999998  5578888873  34555


Q ss_pred             HHHHH
Q 017573          346 MLFDI  350 (369)
Q Consensus       346 ~~~~~  350 (369)
                      .++.+
T Consensus       498 ~~~~~  502 (997)
T 4a4z_A          498 TFKEV  502 (997)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            55444

>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=100.00  E-value=6.8e-42  Score=336.99  Aligned_cols=321  Identities=18%  Similarity=0.206  Sum_probs=248.2

Q ss_pred             CCCHHHHHHH-HhCCCCCCcHhhhhhhhcccc----CC--cEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCH
Q 017573            2 GLQENLLRGI-YAYGFEKPSAIQQRGIVPFCK----GL--DVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTR   74 (369)
Q Consensus         2 ~l~~~i~~~l-~~~~~~~~~~~Q~~~~~~~~~----~~--~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~   74 (369)
                      +.++...+.+ ..++| +++|+|.++++.+.+    ++  ++++++|||+|||.+++.+++..+..+.   +++|++|++
T Consensus       587 ~~~~~~~~~~~~~f~~-~~t~~Q~~ai~~il~~~~~g~p~d~ll~~~TGsGKT~val~aa~~~~~~g~---~vlvlvPt~  662 (1151)
T 2eyq_A          587 KHDREQYQLFCDSFPF-ETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDNHK---QVAVLVPTT  662 (1151)
T ss_dssp             CCCHHHHHHHHHTCCS-CCCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHTTTC---EEEEECSSH
T ss_pred             CCCHHHHHHHHHhCCC-CCCHHHHHHHHHHHHHHhcCCcCcEEEECCCCCCHHHHHHHHHHHHHHhCC---eEEEEechH
Confidence            4556666666 56888 579999999999886    55  8999999999999999888877665443   899999999


Q ss_pred             HHHHHHHHHHHHhccccCcEEEEEECCcchHHHHH----HHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHh
Q 017573           75 ELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQR----ILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEM  150 (369)
Q Consensus        75 ~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~----~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~  150 (369)
                      +|+.|+.+.+.+.....+.++..+.+.........    ...+.++|+|+|++.+.     ......+++++|+||+|++
T Consensus       663 ~La~Q~~~~~~~~~~~~~i~v~~l~~~~~~~~~~~~~~~l~~g~~dIvV~T~~ll~-----~~~~~~~l~lvIiDEaH~~  737 (1151)
T 2eyq_A          663 LLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQ-----SDVKFKDLGLLIVDEEHRF  737 (1151)
T ss_dssp             HHHHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHH-----SCCCCSSEEEEEEESGGGS
T ss_pred             HHHHHHHHHHHHHhhcCCCeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHh-----CCccccccceEEEechHhc
Confidence            99999999999888777888888887665444332    22346899999997663     3456678999999999995


Q ss_pred             hccCcHHHHHHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHH
Q 017573          151 LSRGFKDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLY  230 (369)
Q Consensus       151 ~~~~~~~~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~  230 (369)
                      .     ......+..++...++++|||||.+.........+.....+  .........+..++......    .....++
T Consensus       738 g-----~~~~~~l~~l~~~~~vl~lSATp~p~~l~~~~~~~~~~~~i--~~~~~~r~~i~~~~~~~~~~----~i~~~il  806 (1151)
T 2eyq_A          738 G-----VRHKERIKAMRANVDILTLTATPIPRTLNMAMSGMRDLSII--ATPPARRLAVKTFVREYDSM----VVREAIL  806 (1151)
T ss_dssp             C-----HHHHHHHHHHHTTSEEEEEESSCCCHHHHHHHTTTSEEEEC--CCCCCBCBCEEEEEEECCHH----HHHHHHH
T ss_pred             C-----hHHHHHHHHhcCCCCEEEEcCCCChhhHHHHHhcCCCceEE--ecCCCCccccEEEEecCCHH----HHHHHHH
Confidence            3     22334445555678899999999877666555544333222  11222222334433333221    1222222


Q ss_pred             Hh-ccCCCeEEEeCCHhhHHHHHHHHhhC--CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEE
Q 017573          231 ET-LAITQSVIFVNTRRKVDWLTDKMRSR--DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLV  307 (369)
Q Consensus       231 ~~-~~~~k~lv~~~~~~~~~~~~~~l~~~--~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~v  307 (369)
                      .. ..+++++|||++++.++.+++.|++.  +..+..+||+++..+|.++++.|.+|+.+|||||+++++|+|+|++++|
T Consensus       807 ~~l~~g~qvlvf~~~v~~~~~l~~~L~~~~p~~~v~~lhg~~~~~eR~~il~~F~~g~~~VLVaT~v~e~GiDip~v~~V  886 (1151)
T 2eyq_A          807 REILRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTI  886 (1151)
T ss_dssp             HHHTTTCEEEEECCCSSCHHHHHHHHHHHCTTSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESSTTGGGSCCTTEEEE
T ss_pred             HHHhcCCeEEEEECCHHHHHHHHHHHHHhCCCCeEEEEeCCCCHHHHHHHHHHHHcCCCcEEEECCcceeeecccCCcEE
Confidence            22 24579999999999999999999887  7789999999999999999999999999999999999999999999999


Q ss_pred             EEecC-CCCccchhhhhcccccCCCceeEEEEeccc
Q 017573          308 INYDL-PTQPENYLHRIGRSGRFGRKGVAINFVTRD  342 (369)
Q Consensus       308 i~~~~-~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~  342 (369)
                      |+.+. +++...+.|++||+||.|+.|.|++++++.
T Consensus       887 Ii~~~~~~~l~~l~Qr~GRvgR~g~~g~~~ll~~~~  922 (1151)
T 2eyq_A          887 IIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHP  922 (1151)
T ss_dssp             EETTTTSSCHHHHHHHHTTCCBTTBCEEEEEEECCG
T ss_pred             EEeCCCCCCHHHHHHHHhccCcCCCceEEEEEECCc
Confidence            99887 578899999999999999999999998764

>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=100.00  E-value=2.8e-43  Score=331.82  Aligned_cols=325  Identities=18%  Similarity=0.251  Sum_probs=240.3

Q ss_pred             HHHHHHHHhCCCCCCcHhhhhhhhccccC------CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHH
Q 017573            5 ENLLRGIYAYGFEKPSAIQQRGIVPFCKG------LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQ   78 (369)
Q Consensus         5 ~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~------~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~   78 (369)
                      +.+.+.++.++| +|+++|+++++.+.++      .++++++|||+|||.+++++++..+..+.   +++|++|+++|+.
T Consensus       356 ~~~~~~~~~lpf-~lt~~Q~~ai~~I~~~l~~~~~~~~Ll~a~TGSGKTlvall~il~~l~~g~---qvlvlaPtr~La~  431 (780)
T 1gm5_A          356 KLAEEFIKSLPF-KLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEAGF---QTAFMVPTSILAI  431 (780)
T ss_dssp             HHHHHHHHHSSS-CCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHHTS---CEEEECSCHHHHH
T ss_pred             HHHHHHHHhCCC-CCCHHHHHHHHHHHhhccccCCCcEEEEcCCCCCHHHHHHHHHHHHHHcCC---eEEEEeCcHHHHH
Confidence            345556688999 9999999999998865      58999999999999999999998877654   8999999999999


Q ss_pred             HHHHHHHHhccccCcEEEEEECCcchHHHHH----HHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccC
Q 017573           79 QIEKVMRALGDYLGVKVHACVGGTSVREDQR----ILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRG  154 (369)
Q Consensus        79 q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~----~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~  154 (369)
                      |+.+.+.++....++++..++|+........    ...+.++|+|+||+.+..     .....+++++|+||+|++....
T Consensus       432 Q~~~~l~~~~~~~gi~v~~l~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~-----~~~~~~l~lVVIDEaHr~g~~q  506 (780)
T 1gm5_A          432 QHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQE-----DVHFKNLGLVIIDEQHRFGVKQ  506 (780)
T ss_dssp             HHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHH-----CCCCSCCCEEEEESCCCC----
T ss_pred             HHHHHHHHHhhhcCceEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhh-----hhhccCCceEEecccchhhHHH
Confidence            9999999998888899999999887655432    233568999999987743     3456778999999999863221


Q ss_pred             cHHHHHHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCC-CEEEEecCccccccceeEEEEEccchhhhHHHHHHHHH-h
Q 017573          155 FKDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNK-PVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYE-T  232 (369)
Q Consensus       155 ~~~~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~-~  232 (369)
                           ...+.......++++|||||.+.......  +.. ...... ........+...+.   ... ....+...+. .
T Consensus       507 -----r~~l~~~~~~~~vL~mSATp~p~tl~~~~--~g~~~~s~i~-~~p~~r~~i~~~~~---~~~-~~~~l~~~i~~~  574 (780)
T 1gm5_A          507 -----REALMNKGKMVDTLVMSATPIPRSMALAF--YGDLDVTVID-EMPPGRKEVQTMLV---PMD-RVNEVYEFVRQE  574 (780)
T ss_dssp             ------CCCCSSSSCCCEEEEESSCCCHHHHHHH--TCCSSCEEEC-CCCSSCCCCEECCC---CSS-THHHHHHHHHHH
T ss_pred             -----HHHHHHhCCCCCEEEEeCCCCHHHHHHHH--hCCcceeeee-ccCCCCcceEEEEe---ccc-hHHHHHHHHHHH
Confidence                 11122223468899999999776544332  222 112111 11111112222111   111 2222333332 2


Q ss_pred             c-cCCCeEEEeCCHh--------hHHHHHHHHhh---CCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCC
Q 017573          233 L-AITQSVIFVNTRR--------KVDWLTDKMRS---RDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID  300 (369)
Q Consensus       233 ~-~~~k~lv~~~~~~--------~~~~~~~~l~~---~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d  300 (369)
                      . .+++++|||+..+        .++.+++.|.+   .+..+..+||+++.++|.++++.|++|+.+|||||+++++|+|
T Consensus       575 l~~g~qvlVf~~~ie~se~l~~~~a~~l~~~L~~~~~~~~~v~~lHG~m~~~eR~~v~~~F~~G~~~ILVaT~vie~GID  654 (780)
T 1gm5_A          575 VMRGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDILVSTTVIEVGID  654 (780)
T ss_dssp             TTTSCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHHHHHTTTSSSBCCCSSCCCSCSC
T ss_pred             HhcCCcEEEEecchhhhhhhhHHHHHHHHHHHHhhhcCCCcEEEEeCCCCHHHHHHHHHHHHCCCCeEEEECCCCCcccc
Confidence            2 4568999999654        47788888887   4678999999999999999999999999999999999999999


Q ss_pred             CCCCcEEEEecCCC-CccchhhhhcccccCCCceeEEEEeccccHHHHHHH
Q 017573          301 VQQVSLVINYDLPT-QPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDI  350 (369)
Q Consensus       301 ~~~~~~vi~~~~~~-~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~  350 (369)
                      +|++++||+++++. +...+.|++||+||.|+.|.|++++++.+....+.+
T Consensus       655 iP~v~~VIi~d~~r~~l~~l~Qr~GRaGR~g~~g~~ill~~~~~~~~~~rl  705 (780)
T 1gm5_A          655 VPRANVMVIENPERFGLAQLHQLRGRVGRGGQEAYCFLVVGDVGEEAMERL  705 (780)
T ss_dssp             CTTCCEEEBCSCSSSCTTHHHHHHHTSCCSSTTCEEECCCCSCCHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCHHHHHHHhcccCcCCCCCEEEEEECCCChHHHHHH
Confidence            99999999999985 678899999999999999999999985444443333

>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=100.00  E-value=5.2e-43  Score=343.09  Aligned_cols=321  Identities=19%  Similarity=0.271  Sum_probs=250.1

Q ss_pred             HhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhcccc
Q 017573           12 YAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYL   91 (369)
Q Consensus        12 ~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~   91 (369)
                      +.+||. | ++|.++++.+.+++++++++|||+|||+ +.++++..+..  .+++++|++|+++|+.|+.+.++++....
T Consensus        52 ~~~g~~-p-~iQ~~ai~~il~g~dvlv~apTGSGKTl-~~lp~l~~~~~--~~~~~lil~PtreLa~Q~~~~l~~l~~~~  126 (1054)
T 1gku_B           52 KCVGEP-R-AIQKMWAKRILRKESFAATAPTGVGKTS-FGLAMSLFLAL--KGKRCYVIFPTSLLVIQAAETIRKYAEKA  126 (1054)
T ss_dssp             TTTCSC-C-HHHHHHHHHHHTTCCEECCCCBTSCSHH-HHHHHHHHHHT--TSCCEEEEESCHHHHHHHHHHHHHHHTTT
T ss_pred             HhcCCC-H-HHHHHHHHHHHhCCCEEEEcCCCCCHHH-HHHHHHHHHhh--cCCeEEEEeccHHHHHHHHHHHHHHHhhc
Confidence            458998 9 9999999999999999999999999998 55666655543  23489999999999999999999998877


Q ss_pred             Cc----EEEEEECCcchHHH---HHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHh
Q 017573           92 GV----KVHACVGGTSVRED---QRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQ  164 (369)
Q Consensus        92 ~~----~v~~~~~~~~~~~~---~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~  164 (369)
                      ++    .+..++|+......   ...+.+ ++|+|+||+.|..++.+    +..++++|+||+|++.+  +...+..++.
T Consensus       127 ~i~~~~~v~~~~Gg~~~~~~~~~~~~l~~-~~IlV~TP~~L~~~l~~----L~~l~~lViDEah~~l~--~~~~~~~i~~  199 (1054)
T 1gku_B          127 GVGTENLIGYYHGRIPKREKENFMQNLRN-FKIVITTTQFLSKHYRE----LGHFDFIFVDDVDAILK--ASKNVDKLLH  199 (1054)
T ss_dssp             CCSGGGSEEECCSSCCSHHHHHHHHSGGG-CSEEEEEHHHHHHCSTT----SCCCSEEEESCHHHHHT--STHHHHHHHH
T ss_pred             CCCccceEEEEeCCCChhhHHHHHhhccC-CCEEEEcHHHHHHHHHH----hccCCEEEEeChhhhhh--ccccHHHHHH
Confidence            77    88888988876553   233344 89999999999987665    44789999999999987  4566777766


Q ss_pred             hC-----------CccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHHHhc
Q 017573          165 LL-----------PAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETL  233 (369)
Q Consensus       165 ~~-----------~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  233 (369)
                      .+           +...|++++|||++.. ......++..+..+...........+.+.+..    ..+...+..++...
T Consensus       200 ~lgf~~~~~~~~~~~~~q~~l~SAT~t~~-~~~~~~~~~~~~~i~v~~~~~~~~~i~~~~~~----~~k~~~L~~ll~~~  274 (1054)
T 1gku_B          200 LLGFHYDLKTKSWVGEARGCLMVSTATAK-KGKKAELFRQLLNFDIGSSRITVRNVEDVAVN----DESISTLSSILEKL  274 (1054)
T ss_dssp             HTTEEEETTTTEEEECCSSEEEECCCCSC-CCTTHHHHHHHHCCCCSCCEECCCCEEEEEES----CCCTTTTHHHHTTS
T ss_pred             HhCcchhhhhhhcccCCceEEEEecCCCc-hhHHHHHhhcceEEEccCcccCcCCceEEEec----hhHHHHHHHHHhhc
Confidence            66           3467889999999876 42222232222222223333334455555552    23445556666654


Q ss_pred             cCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEE----ecCCcCCCCCCCC-cEEE
Q 017573          234 AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLIT----TDLLARGIDVQQV-SLVI  308 (369)
Q Consensus       234 ~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~----t~~~~~G~d~~~~-~~vi  308 (369)
                       ++++||||++++.++.+++.|+.. ..+..+||++     .++++.|++|+.+||||    |+++++|+|+|++ ++||
T Consensus       275 -~~~~LVF~~t~~~a~~l~~~L~~~-~~v~~lhg~~-----~~~l~~F~~G~~~VLVaTas~Tdv~~rGIDip~VI~~VI  347 (1054)
T 1gku_B          275 -GTGGIIYARTGEEAEEIYESLKNK-FRIGIVTATK-----KGDYEKFVEGEIDHLIGTAHYYGTLVRGLDLPERIRFAV  347 (1054)
T ss_dssp             -CSCEEEEESSHHHHHHHHHTTTTS-SCEEECTTSS-----SHHHHHHHHTSCSEEEEECC------CCSCCTTTCCEEE
T ss_pred             -CCCEEEEEcCHHHHHHHHHHHhhc-cCeeEEeccH-----HHHHHHHHcCCCcEEEEecCCCCeeEeccccCCcccEEE
Confidence             478999999999999999999988 8999999997     47889999999999999    8999999999995 9999


Q ss_pred             EecCC-----------------------------------------------------------------------CCcc
Q 017573          309 NYDLP-----------------------------------------------------------------------TQPE  317 (369)
Q Consensus       309 ~~~~~-----------------------------------------------------------------------~~~~  317 (369)
                      +++.|                                                                       .+..
T Consensus       348 ~~~~P~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~  427 (1054)
T 1gku_B          348 FVGCPSFRVTIEDIDSLSPQMVKLLAYLYRNVDEIERLLPAVERHIDEVREILKKVMGKERPQAKDVVVREGEVIFPDLR  427 (1054)
T ss_dssp             EESCCEEEEECSCGGGSCHHHHHHHHTTTSCHHHHHTTCTTTSSCHHHHHHHHHHHHTTSCCSCSSSEEETTEEEEECHH
T ss_pred             EeCCCcccccccccccChHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHhccccccccceeEeecceecCcHH
Confidence            99999                                                                       6889


Q ss_pred             chhhhhcccccCCCce--eEEEEeccccHHHHHHHHHHhcc
Q 017573          318 NYLHRIGRSGRFGRKG--VAINFVTRDDERMLFDIQKFYNV  356 (369)
Q Consensus       318 ~~~Q~~GR~~R~~~~~--~~~~~~~~~~~~~~~~~~~~~~~  356 (369)
                      +|.|++||+||.|+.|  .+++++...+.+.++.+.+.++.
T Consensus       428 ~yiQr~GRagR~g~~g~~~g~~~~~~~d~~~~~~l~~~l~~  468 (1054)
T 1gku_B          428 TYIQGSGRTSRLFAGGLTKGASFLLEDDSELLSAFIERAKL  468 (1054)
T ss_dssp             HHHHHHHTTCCEETTEECCEEEEEECSCHHHHHHHHHHHHT
T ss_pred             HHhhhhchhhhccCCCCceEEEEEEecCHHHHHHHHHHHhh
Confidence            9999999999987775  48888888899999989888874

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=100.00  E-value=1.2e-42  Score=320.33  Aligned_cols=311  Identities=16%  Similarity=0.138  Sum_probs=230.2

Q ss_pred             CCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEE
Q 017573           17 EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVH   96 (369)
Q Consensus        17 ~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~   96 (369)
                      .+|+++|.++++.+.+++++++++|||+|||.+++.++...+..+.  +++||++|+++|+.||.+.+.++....+..+.
T Consensus       112 ~~l~~~Q~~ai~~~~~~~~~ll~~~tGsGKT~~~~~~~~~~~~~~~--~~vlvl~P~~~L~~Q~~~~~~~~~~~~~~~v~  189 (510)
T 2oca_A          112 IEPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENYE--GKILIIVPTTALTTQMADDFVDYRLFSHAMIK  189 (510)
T ss_dssp             ECCCHHHHHHHHHHHHHSEEEEECCSTTTHHHHHHHHHHHHHHHCS--SEEEEEESSHHHHHHHHHHHHHTTSSCGGGEE
T ss_pred             CCCCHHHHHHHHHHHhcCCcEEEeCCCCCHHHHHHHHHHHHHhCCC--CeEEEEECcHHHHHHHHHHHHHhhcCCccceE
Confidence            3899999999999999999999999999999999888887765432  28999999999999999999998665556777


Q ss_pred             EEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEE
Q 017573           97 ACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFS  176 (369)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~s  176 (369)
                      .+.++......   .....+|+|+|++.+...   .......+++||+||+|++..    ..+..++..+++..+++++|
T Consensus       190 ~~~~~~~~~~~---~~~~~~I~i~T~~~l~~~---~~~~~~~~~liIiDE~H~~~~----~~~~~il~~~~~~~~~l~lS  259 (510)
T 2oca_A          190 KIGGGASKDDK---YKNDAPVVVGTWQTVVKQ---PKEWFSQFGMMMNDECHLATG----KSISSIISGLNNCMFKFGLS  259 (510)
T ss_dssp             ECGGGCCTTGG---GCTTCSEEEEEHHHHTTS---CGGGGGGEEEEEEETGGGCCH----HHHHHHGGGCTTCCEEEEEE
T ss_pred             EEecCCccccc---cccCCcEEEEeHHHHhhc---hhhhhhcCCEEEEECCcCCCc----ccHHHHHHhcccCcEEEEEE
Confidence            77777654433   346689999999976542   223445689999999999754    45667777887788999999


Q ss_pred             eeCChhHHHHH--HHhcCCCEEEEecCc------cccccceeEEEEEccch--------------------hhhHHHHHH
Q 017573          177 ATMPPEALEIT--RKFMNKPVRILVKRD------ELTLEGIKQFYVNVEKE--------------------EWKLETLCD  228 (369)
Q Consensus       177 aT~~~~~~~~~--~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~--------------------~~~~~~l~~  228 (369)
                      |||+.......  ..++. +..+.....      ...+..........+..                    ..+...+.+
T Consensus       260 ATp~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  338 (510)
T 2oca_A          260 GSLRDGKANIMQYVGMFG-EIFKPVTTSKLMEDGQVTELKINSIFLRYPDEFTTKLKGKTYQEEIKIITGLSKRNKWIAK  338 (510)
T ss_dssp             SCGGGCSSCHHHHHHHHC-SEECCCCCC---------CCEEEEEEEECCHHHHHHHTTCCHHHHHHHHHTCHHHHHHHHH
T ss_pred             eCCCCCcccHHHhHHhhC-CeEEeeCHHHHhhCCcCCCceEEEEeecCChHHhccccccchHHHHHHHhccHHHHHHHHH
Confidence            99965432211  12222 222111111      11111122222222111                    112233444


Q ss_pred             HHHhc--cCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEe-cCCcCCCCCCCCc
Q 017573          229 LYETL--AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITT-DLLARGIDVQQVS  305 (369)
Q Consensus       229 ~~~~~--~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t-~~~~~G~d~~~~~  305 (369)
                      ++...  .+++.+|++.+.++++.+++.|.+.+.++..+||+++..+|.++++.|.+|+.+|||+| +++++|+|+|.++
T Consensus       339 ~l~~~~~~~~~~~ivf~~~~~~~~l~~~L~~~~~~v~~~~g~~~~~~r~~i~~~f~~g~~~vLv~T~~~~~~GiDip~v~  418 (510)
T 2oca_A          339 LAIKLAQKDENAFVMFKHVSHGKAIFDLIKNEYDKVYYVSGEVDTETRNIMKTLAENGKGIIIVASYGVFSTGISVKNLH  418 (510)
T ss_dssp             HHHHHHTTTCEEEEEESSHHHHHHHHHHHHTTCSSEEEESSSTTHHHHHHHHHHHHHCCSCEEEEEHHHHHHSCCCCSEE
T ss_pred             HHHHHHhcCCCeEEEEecHHHHHHHHHHHHHcCCCeEEEECCCCHHHHHHHHHHHhCCCCCEEEEEcChhhcccccccCc
Confidence            44433  23444444455999999999999988899999999999999999999999999999999 9999999999999


Q ss_pred             EEEEecCCCCccchhhhhcccccCCCceeEEEEec
Q 017573          306 LVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVT  340 (369)
Q Consensus       306 ~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~  340 (369)
                      +||+++++++...+.|++||+||.|+.+..+++++
T Consensus       419 ~vi~~~~~~s~~~~~Q~~GR~gR~g~~~~~v~i~~  453 (510)
T 2oca_A          419 HVVLAHGVKSKIIVLQTIGRVLRKHGSKTIATVWD  453 (510)
T ss_dssp             EEEESSCCCSCCHHHHHHHHHHTTTCCCCCCEEEE
T ss_pred             EEEEeCCCCCHHHHHHHHhcccccCCCCceEEEEE
Confidence            99999999999999999999999998774444443

>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=100.00  E-value=2.9e-41  Score=341.33  Aligned_cols=340  Identities=16%  Similarity=0.186  Sum_probs=254.3

Q ss_pred             HHHHHHHHhCCCCCCcHhhhhhhhcccc-CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHH
Q 017573            5 ENLLRGIYAYGFEKPSAIQQRGIVPFCK-GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKV   83 (369)
Q Consensus         5 ~~i~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~   83 (369)
                      .....++...+|..++|+|.++++.+++ +++++++||||||||+++.+++++.+.....+ +++|++|+++|+.|..++
T Consensus       913 ~~~~e~l~~~~f~~fnpiQ~q~~~~l~~~~~nvlv~APTGSGKTliaelail~~l~~~~~~-kavyi~P~raLa~q~~~~  991 (1724)
T 4f92_B          913 NSAFESLYQDKFPFFNPIQTQVFNTVYNSDDNVFVGAPTGSGKTICAEFAILRMLLQSSEG-RCVYITPMEALAEQVYMD  991 (1724)
T ss_dssp             CHHHHTTTTTTCSBCCHHHHHHHHHHHSCCSCEEEECCTTSCCHHHHHHHHHHHHHHCTTC-CEEEECSCHHHHHHHHHH
T ss_pred             CHHHHHHHHhcCCCCCHHHHHHHHHHhcCCCcEEEEeCCCCCchHHHHHHHHHHHHhCCCC-EEEEEcChHHHHHHHHHH
Confidence            4455666667899999999999999976 57899999999999999999999988765433 899999999999999999


Q ss_pred             HHH-hccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCC--CCCccEEEEechhHhhccCcHHHHH
Q 017573           84 MRA-LGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLR--PDYIKMFVLDEADEMLSRGFKDQIY  160 (369)
Q Consensus        84 ~~~-~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~--~~~~~~viiDE~H~~~~~~~~~~~~  160 (369)
                      |.+ +....+.++..++|+...+...   ..+++|+|+||++|..+++++...  .++++++|+||+|.+.+. ....+.
T Consensus       992 ~~~~f~~~~g~~V~~ltGd~~~~~~~---~~~~~IiV~TPEkld~llr~~~~~~~l~~v~lvViDE~H~l~d~-rg~~le 1067 (1724)
T 4f92_B          992 WYEKFQDRLNKKVVLLTGETSTDLKL---LGKGNIIISTPEKWDILSRRWKQRKNVQNINLFVVDEVHLIGGE-NGPVLE 1067 (1724)
T ss_dssp             HHHHHTTTSCCCEEECCSCHHHHHHH---HHHCSEEEECHHHHHHHHTTTTTCHHHHSCSEEEECCGGGGGST-THHHHH
T ss_pred             HHHHhchhcCCEEEEEECCCCcchhh---cCCCCEEEECHHHHHHHHhCcccccccceeeEEEeechhhcCCC-CCccHH
Confidence            976 5556789999998877643321   234799999999998777765432  456899999999988653 333333


Q ss_pred             HH-------HhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhh------HHHHH
Q 017573          161 DI-------FQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWK------LETLC  227 (369)
Q Consensus       161 ~~-------~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~l~  227 (369)
                      .+       ....++..|++++|||.+ +..++..++...+...........+..+.............      ...+.
T Consensus      1068 ~il~rl~~i~~~~~~~~riI~lSATl~-N~~dla~WL~~~~~~~~~~~~~~RPvpL~~~i~~~~~~~~~~~~~~~~~~~~ 1146 (1724)
T 4f92_B         1068 VICSRMRYISSQIERPIRIVALSSSLS-NAKDVAHWLGCSATSTFNFHPNVRPVPLELHIQGFNISHTQTRLLSMAKPVY 1146 (1724)
T ss_dssp             HHHHHHHHHHHTTSSCCEEEEEESCBT-THHHHHHHHTCCSTTEEECCGGGCSSCEEEEEEEECCCSHHHHHHTTHHHHH
T ss_pred             HHHHHHHHHHhhcCCCceEEEEeCCCC-CHHHHHHHhCCCCCCeEEeCCCCCCCCeEEEEEeccCCCchhhhhhhcchHH
Confidence            32       334567889999999986 55666666554443333333344444444444433322111      12222


Q ss_pred             HHH-HhccCCCeEEEeCCHhhHHHHHHHHhhC----------------------------------CCeeEEecCCCCHH
Q 017573          228 DLY-ETLAITQSVIFVNTRRKVDWLTDKMRSR----------------------------------DHTVSATHGDMDQN  272 (369)
Q Consensus       228 ~~~-~~~~~~k~lv~~~~~~~~~~~~~~l~~~----------------------------------~~~~~~~~~~~~~~  272 (369)
                      ..+ ...+.+++||||++++.++..+..|...                                  ...++.+|+++++.
T Consensus      1147 ~~i~~~~~~~~~lVF~~sR~~~~~~A~~L~~~~~~~~~~~~~~~~~~~~l~~~l~~~~d~~L~~~l~~GIa~hHagL~~~ 1226 (1724)
T 4f92_B         1147 HAITKHSPKKPVIVFVPSRKQTRLTAIDILTTCAADIQRQRFLHCTEKDLIPYLEKLSDSTLKETLLNGVGYLHEGLSPM 1226 (1724)
T ss_dssp             HHHHHHCSSSCEEEEESSHHHHHHHHHHHHHHHHHTTCTTTTBCSCHHHHHHHHTTCCCHHHHHHHHTTEEEECTTSCHH
T ss_pred             HHHHHhcCCCCeeeeCCCHHHHHHHHHHHHHHHhhccchhhhhcccHHHHHHHHhhcccHHHHHHHhCCEEEECCCCCHH
Confidence            233 3345679999999999998887666321                                  23588999999999


Q ss_pred             HHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEe----------cCCCCccchhhhhcccccCCC--ceeEEEEec
Q 017573          273 TRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINY----------DLPTQPENYLHRIGRSGRFGR--KGVAINFVT  340 (369)
Q Consensus       273 ~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~----------~~~~~~~~~~Q~~GR~~R~~~--~~~~~~~~~  340 (369)
                      +|..+.+.|++|.++||+||+.++.|+|+|...+||..          ..+.+..+|.||+||+||.|.  .|.+++++.
T Consensus      1227 ~R~~VE~lF~~G~i~VLvaT~tlA~GVnlPa~~VVI~~~~~~dg~~~~~~~~s~~~~~Qm~GRAGR~g~d~~G~avll~~ 1306 (1724)
T 4f92_B         1227 ERRLVEQLFSSGAIQVVVASRSLCWGMNVAAHLVIIMDTQYYNGKIHAYVDYPIYDVLQMVGHANRPLQDDEGRCVIMCQ 1306 (1724)
T ss_dssp             HHHHHHHHHHHTSBCEEEEEGGGSSSCCCCBSEEEEECSEEEETTTTEEEECCHHHHHHHHTTBCCTTTCSCEEEEEEEE
T ss_pred             HHHHHHHHHHCCCCeEEEEChHHHcCCCCCccEEEEecCccccCcccccCCCCHHHHHHhhccccCCCCCCceEEEEEec
Confidence            99999999999999999999999999999988877732          125678899999999999986  599999999


Q ss_pred             cccHHHHHHH
Q 017573          341 RDDERMLFDI  350 (369)
Q Consensus       341 ~~~~~~~~~~  350 (369)
                      +.+...++.+
T Consensus      1307 ~~~~~~~~~l 1316 (1724)
T 4f92_B         1307 GSKKDFFKKF 1316 (1724)
T ss_dssp             GGGHHHHHHH
T ss_pred             chHHHHHHHH
Confidence            8887766544

>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=100.00  E-value=1e-41  Score=344.65  Aligned_cols=341  Identities=18%  Similarity=0.284  Sum_probs=249.9

Q ss_pred             CCHHHHHHHHhCCCCCCcHhhhhhhhcccc-CCcEEEEcCCCChhhHHHHHHHHHhhhcc--------CCCccEEEEcCC
Q 017573            3 LQENLLRGIYAYGFEKPSAIQQRGIVPFCK-GLDVIQQAQSGTGKTATFCSGILQQLDYG--------LVQCQALVLAPT   73 (369)
Q Consensus         3 l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~~li~~~tG~GKT~~~~~~~~~~~~~~--------~~~~~~liv~P~   73 (369)
                      ||++.+..+.  ||.+|+++|.++++.+++ ++|++++||||||||+++.+++++.+.+.        ..+.+++|++|+
T Consensus        66 Lp~~~~~~f~--g~~~ln~iQs~~~~~al~~~~N~lv~APTGsGKTlva~l~il~~l~~~~~~~~~~~~~~~k~lyiaP~  143 (1724)
T 4f92_B           66 LPKYAQAGFE--GFKTLNRIQSKLYRAALETDENLLLCAPTGAGKTNVALMCMLREIGKHINMDGTINVDDFKIIYIAPM  143 (1724)
T ss_dssp             SCGGGSTTCT--TCSBCCHHHHHTHHHHHTCCCCEEEECCTTSCCHHHHHHHHHHHHGGGCCTTSSCCTTSCEEEEECSS
T ss_pred             cCHHHHHhcC--CCCCCCHHHHHHHHHHHcCCCcEEEEeCCcchHHHHHHHHHHHHHHhhccccccccCCCCEEEEECCH
Confidence            4555444332  689999999999998775 68999999999999999999999887542        234589999999


Q ss_pred             HHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCC--CCCCccEEEEechhHhh
Q 017573           74 RELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSL--RPDYIKMFVLDEADEML  151 (369)
Q Consensus        74 ~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~--~~~~~~~viiDE~H~~~  151 (369)
                      ++|+.|..+.|++.....|++|...+|+.......   ..+++|+|+|||++..+++++..  ..+.+++||+||+|.+.
T Consensus       144 kALa~e~~~~l~~~~~~~gi~V~~~tGd~~~~~~~---~~~~~IlVtTpEkld~llr~~~~~~~l~~v~~vIiDEvH~l~  220 (1724)
T 4f92_B          144 RSLVQEMVGSFGKRLATYGITVAELTGDHQLCKEE---ISATQIIVCTPEKWDIITRKGGERTYTQLVRLIILDEIHLLH  220 (1724)
T ss_dssp             HHHHHHHHHHHHHHHTTTTCCEEECCSSCSSCCTT---GGGCSEEEECHHHHHHHTTSSTTHHHHTTEEEEEETTGGGGG
T ss_pred             HHHHHHHHHHHHHHHhhCCCEEEEEECCCCCCccc---cCCCCEEEECHHHHHHHHcCCccchhhcCcCEEEEecchhcC
Confidence            99999999999998888899999999987643321   24589999999999766655432  24568999999999775


Q ss_pred             ccCcHHHHHHHH-------hhCCccCcEEEEEeeCChhHHHHHHHhcCCC-EEEEecCccccccceeEEEEEccch--hh
Q 017573          152 SRGFKDQIYDIF-------QLLPAKVQVGVFSATMPPEALEITRKFMNKP-VRILVKRDELTLEGIKQFYVNVEKE--EW  221 (369)
Q Consensus       152 ~~~~~~~~~~~~-------~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~--~~  221 (369)
                      + .....+..++       ...++..|++++|||.+ +..+...++...+ ...........+..+.+.+......  ..
T Consensus       221 d-~RG~~lE~~l~rl~~~~~~~~~~~riI~LSATl~-N~~dvA~wL~~~~~~~~~~~~~~~RPvpL~~~~~~~~~~~~~~  298 (1724)
T 4f92_B          221 D-DRGPVLEALVARAIRNIEMTQEDVRLIGLSATLP-NYEDVATFLRVDPAKGLFYFDNSFRPVPLEQTYVGITEKKAIK  298 (1724)
T ss_dssp             S-TTHHHHHHHHHHHHHHHHHHTCCCEEEEEECSCT-THHHHHHHTTCCHHHHEEECCGGGCSSCEEEECCEECCCCHHH
T ss_pred             C-ccHHHHHHHHHHHHHHHHhCCCCCcEEEEecccC-CHHHHHHHhCCCCCCCeEEECCCCccCccEEEEeccCCcchhh
Confidence            4 3333333332       34567889999999985 5555555443322 1112222333344455444433321  11


Q ss_pred             hHHH----HHHHHHh-ccCCCeEEEeCCHhhHHHHHHHHhhC-------------------------------------C
Q 017573          222 KLET----LCDLYET-LAITQSVIFVNTRRKVDWLTDKMRSR-------------------------------------D  259 (369)
Q Consensus       222 ~~~~----l~~~~~~-~~~~k~lv~~~~~~~~~~~~~~l~~~-------------------------------------~  259 (369)
                      ..+.    +...+.. ...+++||||++++.++..++.|.+.                                     .
T Consensus       299 ~~~~~~~~~~~~v~~~~~~~~~LVF~~sR~~~~~~A~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~  378 (1724)
T 4f92_B          299 RFQIMNEIVYEKIMEHAGKNQVLVFVHSRKETGKTARAIRDMCLEKDTLGLFLREGSASTEVLRTEAEQCKNLELKDLLP  378 (1724)
T ss_dssp             HHHHHHHHHHHHHTTCCSSCCEEEECSSTTTTHHHHHHHHHHHHHTTSTTCCSSCCTTCSSHHHHTTSCCSTHHHHHHTT
T ss_pred             hhHHHHHHHHHHHHHHhcCCcEEEECCCHHHHHHHHHHHHHHHhhccchhhhcccchhHHHHHHhhhcccccHHHHHHhh
Confidence            1222    2222222 34568999999999988888777531                                     2


Q ss_pred             CeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEE----ec------CCCCccchhhhhcccccC
Q 017573          260 HTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVIN----YD------LPTQPENYLHRIGRSGRF  329 (369)
Q Consensus       260 ~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~----~~------~~~~~~~~~Q~~GR~~R~  329 (369)
                      ..++.+||+++.++|..+.+.|++|.++||+||++++.|+|+|..++||.    ++      .+.+..+|.||+|||||.
T Consensus       379 ~Gva~HHagL~~~~R~~vE~~F~~G~i~vlvaTsTLa~GVNlPa~~vVI~~~~~~~~~~~~~~~ls~~~~~Qm~GRAGR~  458 (1724)
T 4f92_B          379 YGFAIHHAGMTRVDRTLVEDLFADKHIQVLVSTATLAWGVNLPAHTVIIKGTQVYSPEKGRWTELGALDILQMLGRAGRP  458 (1724)
T ss_dssp             TTEEEECSSSCTHHHHHHHHHHHTTCCCEEEECHHHHHHSCCCBSEEEEECCEEEETTTTEEEECCHHHHHHHHTTBSCT
T ss_pred             cCEEEEcCCCCHHHHHHHHHHHHCCCCeEEEEcchhHhhCCCCCceEEEeCCEEecCcCCCcccCCHHHHHHhhhhccCC
Confidence            34889999999999999999999999999999999999999998888874    33      245788999999999998


Q ss_pred             CC--ceeEEEEeccccHHHHHHH
Q 017573          330 GR--KGVAINFVTRDDERMLFDI  350 (369)
Q Consensus       330 ~~--~~~~~~~~~~~~~~~~~~~  350 (369)
                      |.  .|.++++..+.+...+..+
T Consensus       459 g~d~~G~~ii~~~~~~~~~~~~l  481 (1724)
T 4f92_B          459 QYDTKGEGILITSHGELQYYLSL  481 (1724)
T ss_dssp             TTCSCEEEEEEEESTTCCHHHHH
T ss_pred             CCCCccEEEEEecchhHHHHHHH
Confidence            74  5999999998877666554

>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=100.00  E-value=3e-41  Score=308.01  Aligned_cols=296  Identities=18%  Similarity=0.243  Sum_probs=220.9

Q ss_pred             CCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcE-EE
Q 017573           18 KPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVK-VH   96 (369)
Q Consensus        18 ~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~-v~   96 (369)
                      .|+|+|.++++.+.+++++++.+|||+|||++++.++...      +.++||++|+++|+.||.+++.++    +.+ +.
T Consensus        93 ~l~~~Q~~ai~~i~~~~~~ll~~~TGsGKT~~~l~~i~~~------~~~~Lvl~P~~~L~~Q~~~~~~~~----~~~~v~  162 (472)
T 2fwr_A           93 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINEL------STPTLIVVPTLALAEQWKERLGIF----GEEYVG  162 (472)
T ss_dssp             CBCHHHHHHHHHHTTTTEEEEECCTTSCHHHHHHHHHHHH------CSCEEEEESSHHHHHHHHHHGGGG----CGGGEE
T ss_pred             CcCHHHHHHHHHHHhcCCEEEEeCCCCCHHHHHHHHHHHc------CCCEEEEECCHHHHHHHHHHHHhC----CCcceE
Confidence            6999999999999999999999999999999998877754      238999999999999999999884    667 77


Q ss_pred             EEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEE
Q 017573           97 ACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFS  176 (369)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~s  176 (369)
                      .++|+..         ...+|+|+|++.+.......   ..++++||+||+|++.+..+..    +...++ ..+++++|
T Consensus       163 ~~~g~~~---------~~~~Ivv~T~~~l~~~~~~~---~~~~~liIvDEaH~~~~~~~~~----~~~~~~-~~~~l~lS  225 (472)
T 2fwr_A          163 EFSGRIK---------ELKPLTVSTYDSAYVNAEKL---GNRFMLLIFDEVHHLPAESYVQ----IAQMSI-APFRLGLT  225 (472)
T ss_dssp             EBSSSCB---------CCCSEEEEEHHHHHHTHHHH---TTTCSEEEEETGGGTTSTTTHH----HHHTCC-CSEEEEEE
T ss_pred             EECCCcC---------CcCCEEEEEcHHHHHHHHHh---cCCCCEEEEECCcCCCChHHHH----HHHhcC-CCeEEEEe
Confidence            7777654         24689999999997766431   2348999999999998777653    444443 56789999


Q ss_pred             eeCChh-------------------HHHHHHHhcCCCEEE--EecCccc------------------------cccceeE
Q 017573          177 ATMPPE-------------------ALEITRKFMNKPVRI--LVKRDEL------------------------TLEGIKQ  211 (369)
Q Consensus       177 aT~~~~-------------------~~~~~~~~~~~~~~~--~~~~~~~------------------------~~~~~~~  211 (369)
                      |||...                   ..++...++..+...  .......                        .......
T Consensus       226 ATp~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~  305 (472)
T 2fwr_A          226 ATFEREDGRHEILKEVVGGKVFELFPDSLAGKHLAKYTIKRIFVPLAEDERVEYEKREKVYKQFLRARGITLRRAEDFNK  305 (472)
T ss_dssp             SCCCCTTSGGGSHHHHTCCEEEECCHHHHTSCCCCSEEECCEEECCCHHHHHHTTTTTHHHHSCSSSCCCTTTCCSSSTT
T ss_pred             cCccCCCCHHHHHHHHhCCeEeecCHHHHhcCcCCCeEEEEEEcCCCHHHHHHHHHHHHHHHHHHHhcCccccchhhHHH
Confidence            999732                   111111111111110  0000000                        0000000


Q ss_pred             EEE--------------------EccchhhhHHHHHHHHHhccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCH
Q 017573          212 FYV--------------------NVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQ  271 (369)
Q Consensus       212 ~~~--------------------~~~~~~~~~~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~  271 (369)
                      .+.                    .......+...+.+++....++++||||++.+.++.+++.|.     +..+||+++.
T Consensus       306 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~k~lvF~~~~~~~~~l~~~l~-----~~~~~g~~~~  380 (472)
T 2fwr_A          306 IVMASGYDERAYEALRAWEEARRIAFNSKNKIRKLREILERHRKDKIIIFTRHNELVYRISKVFL-----IPAITHRTSR  380 (472)
T ss_dssp             TTTTTCCSSSSSTTTHHHHHHHHHHHSCSHHHHHHHHHHHHTSSSCBCCBCSCHHHHHHHHHHTT-----CCBCCSSSCS
T ss_pred             HHHHhccCHHHHHHHHHHHHHHHHhhcChHHHHHHHHHHHhCCCCcEEEEECCHHHHHHHHHHhC-----cceeeCCCCH
Confidence            000                    000122356777888887778899999999999999999984     5678999999


Q ss_pred             HHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCCCCccchhhhhcccccCCCc-e--eEEEEeccccHH
Q 017573          272 NTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRK-G--VAINFVTRDDER  345 (369)
Q Consensus       272 ~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~-~--~~~~~~~~~~~~  345 (369)
                      .+|.++++.|++|+.+|||+|+++++|+|+|.+++||++++++|+..|.|++||++|.|+. +  .++.+++.+..+
T Consensus       381 ~~R~~~~~~F~~g~~~vLv~T~~~~~Gldlp~~~~Vi~~~~~~s~~~~~Q~~GR~~R~g~~k~~~~i~~lv~~~t~e  457 (472)
T 2fwr_A          381 EEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQRLGRILRPSKGKKEAVLYELISRGTGE  457 (472)
T ss_dssp             HHHHTHHHHHHHSSCSBCBCSSCCCSSSCSCCBSEEEEECCSSCCHHHHHHHHHSBCCCTTTCCEEEEEEEECSCC-
T ss_pred             HHHHHHHHHHhCCCCCEEEEcCchhcCcccccCcEEEEECCCCCHHHHHHHHhhccCCCCCCceEEEEEEEeCCCch
Confidence            9999999999999999999999999999999999999999999999999999999999854 3  444555554433

>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=100.00  E-value=4.1e-40  Score=304.70  Aligned_cols=322  Identities=19%  Similarity=0.229  Sum_probs=242.3

Q ss_pred             hCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccC
Q 017573           13 AYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLG   92 (369)
Q Consensus        13 ~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~   92 (369)
                      ..|+ +|+|.|..+++.+.+|+  +..++||+|||+++.++++.....+   +.++||+|++.|+.|.++++..++..++
T Consensus        79 ~lG~-~pt~VQ~~~ip~ll~G~--Iaea~TGeGKTlaf~LP~~l~aL~g---~~vlVltptreLA~qd~e~~~~l~~~lg  152 (844)
T 1tf5_A           79 VTGM-FPFKVQLMGGVALHDGN--IAEMKTGEGKTLTSTLPVYLNALTG---KGVHVVTVNEYLASRDAEQMGKIFEFLG  152 (844)
T ss_dssp             HHSC-CCCHHHHHHHHHHHTTS--EEECCTTSCHHHHHHHHHHHHHTTS---SCEEEEESSHHHHHHHHHHHHHHHHHTT
T ss_pred             HcCC-CCcHHHHHhhHHHhCCC--EEEccCCcHHHHHHHHHHHHHHHcC---CCEEEEeCCHHHHHHHHHHHHHHHhhcC
Confidence            5799 99999999999999998  9999999999999999988433333   3799999999999999999999999999


Q ss_pred             cEEEEEECCcchHHHHHHHccCCcEEEeccHHH-HHHHHcC------CCCCCCccEEEEechhHhh-ccC----------
Q 017573           93 VKVHACVGGTSVREDQRILQAGVHVVVGTPGRV-FDMLRRQ------SLRPDYIKMFVLDEADEML-SRG----------  154 (369)
Q Consensus        93 ~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l-~~~~~~~------~~~~~~~~~viiDE~H~~~-~~~----------  154 (369)
                      +++..+.|+.......  ....++|+|+||..| +.++...      ......+.++|+||+|++. +..          
T Consensus       153 l~v~~i~gg~~~~~r~--~~~~~dIv~gTpgrlgfD~L~D~m~~~~~~l~lr~~~~lVlDEaD~mLiDea~tplIisg~~  230 (844)
T 1tf5_A          153 LTVGLNLNSMSKDEKR--EAYAADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSILIDEARTPLIISGQA  230 (844)
T ss_dssp             CCEEECCTTSCHHHHH--HHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEEETHHHHHTTTTTCEEEEEEEE
T ss_pred             CeEEEEeCCCCHHHHH--HhcCCCEEEECchhhhHHHHHHhhhcchhhhcccCCCEEEECchhhhhhhccccchhhcCCc
Confidence            9999999987754433  234589999999999 6666543      2445778999999999987 442          


Q ss_pred             -----cHHHHHHHHhhCCc---------cCcEE-----------------EEEeeCChhHHHH-----HHHhcCCC--EE
Q 017573          155 -----FKDQIYDIFQLLPA---------KVQVG-----------------VFSATMPPEALEI-----TRKFMNKP--VR  196 (369)
Q Consensus       155 -----~~~~~~~~~~~~~~---------~~~~i-----------------~~saT~~~~~~~~-----~~~~~~~~--~~  196 (369)
                           +...+..+...+++         ..|+.                 ++|||.+.-....     ...++...  ..
T Consensus       231 ~~~~~~~~~i~~iv~~l~~~~~y~vd~k~rq~~lt~~g~~~~e~~~~i~~Lfsat~~~~~~~i~~al~A~~l~~~d~dYi  310 (844)
T 1tf5_A          231 AKSTKLYVQANAFVRTLKAEKDYTYDIKTKAVQLTEEGMTKAEKAFGIDNLFDVKHVALNHHINQALKAHVAMQKDVDYV  310 (844)
T ss_dssp             ECCCHHHHHHHHHHTTCCSSSSBCCCSSSCCCCBCHHHHHHHHHHTTCSCTTSGGGHHHHHHHHHHHHHHHTCCBTTTEE
T ss_pred             ccchhHHHHHHHHHHhCcccccceeccccceEEecHHHHHHHHHHhCccccCCCccchhHHHHHHHHHHHHHhhcCCceE
Confidence                 56777888888763         45665                 6788854211111     11122110  00


Q ss_pred             E------Eec-----------------------------C----------------------------------------
Q 017573          197 I------LVK-----------------------------R----------------------------------------  201 (369)
Q Consensus       197 ~------~~~-----------------------------~----------------------------------------  201 (369)
                      +      .++                             .                                        
T Consensus       311 v~dg~v~ivDe~tgr~m~grr~sdGLhqaieake~v~I~~e~~t~a~It~q~~fr~y~kl~GmTGTa~te~~e~~~iY~l  390 (844)
T 1tf5_A          311 VEDGQVVIVDSFTGRLMKGRRYSEGLHQAIEAKEGLEIQNESMTLATITFQNYFRMYEKLAGMTGTAKTEEEEFRNIYNM  390 (844)
T ss_dssp             EETTEEEEBCTTTCCBCTTCCCSTTHHHHHHHHTTCCCCCCEEEEEEEEHHHHHTTSSEEEEEESCCGGGHHHHHHHHCC
T ss_pred             EecCeeEEeecccccccCCCccchhhHHHHhhcccceecccccccceeeHHHHHHHHhhhccCCcccchhHHHHHHHhCC
Confidence            0      000                             0                                        


Q ss_pred             ------ccccccceeEEEEEccchhhhHHHHHHHHHh--ccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHH
Q 017573          202 ------DELTLEGIKQFYVNVEKEEWKLETLCDLYET--LAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNT  273 (369)
Q Consensus       202 ------~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~--~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~  273 (369)
                            ...+................+...+...+..  ..+.++||||++++.++.+++.|...|+++..+||++...+
T Consensus       391 ~vv~IPtn~p~~r~d~~d~v~~~~~~K~~al~~~i~~~~~~~~pvLVft~s~~~se~Ls~~L~~~gi~~~vLhg~~~~rE  470 (844)
T 1tf5_A          391 QVVTIPTNRPVVRDDRPDLIYRTMEGKFKAVAEDVAQRYMTGQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHERE  470 (844)
T ss_dssp             CEEECCCSSCCCCEECCCEEESSHHHHHHHHHHHHHHHHHHTCCEEEEESCHHHHHHHHHHHHTTTCCCEEECSSCHHHH
T ss_pred             ceEEecCCCCcccccCCcEEEeCHHHHHHHHHHHHHHHHhcCCcEEEEECCHHHHHHHHHHHHHCCCCEEEeeCCccHHH
Confidence                  0000000000001122345577777776654  24578999999999999999999999999999999988888


Q ss_pred             HHHHHHHHhcCCCcEEEEecCCcCCCCCC--------CCcEEEEecCCCCccchhhhhcccccCCCceeEEEEeccccH
Q 017573          274 RDIIMREFRSGSSRVLITTDLLARGIDVQ--------QVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDE  344 (369)
Q Consensus       274 r~~~~~~f~~~~~~vli~t~~~~~G~d~~--------~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~  344 (369)
                      +..+.+.++.|  .|+|||+++++|+|++        +..+||.++.|.+...|.|++||+||.|.+|.+++|++..|.
T Consensus       471 r~ii~~ag~~g--~VlIATdmAgRG~DI~l~~~V~~~ggl~VIn~d~p~s~r~y~hr~GRTGRqG~~G~s~~~vs~eD~  547 (844)
T 1tf5_A          471 AQIIEEAGQKG--AVTIATNMAGRGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGDPGITQFYLSMEDE  547 (844)
T ss_dssp             HHHHTTTTSTT--CEEEEETTSSTTCCCCCCTTSGGGTSEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEETTSS
T ss_pred             HHHHHHcCCCC--eEEEeCCccccCcCccccchhhhcCCcEEEEecCCCCHHHHHhhcCccccCCCCCeEEEEecHHHH
Confidence            77666555554  6999999999999999        788999999999999999999999999999999999997764

>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=100.00  E-value=2.6e-40  Score=306.39  Aligned_cols=319  Identities=18%  Similarity=0.127  Sum_probs=228.7

Q ss_pred             CCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHH
Q 017573            3 LQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEK   82 (369)
Q Consensus         3 l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~   82 (369)
                      +++.+.+.+... ...+.|.|+.+++.+.+++++++.+|||||||++++++++..+...  +.++||++|+++|+.|+.+
T Consensus       157 ~~~~~~~~l~~~-~~~~lpiq~~~i~~l~~g~dvlv~a~TGSGKT~~~~lpil~~l~~~--~~~vLvl~PtreLa~Qi~~  233 (618)
T 2whx_A          157 KSGDYVSAITQA-ERIGEPDYEVDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALKR--RLRTLILAPTRVVAAEMEE  233 (618)
T ss_dssp             -----CEECBCC-CCCCCCCCCCCGGGGSTTCEEEECCCTTSSTTTTHHHHHHHHHHHT--TCCEEEEESSHHHHHHHHH
T ss_pred             chHHHHHHHhhc-cccCCCccccCHHHHhcCCeEEEEcCCCCCHHHHHHHHHHHHHHhC--CCeEEEEcChHHHHHHHHH
Confidence            333433334332 3778899998999999999999999999999999988888776542  3489999999999999998


Q ss_pred             HHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHH
Q 017573           83 VMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDI  162 (369)
Q Consensus        83 ~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~  162 (369)
                      .+..      ..+........     .....+..+.++|.+.+...+... ....+++++|+||||++ +..+...+..+
T Consensus       234 ~l~~------~~v~~~~~~l~-----~~~tp~~~i~~~t~~~l~~~l~~~-~~l~~~~~iViDEah~~-~~~~~~~~~~i  300 (618)
T 2whx_A          234 ALRG------LPIRYQTPAVK-----SDHTGREIVDLMCHATFTTRLLSS-TRVPNYNLIVMDEAHFT-DPCSVAARGYI  300 (618)
T ss_dssp             HTTT------SCEEECCTTSS-----CCCCSSSCEEEEEHHHHHHHHHHC-SSCCCCSEEEEESTTCC-SHHHHHHHHHH
T ss_pred             HhcC------CceeEecccce-----eccCCCceEEEEChHHHHHHHhcc-ccccCCeEEEEECCCCC-CccHHHHHHHH
Confidence            8763      22322111100     011223467788888887665554 45677999999999997 44455566666


Q ss_pred             HhhCC-ccCcEEEEEeeCChhHHHHHHHhcC-CCEEEEecCccccccceeEEEEEccchhhhHHHHHHHHHhccCCCeEE
Q 017573          163 FQLLP-AKVQVGVFSATMPPEALEITRKFMN-KPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVI  240 (369)
Q Consensus       163 ~~~~~-~~~~~i~~saT~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lv  240 (369)
                      ...++ +..|++++|||++.....    +.. .+..+.....             .+..  ....+...+.. ..+++||
T Consensus       301 ~~~l~~~~~q~il~SAT~~~~~~~----~~~~~~~~~~v~~~-------------~~~~--~~~~ll~~l~~-~~~~~LV  360 (618)
T 2whx_A          301 STRVEMGEAAAIFMTATPPGSTDP----FPQSNSPIEDIERE-------------IPER--SWNTGFDWITD-YQGKTVW  360 (618)
T ss_dssp             HHHHHHTSCEEEEECSSCTTCCCS----SCCCSSCEEEEECC-------------CCSS--CCSSSCHHHHH-CCSCEEE
T ss_pred             HHHhcccCccEEEEECCCchhhhh----hhccCCceeeeccc-------------CCHH--HHHHHHHHHHh-CCCCEEE
Confidence            66654 578999999999765332    111 1211111111             0000  00111122222 2579999


Q ss_pred             EeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEE-------------
Q 017573          241 FVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLV-------------  307 (369)
Q Consensus       241 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~v-------------  307 (369)
                      ||++++.++.+++.|++.+.++..+||+    +|.++++.|++|+.+|||||+++++|+|+| +++|             
T Consensus       361 F~~s~~~a~~l~~~L~~~g~~v~~lhg~----~R~~~l~~F~~g~~~VLVaTdv~~rGiDi~-v~~VId~g~~~~P~~~~  435 (618)
T 2whx_A          361 FVPSIKAGNDIANCLRKSGKRVIQLSRK----TFDTEYPKTKLTDWDFVVTTDISEMGANFR-AGRVIDPRRCLKPVILT  435 (618)
T ss_dssp             ECSSHHHHHHHHHHHHHTTCCEEEECTT----THHHHTTHHHHSCCSEEEECGGGGTTCCCC-CSEEEECCEEEEEEEEC
T ss_pred             EECChhHHHHHHHHHHHcCCcEEEEChH----HHHHHHHhhcCCCcEEEEECcHHHcCcccC-ceEEEECcceecceecc
Confidence            9999999999999999999999999984    678899999999999999999999999997 8888             


Q ss_pred             -------EEecCCCCccchhhhhcccccCCC-ceeEEEEec---cccHHHHHHHHHHhccccccCC
Q 017573          308 -------INYDLPTQPENYLHRIGRSGRFGR-KGVAINFVT---RDDERMLFDIQKFYNVVIEELP  362 (369)
Q Consensus       308 -------i~~~~~~~~~~~~Q~~GR~~R~~~-~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~  362 (369)
                             +.++.|.+..+|.||+||+||.|. .|.+++++.   +.+...+..+++.+.....+++
T Consensus       436 ~~~~~~~i~~d~P~s~~~yiQR~GRaGR~g~~~G~ai~l~~~~~~~d~~~l~~le~~i~l~~~~~~  501 (618)
T 2whx_A          436 DGPERVILAGPIPVTPASAAQRRGRIGRNPAQEDDQYVFSGDPLKNDEDHAHWTEAKMLLDNIYTP  501 (618)
T ss_dssp             SSSCEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECSCCCCCCTTCHHHHHHHHHHTTCCCT
T ss_pred             cCCCceEEcccccCCHHHHHHhccccCCCCCCCCeEEEEccCCchhhHHHHHHHHhHhccccccCC
Confidence                   556668899999999999999964 899999997   7787788888877655444443

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=100.00  E-value=1.3e-39  Score=304.62  Aligned_cols=300  Identities=16%  Similarity=0.219  Sum_probs=189.6

Q ss_pred             CCCcHhhhhhhhcccc----C-CcEEEEcCCCChhhHHHHHHHHHhhhcc------CCCccEEEEcCCHHHHHHHH-HHH
Q 017573           17 EKPSAIQQRGIVPFCK----G-LDVIQQAQSGTGKTATFCSGILQQLDYG------LVQCQALVLAPTRELAQQIE-KVM   84 (369)
Q Consensus        17 ~~~~~~Q~~~~~~~~~----~-~~~li~~~tG~GKT~~~~~~~~~~~~~~------~~~~~~liv~P~~~l~~q~~-~~~   84 (369)
                      ..||++|.++++.+.+    + +++++++|||+|||++++..+...+..+      ...+++||++|+++|+.|+. +.+
T Consensus       177 ~~lr~~Q~~ai~~~~~~~~~~~~~~ll~~~TGsGKT~~~~~~~~~l~~~~~~~~~~~~~~~vlil~P~~~L~~Q~~~~~~  256 (590)
T 3h1t_A          177 YSPRYYQQIAINRAVQSVLQGKKRSLITMATGTGKTVVAFQISWKLWSARWNRTGDYRKPRILFLADRNVLVDDPKDKTF  256 (590)
T ss_dssp             --CCHHHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHHHHHHHHHTTCCSSCSSSCCCEEEEEC-----------CC
T ss_pred             CCchHHHHHHHHHHHHHHhcCCCceEEEecCCCChHHHHHHHHHHHHhcccccccccCCCeEEEEeCCHHHHHHHHHHHH
Confidence            3799999999998876    4 6689999999999999776666555433      13458999999999999999 777


Q ss_pred             HHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHH----cCCCCCCCccEEEEechhHhhccCcHHHHH
Q 017573           85 RALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLR----RQSLRPDYIKMFVLDEADEMLSRGFKDQIY  160 (369)
Q Consensus        85 ~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~----~~~~~~~~~~~viiDE~H~~~~~~~~~~~~  160 (369)
                      ..+..    .+..+.++.        ...+.+|+|+|++.+.....    ...+....+++||+||||++.... ...+.
T Consensus       257 ~~~~~----~~~~~~~~~--------~~~~~~I~v~T~~~l~~~~~~~~~~~~~~~~~~~lvIiDEaH~~~~~~-~~~~~  323 (590)
T 3h1t_A          257 TPFGD----ARHKIEGGK--------VVKSREIYFAIYQSIASDERRPGLYKEFPQDFFDLIIIDECHRGSARD-NSNWR  323 (590)
T ss_dssp             TTTCS----SEEECCC----------CCSSCSEEEEEGGGC------CCGGGGSCTTSCSEEEESCCC----------CH
T ss_pred             Hhcch----hhhhhhccC--------CCCCCcEEEEEhhhhccccccccccccCCCCccCEEEEECCccccccc-hHHHH
Confidence            76532    233322221        23467999999999987654    223445668999999999986542 24455


Q ss_pred             HHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccc-----cccceeEEEE---------------------
Q 017573          161 DIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDEL-----TLEGIKQFYV---------------------  214 (369)
Q Consensus       161 ~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~---------------------  214 (369)
                      .++..++ ..+++++||||..........++..+..........     .+........                     
T Consensus       324 ~il~~~~-~~~~l~lTATP~~~~~~~~~~~f~~~~~~~~~~~~i~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  402 (590)
T 3h1t_A          324 EILEYFE-PAFQIGMTATPLREDNRDTYRYFGNPIYTYSLRQGIDDGFLAPYRVHRVISEVDAAGWRPSKGDVDRFGREI  402 (590)
T ss_dssp             HHHHHST-TSEEEEEESSCSCTTTHHHHHHSCSCSEEECHHHHHHHTSSCCEEEEEEEETTCC-----------------
T ss_pred             HHHHhCC-cceEEEeccccccccchhHHHHcCCceEecCHHHHhhCCccCCcEEEEeeeeeecccccccccccccccccc
Confidence            6666665 467899999998544433444444332221110000     0000000000                     


Q ss_pred             -----Eccc----------hhhhHHHHHHHHHh-ccCCCeEEEeCCHhhHHHHHHHHhhCCCe--------eEEecCCCC
Q 017573          215 -----NVEK----------EEWKLETLCDLYET-LAITQSVIFVNTRRKVDWLTDKMRSRDHT--------VSATHGDMD  270 (369)
Q Consensus       215 -----~~~~----------~~~~~~~l~~~~~~-~~~~k~lv~~~~~~~~~~~~~~l~~~~~~--------~~~~~~~~~  270 (369)
                           ....          .....+.+.+.+.. ...+++||||+++++++.+++.|.+.+..        +..+||+++
T Consensus       403 ~~~~~~~~~~~~~~~~~~r~~~i~~~l~~~l~~~~~~~k~lVF~~~~~~a~~l~~~L~~~~~~~~~~~~~~~~~i~g~~~  482 (590)
T 3h1t_A          403 PDGEYQTKDFERVIALKARTDAFAKHLTDFMKRTDRFAKTIVFCVDQEHADEMRRALNNLNSDLSRKHPDYVARVTSEEG  482 (590)
T ss_dssp             ------CCSHHHHHHHHHTHHHHHHHHHHHHHHHCTTSEEEEEESSHHHHHHHHHHHHHHTHHHHTTCTTSEEECSSTTH
T ss_pred             ccccCCHHHhhhHhcChHHHHHHHHHHHHHHHhcCCCccEEEEECCHHHHHHHHHHHHHhhhhhhccCCCeEEEEeCCCh
Confidence                 0000          00011223333333 34479999999999999999999875432        778888865


Q ss_pred             HHHHHHHHHHHhcCCCc---EEEEecCCcCCCCCCCCcEEEEecCCCCccchhhhhcccccCCC
Q 017573          271 QNTRDIIMREFRSGSSR---VLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGR  331 (369)
Q Consensus       271 ~~~r~~~~~~f~~~~~~---vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~  331 (369)
                       ++|.++++.|++|+.+   |+++|+++++|+|+|.+++||++++++|...|.|++||++|.++
T Consensus       483 -~~r~~~l~~F~~~~~~~~~ilvtt~~l~~GiDip~v~~Vi~~~~~~s~~~~~Q~iGR~~R~~~  545 (590)
T 3h1t_A          483 -KIGKGHLSRFQELETSTPVILTTSQLLTTGVDAPTCKNVVLARVVNSMSEFKQIVGRGTRLRE  545 (590)
T ss_dssp             -HHHHHHHHHHHCTTCCCCCEEEESSTTTTTCCCTTEEEEEEESCCCCHHHHHHHHTTSCCCBG
T ss_pred             -HHHHHHHHHHhCCCCCCCEEEEECChhhcCccchheeEEEEEecCCChHHHHHHHhhhcccCc
Confidence             4799999999998755   77888999999999999999999999999999999999999875

>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=100.00  E-value=1.1e-37  Score=287.67  Aligned_cols=322  Identities=18%  Similarity=0.212  Sum_probs=224.4

Q ss_pred             CCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCc
Q 017573           14 YGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGV   93 (369)
Q Consensus        14 ~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~   93 (369)
                      .|. +|++.|..+++.+.+|+  +..++||+|||++++++++.....+   +.++|++||+.|+.|..+++..++..+++
T Consensus        71 lg~-~p~~VQ~~~i~~ll~G~--Iaem~TGsGKTlaf~LP~l~~~l~g---~~vlVltPTreLA~Q~~e~~~~l~~~lgl  144 (853)
T 2fsf_A           71 FGM-RHFDVQLLGGMVLNERC--IAEMRTGEGKTLTATLPAYLNALTG---KGVHVVTVNDYLAQRDAENNRPLFEFLGL  144 (853)
T ss_dssp             HSC-CCCHHHHHHHHHHHSSE--EEECCTTSCHHHHHHHHHHHHHTTS---SCCEEEESSHHHHHHHHHHHHHHHHHTTC
T ss_pred             cCC-CCChHHHhhcccccCCe--eeeecCCchHHHHHHHHHHHHHHcC---CcEEEEcCCHHHHHHHHHHHHHHHHhcCC
Confidence            464 99999999999999988  9999999999999999988544333   38999999999999999999999999999


Q ss_pred             EEEEEECCcchHHHHHHHccCCcEEEeccHHH-HHHHHcCC------CCCCCccEEEEechhHhh-ccC-----------
Q 017573           94 KVHACVGGTSVREDQRILQAGVHVVVGTPGRV-FDMLRRQS------LRPDYIKMFVLDEADEML-SRG-----------  154 (369)
Q Consensus        94 ~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l-~~~~~~~~------~~~~~~~~viiDE~H~~~-~~~-----------  154 (369)
                      ++..+.|+.......  ....++|+|+||..| +.++....      .....++++|+||+|++. +..           
T Consensus       145 ~v~~i~GG~~~~~r~--~~~~~dIvvgTpgrl~fDyLrd~~~~~~~~~~~~~l~~lVlDEaD~mLiD~a~tpLIiSg~~~  222 (853)
T 2fsf_A          145 TVGINLPGMPAPAKR--EAYAADITYGTNNEYGFDYLRDNMAFSPEERVQRKLHYALVDEVDSILIDEARTPLIISGPAE  222 (853)
T ss_dssp             CEEECCTTCCHHHHH--HHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCSCCEEEESCHHHHTTTTTTCEEEEEEC--
T ss_pred             eEEEEeCCCCHHHHH--HhcCCCEEEECCchhhHHHHHhhhhccHhHhcccCCcEEEECchHHHHHhcCcccccccCCCc
Confidence            999999988754332  334589999999999 67776542      455778999999999987 332           


Q ss_pred             ----cHHHHHHHHhhCCc--------------------cCcEE------------------------EEEeeCChhHHHH
Q 017573          155 ----FKDQIYDIFQLLPA--------------------KVQVG------------------------VFSATMPPEALEI  186 (369)
Q Consensus       155 ----~~~~~~~~~~~~~~--------------------~~~~i------------------------~~saT~~~~~~~~  186 (369)
                          +...+..+...+++                    ..|+.                        ++|||.+.-....
T Consensus       223 ~~~~~y~~i~~iv~~L~~~~~~~~~~~~~~~dy~vdek~rqv~lte~g~~~~e~~l~~~~l~~~~~~Lfsat~~~~~~~i  302 (853)
T 2fsf_A          223 DSSEMYKRVNKIIPHLIRQEKEDSETFQGEGHFSVDEKSRQVNLTERGLVLIEELLVKEGIMDEGESLYSPANIMLMHHV  302 (853)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cchhHHHHHHHHHHhchhhhccccccccccccceeccccceEEEcHHHHHHHHHHHHhCCcccccccccCcccchHHHHH
Confidence                34556666666653                    33332                        5677753211000


Q ss_pred             -----HHHhcCCC-------------------------------------EEEEecCcccccccee--------------
Q 017573          187 -----TRKFMNKP-------------------------------------VRILVKRDELTLEGIK--------------  210 (369)
Q Consensus       187 -----~~~~~~~~-------------------------------------~~~~~~~~~~~~~~~~--------------  210 (369)
                           ...++...                                     ..+.+..+......+.              
T Consensus       303 ~~al~A~~l~~~d~dYiV~d~~vviVde~tgR~m~grr~sdGLhQaieake~v~I~~e~~tla~It~qnyfr~Y~kl~Gm  382 (853)
T 2fsf_A          303 TAALRAHALFTRDVDYIVKDGEVIIVDEHTGRTMQGRRWSDGLHQAVEAKEGVQIQNENQTLASITFQNYFRLYEKLAGM  382 (853)
T ss_dssp             ------------------------------------------------------CCCCCEEEEEEEHHHHHTTSSEEEEE
T ss_pred             HHHHHHHHHhhcCccceeecCcEEEEecccCcccCCCccchhhhHHHHhcccceecccccccceeehHHHHhhhhhhhcC
Confidence                 00011000                                     0111111111111111              


Q ss_pred             --------------------------------EEEEEccchhhhHHHHHHHHHh-c-cCCCeEEEeCCHhhHHHHHHHHh
Q 017573          211 --------------------------------QFYVNVEKEEWKLETLCDLYET-L-AITQSVIFVNTRRKVDWLTDKMR  256 (369)
Q Consensus       211 --------------------------------~~~~~~~~~~~~~~~l~~~~~~-~-~~~k~lv~~~~~~~~~~~~~~l~  256 (369)
                                                      ...........+...+...+.. + .+.++||||++++.++.+++.|+
T Consensus       383 TGTa~te~~ef~~iY~l~vv~IPtn~p~~R~d~~d~v~~~~~~K~~al~~~i~~~~~~gqpvLVft~sie~se~Ls~~L~  462 (853)
T 2fsf_A          383 TGTADTEAFEFSSIYKLDTVVVPTNRPMIRKDLPDLVYMTEAEKIQAIIEDIKERTAKGQPVLVGTISIEKSELVSNELT  462 (853)
T ss_dssp             ECTTCCCHHHHHHHHCCEEEECCCSSCCCCEECCCEEESSHHHHHHHHHHHHHHHHTTTCCEEEEESSHHHHHHHHHHHH
T ss_pred             CCCchhHHHHHHHHhCCcEEEcCCCCCceeecCCcEEEeCHHHHHHHHHHHHHHHhcCCCCEEEEECcHHHHHHHHHHHH
Confidence                                            1011123445577777776654 2 45689999999999999999999


Q ss_pred             hCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCC--------------------------------
Q 017573          257 SRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQV--------------------------------  304 (369)
Q Consensus       257 ~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~--------------------------------  304 (369)
                      +.|+++..+||+....++..+.+.|+.|  .|+|||+++++|+|++..                                
T Consensus       463 ~~gi~~~vLnak~~~rEa~iia~agr~G--~VtIATnmAgRGtDI~l~gn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V  540 (853)
T 2fsf_A          463 KAGIKHNVLNAKFHANEAAIVAQAGYPA--AVTIATNMAGRGTDIVLGGSWQAEVAALENPTAEQIEKIKADWQVRHDAV  540 (853)
T ss_dssp             HTTCCCEECCTTCHHHHHHHHHTTTSTT--CEEEEESCCSSCSCCCTTCCHHHHHHHCSSCCSSHHHHHHHHHHHHHHHH
T ss_pred             HCCCCEEEecCChhHHHHHHHHhcCCCC--eEEEecccccCCcCccCCCchHhhhhhcccchhHHHHHHHHHhhhhhhHH
Confidence            9999999999999888888888888877  599999999999999863                                


Q ss_pred             -----cEEEEecCCCCccchhhhhcccccCCCceeEEEEeccccHH
Q 017573          305 -----SLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDER  345 (369)
Q Consensus       305 -----~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~  345 (369)
                           .+||.++.|.|...|.|++||+||.|.+|.+++|++..|.-
T Consensus       541 ~~~GGl~VI~te~pes~riy~qr~GRTGRqGd~G~s~~fls~eD~l  586 (853)
T 2fsf_A          541 LEAGGLHIIGTERHESRRIDNQLRGRSGRQGDAGSSRFYLSMEDAL  586 (853)
T ss_dssp             HHTTSEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEETTSGG
T ss_pred             HhcCCcEEEEccCCCCHHHHHhhccccccCCCCeeEEEEecccHHH
Confidence                 59999999999999999999999999999999999987643

>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=100.00  E-value=5.5e-37  Score=283.53  Aligned_cols=324  Identities=20%  Similarity=0.259  Sum_probs=245.6

Q ss_pred             hCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccC
Q 017573           13 AYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLG   92 (369)
Q Consensus        13 ~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~   92 (369)
                      ..|+ +|++.|..+++.+.+|+  +..++||+|||+++.++++.....+   ..++||+|++.|+.|..+++..+...++
T Consensus       107 ~lG~-rP~~VQ~~~ip~Ll~G~--Iaem~TGeGKTLa~~LP~~l~aL~g---~~v~VvTpTreLA~Qdae~m~~l~~~lG  180 (922)
T 1nkt_A          107 VLDQ-RPFDVQVMGAAALHLGN--VAEMKTGEGKTLTCVLPAYLNALAG---NGVHIVTVNDYLAKRDSEWMGRVHRFLG  180 (922)
T ss_dssp             HHSC-CCCHHHHHHHHHHHTTE--EEECCTTSCHHHHTHHHHHHHHTTT---SCEEEEESSHHHHHHHHHHHHHHHHHTT
T ss_pred             HcCC-CCCHHHHHHHHhHhcCC--EEEecCCCccHHHHHHHHHHHHHhC---CCeEEEeCCHHHHHHHHHHHHHHHhhcC
Confidence            4687 99999999999999888  9999999999999999986433333   3799999999999999999999999999


Q ss_pred             cEEEEEECCcchHHHHHHHccCCcEEEeccHHH-HHHHHcC------CCCCCCccEEEEechhHhh-cc-----------
Q 017573           93 VKVHACVGGTSVREDQRILQAGVHVVVGTPGRV-FDMLRRQ------SLRPDYIKMFVLDEADEML-SR-----------  153 (369)
Q Consensus        93 ~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l-~~~~~~~------~~~~~~~~~viiDE~H~~~-~~-----------  153 (369)
                      +++..+.|+........  ...++|+++||..| +.++...      ......+.++|+||+|++. +.           
T Consensus       181 Lsv~~i~gg~~~~~r~~--~y~~DIvygTpgrlgfDyLrD~m~~~~~~l~lr~l~~lIVDEaDsmLiDeartPLiiSg~~  258 (922)
T 1nkt_A          181 LQVGVILATMTPDERRV--AYNADITYGTNNEFGFDYLRDNMAHSLDDLVQRGHHYAIVDEVDSILIDEARTPLIISGPA  258 (922)
T ss_dssp             CCEEECCTTCCHHHHHH--HHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEETTHHHHHTTGGGSCEEEEEEC
T ss_pred             CeEEEEeCCCCHHHHHH--hcCCCEEEECchHhhHHHHHhhhhccHhhhccCCCCEEEEeChHHHHHhcCccceeecCCC
Confidence            99999999887543332  33589999999999 6777654      3455678999999999987 32           


Q ss_pred             ----CcHHHHHHHHhhCC---------ccCcEE-----------------EEEeeCChhHHHH-----HHHhcCCCE---
Q 017573          154 ----GFKDQIYDIFQLLP---------AKVQVG-----------------VFSATMPPEALEI-----TRKFMNKPV---  195 (369)
Q Consensus       154 ----~~~~~~~~~~~~~~---------~~~~~i-----------------~~saT~~~~~~~~-----~~~~~~~~~---  195 (369)
                          ++...+..+...++         +..++.                 ++|||.+.-....     ...++....   
T Consensus       259 ~~~~~~y~~i~~iv~~L~~~~dy~vDek~rqv~Lte~G~~~~e~~l~i~~Lfsat~~~l~~~i~~aL~A~~l~~~d~dYi  338 (922)
T 1nkt_A          259 DGASNWYTEFARLAPLMEKDVHYEVDLRKRTVGVHEKGVEFVEDQLGIDNLYEAANSPLVSYLNNALKAKELFSRDKDYI  338 (922)
T ss_dssp             CCCHHHHHHHHHHHHHSCBTTTEEEETTTTEEEECHHHHHHHHHHHTCSSTTCSTTCCHHHHHHHHHHHHHHCCBTTTEE
T ss_pred             CcchhHHHHHHHHHHhCcccccceeccCcceEEecHhHHHHHHHHhCCccccCCcchhHHHHHHHHHHHHHHhhccccee
Confidence                36678888888887         566776                 6788865311111     111221110   


Q ss_pred             -----EEEecC-----------------------------ccccc-----------------------------------
Q 017573          196 -----RILVKR-----------------------------DELTL-----------------------------------  206 (369)
Q Consensus       196 -----~~~~~~-----------------------------~~~~~-----------------------------------  206 (369)
                           .+.+..                             +....                                   
T Consensus       339 V~dg~vviVDe~TGR~m~grr~sdGLHQaieaKe~V~I~~e~~TlatIt~Qnyfr~Y~kL~GMTGTa~te~~Ef~~iY~l  418 (922)
T 1nkt_A          339 VRDGEVLIVDEFTGRVLIGRRYNEGMHQAIEAKEHVEIKAENQTLATITLQNYFRLYDKLAGMTGTAQTEAAELHEIYKL  418 (922)
T ss_dssp             ECSSCEEEBCSSSCCBCTTCCCSTTHHHHHHHHTTCCCCCCEEEEEEECHHHHHTTSSEEEEEESCCGGGHHHHHHHHCC
T ss_pred             eecCceEEEecccCcccCCccccchhhHHHhccccccccccccccceeehHHHHHhhhhhhccccCchhHHHHHHHHhCC
Confidence                 000000                             00000                                   


Q ss_pred             -----------cceeEEEEEccchhhhHHHHHHHHHh-c-cCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHH
Q 017573          207 -----------EGIKQFYVNVEKEEWKLETLCDLYET-L-AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNT  273 (369)
Q Consensus       207 -----------~~~~~~~~~~~~~~~~~~~l~~~~~~-~-~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~  273 (369)
                                 ...............+...+...+.. + .+.++||||++++.++.+++.|.+.|+++..+||+....+
T Consensus       419 ~vv~IPtn~p~~R~d~~d~v~~t~~~K~~al~~~i~~~~~~gqpvLVft~Sie~sE~Ls~~L~~~Gi~~~vLnak~~~rE  498 (922)
T 1nkt_A          419 GVVSIPTNMPMIREDQSDLIYKTEEAKYIAVVDDVAERYAKGQPVLIGTTSVERSEYLSRQFTKRRIPHNVLNAKYHEQE  498 (922)
T ss_dssp             EEEECCCSSCCCCEECCCEEESCHHHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHTTCCCEEECSSCHHHH
T ss_pred             CeEEeCCCCCcccccCCcEEEeCHHHHHHHHHHHHHHHHhcCCcEEEEECCHHHHHHHHHHHHHCCCCEEEecCChhHHH
Confidence                       00000001122344567777666643 2 4568999999999999999999999999999999988777


Q ss_pred             HHHHHHHHhcCCCcEEEEecCCcCCCCCCCC-------------------------------------------------
Q 017573          274 RDIIMREFRSGSSRVLITTDLLARGIDVQQV-------------------------------------------------  304 (369)
Q Consensus       274 r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~-------------------------------------------------  304 (369)
                      +..+.+.|+.|  .|+|||+++++|+|++..                                                 
T Consensus       499 a~iia~agr~G--~VtIATnmAgRGtDI~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~  576 (922)
T 1nkt_A          499 ATIIAVAGRRG--GVTVATNMAGRGTDIVLGGNVDFLTDQRLRERGLDPVETPEEYEAAWHSELPIVKEEASKEAKEVIE  576 (922)
T ss_dssp             HHHHHTTTSTT--CEEEEETTCSTTCCCCTTCCHHHHHHHHHHHTTCCTTTSHHHHHHHHHHHHHHHHHHTTHHHHHHHH
T ss_pred             HHHHHhcCCCC--eEEEecchhhcCccccCCCCHHHHHHHHHhhccccccccchhhHHHHHHHHHHHHHHHHHhhhHHHh
Confidence            77777777776  599999999999999964                                                 


Q ss_pred             ---cEEEEecCCCCccchhhhhcccccCCCceeEEEEeccccHHH
Q 017573          305 ---SLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERM  346 (369)
Q Consensus       305 ---~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~  346 (369)
                         .+||.++.|.|...|.|++||+||.|.+|.+++|++..|.-+
T Consensus       577 ~GGlhVI~te~pes~riy~qr~GRTGRqGdpG~s~fflSleD~l~  621 (922)
T 1nkt_A          577 AGGLYVLGTERHESRRIDNQLRGRSGRQGDPGESRFYLSLGDELM  621 (922)
T ss_dssp             TTSEEEEECSCCSSHHHHHHHHHTSSGGGCCEEEEEEEETTSHHH
T ss_pred             cCCcEEEeccCCCCHHHHHHHhcccccCCCCeeEEEEechhHHHH
Confidence               489999999999999999999999999999999999877643

>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=100.00  E-value=6.3e-39  Score=312.20  Aligned_cols=333  Identities=17%  Similarity=0.133  Sum_probs=231.2

Q ss_pred             CCCcHhhhhhhhccccC--CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcE
Q 017573           17 EKPSAIQQRGIVPFCKG--LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVK   94 (369)
Q Consensus        17 ~~~~~~Q~~~~~~~~~~--~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~   94 (369)
                      .+|+|||.+++..+...  .++++.++||+|||.+++..+...+..+..+ ++|||||+ +|+.||.+++.+.+   +++
T Consensus       152 ~~LrpyQ~eav~~~l~~~~~~~LLad~tGlGKTi~Ai~~i~~l~~~g~~~-rvLIVvP~-sLl~Qw~~E~~~~f---~l~  226 (968)
T 3dmq_A          152 TSLIPHQLNIAHDVGRRHAPRVLLADEVGLGKTIEAGMILHQQLLSGAAE-RVLIIVPE-TLQHQWLVEMLRRF---NLR  226 (968)
T ss_dssp             SCCCHHHHHHHHHHHHSSSCEEEECCCTTSCHHHHHHHHHHHHHHTSSCC-CEEEECCT-TTHHHHHHHHHHHS---CCC
T ss_pred             CCCcHHHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHHhCCCC-eEEEEeCH-HHHHHHHHHHHHHh---CCC
Confidence            47999999999988764  5899999999999999988877766655443 89999999 99999999997765   455


Q ss_pred             EEEEECCcchHHHHH--HHccCCcEEEeccHHHHHHHHc-CCCCCCCccEEEEechhHhhccCcH--HHHHHHHhhCCcc
Q 017573           95 VHACVGGTSVREDQR--ILQAGVHVVVGTPGRVFDMLRR-QSLRPDYIKMFVLDEADEMLSRGFK--DQIYDIFQLLPAK  169 (369)
Q Consensus        95 v~~~~~~~~~~~~~~--~~~~~~~iiv~t~~~l~~~~~~-~~~~~~~~~~viiDE~H~~~~~~~~--~~~~~~~~~~~~~  169 (369)
                      +..++++........  ......+|+|+|++.+...... ..+....+++||+||||++.+....  .....+.......
T Consensus       227 v~v~~~~~~~~~~~~~~~~~~~~dIvI~T~~~L~~~~~~~~~l~~~~~dlVIvDEAH~~kn~~~~~s~~~~~l~~L~~~~  306 (968)
T 3dmq_A          227 FALFDDERYAEAQHDAYNPFDTEQLVICSLDFARRSKQRLEHLCEAEWDLLVVDEAHHLVWSEDAPSREYQAIEQLAEHV  306 (968)
T ss_dssp             CEECCHHHHHHHHHTTCSSSTTCSEEEECHHHHHTSTTTTHHHHTSCCCEEEECCSSCCCCBTTBCCHHHHHHHHHHTTC
T ss_pred             EEEEccchhhhhhhhcccccccCCEEEEcHHHHhhCHHHHHHhhhcCCCEEEehhhHhhcCCCCcchHHHHHHHHHhhcC
Confidence            555544332211111  1123568999999988542111 1122345899999999999754422  1122222222345


Q ss_pred             CcEEEEEeeCChh----HHHHHH----------------------------HhcCC------------------------
Q 017573          170 VQVGVFSATMPPE----ALEITR----------------------------KFMNK------------------------  193 (369)
Q Consensus       170 ~~~i~~saT~~~~----~~~~~~----------------------------~~~~~------------------------  193 (369)
                      .+++++||||..+    ...+..                            .+...                        
T Consensus       307 ~~~L~LTATPi~n~~~el~sll~~L~p~~~~~~~~f~~~~~~~~~i~~~~~~l~~~~~~~~~~~~~L~~~l~~~~~~~l~  386 (968)
T 3dmq_A          307 PGVLLLTATPEQLGMESHFARLRLLDPNRFHDFAQFVEEQKNYCPVADAVAMLLAGNKLSNDELNMLGEMIGEQDIEPLL  386 (968)
T ss_dssp             SSEEESCSSCSSSCSSCTHHHHHHHCTTTCSSTHHHHHHHHHHHHHHHHHHTTTTSCCCCGGGTTSSTTTTCTTCSSTTG
T ss_pred             CcEEEEEcCCccCCHHHHHHHHHhcCccccCCHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHHHhcchhhHHHH
Confidence            5689999999531    111100                            00000                        


Q ss_pred             ----------------------------CEEEEecCc---cccccceeEEEEE---------------------------
Q 017573          194 ----------------------------PVRILVKRD---ELTLEGIKQFYVN---------------------------  215 (369)
Q Consensus       194 ----------------------------~~~~~~~~~---~~~~~~~~~~~~~---------------------------  215 (369)
                                                  ...+.....   .............                           
T Consensus       387 ~~~~~~~~~~~~~~~~~i~~lld~~g~~~~l~r~~r~~i~~~p~r~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~  466 (968)
T 3dmq_A          387 QAANSDSEDAQSARQELVSMLMDRHGTSRVLFRNTRNGVKGFPKRELHTIKLPLPTQYQTAIKVSGIMGARKSAEDRARD  466 (968)
T ss_dssp             GGTCCCSSCSTTTHHHHHHHHGGGCTTTTTEECCCTTTCCCCCCCCCCEEEECCCHHHHHHHHHHHHTTCCSSGGGGTHH
T ss_pred             hcccchhhhhHHHHHHHHHHHHHhhCcchhhhhhhhhhhcccChhheEeeecCCCHHHHHHHHHHhhhhhhhhhHHHHhh
Confidence                                        000000000   0000001111111                           


Q ss_pred             -----------------ccchhhhHHHHHHHHHhccCCCeEEEeCCHhhHHHHHHHHhh-CCCeeEEecCCCCHHHHHHH
Q 017573          216 -----------------VEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRS-RDHTVSATHGDMDQNTRDII  277 (369)
Q Consensus       216 -----------------~~~~~~~~~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~-~~~~~~~~~~~~~~~~r~~~  277 (369)
                                       ......+...+.+++....++++||||++.+.++.+++.|.. .+.++..+||+++..+|.++
T Consensus       467 ~l~pe~~~~~l~~~~~~~~~~~~K~~~L~~ll~~~~~~k~iVF~~~~~~~~~l~~~L~~~~g~~~~~lhG~~~~~~R~~~  546 (968)
T 3dmq_A          467 MLYPERIYQEFEGDNATWWNFDPRVEWLMGYLTSHRSQKVLVICAKAATALQLEQVLREREGIRAAVFHEGMSIIERDRA  546 (968)
T ss_dssp             HHCSGGGTTTTTSSSCCTTTTSHHHHHHHHHHHHTSSSCCCEECSSTHHHHHHHHHHHTTTCCCEEEECTTSCTTHHHHH
T ss_pred             hcChHHHHHHhhhhhhcccCccHHHHHHHHHHHhCCCCCEEEEeCcHHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHH
Confidence                             112234677788888887788999999999999999999994 59999999999999999999


Q ss_pred             HHHHhcCC--CcEEEEecCCcCCCCCCCCcEEEEecCCCCccchhhhhcccccCCCceeEEEEeccccHHHHHHHHHHh
Q 017573          278 MREFRSGS--SRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFY  354 (369)
Q Consensus       278 ~~~f~~~~--~~vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~~  354 (369)
                      ++.|++|+  ++|||+|+++++|+|+|.+++||++++|+++..|.|++||++|.|+.+.++++.........+.+.+.+
T Consensus       547 l~~F~~g~~~~~vLvaT~v~~~GlDl~~~~~VI~~d~p~~~~~~~Q~~GR~~R~Gq~~~v~v~~~~~~~t~ee~i~~~~  625 (968)
T 3dmq_A          547 AAWFAEEDTGAQVLLCSEIGSEGRNFQFASHMVMFDLPFNPDLLEQRIGRLDRIGQAHDIQIHVPYLEKTAQSVLVRWY  625 (968)
T ss_dssp             HHHHHSTTSSCEEEECSCCTTCSSCCTTCCEEECSSCCSSHHHHHHHHHTTSCSSSCSCCEEEEEEETTSHHHHHHHHH
T ss_pred             HHHHhCCCCcccEEEecchhhcCCCcccCcEEEEecCCCCHHHHHHHhhccccCCCCceEEEEEecCCChHHHHHHHHH
Confidence            99999998  999999999999999999999999999999999999999999999998777665544333334444444

>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=100.00  E-value=1.1e-37  Score=286.36  Aligned_cols=311  Identities=16%  Similarity=0.198  Sum_probs=214.9

Q ss_pred             CCCcHhhhhhhhccc----cCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccC
Q 017573           17 EKPSAIQQRGIVPFC----KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLG   92 (369)
Q Consensus        17 ~~~~~~Q~~~~~~~~----~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~   92 (369)
                      ..|+|||.++++.+.    .++++++.++||+|||++++..+......+ ...++|||||. +|+.||.+++.++...  
T Consensus        36 ~~L~~~Q~~~v~~l~~~~~~~~~~ilad~~GlGKT~~ai~~i~~~~~~~-~~~~~LIv~P~-~l~~qw~~e~~~~~~~--  111 (500)
T 1z63_A           36 ANLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAVFSDAKKEN-ELTPSLVICPL-SVLKNWEEELSKFAPH--  111 (500)
T ss_dssp             SCCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHHHHHHHHHHTT-CCSSEEEEECS-TTHHHHHHHHHHHCTT--
T ss_pred             ccchHHHHHHHHHHHHHhhCCCCEEEEeCCCCcHHHHHHHHHHHHHhcC-CCCCEEEEccH-HHHHHHHHHHHHHCCC--
Confidence            369999999998763    578999999999999999876665544333 33489999995 6899999999998753  


Q ss_pred             cEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCccCcE
Q 017573           93 VKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQV  172 (369)
Q Consensus        93 ~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~  172 (369)
                      .++...+++...     ....+++|+|+||+.+.....   +....+++||+||||++.+..  ......+..++ ..+.
T Consensus       112 ~~v~~~~g~~~~-----~~~~~~~ivi~t~~~l~~~~~---l~~~~~~~vIvDEaH~~kn~~--~~~~~~l~~l~-~~~~  180 (500)
T 1z63_A          112 LRFAVFHEDRSK-----IKLEDYDIILTTYAVLLRDTR---LKEVEWKYIVIDEAQNIKNPQ--TKIFKAVKELK-SKYR  180 (500)
T ss_dssp             SCEEECSSSTTS-----CCGGGSSEEEEEHHHHTTCHH---HHTCCEEEEEEETGGGGSCTT--SHHHHHHHTSC-EEEE
T ss_pred             ceEEEEecCchh-----ccccCCcEEEeeHHHHhccch---hcCCCcCEEEEeCccccCCHh--HHHHHHHHhhc-cCcE
Confidence            455555554421     122457999999999865432   223458999999999997554  23444555554 4567


Q ss_pred             EEEEeeCChhHHHH-------------------------------------HHHhcCCCEEEEe-cCc----ccccccee
Q 017573          173 GVFSATMPPEALEI-------------------------------------TRKFMNKPVRILV-KRD----ELTLEGIK  210 (369)
Q Consensus       173 i~~saT~~~~~~~~-------------------------------------~~~~~~~~~~~~~-~~~----~~~~~~~~  210 (369)
                      +++||||..+....                                     ....+. +..+.. ..+    ...+....
T Consensus       181 l~LTaTP~~n~~~el~~ll~~l~p~~~~~~~~f~~~~~~~~~~~~~~~~~~l~~~l~-~~~lrr~k~~~~~~~~lp~~~~  259 (500)
T 1z63_A          181 IALTGTPIENKVDDLWSIMTFLNPGLLGSYSEFKSKFATPIKKGDNMAKEELKAIIS-PFILRRTKYDKAIINDLPDKIE  259 (500)
T ss_dssp             EEECSSCSTTCHHHHHHHHHHHSTTTTCCHHHHHTTTHHHHHTTCHHHHHHHHHHHT-TTEECCCTTCHHHHTTSCSEEE
T ss_pred             EEEecCCCCCCHHHHHHHHHHhCCCcCCCHHHHHHHhccccccccHHHHHHHHHHHh-hHeeeecccccchhhcCCCCeE
Confidence            99999996432111                                     111111 111111 100    00111111


Q ss_pred             -EEEEEccc------------------------------------------------------hhhhHHHHHHHHHhc--
Q 017573          211 -QFYVNVEK------------------------------------------------------EEWKLETLCDLYETL--  233 (369)
Q Consensus       211 -~~~~~~~~------------------------------------------------------~~~~~~~l~~~~~~~--  233 (369)
                       ..+.....                                                      ...+...+.+++...  
T Consensus       260 ~~v~~~l~~~~~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~l~~lr~~~~~p~l~~~~~~~~~~s~K~~~l~~~l~~~~~  339 (500)
T 1z63_A          260 TNVYCNLTPEQAAMYKAEVENLFNNIDSVTGIKRKGMILSTLLKLKQIVDHPALLKGGEQSVRRSGKMIRTMEIIEEALD  339 (500)
T ss_dssp             EEEEECCCHHHHHHHHHHHHHHTTTTTTCCTHHHHHHHHHHHHHHHHHTTCTHHHHCSCCCSTTCHHHHHHHHHHHHHHT
T ss_pred             EEEEcCCCHHHHHHHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhCCHHHhcCccchhhcchhHHHHHHHHHHHHc
Confidence             11111111                                                      112334444555443  


Q ss_pred             cCCCeEEEeCCHhhHHHHHHHHhhC-CCeeEEecCCCCHHHHHHHHHHHhcC-CCc-EEEEecCCcCCCCCCCCcEEEEe
Q 017573          234 AITQSVIFVNTRRKVDWLTDKMRSR-DHTVSATHGDMDQNTRDIIMREFRSG-SSR-VLITTDLLARGIDVQQVSLVINY  310 (369)
Q Consensus       234 ~~~k~lv~~~~~~~~~~~~~~l~~~-~~~~~~~~~~~~~~~r~~~~~~f~~~-~~~-vli~t~~~~~G~d~~~~~~vi~~  310 (369)
                      .+.|+|||+++...++.+.+.|... +..+..++|+++..+|.++++.|+++ +.+ +|++|.++++|+|+|.+++||++
T Consensus       340 ~~~k~lvF~~~~~~~~~l~~~l~~~~~~~~~~~~g~~~~~~R~~~~~~F~~~~~~~vil~st~~~~~Glnl~~~~~vi~~  419 (500)
T 1z63_A          340 EGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVKAGGFGINLTSANRVIHF  419 (500)
T ss_dssp             TTCCEEEECSCHHHHHHHHHHHHHHHTCCCCEEETTSCHHHHHHHHHHHHHCTTCCCCEEECCCC-CCCCCTTCSEEEES
T ss_pred             cCCcEEEEEehHHHHHHHHHHHHHhhCCCeEEEECCCCHHHHHHHHHHhcCCCCCCEEEEecccccCCCchhhCCEEEEe
Confidence            5679999999999999999999885 88999999999999999999999988 455 78899999999999999999999


Q ss_pred             cCCCCccchhhhhcccccCCCceeE--EEEecccc
Q 017573          311 DLPTQPENYLHRIGRSGRFGRKGVA--INFVTRDD  343 (369)
Q Consensus       311 ~~~~~~~~~~Q~~GR~~R~~~~~~~--~~~~~~~~  343 (369)
                      ++|||+..+.|++||++|.|+.+.+  +.++..+.
T Consensus       420 d~~~~~~~~~Q~~gR~~R~Gq~~~v~v~~lv~~~t  454 (500)
T 1z63_A          420 DRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVGT  454 (500)
T ss_dssp             SCCSCC---CHHHHTTTTTTTTSCEEEEEEEETTS
T ss_pred             CCCCCcchHHHHHHHHHHcCCCCeeEEEEEEeCCC
Confidence            9999999999999999999987655  44555554

>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=100.00  E-value=1.7e-38  Score=286.25  Aligned_cols=287  Identities=18%  Similarity=0.155  Sum_probs=206.8

Q ss_pred             CCCCCcHhhhhhhhccccCCcE-EEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCc
Q 017573           15 GFEKPSAIQQRGIVPFCKGLDV-IQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGV   93 (369)
Q Consensus        15 ~~~~~~~~Q~~~~~~~~~~~~~-li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~   93 (369)
                      |+.+++|.|+ +++.++++++. ++.+|||||||++++++++..+...  +++++|++|+++|+.|+.+.+.      +.
T Consensus         1 G~~q~~~iq~-~i~~~l~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~~--~~~~lvl~Ptr~La~Q~~~~l~------g~   71 (451)
T 2jlq_A            1 GSAMGEPDYE-VDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALLR--RLRTLILAPTRVVAAEMEEALR------GL   71 (451)
T ss_dssp             CCCCCSCCCC-CCGGGGSTTCEEEECCCTTSSCCTTHHHHHHHHHHHT--TCCEEEEESSHHHHHHHHHHTT------TS
T ss_pred             CCCCCCCcHH-HHHHHHhcCCeEEEECCCCCCHhhHHHHHHHHHHHhc--CCcEEEECCCHHHHHHHHHHhc------Cc
Confidence            6788999985 78999988776 9999999999998888887665432  2489999999999999999875      23


Q ss_pred             EEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHH-hhCCccCcE
Q 017573           94 KVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIF-QLLPAKVQV  172 (369)
Q Consensus        94 ~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~-~~~~~~~~~  172 (369)
                      .+.........     .......+.++|++.+.+.+... ....+++++|+||+|++ +..+......+. ...++..++
T Consensus        72 ~v~~~~~~~~~-----~~~~~~~i~~~t~~~l~~~l~~~-~~l~~~~~iViDEah~~-~~~~~~~~~~~~~~~~~~~~~~  144 (451)
T 2jlq_A           72 PIRYQTPAVKS-----DHTGREIVDLMCHATFTTRLLSS-TRVPNYNLIVMDEAHFT-DPCSVAARGYISTRVEMGEAAA  144 (451)
T ss_dssp             CEEECCTTCSC-----CCCSSCCEEEEEHHHHHHHHHHC-SCCCCCSEEEEETTTCC-SHHHHHHHHHHHHHHHTTSCEE
T ss_pred             eeeeeeccccc-----cCCCCceEEEEChHHHHHHhhCc-ccccCCCEEEEeCCccC-CcchHHHHHHHHHhhcCCCceE
Confidence            33322221110     11234578899999988777654 45677899999999976 222122222222 223457899


Q ss_pred             EEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHHHhccCCCeEEEeCCHhhHHHHH
Q 017573          173 GVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLT  252 (369)
Q Consensus       173 i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lv~~~~~~~~~~~~  252 (369)
                      ++||||++......   +...+..+..... .....    +      .    .+...+.. ..+++||||++++.++.++
T Consensus       145 i~~SAT~~~~~~~~---~~~~~~~~~~~~~-~p~~~----~------~----~~~~~l~~-~~~~~lVF~~s~~~a~~l~  205 (451)
T 2jlq_A          145 IFMTATPPGSTDPF---PQSNSPIEDIERE-IPERS----W------N----TGFDWITD-YQGKTVWFVPSIKAGNDIA  205 (451)
T ss_dssp             EEECSSCTTCCCSS---CCCSSCEEEEECC-CCSSC----C------S----SSCHHHHH-CCSCEEEECSSHHHHHHHH
T ss_pred             EEEccCCCccchhh---hcCCCceEecCcc-CCchh----h------H----HHHHHHHh-CCCCEEEEcCCHHHHHHHH
Confidence            99999997643221   1122222221110 00000    0      0    01122222 2569999999999999999


Q ss_pred             HHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEec--------------------C
Q 017573          253 DKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYD--------------------L  312 (369)
Q Consensus       253 ~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~--------------------~  312 (369)
                      +.|++.+..+..+|+++    +.++++.|++|+.+|||||+++++|+|+|+ ++||.++                    .
T Consensus       206 ~~L~~~g~~~~~lh~~~----~~~~~~~f~~g~~~vLVaT~v~~~GiDip~-~~VI~~~~~~~~~~d~~~~~~l~~~~~~  280 (451)
T 2jlq_A          206 NCLRKSGKRVIQLSRKT----FDTEYPKTKLTDWDFVVTTDISEMGANFRA-GRVIDPRRCLKPVILTDGPERVILAGPI  280 (451)
T ss_dssp             HHHHTTTCCEEEECTTT----HHHHGGGGGSSCCSEEEECGGGGSSCCCCC-SEEEECCEEEEEEEECSSSCEEEEEEEE
T ss_pred             HHHHHcCCeEEECCHHH----HHHHHHhhccCCceEEEECCHHHhCcCCCC-CEEEECCCcccccccccccceeeecccc
Confidence            99999999999999975    357899999999999999999999999999 9999887                    8


Q ss_pred             CCCccchhhhhcccccCCC-ceeEEEEecc
Q 017573          313 PTQPENYLHRIGRSGRFGR-KGVAINFVTR  341 (369)
Q Consensus       313 ~~~~~~~~Q~~GR~~R~~~-~~~~~~~~~~  341 (369)
                      |.+..+|.||+||+||.|+ .|.++++...
T Consensus       281 p~s~~~y~Qr~GRaGR~g~~~g~~~~~~~~  310 (451)
T 2jlq_A          281 PVTPASAAQRRGRIGRNPAQEDDQYVFSGD  310 (451)
T ss_dssp             ECCHHHHHHHHTTSSCCTTCCCEEEEECSC
T ss_pred             cCCHHHHHHhccccCCCCCCCccEEEEeCC
Confidence            8999999999999999998 7888888754

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=100.00  E-value=1.1e-38  Score=297.28  Aligned_cols=300  Identities=20%  Similarity=0.180  Sum_probs=209.2

Q ss_pred             CCcHhhh-----hhhhccc------cCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHH
Q 017573           18 KPSAIQQ-----RGIVPFC------KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRA   86 (369)
Q Consensus        18 ~~~~~Q~-----~~~~~~~------~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~   86 (369)
                      .|+++|+     ++++.++      +++++++++|||+|||++++++++..+...  +.+++|++|+++|+.|+.+.+..
T Consensus       215 ~pt~IQ~~~r~~~aIp~~l~~~~l~~g~dvlv~apTGSGKTl~~ll~il~~l~~~--~~~~lilaPTr~La~Q~~~~l~~  292 (673)
T 2wv9_A          215 YVSAIVQGERVEEPVPEAYNPEMLKKRQLTVLDLHPGAGKTRRILPQIIKDAIQK--RLRTAVLAPTRVVAAEMAEALRG  292 (673)
T ss_dssp             EEEEEECC-------CCCCCGGGGSTTCEEEECCCTTTTTTTTHHHHHHHHHHHT--TCCEEEEESSHHHHHHHHHHTTT
T ss_pred             ccCceeeccccccchHHHhhHHHHhcCCeEEEEeCCCCCHHHHHHHHHHHHHHhC--CCcEEEEccHHHHHHHHHHHHhc
Confidence            8999999     9999888      899999999999999999988888775543  23899999999999999998875


Q ss_pred             hccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhC
Q 017573           87 LGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLL  166 (369)
Q Consensus        87 ~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~  166 (369)
                      +    ++.  ...+...     .....+.-+-+.+...+.+.+... ....+++++|+||+|++. ..+......+....
T Consensus       293 ~----~i~--~~~~~l~-----~v~tp~~ll~~l~~~~l~~~l~~~-~~l~~l~lvViDEaH~~~-~~~~~~~~~l~~~~  359 (673)
T 2wv9_A          293 L----PVR--YLTPAVQ-----REHSGNEIVDVMCHATLTHRLMSP-LRVPNYNLFVMDEAHFTD-PASIAARGYIATRV  359 (673)
T ss_dssp             S----CCE--ECCC--------CCCCSCCCEEEEEHHHHHHHHHSS-SCCCCCSEEEEESTTCCC-HHHHHHHHHHHHHH
T ss_pred             C----Cee--eeccccc-----ccCCHHHHHHHHHhhhhHHHHhcc-cccccceEEEEeCCcccC-ccHHHHHHHHHHhc
Confidence            4    221  1111000     011122334555666665555543 556779999999999971 11122222333333


Q ss_pred             -CccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHHHhccCCCeEEEeCCH
Q 017573          167 -PAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTR  245 (369)
Q Consensus       167 -~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lv~~~~~  245 (369)
                       +...++++||||+++....+...  ..++.              ........ ......+. .+.. ..+++||||+++
T Consensus       360 ~~~~~~vl~~SAT~~~~i~~~~~~--~~~i~--------------~v~~~~~~-~~~~~~l~-~l~~-~~~~~lVF~~s~  420 (673)
T 2wv9_A          360 EAGEAAAIFMTATPPGTSDPFPDT--NSPVH--------------DVSSEIPD-RAWSSGFE-WITD-YAGKTVWFVASV  420 (673)
T ss_dssp             HTTSCEEEEECSSCTTCCCSSCCC--SSCEE--------------EEECCCCS-SCCSSCCH-HHHS-CCSCEEEECSSH
T ss_pred             cccCCcEEEEcCCCChhhhhhccc--CCceE--------------EEeeecCH-HHHHHHHH-HHHh-CCCCEEEEECCH
Confidence             25789999999997653211100  01111              11100111 00111111 2222 467999999999


Q ss_pred             hhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEE----------------
Q 017573          246 RKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVIN----------------  309 (369)
Q Consensus       246 ~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~----------------  309 (369)
                      +.++.+++.|++.+..+..+||+    +|.++++.|++|+.+|||||+++++|+|+| +++||+                
T Consensus       421 ~~~e~la~~L~~~g~~v~~lHg~----eR~~v~~~F~~g~~~VLVaTdv~e~GIDip-v~~VI~~g~~~~p~vi~da~~r  495 (673)
T 2wv9_A          421 KMSNEIAQCLQRAGKRVIQLNRK----SYDTEYPKCKNGDWDFVITTDISEMGANFG-ASRVIDCRKSVKPTILDEGEGR  495 (673)
T ss_dssp             HHHHHHHHHHHTTTCCEEEECSS----SHHHHGGGGGTCCCSEEEECGGGGTTCCCC-CSEEEECCEECCEEEECSTTCE
T ss_pred             HHHHHHHHHHHhCCCeEEEeChH----HHHHHHHHHHCCCceEEEECchhhcceeeC-CcEEEECCCcccceeeeccccc
Confidence            99999999999999999999994    688999999999999999999999999999 999997                


Q ss_pred             ----ecCCCCccchhhhhcccccC-CCceeEEEEe---ccccHHHHHHHHHHhcc
Q 017573          310 ----YDLPTQPENYLHRIGRSGRF-GRKGVAINFV---TRDDERMLFDIQKFYNV  356 (369)
Q Consensus       310 ----~~~~~~~~~~~Q~~GR~~R~-~~~~~~~~~~---~~~~~~~~~~~~~~~~~  356 (369)
                          ++.|.+..+|.|++||+||. ++.|.+++++   ++.+...+..++..+..
T Consensus       496 ~~ll~d~P~s~~~y~Qr~GRaGR~~g~~G~ai~l~~~~~~~d~~~l~~ie~~~~l  550 (673)
T 2wv9_A          496 VILSVPSAITSASAAQRRGRVGRNPSQIGDEYHYGGGTSEDDTMLAHWTEAKILL  550 (673)
T ss_dssp             EEECCSEECCHHHHHHHHTTSSCCSSCCCEEEEECSCCCCCCTTBHHHHHHHHHH
T ss_pred             ceecccCCCCHHHHHHHhhccCCCCCCCCEEEEEEecCChhHHHHHHHHHHHHhh
Confidence                45788889999999999999 7899999996   56676666666665533

>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=100.00  E-value=1.3e-39  Score=292.19  Aligned_cols=295  Identities=16%  Similarity=0.163  Sum_probs=194.2

Q ss_pred             ccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHH
Q 017573           29 PFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQ  108 (369)
Q Consensus        29 ~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~  108 (369)
                      .+.+++++++++|||||||++++++++..+...  +++++|++|+++|+.|+.+.+..+      .+....+....    
T Consensus         4 ~l~~g~~vlv~a~TGSGKT~~~l~~~l~~~~~~--~~~~lil~Ptr~La~Q~~~~l~~~------~v~~~~~~~~~----   71 (440)
T 1yks_A            4 MLKKGMTTVLDFHPGAGKTRRFLPQILAECARR--RLRTLVLAPTRVVLSEMKEAFHGL------DVKFHTQAFSA----   71 (440)
T ss_dssp             TTSTTCEEEECCCTTSSTTTTHHHHHHHHHHHT--TCCEEEEESSHHHHHHHHHHTTTS------CEEEESSCCCC----
T ss_pred             HhhCCCCEEEEcCCCCCHHHHHHHHHHHHHHhc--CCeEEEEcchHHHHHHHHHHHhcC------CeEEeccccee----
Confidence            467899999999999999999988888866543  238999999999999999988743      22222211100    


Q ss_pred             HHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhC-CccCcEEEEEeeCChhHHHHH
Q 017573          109 RILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLL-PAKVQVGVFSATMPPEALEIT  187 (369)
Q Consensus       109 ~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~-~~~~~~i~~saT~~~~~~~~~  187 (369)
                       ....+.-+-..+...+...+. ......+++++|+||+|++ +..+......+.... +...++++||||+++....+.
T Consensus        72 -v~Tp~~l~~~l~~~~l~~~~~-~~~~~~~l~~vViDEah~~-~~~~~~~~~~~~~~~~~~~~~~l~~SAT~~~~~~~~~  148 (440)
T 1yks_A           72 -HGSGREVIDAMCHATLTYRML-EPTRVVNWEVIIMDEAHFL-DPASIAARGWAAHRARANESATILMTATPPGTSDEFP  148 (440)
T ss_dssp             -CCCSSCCEEEEEHHHHHHHHT-SSSCCCCCSEEEETTTTCC-SHHHHHHHHHHHHHHHTTSCEEEEECSSCTTCCCSSC
T ss_pred             -ccCCccceeeecccchhHhhh-CcccccCccEEEEECcccc-CcchHHHHHHHHHHhccCCceEEEEeCCCCchhhhhh
Confidence             000111122333333333222 2345677899999999997 222222222222222 357899999999976543211


Q ss_pred             HHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHHHhccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecC
Q 017573          188 RKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHG  267 (369)
Q Consensus       188 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~  267 (369)
                      ..  ..+.              .......... .....+. .+.. ..++++|||++++.++.+++.|+..+.++..+||
T Consensus       149 ~~--~~~~--------------~~~~~~~~~~-~~~~~~~-~l~~-~~~~~lVF~~s~~~a~~l~~~L~~~~~~v~~lhg  209 (440)
T 1yks_A          149 HS--NGEI--------------EDVQTDIPSE-PWNTGHD-WILA-DKRPTAWFLPSIRAANVMAASLRKAGKSVVVLNR  209 (440)
T ss_dssp             CC--SSCE--------------EEEECCCCSS-CCSSSCH-HHHH-CCSCEEEECSCHHHHHHHHHHHHHTTCCEEECCS
T ss_pred             hc--CCCe--------------eEeeeccChH-HHHHHHH-HHHh-cCCCEEEEeCCHHHHHHHHHHHHHcCCCEEEecc
Confidence            10  0111              1111111110 0111111 1222 2579999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEE-------------------ecCCCCccchhhhhccccc
Q 017573          268 DMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVIN-------------------YDLPTQPENYLHRIGRSGR  328 (369)
Q Consensus       268 ~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~-------------------~~~~~~~~~~~Q~~GR~~R  328 (369)
                          ++|.++++.|++|+.+|||||+++++|+|+| +++||+                   ++.|.+..+|.|++||+||
T Consensus       210 ----~~R~~~~~~F~~g~~~vLVaT~v~e~GiDip-v~~VI~~g~~~~pv~~~~~~~~vi~~~~p~~~~~~~Qr~GR~GR  284 (440)
T 1yks_A          210 ----KTFEREYPTIKQKKPDFILATDIAEMGANLC-VERVLDCRTAFKPVLVDEGRKVAIKGPLRISASSAAQRRGRIGR  284 (440)
T ss_dssp             ----SSCC--------CCCSEEEESSSTTCCTTCC-CSEEEECCEEEEEEEETTTTEEEEEEEEECCHHHHHHHHTTSSC
T ss_pred             ----hhHHHHHhhhcCCCceEEEECChhheeeccC-ceEEEeCCccceeeecccccceeeccccccCHHHHHHhccccCC
Confidence                3578899999999999999999999999999 999986                   7788999999999999999


Q ss_pred             C-CCceeEEEEe---ccccHHHHHHHHHHhccccccCC
Q 017573          329 F-GRKGVAINFV---TRDDERMLFDIQKFYNVVIEELP  362 (369)
Q Consensus       329 ~-~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~  362 (369)
                      . ++.|.|++++   ++.+...+..++..+.....+++
T Consensus       285 ~g~~~g~~~~l~~~~~~~~~~~l~~l~~~~~~~~~~l~  322 (440)
T 1yks_A          285 NPNRDGDSYYYSEPTSENNAHHVCWLEASMLLDNMEVR  322 (440)
T ss_dssp             CTTCCCEEEEECSCCCCCCTTBHHHHHHHHHHTTSCCG
T ss_pred             CCCCCceEEEEeccCChhhhhhhhhhhHHhcccccccc
Confidence            7 6899999996   67777777878777654444443

>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=100.00  E-value=1.1e-37  Score=295.89  Aligned_cols=328  Identities=16%  Similarity=0.216  Sum_probs=236.4

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhcccc-CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCK-GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQ   79 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q   79 (369)
                      +++++.+.+.++..+ ..|.+.|++++..++. ++++++.||||+|||+..-..+.........+.++++++|+++++.|
T Consensus        77 ~~l~~~~~~~l~~r~-~lP~~~q~~~i~~~l~~~~~vii~gpTGSGKTtllp~ll~~~~~~~~~g~~ilvl~P~r~La~q  155 (773)
T 2xau_A           77 REFTPKYVDILKIRR-ELPVHAQRDEFLKLYQNNQIMVFVGETGSGKTTQIPQFVLFDEMPHLENTQVACTQPRRVAAMS  155 (773)
T ss_dssp             SBCCHHHHHHHHHHT-TSGGGGGHHHHHHHHHHCSEEEEECCTTSSHHHHHHHHHHHHHCGGGGTCEEEEEESCHHHHHH
T ss_pred             cCCCHHHHHHHHHhh-cCChHHHHHHHHHHHhCCCeEEEECCCCCCHHHHHHHHHHHhccccCCCceEEecCchHHHHHH
Confidence            578999999998887 7899999999988775 56799999999999984322222221111123369999999999999


Q ss_pred             HHHHHHHhcc-ccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhH-hhccC-cH
Q 017573           80 IEKVMRALGD-YLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADE-MLSRG-FK  156 (369)
Q Consensus        80 ~~~~~~~~~~-~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~-~~~~~-~~  156 (369)
                      +.+.+.+... ..+..+........      ....+.+|+++|++.+.+.+... ....+++++|+||+|. ..+.. ..
T Consensus       156 ~~~~l~~~~~~~v~~~vG~~i~~~~------~~~~~~~I~v~T~G~l~r~l~~~-~~l~~~~~lIlDEah~R~ld~d~~~  228 (773)
T 2xau_A          156 VAQRVAEEMDVKLGEEVGYSIRFEN------KTSNKTILKYMTDGMLLREAMED-HDLSRYSCIILDEAHERTLATDILM  228 (773)
T ss_dssp             HHHHHHHHTTCCBTTTEEEEETTEE------ECCTTCSEEEEEHHHHHHHHHHS-TTCTTEEEEEECSGGGCCHHHHHHH
T ss_pred             HHHHHHHHhCCchhheecceecccc------ccCCCCCEEEECHHHHHHHHhhC-ccccCCCEEEecCccccccchHHHH
Confidence            9887765432 22333332211111      01235789999999998877664 4567789999999996 33322 22


Q ss_pred             HHHHHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhh---hHHHHHHHHHhc
Q 017573          157 DQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEW---KLETLCDLYETL  233 (369)
Q Consensus       157 ~~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~l~~~~~~~  233 (369)
                      ..+..+.... +..+++++|||++.+  .+ ..++.....+......   ..+..++........   ....+..++...
T Consensus       229 ~~l~~l~~~~-~~~~iIl~SAT~~~~--~l-~~~~~~~~vi~v~gr~---~pv~~~~~~~~~~~~~~~~l~~l~~~~~~~  301 (773)
T 2xau_A          229 GLLKQVVKRR-PDLKIIIMSATLDAE--KF-QRYFNDAPLLAVPGRT---YPVELYYTPEFQRDYLDSAIRTVLQIHATE  301 (773)
T ss_dssp             HHHHHHHHHC-TTCEEEEEESCSCCH--HH-HHHTTSCCEEECCCCC---CCEEEECCSSCCSCHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHhC-CCceEEEEeccccHH--HH-HHHhcCCCcccccCcc---cceEEEEecCCchhHHHHHHHHHHHHHHhc
Confidence            3344444433 477899999999642  33 3445443333332222   223444433333222   233444444445


Q ss_pred             cCCCeEEEeCCHhhHHHHHHHHhh-----------CCCeeEEecCCCCHHHHHHHHHHHh-----cCCCcEEEEecCCcC
Q 017573          234 AITQSVIFVNTRRKVDWLTDKMRS-----------RDHTVSATHGDMDQNTRDIIMREFR-----SGSSRVLITTDLLAR  297 (369)
Q Consensus       234 ~~~k~lv~~~~~~~~~~~~~~l~~-----------~~~~~~~~~~~~~~~~r~~~~~~f~-----~~~~~vli~t~~~~~  297 (369)
                      ..+++|||++++++++.+++.|.+           .+..+..+||+++.++|.++++.|.     +|..+|||||+++++
T Consensus       302 ~~g~iLVF~~~~~~i~~l~~~L~~~~~~l~~~~~~~~~~v~~lhg~l~~~eR~~v~~~f~~~~~~~g~~kVlVAT~iae~  381 (773)
T 2xau_A          302 EAGDILLFLTGEDEIEDAVRKISLEGDQLVREEGCGPLSVYPLYGSLPPHQQQRIFEPAPESHNGRPGRKVVISTNIAET  381 (773)
T ss_dssp             CSCEEEEECSCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECTTCCHHHHGGGGSCCCCCSSSSCCEEEEEECTHHHH
T ss_pred             CCCCEEEECCCHHHHHHHHHHHHHHHHhhcccccCCCeEEEEeCCCCCHHHHHHHHhhcccccCCCCceEEEEeCcHHHh
Confidence            678999999999999999999975           5778999999999999999999999     999999999999999


Q ss_pred             CCCCCCCcEEEEecC------------------CCCccchhhhhcccccCCCceeEEEEeccccH
Q 017573          298 GIDVQQVSLVINYDL------------------PTQPENYLHRIGRSGRFGRKGVAINFVTRDDE  344 (369)
Q Consensus       298 G~d~~~~~~vi~~~~------------------~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~  344 (369)
                      |+|+|++++||.++.                  |.|..+|.||+||+||. +.|.|+.++++.+.
T Consensus       382 GidIp~v~~VId~g~~k~~~yd~~~g~~~L~~~p~S~~s~~QR~GRaGR~-~~G~~~~l~~~~~~  445 (773)
T 2xau_A          382 SLTIDGIVYVVDPGFSKQKVYNPRIRVESLLVSPISKASAQQRAGRAGRT-RPGKCFRLYTEEAF  445 (773)
T ss_dssp             TCCCTTEEEEEECSEEEEEEEETTTTEEEEEEEECCHHHHHHHHHGGGSS-SSEEEEESSCHHHH
T ss_pred             CcCcCCeEEEEeCCCccceeeccccCccccccccCCHHHHHhhccccCCC-CCCEEEEEecHHHh
Confidence            999999999999877                  78999999999999999 88999999976554

>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=100.00  E-value=8.4e-38  Score=286.93  Aligned_cols=292  Identities=20%  Similarity=0.209  Sum_probs=214.8

Q ss_pred             CCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEE
Q 017573           18 KPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHA   97 (369)
Q Consensus        18 ~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~   97 (369)
                      .++++|+++++.+.++++++++||||+|||.++.+++++.      +.+++|++|+++|+.|+.+.+.+..   +..+..
T Consensus       217 P~~~~q~~i~~~L~~~~~vlv~ApTGSGKT~a~~l~ll~~------g~~vLVl~PTReLA~Qia~~l~~~~---g~~vg~  287 (666)
T 3o8b_A          217 PVFTDNSSPPAVPQSFQVAHLHAPTGSGKSTKVPAAYAAQ------GYKVLVLNPSVAATLGFGAYMSKAH---GIDPNI  287 (666)
T ss_dssp             CSCCCCCSCCCCCSSCEEEEEECCTTSCTTTHHHHHHHHT------TCCEEEEESCHHHHHHHHHHHHHHH---SCCCEE
T ss_pred             CcHHHHHHHHHHHHcCCeEEEEeCCchhHHHHHHHHHHHC------CCeEEEEcchHHHHHHHHHHHHHHh---CCCeeE
Confidence            4677888888888889999999999999999888777652      2389999999999999999887654   344555


Q ss_pred             EECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCccCc--EEEE
Q 017573           98 CVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQ--VGVF  175 (369)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~--~i~~  175 (369)
                      ..++..       ...+.+|+|+||+.|   +.+..+...+++++|+||+|.+ +.++...+..+.+.++...+  ++++
T Consensus       288 ~vG~~~-------~~~~~~IlV~TPGrL---l~~~~l~l~~l~~lVlDEAH~l-~~~~~~~l~~Il~~l~~~~~~llil~  356 (666)
T 3o8b_A          288 RTGVRT-------ITTGAPVTYSTYGKF---LADGGCSGGAYDIIICDECHST-DSTTILGIGTVLDQAETAGARLVVLA  356 (666)
T ss_dssp             ECSSCE-------ECCCCSEEEEEHHHH---HHTTSCCTTSCSEEEETTTTCC-SHHHHHHHHHHHHHTTTTTCSEEEEE
T ss_pred             EECcEe-------ccCCCCEEEECcHHH---HhCCCcccCcccEEEEccchhc-CccHHHHHHHHHHhhhhcCCceEEEE
Confidence            555543       345689999999997   4566677778999999999865 44556677788888876665  6778


Q ss_pred             EeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHHHhccCCCeEEEeCCHhhHHHHHHHH
Q 017573          176 SATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKM  255 (369)
Q Consensus       176 saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l  255 (369)
                      |||++....      ...+..........  ..+    ....... .       +.....+++||||++++.++.+++.|
T Consensus       357 SAT~~~~i~------~~~p~i~~v~~~~~--~~i----~~~~~~~-~-------l~~~~~~~vLVFv~Tr~~ae~la~~L  416 (666)
T 3o8b_A          357 TATPPGSVT------VPHPNIEEVALSNT--GEI----PFYGKAI-P-------IEAIRGGRHLIFCHSKKKCDELAAKL  416 (666)
T ss_dssp             ESSCTTCCC------CCCTTEEEEECBSC--SSE----EETTEEE-C-------GGGSSSSEEEEECSCHHHHHHHHHHH
T ss_pred             CCCCCcccc------cCCcceEEEeeccc--chh----HHHHhhh-h-------hhhccCCcEEEEeCCHHHHHHHHHHH
Confidence            999976311      11111111000000  000    0000000 0       12335679999999999999999999


Q ss_pred             hhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEE----------ec-----------CCC
Q 017573          256 RSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVIN----------YD-----------LPT  314 (369)
Q Consensus       256 ~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~----------~~-----------~~~  314 (369)
                      ++.+..+..+||++++++       |.++..+|||+|+++++|+|+| ++.||+          ++           .|.
T Consensus       417 ~~~g~~v~~lHG~l~q~e-------r~~~~~~VLVATdVaerGIDId-V~~VI~~Gl~~~~ViNyDydP~~gl~~~~~P~  488 (666)
T 3o8b_A          417 SGLGINAVAYYRGLDVSV-------IPTIGDVVVVATDALMTGYTGD-FDSVIDCNTCVTQTVDFSLDPTFTIETTTVPQ  488 (666)
T ss_dssp             HTTTCCEEEECTTSCGGG-------SCSSSCEEEEECTTHHHHCCCC-BSEEEECCEEEEEEEECCCSSSCEEEEEEEEC
T ss_pred             HhCCCcEEEecCCCCHHH-------HHhCCCcEEEECChHHccCCCC-CcEEEecCcccccccccccccccccccccCcC
Confidence            999999999999998875       4556669999999999999997 999984          44           788


Q ss_pred             CccchhhhhcccccCCCceeEEEEeccccHHH--H--HHHHHHhccccc
Q 017573          315 QPENYLHRIGRSGRFGRKGVAINFVTRDDERM--L--FDIQKFYNVVIE  359 (369)
Q Consensus       315 ~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~--~--~~~~~~~~~~~~  359 (369)
                      +..+|.||+||+|| |+.|. +.++++.+...  +  ..+.+..+..+.
T Consensus       489 s~~syiQRiGRtGR-g~~G~-i~lvt~~e~~~~~l~~~~i~~~~~~~~~  535 (666)
T 3o8b_A          489 DAVSRSQRRGRTGR-GRRGI-YRFVTPGERPSGMFDSSVLCECYDAGCA  535 (666)
T ss_dssp             BHHHHHHHHTTBCS-SSCEE-EEESCCCCBCSSBCCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHhccCCC-CCCCE-EEEEecchhhcccccHHHHHHHhcCCcc
Confidence            89999999999999 89999 88988776554  3  445555554443

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=100.00  E-value=1.8e-36  Score=271.21  Aligned_cols=270  Identities=16%  Similarity=0.133  Sum_probs=186.8

Q ss_pred             cCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHH
Q 017573           32 KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL  111 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~  111 (369)
                      +++++++++|||+|||.++++++++.+...  +.+++|++|+++|+.|+.+.+.      +..+....++...     ..
T Consensus         1 kg~~~lv~a~TGsGKT~~~l~~~l~~~~~~--g~~~lvl~Pt~~La~Q~~~~~~------~~~v~~~~~~~~~-----~~   67 (431)
T 2v6i_A            1 KRELTVLDLHPGAGKTRRVLPQLVREAVKK--RLRTVILAPTRVVASEMYEALR------GEPIRYMTPAVQS-----ER   67 (431)
T ss_dssp             -CCEEEEECCTTSCTTTTHHHHHHHHHHHT--TCCEEEEESSHHHHHHHHHHTT------TSCEEEC-------------
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHHHhC--CCCEEEECcHHHHHHHHHHHhC------CCeEEEEecCccc-----cC
Confidence            368999999999999999988888554432  2389999999999999988775      3445444443221     11


Q ss_pred             ccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhC-CccCcEEEEEeeCChhHHHHHHHh
Q 017573          112 QAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLL-PAKVQVGVFSATMPPEALEITRKF  190 (369)
Q Consensus       112 ~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~-~~~~~~i~~saT~~~~~~~~~~~~  190 (369)
                      ..+..+.++|...+.+.+.. .....+++++|+||+|++ +..+......+.... ++..++++|||||++....    +
T Consensus        68 ~~~~~~~~~~~~~l~~~l~~-~~~~~~l~~vViDEaH~~-~~~~~~~~~~l~~~~~~~~~~~l~~SAT~~~~~~~----~  141 (431)
T 2v6i_A           68 TGNEIVDFMCHSTFTMKLLQ-GVRVPNYNLYIMDEAHFL-DPASVAARGYIETRVSMGDAGAIFMTATPPGTTEA----F  141 (431)
T ss_dssp             -CCCSEEEEEHHHHHHHHHH-TCCCCCCSEEEEESTTCC-SHHHHHHHHHHHHHHHTTSCEEEEEESSCTTCCCS----S
T ss_pred             CCCceEEEEchHHHHHHHhc-CccccCCCEEEEeCCccC-CccHHHHHHHHHHHhhCCCCcEEEEeCCCCcchhh----h
Confidence            22345777788888766665 455777999999999997 322223333333332 4578999999999864221    1


Q ss_pred             cCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHHHhccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCC
Q 017573          191 MNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMD  270 (369)
Q Consensus       191 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~  270 (369)
                      ...            ...+.......+.  .....+...+.. ..++++|||+++++++.+++.|++.+..+..+||+  
T Consensus       142 ~~~------------~~~i~~~~~~~~~--~~~~~~~~~l~~-~~~~~lVF~~~~~~~~~l~~~L~~~~~~v~~lhg~--  204 (431)
T 2v6i_A          142 PPS------------NSPIIDEETRIPD--KAWNSGYEWITE-FDGRTVWFVHSIKQGAEIGTCLQKAGKKVLYLNRK--  204 (431)
T ss_dssp             CCC------------SSCCEEEECCCCS--SCCSSCCHHHHS-CSSCEEEECSSHHHHHHHHHHHHHTTCCEEEESTT--
T ss_pred             cCC------------CCceeeccccCCH--HHHHHHHHHHHc-CCCCEEEEeCCHHHHHHHHHHHHHcCCeEEEeCCc--
Confidence            100            0001110000111  011111222333 25689999999999999999999999999999997  


Q ss_pred             HHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcE-----------------EEEecCCCCccchhhhhcccccCCC-c
Q 017573          271 QNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSL-----------------VINYDLPTQPENYLHRIGRSGRFGR-K  332 (369)
Q Consensus       271 ~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~-----------------vi~~~~~~~~~~~~Q~~GR~~R~~~-~  332 (369)
                        +|.++++.|++|+.+|||||+++++|+|+| +.+                 ++.++.|.+..+|.|++||+||.|+ .
T Consensus       205 --~r~~~~~~f~~g~~~vLVaT~v~e~GiDip-~~~VI~~g~~~~~v~d~~~~vi~~~~p~~~~~~~Qr~GR~GR~g~~~  281 (431)
T 2v6i_A          205 --TFESEYPKCKSEKWDFVITTDISEMGANFK-ADRVIDPRKTIKPILLDGRVSMQGPIAITPASAAQRRGRIGRNPEKL  281 (431)
T ss_dssp             --THHHHTTHHHHSCCSEEEECGGGGTSCCCC-CSEEEECCEEEEEEEETTEEEEEEEEECCHHHHHHHHTTSSCCTTCC
T ss_pred             --cHHHHHHhhcCCCCeEEEECchHHcCcccC-CcEEEecCccccceecccceeecccccCCHHHHHHhhhccCCCCCCC
Confidence              477899999999999999999999999999 555                 4667788899999999999999985 4


Q ss_pred             eeEEEEec
Q 017573          333 GVAINFVT  340 (369)
Q Consensus       333 ~~~~~~~~  340 (369)
                      +.++++..
T Consensus       282 ~~~~~~~~  289 (431)
T 2v6i_A          282 GDIYAYSG  289 (431)
T ss_dssp             CCEEEECS
T ss_pred             CeEEEEcC
Confidence            56666653

>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19

Probab=100.00  E-value=2.2e-35  Score=239.24  Aligned_cols=197  Identities=38%  Similarity=0.629  Sum_probs=178.6

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQI   80 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~   80 (369)
                      ++|++++.+.|.++|+..|+++|+++++.+.+++++++.+|||+|||++++++++..+.....+++++|++|+++|+.|+
T Consensus         8 ~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~   87 (206)
T 1vec_A            8 YCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRELALQV   87 (206)
T ss_dssp             SCCCHHHHHHHHTTTCCSCCHHHHHHHHHHHTTCCEEEECCSSSTTHHHHHHHHHHHCCTTSCSCCEEEECSCHHHHHHH
T ss_pred             cCCCHHHHHHHHHCCCCCCCHHHHHHHHHHccCCCEEEECCCCCchHHHHHHHHHHHhcccCCCeeEEEEeCcHHHHHHH
Confidence            58999999999999999999999999999999999999999999999999999998876655566899999999999999


Q ss_pred             HHHHHHhcccc-CcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHH
Q 017573           81 EKVMRALGDYL-GVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQI  159 (369)
Q Consensus        81 ~~~~~~~~~~~-~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~  159 (369)
                      .+.+.++.... +..+....|+............+++|+|+||+.+...+.+......+++++|+||+|++.+.++...+
T Consensus        88 ~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~lViDEah~~~~~~~~~~l  167 (206)
T 1vec_A           88 SQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVQIM  167 (206)
T ss_dssp             HHHHHHHTTTSSSCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEEETHHHHTSTTTHHHH
T ss_pred             HHHHHHHHhhcCCceEEEEeCCccHHHHHHhcCCCCCEEEeCHHHHHHHHHcCCcCcccCCEEEEEChHHhHhhCcHHHH
Confidence            99999988766 77888888888776666666678899999999999999888778888999999999999988899999


Q ss_pred             HHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEE
Q 017573          160 YDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRI  197 (369)
Q Consensus       160 ~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~  197 (369)
                      ..+...+++..|++++|||++.+..+....++.+|..+
T Consensus       168 ~~i~~~~~~~~~~l~~SAT~~~~~~~~~~~~l~~p~~i  205 (206)
T 1vec_A          168 EDIILTLPKNRQILLYSATFPLSVQKFMNSHLEKPYEI  205 (206)
T ss_dssp             HHHHHHSCTTCEEEEEESCCCHHHHHHHHHHCSSCEEE
T ss_pred             HHHHHhCCccceEEEEEeeCCHHHHHHHHHHcCCCeEe
Confidence            99999999899999999999999999999999888654

>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=100.00  E-value=5e-35  Score=274.36  Aligned_cols=319  Identities=17%  Similarity=0.169  Sum_probs=219.8

Q ss_pred             CCcHhhhhhhhccc---------cCCcEEEEcCCCChhhHHHHHHHHHhhhccC----CCccEEEEcCCHHHHHHHHHHH
Q 017573           18 KPSAIQQRGIVPFC---------KGLDVIQQAQSGTGKTATFCSGILQQLDYGL----VQCQALVLAPTRELAQQIEKVM   84 (369)
Q Consensus        18 ~~~~~Q~~~~~~~~---------~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~----~~~~~liv~P~~~l~~q~~~~~   84 (369)
                      .|+|||.+++..+.         .+.++++.++||+|||+.++..+...+..++    ...++|||||+ +|+.||.+++
T Consensus        55 ~LrpyQ~~gv~~l~~~~~~~~~~~~~g~ILad~mGlGKT~~~i~~i~~l~~~~~~~~p~~~~~LiV~P~-sll~qW~~E~  133 (644)
T 1z3i_X           55 VLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLIWTLLKQSPDCKPEIDKVIVVSPS-SLVRNWYNEV  133 (644)
T ss_dssp             TCCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHHHHHHHHHHHCCTTSSCSCSCEEEEECH-HHHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHhhhcccccCCCCeEeeeCCCchHHHHHHHHHHHHHHhCccccCCCCcEEEEecH-HHHHHHHHHH
Confidence            69999999998874         4567999999999999998887776665442    12369999996 8999999999


Q ss_pred             HHhccccCcEEEEEECCcchHHHHH---HHc-----cCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcH
Q 017573           85 RALGDYLGVKVHACVGGTSVREDQR---ILQ-----AGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFK  156 (369)
Q Consensus        85 ~~~~~~~~~~v~~~~~~~~~~~~~~---~~~-----~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~  156 (369)
                      .++... .+.+...+++........   ...     ...+|+|+|++.+.....  .+....|++||+||+|++.+..  
T Consensus       134 ~~~~~~-~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~vvi~ty~~l~~~~~--~l~~~~~~~vI~DEaH~ikn~~--  208 (644)
T 1z3i_X          134 GKWLGG-RVQPVAIDGGSKDEIDSKLVNFISQQGMRIPTPILIISYETFRLHAE--VLHKGKVGLVICDEGHRLKNSD--  208 (644)
T ss_dssp             HHHHGG-GCCEEEECSSCHHHHHHHHHHHHCCCSSCCSCCEEEEEHHHHHHHTT--TTTTSCCCEEEETTGGGCCTTC--
T ss_pred             HHHcCC-CeeEEEEeCCCHHHHHHHHHHHHHhcCCCCCCcEEEeeHHHHHhhHH--HhhcCCccEEEEECceecCChh--
Confidence            998765 455555555544322211   111     147899999999976432  2444568999999999986544  


Q ss_pred             HHHHHHHhhCCccCcEEEEEeeCChhHHH-------------------HHHHhcC-------------------------
Q 017573          157 DQIYDIFQLLPAKVQVGVFSATMPPEALE-------------------ITRKFMN-------------------------  192 (369)
Q Consensus       157 ~~~~~~~~~~~~~~~~i~~saT~~~~~~~-------------------~~~~~~~-------------------------  192 (369)
                      ......+..++ ....+++||||..+...                   +...+..                         
T Consensus       209 ~~~~~al~~l~-~~~rl~LTgTPiqN~l~El~sll~fl~p~~l~~~~~F~~~f~~pi~~~~~~~~~~~~~~~~~~~~~~L  287 (644)
T 1z3i_X          209 NQTYLALNSMN-AQRRVLISGTPIQNDLLEYFSLVHFVNSGILGTAQEFKKRFEIPILKGRDADASDKDRAAGEQKLQEL  287 (644)
T ss_dssp             HHHHHHHHHHC-CSEEEEECSSCSGGGGGGCHHHHHHHHHHHHCCHHHHHHHTHHHHHHHHSTTCCSHHHHHHHHHHHHH
T ss_pred             hHHHHHHHhcc-cCcEEEEecCcccCCHHHHHHHHHhhCCCcCCCHHHHHHhhcchhhhcCCcCCCHHHHHHHHHHHHHH
Confidence            23333334444 44679999999643210                   0000000                         


Q ss_pred             ----CCEEEEecCcc---ccccceeEE-EEEcc-----------------------------------------------
Q 017573          193 ----KPVRILVKRDE---LTLEGIKQF-YVNVE-----------------------------------------------  217 (369)
Q Consensus       193 ----~~~~~~~~~~~---~~~~~~~~~-~~~~~-----------------------------------------------  217 (369)
                          .+.........   ..+...... +....                                               
T Consensus       288 ~~~l~~~~lRR~k~~v~~~LP~k~~~~v~~~ls~~q~~lY~~~~~~~~~~~~~~~g~~~~~~l~~l~~Lrk~c~hp~l~~  367 (644)
T 1z3i_X          288 ISIVNRCLIRRTSDILSKYLPVKIEQVVCCNLTPLQKELYKLFLKQAKPVESLQTGKISVSSLSSITSLKKLCNHPALIY  367 (644)
T ss_dssp             HHHHHHHEECCCGGGGGGTSCCEEEEEEEECCCHHHHHHHHHHHHHHCGGGSSCTTCCCHHHHHHHHHHHHHHHCTHHHH
T ss_pred             HHHHHHHHHHhhHHhHhhhCCCceEEEEEeCCCHHHHHHHHHHHHHHHHHHHHhcCccchhHHHHHHHHHHHhCCHHHHH
Confidence                00000000000   000011100 00000                                               


Q ss_pred             ----------------------------chhhhHHHHHHHHHh---ccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEec
Q 017573          218 ----------------------------KEEWKLETLCDLYET---LAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATH  266 (369)
Q Consensus       218 ----------------------------~~~~~~~~l~~~~~~---~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~  266 (369)
                                                  ....+...+..++..   ..+.|+|||++....++.+.+.|...++.+..++
T Consensus       368 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~K~~~l~~ll~~~~~~~~~k~lIFs~~~~~~~~l~~~l~~~g~~~~~l~  447 (644)
T 1z3i_X          368 EKCLTGEEGFDGALDLFPQNYSTKAVEPQLSGKMLVLDYILAMTRTTTSDKVVLVSNYTQTLDLFEKLCRNRRYLYVRLD  447 (644)
T ss_dssp             HHHHHTCTTCTTGGGTSCSSCCSSSCCGGGSHHHHHHHHHHHHHHHHCCCEEEEEESCHHHHHHHHHHHHHHTCCEEEEC
T ss_pred             HHHhcccchhhhHHhhccccccccccCcccChHHHHHHHHHHHHhhcCCCEEEEEEccHHHHHHHHHHHHHCCCCEEEEe
Confidence                                        011233344444433   3467999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHhcCCCc---EEEEecCCcCCCCCCCCcEEEEecCCCCccchhhhhcccccCCCcee--EEEEecc
Q 017573          267 GDMDQNTRDIIMREFRSGSSR---VLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGV--AINFVTR  341 (369)
Q Consensus       267 ~~~~~~~r~~~~~~f~~~~~~---vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~--~~~~~~~  341 (369)
                      |+++.++|.++++.|++++..   +|++|.++++|+|++.+++||+++++||+..+.|++||++|.|+...  ++.++..
T Consensus       448 G~~~~~~R~~~i~~F~~~~~~~~v~L~st~a~g~Glnl~~a~~Vi~~d~~wnp~~~~Qa~gR~~R~Gq~~~v~v~~lv~~  527 (644)
T 1z3i_X          448 GTMSIKKRAKIVERFNNPSSPEFIFMLSSKAGGCGLNLIGANRLVMFDPDWNPANDEQAMARVWRDGQKKTCYIYRLLST  527 (644)
T ss_dssp             SSCCHHHHHHHHHHHHSTTCCCCEEEEEGGGSCTTCCCTTEEEEEECSCCSSHHHHHHHHTTSSSTTCCSCEEEEEEEET
T ss_pred             CCCCHHHHHHHHHHhcCCCCCcEEEEEecccccCCcccccCCEEEEECCCCCccHHHHHHHhhhhcCCCCceEEEEEEEC
Confidence            999999999999999998754   78899999999999999999999999999999999999999997754  4445555


Q ss_pred             cc
Q 017573          342 DD  343 (369)
Q Consensus       342 ~~  343 (369)
                      ..
T Consensus       528 ~t  529 (644)
T 1z3i_X          528 GT  529 (644)
T ss_dssp             TS
T ss_pred             CC
Confidence            53

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=100.00  E-value=7.5e-36  Score=286.74  Aligned_cols=330  Identities=18%  Similarity=0.215  Sum_probs=230.6

Q ss_pred             CCCcHhhhhhhhccc----cCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccC
Q 017573           17 EKPSAIQQRGIVPFC----KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLG   92 (369)
Q Consensus        17 ~~~~~~Q~~~~~~~~----~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~   92 (369)
                      .+|+|||.+++..+.    .++++++.++||+|||++++..+...+.......++||||| .+++.||.+++.++..  +
T Consensus       235 ~~Lr~yQ~egv~~l~~~~~~~~~~ILademGlGKT~~ai~~i~~l~~~~~~~~~~LIV~P-~sll~qW~~E~~~~~p--~  311 (800)
T 3mwy_W          235 GELRDFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFISWLIFARRQNGPHIIVVP-LSTMPAWLDTFEKWAP--D  311 (800)
T ss_dssp             SCCCTHHHHHHHHHHHHHTTTCCEEECCCTTSSTTHHHHHHHHHHHHHHSCCSCEEEECC-TTTHHHHHHHHHHHST--T
T ss_pred             CCcCHHHHHHHHHHHHHhhcCCCEEEEeCCCcchHHHHHHHHHHHHHhcCCCCCEEEEEC-chHHHHHHHHHHHHCC--C
Confidence            479999999998765    78999999999999999987777666544444448999999 6889999999999875  4


Q ss_pred             cEEEEEECCcchHHHHHH------------HccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHH
Q 017573           93 VKVHACVGGTSVREDQRI------------LQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIY  160 (369)
Q Consensus        93 ~~v~~~~~~~~~~~~~~~------------~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~  160 (369)
                      +++...+|+.........            ....++|+|+|++.+......  +....|++||+||||++.+..  ....
T Consensus       312 ~~v~~~~g~~~~r~~~~~~~~~~~~~~~~~~~~~~dvvitTy~~l~~~~~~--l~~~~w~~vIvDEaH~lkn~~--s~~~  387 (800)
T 3mwy_W          312 LNCICYMGNQKSRDTIREYEFYTNPRAKGKKTMKFNVLLTTYEYILKDRAE--LGSIKWQFMAVDEAHRLKNAE--SSLY  387 (800)
T ss_dssp             CCEEECCCSSHHHHHHHHHHSCSCC-----CCCCCSEEEECTTHHHHTHHH--HHTSEEEEEEETTGGGGCCSS--SHHH
T ss_pred             ceEEEEeCCHHHHHHHHHHHhhccccccccccccCCEEEecHHHHHhhHHH--HhcCCcceeehhhhhhhcCch--hHHH
Confidence            566666666553332211            123578999999999764332  223358999999999996543  3445


Q ss_pred             HHHhhCCccCcEEEEEeeCChhH----HHHHHHhcCC-----------------------------CEEEEecCccc--c
Q 017573          161 DIFQLLPAKVQVGVFSATMPPEA----LEITRKFMNK-----------------------------PVRILVKRDEL--T  205 (369)
Q Consensus       161 ~~~~~~~~~~~~i~~saT~~~~~----~~~~~~~~~~-----------------------------~~~~~~~~~~~--~  205 (369)
                      ..+..++ ....+++||||..+.    ..++..+...                             +..........  .
T Consensus       388 ~~l~~l~-~~~rl~LTgTPiqN~l~el~~ll~fL~p~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~p~~lRR~k~dv~~~  466 (800)
T 3mwy_W          388 ESLNSFK-VANRMLITGTPLQNNIKELAALVNFLMPGRFTIDQEIDFENQDEEQEEYIHDLHRRIQPFILRRLKKDVEKS  466 (800)
T ss_dssp             HHHTTSE-EEEEEEECSCCCSSCSHHHHHHHHHHCSCCC---------CCTTHHHHHHHHHHHTTGGGEEECCGGGGTTT
T ss_pred             HHHHHhh-hccEEEeeCCcCCCCHHHHHHHHHHhCccccCchhhhcccccchhHHHHHHHHHHHHhHHHhhhhHHhhhhc
Confidence            5555564 445788999994321    1111111110                             00000000000  0


Q ss_pred             ccceeEE--EEEccc-----------------------------------------------------------------
Q 017573          206 LEGIKQF--YVNVEK-----------------------------------------------------------------  218 (369)
Q Consensus       206 ~~~~~~~--~~~~~~-----------------------------------------------------------------  218 (369)
                      .+.....  ++....                                                                 
T Consensus       467 LP~k~~~~v~v~ls~~q~~~Y~~i~~~~~~~l~~~~~~~~~~~l~~l~~Lrk~~~hp~l~~~~~~~~~~~~~~~~~~~~~  546 (800)
T 3mwy_W          467 LPSKTERILRVELSDVQTEYYKNILTKNYSALTAGAKGGHFSLLNIMNELKKASNHPYLFDNAEERVLQKFGDGKMTREN  546 (800)
T ss_dssp             SCCEEEEEEEECCCHHHHHHHHHHHHHCCC----------CTHHHHHHHHHHHHHCGGGSSSHHHHHCCCC----CCSHH
T ss_pred             cCCcEEEEEEeCCCHHHHHHHHHHHHHHHHHHhhccccchhhHHHHHHHHHHHhcChhhhcchHHHHHHhcccccccHHH
Confidence            0011111  111000                                                                 


Q ss_pred             -------hhhhHHHHHHHHHhc--cCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCC---
Q 017573          219 -------EEWKLETLCDLYETL--AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSS---  286 (369)
Q Consensus       219 -------~~~~~~~l~~~~~~~--~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~---  286 (369)
                             ...++..+..++...  .+.|+|||+.....+..+.+.|...++.+..++|.++..+|.++++.|++++.   
T Consensus       547 ~~~~l~~~s~K~~~L~~lL~~~~~~g~kvLIFsq~~~~ld~L~~~L~~~g~~~~~i~G~~~~~eR~~~i~~F~~~~~~~~  626 (800)
T 3mwy_W          547 VLRGLIMSSGKMVLLDQLLTRLKKDGHRVLIFSQMVRMLDILGDYLSIKGINFQRLDGTVPSAQRRISIDHFNSPDSNDF  626 (800)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHTTTTCCEEEEESCHHHHHHHHHHHHHHTCCCEEESTTSCHHHHHHHHHTTSSTTCSCC
T ss_pred             HHHHhhhcChHHHHHHHHHHHHhhCCCeEEEEechHHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHhhCCCCCce
Confidence                   122455566666554  45699999999999999999999999999999999999999999999998654   


Q ss_pred             cEEEEecCCcCCCCCCCCcEEEEecCCCCccchhhhhcccccCCCcee--EEEEeccc--cHHHHHHHHHHh
Q 017573          287 RVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGV--AINFVTRD--DERMLFDIQKFY  354 (369)
Q Consensus       287 ~vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~--~~~~~~~~--~~~~~~~~~~~~  354 (369)
                      .+|++|.++++|+|++.+++||+++++||+..+.|++||++|.|+...  ++.+++..  +..+++...+..
T Consensus       627 v~LlSt~agg~GlNL~~a~~VI~~D~~wnp~~~~Qa~gR~~RiGQ~k~V~Vyrlv~~~TiEe~i~~~~~~K~  698 (800)
T 3mwy_W          627 VFLLSTRAGGLGINLMTADTVVIFDSDWNPQADLQAMARAHRIGQKNHVMVYRLVSKDTVEEEVLERARKKM  698 (800)
T ss_dssp             CEEEEHHHHTTTCCCTTCCEEEESSCCSCSHHHHHHHTTTSCSSCCSCEEEEEEEETTSHHHHHHHHHHHHT
T ss_pred             EEEEecccccCCCCccccceEEEecCCCChhhHHHHHHHHHhcCCCceEEEEEEecCCCHHHHHHHHHHHHH
Confidence            488999999999999999999999999999999999999999997754  45556655  444555444443

>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=100.00  E-value=4.5e-37  Score=277.40  Aligned_cols=273  Identities=20%  Similarity=0.211  Sum_probs=191.0

Q ss_pred             hhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHH
Q 017573           27 IVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVRE  106 (369)
Q Consensus        27 ~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~  106 (369)
                      ...+.+++++++.+|||+|||++++++++..+...  +++++|++|+++|+.|+.+.+..      ..+....+....  
T Consensus        15 ~~~l~~~~~vlv~a~TGsGKT~~~~l~il~~~~~~--~~~~lvl~Ptr~La~Q~~~~l~g------~~v~~~~~~~~~--   84 (459)
T 2z83_A           15 PNMLRKRQMTVLDLHPGSGKTRKILPQIIKDAIQQ--RLRTAVLAPTRVVAAEMAEALRG------LPVRYQTSAVQR--   84 (459)
T ss_dssp             CGGGSTTCEEEECCCTTSCTTTTHHHHHHHHHHHT--TCCEEEEECSHHHHHHHHHHTTT------SCEEECC-------
T ss_pred             HHHHhcCCcEEEECCCCCCHHHHHHHHHHHHHHhC--CCcEEEECchHHHHHHHHHHhcC------ceEeEEeccccc--
Confidence            44456789999999999999999988888776532  23899999999999999998862      233222111110  


Q ss_pred             HHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHh-----hccCcHHHHHHHHhhCCccCcEEEEEeeCCh
Q 017573          107 DQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEM-----LSRGFKDQIYDIFQLLPAKVQVGVFSATMPP  181 (369)
Q Consensus       107 ~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~-----~~~~~~~~~~~~~~~~~~~~~~i~~saT~~~  181 (369)
                         ....+..+.++|...+...+... ....+++++|+||+|+.     ...++....     ..++..|+++||||++.
T Consensus        85 ---~~t~~~~i~~~~~~~l~~~l~~~-~~l~~~~~iViDEaH~~~~~~~~~~~~~~~~-----~~~~~~~~il~SAT~~~  155 (459)
T 2z83_A           85 ---EHQGNEIVDVMCHATLTHRLMSP-NRVPNYNLFVMDEAHFTDPASIAARGYIATK-----VELGEAAAIFMTATPPG  155 (459)
T ss_dssp             ------CCCSEEEEEHHHHHHHHHSC-C-CCCCSEEEESSTTCCSHHHHHHHHHHHHH-----HHTTSCEEEEECSSCTT
T ss_pred             ---CCCCCcEEEEEchHHHHHHhhcc-ccccCCcEEEEECCccCCchhhHHHHHHHHH-----hccCCccEEEEEcCCCc
Confidence               01233457788888877666554 45677899999999983     222222211     11357899999999986


Q ss_pred             hHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHHHhccCCCeEEEeCCHhhHHHHHHHHhhCCCe
Q 017573          182 EALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHT  261 (369)
Q Consensus       182 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~~~~  261 (369)
                      ....+...  ..++.....              ..+..  ....+..++... .+++||||++++.++.+++.|+..+..
T Consensus       156 ~~~~~~~~--~~pi~~~~~--------------~~~~~--~~~~~~~~l~~~-~~~~LVF~~s~~~~~~l~~~L~~~g~~  216 (459)
T 2z83_A          156 TTDPFPDS--NAPIHDLQD--------------EIPDR--AWSSGYEWITEY-AGKTVWFVASVKMGNEIAMCLQRAGKK  216 (459)
T ss_dssp             CCCSSCCC--SSCEEEEEC--------------CCCSS--CCSSCCHHHHHC-CSCEEEECSCHHHHHHHHHHHHHTTCC
T ss_pred             chhhhccC--CCCeEEecc--------------cCCcc--hhHHHHHHHHhc-CCCEEEEeCChHHHHHHHHHHHhcCCc
Confidence            53211110  122221110              00000  000011222222 579999999999999999999999999


Q ss_pred             eEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEE--------------------ecCCCCccchhh
Q 017573          262 VSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVIN--------------------YDLPTQPENYLH  321 (369)
Q Consensus       262 ~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~--------------------~~~~~~~~~~~Q  321 (369)
                      +..+|++    +|.++++.|++|+.+|||||+++++|+|+|+ +.||.                    ++.|.+..+|.|
T Consensus       217 v~~lh~~----~R~~~~~~f~~g~~~iLVaT~v~~~GiDip~-~~VI~~G~~~~~~~~~~~~~~~~~~~d~p~s~~~~~Q  291 (459)
T 2z83_A          217 VIQLNRK----SYDTEYPKCKNGDWDFVITTDISEMGANFGA-SRVIDCRKSVKPTILEEGEGRVILGNPSPITSASAAQ  291 (459)
T ss_dssp             EEEESTT----CCCCCGGGSSSCCCSEEEESSCC---CCCSC-SEEEECCEECCEEEECSSSCEEEECSCEECCHHHHHH
T ss_pred             EEecCHH----HHHHHHhhccCCCceEEEECChHHhCeecCC-CEEEECCcccccccccccccccccccCCCCCHHHHHH
Confidence            9999995    5778899999999999999999999999999 99998                    568999999999


Q ss_pred             hhcccccCCC-ceeEEEEeccc
Q 017573          322 RIGRSGRFGR-KGVAINFVTRD  342 (369)
Q Consensus       322 ~~GR~~R~~~-~~~~~~~~~~~  342 (369)
                      |+||+||.|+ .|.+++++...
T Consensus       292 R~GRaGR~g~~~G~~~~~~~~~  313 (459)
T 2z83_A          292 RRGRVGRNPNQVGDEYHYGGAT  313 (459)
T ss_dssp             HHTTSSCCTTCCCEEEEECSCC
T ss_pred             hccccCCCCCCCCeEEEEEccc
Confidence            9999999987 89999999875

>3fe2_A Probable ATP-dependent RNA helicase DDX5; DEAD, ADP, ATP-binding, hydrolase, nucleotide- RNA-binding, methylation, mRNA processing, mRNA S nucleus; HET: ADP; 2.60A {Homo sapiens} PDB: 4a4d_A

Probab=100.00  E-value=1.9e-35  Score=245.28  Aligned_cols=202  Identities=32%  Similarity=0.435  Sum_probs=183.9

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhcc-----CCCccEEEEcCCHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYG-----LVQCQALVLAPTRE   75 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~-----~~~~~~liv~P~~~   75 (369)
                      ++|++.+.+.+.++||.+|+++|.++++.+.+++++++.+|||+|||++++++++..+...     ..+++++|++|+++
T Consensus        34 ~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~g~~~l~~apTGsGKT~~~~l~~l~~l~~~~~~~~~~~~~~lil~Pt~~  113 (242)
T 3fe2_A           34 ANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPFLERGDGPICLVLAPTRE  113 (242)
T ss_dssp             TTCCHHHHHHHHTTTCCSCCHHHHHHHHHHHHTCCEEEEECTTSCHHHHHHHHHHHHHHTSCCCCTTCCCSEEEECSSHH
T ss_pred             cCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCcCHHHHHHHHHHHHHHHhccccccCCCCEEEEEeCcHH
Confidence            5799999999999999999999999999999999999999999999999999999887632     23458999999999


Q ss_pred             HHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCc
Q 017573           76 LAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGF  155 (369)
Q Consensus        76 l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~  155 (369)
                      |+.|+.+.++++....++.+....|+.........+..+++|+|+||+.+...+........+++++|+||||++.+.++
T Consensus       114 L~~Q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~~~~~~lViDEah~l~~~~~  193 (242)
T 3fe2_A          114 LAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLECGKTNLRRTTYLVLDEADRMLDMGF  193 (242)
T ss_dssp             HHHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHHTSCCCTTCCEEEETTHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHhhcCceEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHHcCCCCcccccEEEEeCHHHHhhhCc
Confidence            99999999999988888999999999887777666777899999999999999998888888899999999999999999


Q ss_pred             HHHHHHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCc
Q 017573          156 KDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRD  202 (369)
Q Consensus       156 ~~~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~  202 (369)
                      ...+..++..+++..|++++|||+++....+...++.++..+.....
T Consensus       194 ~~~~~~i~~~~~~~~q~~~~SAT~~~~~~~~~~~~l~~~~~i~~~~~  240 (242)
T 3fe2_A          194 EPQIRKIVDQIRPDRQTLMWSATWPKEVRQLAEDFLKDYIHINIGAL  240 (242)
T ss_dssp             HHHHHHHHTTSCSSCEEEEEESCCCHHHHHHHHHHCSSCEEEEECC-
T ss_pred             HHHHHHHHHhCCccceEEEEEeecCHHHHHHHHHHCCCCEEEEecCC
Confidence            99999999999999999999999999999999999999988876543

>3ber_A Probable ATP-dependent RNA helicase DDX47; DEAD, AMP, structural genomics, structural GEN consortium, SGC, ATP-binding, hydrolase; HET: AMP PGE; 1.40A {Homo sapiens}

Probab=100.00  E-value=6.9e-35  Score=242.29  Aligned_cols=199  Identities=34%  Similarity=0.524  Sum_probs=180.2

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQI   80 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~   80 (369)
                      +||++.+.+.|+.+|+..|+++|+++++.+.+++++++.+|||+|||++++++++..+.....+.+++|++|+++|+.|+
T Consensus        48 l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~~~il~~l~~~~~~~~~lil~Ptr~L~~q~  127 (249)
T 3ber_A           48 LGVTDVLCEACDQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPILNALLETPQRLFALVLTPTRELAFQI  127 (249)
T ss_dssp             GTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHSCCSSCEEEECSSHHHHHHH
T ss_pred             cCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEEcCCCCCchhHhHHHHHHHHhcCCCCceEEEEeCCHHHHHHH
Confidence            58999999999999999999999999999999999999999999999999999998877666556899999999999999


Q ss_pred             HHHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHc-CCCCCCCccEEEEechhHhhccCcHHHH
Q 017573           81 EKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRR-QSLRPDYIKMFVLDEADEMLSRGFKDQI  159 (369)
Q Consensus        81 ~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~-~~~~~~~~~~viiDE~H~~~~~~~~~~~  159 (369)
                      .+.++++....++.+..+.|+............+++|+|+||+++...+.+ .......++++|+||||++.+.++...+
T Consensus       128 ~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~l~~~~~lViDEah~l~~~~~~~~l  207 (249)
T 3ber_A          128 SEQFEALGSSIGVQSAVIVGGIDSMSQSLALAKKPHIIIATPGRLIDHLENTKGFNLRALKYLVMDEADRILNMDFETEV  207 (249)
T ss_dssp             HHHHHHHHGGGTCCEEEECTTSCHHHHHHHHHTCCSEEEECHHHHHHHHHHSTTCCCTTCCEEEECSHHHHHHTTCHHHH
T ss_pred             HHHHHHHhccCCeeEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHHcCCCcCccccCEEEEcChhhhhccChHHHH
Confidence            999999988888899999998876666666667899999999999988876 4456778999999999999999999999


Q ss_pred             HHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEe
Q 017573          160 YDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILV  199 (369)
Q Consensus       160 ~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~  199 (369)
                      ..++..+++..+++++|||++....++...++.+|..+.+
T Consensus       208 ~~i~~~~~~~~~~l~~SAT~~~~v~~~~~~~l~~p~~i~v  247 (249)
T 3ber_A          208 DKILKVIPRDRKTFLFSATMTKKVQKLQRAALKNPVKCAV  247 (249)
T ss_dssp             HHHHHSSCSSSEEEEEESSCCHHHHHHHHHHCSSCEEEEC
T ss_pred             HHHHHhCCCCCeEEEEeccCCHHHHHHHHHHCCCCEEEEe
Confidence            9999999989999999999999999999999999987654

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=100.00  E-value=1.9e-35  Score=241.62  Aligned_cols=201  Identities=33%  Similarity=0.502  Sum_probs=178.2

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQI   80 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~   80 (369)
                      ++|++.+.++|.++|+..|+++|+++++.+.+++++++.+|||+|||++++++++..+.....+.+++|++|+++|+.|+
T Consensus         9 ~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~   88 (219)
T 1q0u_A            9 FPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPERAEVQAVITAPTRELATQI   88 (219)
T ss_dssp             SCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHH
T ss_pred             CCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhCcCCceEEEEcCcHHHHHHH
Confidence            58999999999999999999999999999999999999999999999999999998887655566899999999999999


Q ss_pred             HHHHHHhcccc----CcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcH
Q 017573           81 EKVMRALGDYL----GVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFK  156 (369)
Q Consensus        81 ~~~~~~~~~~~----~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~  156 (369)
                      .+.+.++....    +..+....|+.........+..+++|+|+||+.+...+.........++++|+||+|.+.++++.
T Consensus        89 ~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~l~~~~~~~~~~~~lViDEah~~~~~~~~  168 (219)
T 1q0u_A           89 YHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLNVQPHIVIGTPGRINDFIREQALDVHTAHILVVDEADLMLDMGFI  168 (219)
T ss_dssp             HHHHHHHHTTSCGGGCCCEEEECCCSHHHHTTCCCSSCCSEEEECHHHHHHHHHTTCCCGGGCCEEEECSHHHHHHTTCH
T ss_pred             HHHHHHHhhhcccccceEEEEEeCCCCHHHHHHHcCCCCCEEEeCHHHHHHHHHcCCCCcCcceEEEEcCchHHhhhChH
Confidence            99999987665    67788888877655444444457899999999999999887777788999999999999999999


Q ss_pred             HHHHHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecC
Q 017573          157 DQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKR  201 (369)
Q Consensus       157 ~~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~  201 (369)
                      ..+..+...+++..|++++|||++.+..+....++.+|..+....
T Consensus       169 ~~l~~i~~~~~~~~~~l~~SAT~~~~~~~~~~~~~~~p~~~~~~~  213 (219)
T 1q0u_A          169 TDVDQIAARMPKDLQMLVFSATIPEKLKPFLKKYMENPTFVHVLE  213 (219)
T ss_dssp             HHHHHHHHTSCTTCEEEEEESCCCGGGHHHHHHHCSSCEEEECC-
T ss_pred             HHHHHHHHhCCcccEEEEEecCCCHHHHHHHHHHcCCCeEEEeec
Confidence            999999999998999999999999999999999999998776543

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A

Probab=100.00  E-value=5.5e-35  Score=240.05  Aligned_cols=201  Identities=62%  Similarity=0.954  Sum_probs=172.2

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQI   80 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~   80 (369)
                      ++|++.+.+.|.++|+..|+++|.++++.+.+++++++.+|||+|||++++++++..+.....+++++|++|+++|+.|+
T Consensus        19 l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~~pTGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~   98 (224)
T 1qde_A           19 MELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQI   98 (224)
T ss_dssp             GTCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEEECSSHHHHHHH
T ss_pred             cCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHhccCCCceEEEEECCHHHHHHH
Confidence            57999999999999999999999999999999999999999999999999999998887666666999999999999999


Q ss_pred             HHHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHH
Q 017573           81 EKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIY  160 (369)
Q Consensus        81 ~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~  160 (369)
                      .+.+.++....+..+....|+.........+. .++|+|+||+.+...+.+......+++++|+||||++.+.++...+.
T Consensus        99 ~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~-~~~iiv~Tp~~l~~~~~~~~~~~~~~~~iViDEah~~~~~~~~~~l~  177 (224)
T 1qde_A           99 QKVVMALAFHMDIKVHACIGGTSFVEDAEGLR-DAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIY  177 (224)
T ss_dssp             HHHHHHHTTTSCCCEEEECC----------CT-TCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHHHTTCHHHHH
T ss_pred             HHHHHHHhcccCceEEEEeCCcchHHHHhcCC-CCCEEEECHHHHHHHHHhCCcchhhCcEEEEcChhHHhhhhhHHHHH
Confidence            99999998877888888888776555444333 38999999999999998888888889999999999999989999999


Q ss_pred             HHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCc
Q 017573          161 DIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRD  202 (369)
Q Consensus       161 ~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~  202 (369)
                      .+...+++..|++++|||++.+..++...++..|..+....+
T Consensus       178 ~i~~~~~~~~~~i~lSAT~~~~~~~~~~~~~~~p~~i~~~~~  219 (224)
T 1qde_A          178 QIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKD  219 (224)
T ss_dssp             HHHHHSCTTCEEEEEESSCCHHHHHHHHHHCSSCEEEC----
T ss_pred             HHHHhCCccCeEEEEEeecCHHHHHHHHHHCCCCEEEEecCC
Confidence            999999999999999999999999999999999887765443

>3bor_A Human initiation factor 4A-II; translation initiation, DEAD BOX, structural genomics, helic binding, HOST-virus interaction, hydrolase; 1.85A {Homo sapiens} PDB: 2g9n_A*

Probab=100.00  E-value=5.7e-35  Score=241.52  Aligned_cols=199  Identities=70%  Similarity=1.077  Sum_probs=170.7

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQI   80 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~   80 (369)
                      ++|++.+.++|.++||..|+++|.++++.+.+++++++.+|||+|||++++++++..+.....+.+++|++|+++|+.|+
T Consensus        35 l~l~~~l~~~l~~~g~~~~~~~Q~~ai~~i~~~~~~li~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~  114 (237)
T 3bor_A           35 MNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQLEIEFKETQALVLAPTRELAQQI  114 (237)
T ss_dssp             SCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEECCCSSHHHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHH
T ss_pred             cCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhcCCCceEEEEECcHHHHHHH
Confidence            58999999999999999999999999999999999999999999999999999998876655556899999999999999


Q ss_pred             HHHHHHhccccCcEEEEEECCcchHHHHHHHc-cCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHH
Q 017573           81 EKVMRALGDYLGVKVHACVGGTSVREDQRILQ-AGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQI  159 (369)
Q Consensus        81 ~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~-~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~  159 (369)
                      .+.++++....+..+....++.........+. ..++|+|+||+.+...+.+.......++++|+||||++.+.++...+
T Consensus       115 ~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~~~~lViDEah~~~~~~~~~~l  194 (237)
T 3bor_A          115 QKVILALGDYMGATCHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSRGFKDQI  194 (237)
T ss_dssp             HHHHHHHTTTTTCCEEEECC-------------CCCSEEEECHHHHHHHHHTTSSCSTTCCEEEEESHHHHHHTTCHHHH
T ss_pred             HHHHHHHhhhcCceEEEEECCCchHHHHHHHhcCCCCEEEECHHHHHHHHHhCCcCcccCcEEEECCchHhhccCcHHHH
Confidence            99999998877888888887766544433333 34899999999999999888777888999999999999988899999


Q ss_pred             HHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEe
Q 017573          160 YDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILV  199 (369)
Q Consensus       160 ~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~  199 (369)
                      ..++..+++..|++++|||++++..++...++.+|..+.+
T Consensus       195 ~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~l~~p~~i~v  234 (237)
T 3bor_A          195 YEIFQKLNTSIQVVLLSATMPTDVLEVTKKFMRDPIRILV  234 (237)
T ss_dssp             HHHHHHSCTTCEEEEECSSCCHHHHHHHHHHCSSCEEEC-
T ss_pred             HHHHHhCCCCCeEEEEEEecCHHHHHHHHHHCCCCEEEEe
Confidence            9999999989999999999999999999999998877654

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=100.00  E-value=1.6e-34  Score=268.51  Aligned_cols=290  Identities=17%  Similarity=0.187  Sum_probs=209.1

Q ss_pred             ccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHH
Q 017573           29 PFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQ  108 (369)
Q Consensus        29 ~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~  108 (369)
                      ..+++++++++||||||||..++..+..    ..   ..+|++|+++|+.|+++.+.+.    +.++....|+...... 
T Consensus       151 r~l~rk~vlv~apTGSGKT~~al~~l~~----~~---~gl~l~PtR~LA~Qi~~~l~~~----g~~v~lltG~~~~iv~-  218 (677)
T 3rc3_A          151 RAMQRKIIFHSGPTNSGKTYHAIQKYFS----AK---SGVYCGPLKLLAHEIFEKSNAA----GVPCDLVTGEERVTVQ-  218 (677)
T ss_dssp             HTSCCEEEEEECCTTSSHHHHHHHHHHH----SS---SEEEEESSHHHHHHHHHHHHHT----TCCEEEECSSCEECCS-
T ss_pred             HhcCCCEEEEEcCCCCCHHHHHHHHHHh----cC---CeEEEeCHHHHHHHHHHHHHhc----CCcEEEEECCeeEEec-
Confidence            3457789999999999999854443332    22   5699999999999999999886    6778888887653100 


Q ss_pred             HHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCC-ccCcEEEEEeeCChhHHHHH
Q 017573          109 RILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLP-AKVQVGVFSATMPPEALEIT  187 (369)
Q Consensus       109 ~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~-~~~~~i~~saT~~~~~~~~~  187 (369)
                       .-.+..+++++|++.+.        ....++++|+||+|++.+.++...+..++..++ ...+++++|||. +....+.
T Consensus       219 -TpGr~~~il~~T~e~~~--------l~~~v~lvVIDEaH~l~d~~~g~~~~~~l~~l~~~~i~il~~SAT~-~~i~~l~  288 (677)
T 3rc3_A          219 -PNGKQASHVSCTVEMCS--------VTTPYEVAVIDEIQMIRDPARGWAWTRALLGLCAEEVHLCGEPAAI-DLVMELM  288 (677)
T ss_dssp             -TTCCCCSEEEEEGGGCC--------SSSCEEEEEECSGGGGGCTTTHHHHHHHHHHCCEEEEEEEECGGGH-HHHHHHH
T ss_pred             -CCCcccceeEecHhHhh--------hcccCCEEEEecceecCCccchHHHHHHHHccCccceEEEeccchH-HHHHHHH
Confidence             00123679999986553        235579999999999988888888888888887 677889999994 2333333


Q ss_pred             HHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHHHhccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecC
Q 017573          188 RKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHG  267 (369)
Q Consensus       188 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~  267 (369)
                      .. ......+........      .......    .    ..+... .+..+|||+++++++.+++.|.+.+..+..+||
T Consensus       289 ~~-~~~~~~v~~~~r~~~------l~~~~~~----l----~~l~~~-~~g~iIf~~s~~~ie~la~~L~~~g~~v~~lHG  352 (677)
T 3rc3_A          289 YT-TGEEVEVRDYKRLTP------ISVLDHA----L----ESLDNL-RPGDCIVCFSKNDIYSVSRQIEIRGLESAVIYG  352 (677)
T ss_dssp             HH-HTCCEEEEECCCSSC------EEECSSC----C----CSGGGC-CTTEEEECSSHHHHHHHHHHHHHTTCCCEEECT
T ss_pred             Hh-cCCceEEEEeeecch------HHHHHHH----H----HHHHhc-CCCCEEEEcCHHHHHHHHHHHHhcCCCeeeeec
Confidence            32 333333322111100      0000000    0    011112 245588999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHhc--CCCcEEEEecCCcCCCCCCCCcEEEEecC--------------CCCccchhhhhcccccCCC
Q 017573          268 DMDQNTRDIIMREFRS--GSSRVLITTDLLARGIDVQQVSLVINYDL--------------PTQPENYLHRIGRSGRFGR  331 (369)
Q Consensus       268 ~~~~~~r~~~~~~f~~--~~~~vli~t~~~~~G~d~~~~~~vi~~~~--------------~~~~~~~~Q~~GR~~R~~~  331 (369)
                      ++++++|.++++.|++  |..+|||||+++++|+|+ +++.||+++.              |.+..+|.||+||+||.|+
T Consensus       353 ~L~~~~R~~~~~~F~~~~g~~~VLVATdi~e~GlDi-~v~~VI~~~~~k~~~~~~G~~~~~p~s~~~~~QR~GRAGR~g~  431 (677)
T 3rc3_A          353 SLPPGTKLAQAKKFNDPNDPCKILVATDAIGMGLNL-SIRRIIFYSLIKPSINEKGERELEPITTSQALQIAGRAGRFSS  431 (677)
T ss_dssp             TSCHHHHHHHHHHHHCTTSSCCEEEECGGGGSSCCC-CBSEEEESCSBC-----------CBCCHHHHHHHHTTBTCTTS
T ss_pred             cCCHHHHHHHHHHHHccCCCeEEEEeCcHHHCCcCc-CccEEEECCccccccccCCccccccCCHHHHHHHhcCCCCCCC
Confidence            9999999999999999  889999999999999999 8999999998              6789999999999999986


Q ss_pred             c---eeEEEEeccccHHHHHHHHHHhcccc
Q 017573          332 K---GVAINFVTRDDERMLFDIQKFYNVVI  358 (369)
Q Consensus       332 ~---~~~~~~~~~~~~~~~~~~~~~~~~~~  358 (369)
                      .   |.|+.+ .+.+...++.+.......+
T Consensus       432 ~g~~G~v~~l-~~~d~~~~~~~~~~~~~~i  460 (677)
T 3rc3_A          432 RFKEGEVTTM-NHEDLSLLKEILKRPVDPI  460 (677)
T ss_dssp             SCSSEEEEES-STTHHHHHHHHHHSCCCCC
T ss_pred             CCCCEEEEEE-ecchHHHHHHHHhcCcchh
Confidence            5   555544 3444445555544444333

>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX, structural genomics, structural genomi consortium, SGC, ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens}

Probab=100.00  E-value=1.3e-34  Score=238.25  Aligned_cols=197  Identities=31%  Similarity=0.437  Sum_probs=170.9

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhcc------CCCccEEEEcCCH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYG------LVQCQALVLAPTR   74 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~------~~~~~~liv~P~~   74 (369)
                      +++++.+.++|.++||.+|+++|.++++.+.+++++++.+|||+|||++++++++..+...      ..+++++|++|++
T Consensus        25 ~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~apTGsGKT~~~~l~~~~~l~~~~~~~~~~~~~~~lil~Pt~  104 (228)
T 3iuy_A           25 FQQYPDLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIHLDSQPISREQRNGPGMLVLTPTR  104 (228)
T ss_dssp             HTTCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHC---------CCCSEEEECSSH
T ss_pred             hccCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhccchhhccCCCcEEEEeCCH
Confidence            4789999999999999999999999999999999999999999999999999988776432      2445899999999


Q ss_pred             HHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccC
Q 017573           75 ELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRG  154 (369)
Q Consensus        75 ~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~  154 (369)
                      +|+.|+.+.+.++. ..+..+....++.........+..+++|+|+||+.+...+........+++++|+||||++.+.+
T Consensus       105 ~L~~q~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~Tp~~l~~~~~~~~~~~~~~~~lViDEah~~~~~~  183 (228)
T 3iuy_A          105 ELALHVEAECSKYS-YKGLKSICIYGGRNRNGQIEDISKGVDIIIATPGRLNDLQMNNSVNLRSITYLVIDEADKMLDME  183 (228)
T ss_dssp             HHHHHHHHHHHHHC-CTTCCEEEECC------CHHHHHSCCSEEEECHHHHHHHHHTTCCCCTTCCEEEECCHHHHHHTT
T ss_pred             HHHHHHHHHHHHhc-ccCceEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHHcCCcCcccceEEEEECHHHHhccc
Confidence            99999999999986 34778888888877666666667788999999999999998888888889999999999999999


Q ss_pred             cHHHHHHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEE
Q 017573          155 FKDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRIL  198 (369)
Q Consensus       155 ~~~~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~  198 (369)
                      +...+..++..+++..|++++|||+++...+....++.+|..+.
T Consensus       184 ~~~~~~~i~~~~~~~~~~l~~SAT~~~~~~~~~~~~l~~p~~i~  227 (228)
T 3iuy_A          184 FEPQIRKILLDVRPDRQTVMTSATWPDTVRQLALSYLKDPMIVY  227 (228)
T ss_dssp             CHHHHHHHHHHSCSSCEEEEEESCCCHHHHHHHHTTCSSCEEEE
T ss_pred             hHHHHHHHHHhCCcCCeEEEEEeeCCHHHHHHHHHHCCCCEEEe
Confidence            99999999999999999999999999999999999999887654

>2oxc_A Probable ATP-dependent RNA helicase DDX20; DEAD, structural genomics, structural genomics consortium, SGC, hydrolase; HET: ADP; 1.30A {Homo sapiens} PDB: 3b7g_A*

Probab=100.00  E-value=1.7e-34  Score=237.59  Aligned_cols=197  Identities=40%  Similarity=0.621  Sum_probs=174.8

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQI   80 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~   80 (369)
                      ++|++.+.+.|.++||..|+++|.++++.+.+++++++.+|||+|||++++++++..+.....+++++|++|+++|+.|+
T Consensus        29 l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~  108 (230)
T 2oxc_A           29 LLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDSLVLENLSTQILILAPTREIAVQI  108 (230)
T ss_dssp             GTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHH
T ss_pred             cCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhcCCCceEEEEeCCHHHHHHH
Confidence            57999999999999999999999999999999999999999999999999999988876555556999999999999999


Q ss_pred             HHHHHHhcccc-CcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccC-cHHH
Q 017573           81 EKVMRALGDYL-GVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRG-FKDQ  158 (369)
Q Consensus        81 ~~~~~~~~~~~-~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~-~~~~  158 (369)
                      .+.++++.... ++++....|+.....+.... .+++|+|+||+.+...+........+++++|+||+|++.+.+ +...
T Consensus       109 ~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~-~~~~Iiv~Tp~~l~~~~~~~~~~~~~~~~lViDEah~~~~~~~~~~~  187 (230)
T 2oxc_A          109 HSVITAIGIKMEGLECHVFIGGTPLSQDKTRL-KKCHIAVGSPGRIKQLIELDYLNPGSIRLFILDEADKLLEEGSFQEQ  187 (230)
T ss_dssp             HHHHHHHTTTSTTCCEEEECTTSCHHHHHHHT-TSCSEEEECHHHHHHHHHTTSSCGGGCCEEEESSHHHHHSTTSSHHH
T ss_pred             HHHHHHHhcccCCceEEEEeCCCCHHHHHHhc-cCCCEEEECHHHHHHHHhcCCcccccCCEEEeCCchHhhcCcchHHH
Confidence            99999987654 78888888888766555444 468999999999999988877777889999999999998886 8899


Q ss_pred             HHHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEE
Q 017573          159 IYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRIL  198 (369)
Q Consensus       159 ~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~  198 (369)
                      +..+...+++..|++++|||++....+....++.+|..+.
T Consensus       188 ~~~i~~~~~~~~~~l~lSAT~~~~~~~~~~~~~~~p~~i~  227 (230)
T 2oxc_A          188 INWIYSSLPASKQMLAVSATYPEFLANALTKYMRDPTFVR  227 (230)
T ss_dssp             HHHHHHHSCSSCEEEEEESCCCHHHHHHHTTTCSSCEEEC
T ss_pred             HHHHHHhCCCCCeEEEEEeccCHHHHHHHHHHcCCCeEEE
Confidence            9999999998999999999999888888888888887654

>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic resolution, AMP complex, ribosome biogenesis, thermophilic, hydrolase; HET: AMP; 1.20A {Thermus thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A* 3mwl_A* 3nbf_A* 3nej_A

Probab=100.00  E-value=3.9e-34  Score=232.14  Aligned_cols=197  Identities=38%  Similarity=0.547  Sum_probs=174.9

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhcc---CCCccEEEEcCCHHHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYG---LVQCQALVLAPTRELA   77 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~---~~~~~~liv~P~~~l~   77 (369)
                      +||++.+.+.|.++|+..|+++|+++++.+.+++++++.+|||+|||++++++++..+...   ..+++++|++|+++|+
T Consensus         6 ~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~l~~~~~~~~~~~~lil~P~~~L~   85 (207)
T 2gxq_A            6 FPLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAERLAPSQERGRKPRALVLTPTRELA   85 (207)
T ss_dssp             SCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCCCTTCCCSEEEECSSHHHH
T ss_pred             cCCCHHHHHHHHHcCCCCCCHHHHHHHHHHcCCCCEEEECCCCChHHHHHHHHHHHHHhhccccCCCCcEEEEECCHHHH
Confidence            5899999999999999999999999999999999999999999999999999998887532   2345899999999999


Q ss_pred             HHHHHHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHH
Q 017573           78 QQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKD  157 (369)
Q Consensus        78 ~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~  157 (369)
                      .|+.+.+.++...  .++....++............+++|+|+||+.+...+.........++++|+||+|++.+.++..
T Consensus        86 ~q~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~iViDEah~~~~~~~~~  163 (207)
T 2gxq_A           86 LQVASELTAVAPH--LKVVAVYGGTGYGKQKEALLRGADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSMGFEE  163 (207)
T ss_dssp             HHHHHHHHHHCTT--SCEEEECSSSCSHHHHHHHHHCCSEEEECHHHHHHHHHHTSSCCTTCSEEEEESHHHHHHTTCHH
T ss_pred             HHHHHHHHHHhhc--ceEEEEECCCChHHHHHHhhCCCCEEEECHHHHHHHHHcCCcchhhceEEEEEChhHhhccchHH
Confidence            9999999998754  56777788777666655566678999999999999998887888889999999999999888999


Q ss_pred             HHHHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEe
Q 017573          158 QIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILV  199 (369)
Q Consensus       158 ~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~  199 (369)
                      .+..++..+++..|++++|||++.+..++...++.+|..+..
T Consensus       164 ~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~p~~i~~  205 (207)
T 2gxq_A          164 EVEALLSATPPSRQTLLFSATLPSWAKRLAERYMKNPVLINV  205 (207)
T ss_dssp             HHHHHHHTSCTTSEEEEECSSCCHHHHHHHHHHCSSCEEEEC
T ss_pred             HHHHHHHhCCccCeEEEEEEecCHHHHHHHHHHcCCCeEEEc
Confidence            999999999989999999999999999999999998876653

>1wrb_A DJVLGB; RNA helicase, DEAD BOX, VASA, structural genomics, NPPSFA, N project on protein structural and functional analyses; 2.40A {Dugesia japonica} SCOP: c.37.1.19

Probab=100.00  E-value=9.5e-35  Score=242.94  Aligned_cols=210  Identities=32%  Similarity=0.493  Sum_probs=178.0

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccC---------CCccEEEEc
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGL---------VQCQALVLA   71 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~---------~~~~~liv~   71 (369)
                      ++|++.+.++|..+|+..|+++|.++++.+.+++++++++|||+|||++++++++..+....         .++++||++
T Consensus        28 l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~l~~a~TGsGKT~~~~~~~l~~l~~~~~~~~~~~~~~~~~~lil~  107 (253)
T 1wrb_A           28 LKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILA  107 (253)
T ss_dssp             GSCCCSTTTTTTTTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHTTCC------CCBCCSEEEEC
T ss_pred             CCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhhccccccccccCCceEEEEE
Confidence            47899999999999999999999999999999999999999999999999999998875432         234899999


Q ss_pred             CCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhh
Q 017573           72 PTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEML  151 (369)
Q Consensus        72 P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~  151 (369)
                      |+++|+.|+.+.++++....++.+....|+.........+..+++|+|+||+.+...+.........++++|+||||++.
T Consensus       108 Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~~lViDEah~~~  187 (253)
T 1wrb_A          108 PTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEKNKISLEFCKYIVLDEADRML  187 (253)
T ss_dssp             SSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCSHHHHHHHSSCCSEEEECHHHHHHHHHTTSBCCTTCCEEEEETHHHHH
T ss_pred             CCHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHhCCCCCEEEECHHHHHHHHHcCCCChhhCCEEEEeCHHHHH
Confidence            99999999999999998877888888888887766666667788999999999999998888888889999999999999


Q ss_pred             ccCcHHHHHHHHhh--CCc--cCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCcccccccee
Q 017573          152 SRGFKDQIYDIFQL--LPA--KVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIK  210 (369)
Q Consensus       152 ~~~~~~~~~~~~~~--~~~--~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  210 (369)
                      +.++...+..++..  .+.  ..|++++|||++.+...+...++.++..+...........+.
T Consensus       188 ~~~~~~~~~~i~~~~~~~~~~~~q~l~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~i~  250 (253)
T 1wrb_A          188 DMGFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTVGRVGSTSDSIK  250 (253)
T ss_dssp             HTTCHHHHHHHHHSSCCCCGGGCEEEEEESSCCHHHHHHHHHHCSSCEEEEEC----------
T ss_pred             hCchHHHHHHHHhhccCCCCCCcEEEEEEEeCCHHHHHHHHHHcCCCEEEEECCCCCCcCCce
Confidence            99999999999885  343  678999999999999999999999998887766554444443

>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP: c.37.1.19

Probab=100.00  E-value=3.7e-34  Score=234.34  Aligned_cols=198  Identities=42%  Similarity=0.647  Sum_probs=174.4

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQI   80 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~   80 (369)
                      ++|++.+.++|.++|+..|+++|.++++.+.+++++++.+|||+|||++++++++..+.....+.+++|++|+++|+.|+
T Consensus        19 ~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~   98 (220)
T 1t6n_A           19 FLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQI   98 (220)
T ss_dssp             SCCCHHHHHHHHHTTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCTTCCCEEEECSCHHHHHHH
T ss_pred             cCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCchhhhhhHHHHHhhhccCCCEEEEEEeCCHHHHHHH
Confidence            58999999999999999999999999999999999999999999999999999998876655555899999999999999


Q ss_pred             HHHHHHhcccc-CcEEEEEECCcchHHHHHHHc-cCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhc-cCcHH
Q 017573           81 EKVMRALGDYL-GVKVHACVGGTSVREDQRILQ-AGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLS-RGFKD  157 (369)
Q Consensus        81 ~~~~~~~~~~~-~~~v~~~~~~~~~~~~~~~~~-~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~-~~~~~  157 (369)
                      .+.++++.... +.++..+.|+.....+...+. ..++|+|+||+.+...+.........++++|+||||++.+ .++..
T Consensus        99 ~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~lViDEah~~~~~~~~~~  178 (220)
T 1t6n_A           99 SKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRR  178 (220)
T ss_dssp             HHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEESHHHHHSSHHHHH
T ss_pred             HHHHHHHHhhCCCceEEEEeCCCChHHHHHHHhcCCCCEEEeCHHHHHHHHHhCCCCcccCCEEEEcCHHHHhcccCcHH
Confidence            99999987765 788888888877655544443 4579999999999999988878888899999999999986 46778


Q ss_pred             HHHHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEE
Q 017573          158 QIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRIL  198 (369)
Q Consensus       158 ~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~  198 (369)
                      .+..+...+++..|++++|||++.+..++...++.+|..+.
T Consensus       179 ~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~p~~i~  219 (220)
T 1t6n_A          179 DVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIF  219 (220)
T ss_dssp             HHHHHHHTSCSSSEEEEEESCCCTTTHHHHHTTCSSCEEEE
T ss_pred             HHHHHHHhCCCcCeEEEEEeecCHHHHHHHHHHcCCCeEEe
Confidence            88888888888999999999999999999999998887653

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=100.00  E-value=1.5e-33  Score=233.27  Aligned_cols=199  Identities=29%  Similarity=0.468  Sum_probs=173.3

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhcc----CCCccEEEEcCCHHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYG----LVQCQALVLAPTREL   76 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~----~~~~~~liv~P~~~l   76 (369)
                      ++|++.+.+.|.++|+..|+++|.++++.+.+++++++.+|||+|||++++++++..+...    ..+++++|++|+++|
T Consensus        30 ~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~li~a~TGsGKT~~~~~~~l~~l~~~~~~~~~~~~~lil~Pt~~L  109 (236)
T 2pl3_A           30 FPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEALYRLQWTSTDGLGVLIISPTREL  109 (236)
T ss_dssp             SCCCHHHHHHHHHTTCCBCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHTTCCGGGCCCEEEECSSHHH
T ss_pred             cCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEEeCCCCcHHHHHHHHHHHHHHhhcccccCCceEEEEeCCHHH
Confidence            5899999999999999999999999999999999999999999999999999988776431    234489999999999


Q ss_pred             HHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcC-CCCCCCccEEEEechhHhhccCc
Q 017573           77 AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQ-SLRPDYIKMFVLDEADEMLSRGF  155 (369)
Q Consensus        77 ~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~-~~~~~~~~~viiDE~H~~~~~~~  155 (369)
                      +.|+.+.+.++....++.+....|+.......... .+++|+|+||+.+...+... ......++++|+||+|++.+.++
T Consensus       110 ~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~-~~~~iiv~Tp~~l~~~l~~~~~~~~~~~~~lViDEah~~~~~~~  188 (236)
T 2pl3_A          110 AYQTFEVLRKVGKNHDFSAGLIIGGKDLKHEAERI-NNINILVCTPGRLLQHMDETVSFHATDLQMLVLDEADRILDMGF  188 (236)
T ss_dssp             HHHHHHHHHHHTTTSSCCEEEECCC--CHHHHHHH-TTCSEEEECHHHHHHHHHHCSSCCCTTCCEEEETTHHHHHHTTT
T ss_pred             HHHHHHHHHHHhCCCCeeEEEEECCCCHHHHHHhC-CCCCEEEECHHHHHHHHHhcCCcccccccEEEEeChHHHhcCCc
Confidence            99999999999887788888888887765554444 46899999999999887764 45667899999999999999999


Q ss_pred             HHHHHHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEec
Q 017573          156 KDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVK  200 (369)
Q Consensus       156 ~~~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~  200 (369)
                      ...+..++..+++..|++++|||++++..++...++.+|..+...
T Consensus       189 ~~~~~~i~~~~~~~~~~l~~SAT~~~~~~~~~~~~~~~p~~i~~~  233 (236)
T 2pl3_A          189 ADTMNAVIENLPKKRQTLLFSATQTKSVKDLARLSLKNPEYVWVH  233 (236)
T ss_dssp             HHHHHHHHHTSCTTSEEEEEESSCCHHHHHHHHHSCSSCEEEECC
T ss_pred             HHHHHHHHHhCCCCCeEEEEEeeCCHHHHHHHHHhCCCCEEEEeC
Confidence            999999999999999999999999999999999999988877653

>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=100.00  E-value=1.1e-33  Score=273.40  Aligned_cols=311  Identities=13%  Similarity=0.117  Sum_probs=204.4

Q ss_pred             CCcHhhhhhhhcccc--------------CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHH
Q 017573           18 KPSAIQQRGIVPFCK--------------GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKV   83 (369)
Q Consensus        18 ~~~~~Q~~~~~~~~~--------------~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~   83 (369)
                      .|||+|.++++.+.+              +++++++++||||||+++ ++++..+.......++|||||+++|+.|+.+.
T Consensus       271 ~~R~~Q~~AI~~il~~i~~~~~~~~~~~~~~~gli~~~TGSGKT~t~-~~l~~ll~~~~~~~rvLvlvpr~eL~~Q~~~~  349 (1038)
T 2w00_A          271 VMRPYQIAATERILWKIKSSFTAKNWSKPESGGYIWHTTGSGKTLTS-FKAARLATELDFIDKVFFVVDRKDLDYQTMKE  349 (1038)
T ss_dssp             ECCHHHHHHHHHHHHHHHHHHHHTCCSSGGGSEEEEECTTSSHHHHH-HHHHHHHTTCTTCCEEEEEECGGGCCHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHHHhcccccccccCCCCEEEEecCCCCHHHHH-HHHHHHHHhcCCCceEEEEeCcHHHHHHHHHH
Confidence            599999999998875              368999999999999997 44455554333334899999999999999999


Q ss_pred             HHHhccccCcEEEEEECCcchHHHHHHH-ccCCcEEEeccHHHHHHHHcCC--CCCCCccEEEEechhHhhccCcHHHHH
Q 017573           84 MRALGDYLGVKVHACVGGTSVREDQRIL-QAGVHVVVGTPGRVFDMLRRQS--LRPDYIKMFVLDEADEMLSRGFKDQIY  160 (369)
Q Consensus        84 ~~~~~~~~~~~v~~~~~~~~~~~~~~~~-~~~~~iiv~t~~~l~~~~~~~~--~~~~~~~~viiDE~H~~~~~~~~~~~~  160 (369)
                      +.++....      ..++.........+ ....+|+|+|+++|...+....  .....+.+||+||||++...   ....
T Consensus       350 f~~f~~~~------v~~~~s~~~l~~~L~~~~~~IiVtTiqkl~~~l~~~~~~~~~~~~~lvIiDEAHrs~~~---~~~~  420 (1038)
T 2w00_A          350 YQRFSPDS------VNGSENTAGLKRNLDKDDNKIIVTTIQKLNNLMKAESDLPVYNQQVVFIFDECHRSQFG---EAQK  420 (1038)
T ss_dssp             HHTTSTTC------SSSSCCCHHHHHHHHCSSCCEEEEEHHHHHHHHHHCCCCGGGGSCEEEEEESCCTTHHH---HHHH
T ss_pred             HHHhcccc------cccccCHHHHHHHhcCCCCCEEEEEHHHHHHHHhcccchhccccccEEEEEccchhcch---HHHH
Confidence            99876431      12333333333333 3568999999999988776532  12345789999999997532   3345


Q ss_pred             HHHhhCCccCcEEEEEeeCChhHH----HHHHHhcCCCEEEEecCccccccceeEE---EEEc-----------c-----
Q 017573          161 DIFQLLPAKVQVGVFSATMPPEAL----EITRKFMNKPVRILVKRDELTLEGIKQF---YVNV-----------E-----  217 (369)
Q Consensus       161 ~~~~~~~~~~~~i~~saT~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~-----------~-----  217 (369)
                      .+...++ +.+++++||||.....    .....+++.++.............+..+   +...           .     
T Consensus       421 ~I~~~~p-~a~~lgfTATP~~~~~~~~~~~t~~~FG~~i~~Y~l~~AI~dg~l~p~~v~y~~v~~~~~~~~~e~d~~~~~  499 (1038)
T 2w00_A          421 NLKKKFK-RYYQFGFTGTPIFPENALGSETTASVFGRELHSYVITDAIRDEKVLKFKVDYNDVRPQFKSLETETDEKKLS  499 (1038)
T ss_dssp             HHHHHCS-SEEEEEEESSCCCSTTCTTSCCHHHHHCSEEEEECHHHHHHHTSSCCEEEEECCCCGGGHHHHTCCCHHHHH
T ss_pred             HHHHhCC-cccEEEEeCCccccccchhhhHHHHHhCCeeEeecHHHHHhCCCcCCeEEEEEeccchhhhccccccHHHHH
Confidence            5666665 4689999999974321    1222233332222111000000000000   0000           0     


Q ss_pred             --------chhhhHHHHH-HHHHhc-----------cCCCeEEEeCCHhhHHHHHHHHhhCC------------Cee-EE
Q 017573          218 --------KEEWKLETLC-DLYETL-----------AITQSVIFVNTRRKVDWLTDKMRSRD------------HTV-SA  264 (369)
Q Consensus       218 --------~~~~~~~~l~-~~~~~~-----------~~~k~lv~~~~~~~~~~~~~~l~~~~------------~~~-~~  264 (369)
                              ........+. .++...           .+.+++|||++++.|..+++.|.+.+            .++ .+
T Consensus       500 ~i~~~~~l~~~~ri~~I~~~Il~~~~~~~~~~~~~~~g~kamVf~~S~~~A~~~~~~l~~~~~~~~~~~~~~~~~k~avv  579 (1038)
T 2w00_A          500 AAENQQAFLHPMRIQEITQYILNNFRQKTHRTFPGSKGFNAMLAVSSVDAAKAYYATFKRLQEEAANKSATYKPLRIATI  579 (1038)
T ss_dssp             HTCSTTTTTCHHHHHHHHHHHHHHHHHHTTCSSSSCCCCEEEEEESSHHHHHHHHHHHHHHHHHHTTTSSSCCCCCEEEE
T ss_pred             HHHHHHHhcCHHHHHHHHHHHHHHHHHhhhhhcccCCCCcEEEEECCHHHHHHHHHHHHhhhhhhcccccccccCcEEEE
Confidence                    0011122222 232211           23479999999999999999997653            344 34


Q ss_pred             ecCC----------C----------CH-----------------------------HHHHHHHHHHhcCCCcEEEEecCC
Q 017573          265 THGD----------M----------DQ-----------------------------NTRDIIMREFRSGSSRVLITTDLL  295 (369)
Q Consensus       265 ~~~~----------~----------~~-----------------------------~~r~~~~~~f~~~~~~vli~t~~~  295 (369)
                      +++.          +          +.                             ..|..+++.|++|++++||+|+++
T Consensus       580 ~s~~~~~~~~~~G~~~~e~~~~~~~~~~~r~~l~~~I~dyn~~f~~~~~~~~~~~~~~R~~i~~~Fk~g~i~ILIvvd~l  659 (1038)
T 2w00_A          580 FSFAANEEQNAIGEISDETFDTSAMDSSAKEFLDAAIREYNSHFKTNFSTDSNGFQNYYRDLAQRVKNQDIDLLIVVGMF  659 (1038)
T ss_dssp             CCCCC------CCCCCCCCSCGGGSCHHHHHHHHHHHHHHHHHHTCCCCSSHHHHHHHHHHHHHHHHTTSSSEEEESSTT
T ss_pred             EeCCCccccccccccccccccccccchhHHHHHHHHHHHHHHHhcccccccchhhhHHHHHHHHHHHcCCCeEEEEcchH
Confidence            4542          1          11                             137788999999999999999999


Q ss_pred             cCCCCCCCCcEEEEecCCCCccchhhhhcccccCCCc----eeEEEEec
Q 017573          296 ARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRK----GVAINFVT  340 (369)
Q Consensus       296 ~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~----~~~~~~~~  340 (369)
                      .+|+|+|.+ +++.++.|.+...++|++||++|.++.    |.++.|..
T Consensus       660 ltGfDiP~l-~tlylDkpl~~~~liQaIGRtnR~~~~~K~~G~IVdf~~  707 (1038)
T 2w00_A          660 LTGFDAPTL-NTLFVDKNLRYHGLMQAFSRTNRIYDATKTFGNIVTFRD  707 (1038)
T ss_dssp             SSSCCCTTE-EEEEEESCCCHHHHHHHHHTTCCCCCTTCCSEEEEESSC
T ss_pred             HhCcCcccc-cEEEEccCCCccceeehhhccCcCCCCCCCcEEEEEccc
Confidence            999999999 556788889999999999999998653    55665554

>3ly5_A ATP-dependent RNA helicase DDX18; alpha-beta, structural genomics, structural genomics consort ATP-binding, hydrolase, nucleotide-binding, RNA-B; 2.80A {Homo sapiens}

Probab=100.00  E-value=2.3e-33  Score=234.97  Aligned_cols=192  Identities=30%  Similarity=0.489  Sum_probs=171.6

Q ss_pred             CCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhcc----CCCccEEEEcCCHHHHH
Q 017573            3 LQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYG----LVQCQALVLAPTRELAQ   78 (369)
Q Consensus         3 l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~----~~~~~~liv~P~~~l~~   78 (369)
                      +++.+.+.|..+||.+|+++|.++++.+..++++++++|||+|||++++++++..+...    ..+.+++|++|+++|+.
T Consensus        61 l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~l~~l~~l~~~~~~~~~~~~~lil~Pt~~La~  140 (262)
T 3ly5_A           61 VNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRFMPRNGTGVLILSPTRELAM  140 (262)
T ss_dssp             CCHHHHHHHHHTTCCBCCHHHHHHHHHHHHTCCCEECCCTTSCHHHHHHHHHHHHHHHTTCCGGGCCCEEEECSSHHHHH
T ss_pred             cCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCcEEEEccCCCCchHHHHHHHHHHHHhccccccCCceEEEEeCCHHHHH
Confidence            89999999999999999999999999999999999999999999999999999877542    13448999999999999


Q ss_pred             HHHHHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCC-CCCCCccEEEEechhHhhccCcHH
Q 017573           79 QIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQS-LRPDYIKMFVLDEADEMLSRGFKD  157 (369)
Q Consensus        79 q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~-~~~~~~~~viiDE~H~~~~~~~~~  157 (369)
                      |+.+.++++....+..+..+.|+.........+..+++|+|+||+++...+.... ....+++++|+||+|++.+.++..
T Consensus       141 q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~~~~~~~~~~~~l~~lViDEah~l~~~~~~~  220 (262)
T 3ly5_A          141 QTFGVLKELMTHHVHTYGLIMGGSNRSAEAQKLGNGINIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEADRILDVGFEE  220 (262)
T ss_dssp             HHHHHHHHHTTTCCSCEEEECSSSCHHHHHHHHHHCCSEEEECHHHHHHHHHHCTTCCCTTCCEEEECSHHHHHHTTCHH
T ss_pred             HHHHHHHHHHhhcCceEEEEECCCCHHHHHHHhcCCCCEEEEcHHHHHHHHHccCCcccccCCEEEEcChHHHhhhhHHH
Confidence            9999999998888888989999888766666666678999999999998877654 567789999999999999999999


Q ss_pred             HHHHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCC
Q 017573          158 QIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKP  194 (369)
Q Consensus       158 ~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~  194 (369)
                      .+..+...+++..|++++|||++....++.+..+.++
T Consensus       221 ~l~~i~~~~~~~~q~l~~SAT~~~~v~~~~~~~l~~~  257 (262)
T 3ly5_A          221 ELKQIIKLLPTRRQTMLFSATQTRKVEDLARISLKKE  257 (262)
T ss_dssp             HHHHHHHHSCSSSEEEEECSSCCHHHHHHHHHHCSSC
T ss_pred             HHHHHHHhCCCCCeEEEEEecCCHHHHHHHHHHcCCC
Confidence            9999999999999999999999999998888877654

>3fmo_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 2.51A {Homo sapiens}

Probab=100.00  E-value=3.5e-33  Score=237.90  Aligned_cols=197  Identities=38%  Similarity=0.595  Sum_probs=173.3

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccC--CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKG--LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQ   78 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~--~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~   78 (369)
                      ++|++.+.++|.++||..|+++|.++++.+..+  +++++++|||+|||++++++++..+.....++++||++|+++|+.
T Consensus        97 l~l~~~l~~~l~~~g~~~pt~iQ~~ai~~il~~~~~~~l~~a~TGsGKT~a~~lp~l~~l~~~~~~~~~lil~PtreLa~  176 (300)
T 3fmo_B           97 LRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELAL  176 (300)
T ss_dssp             GTCCHHHHHHHHHTTCCSCCHHHHHHHHHHTSSSCCCEEEECCTTSSHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHH
T ss_pred             cCCCHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCCccHHHHHHHHHhhhccCCCceEEEEcCcHHHHH
Confidence            579999999999999999999999999999987  999999999999999999999999877666678999999999999


Q ss_pred             HHHHHHHHhcccc-CcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHc-CCCCCCCccEEEEechhHhhc-cCc
Q 017573           79 QIEKVMRALGDYL-GVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRR-QSLRPDYIKMFVLDEADEMLS-RGF  155 (369)
Q Consensus        79 q~~~~~~~~~~~~-~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~-~~~~~~~~~~viiDE~H~~~~-~~~  155 (369)
                      |+.+.+.++.... ++.+....++.......   ...++|+|+||+++..++.+ ..+...+++++|+||+|++.+ .++
T Consensus       177 Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~---~~~~~IlV~TP~~l~~~l~~~~~~~l~~l~~lVlDEad~l~~~~~~  253 (300)
T 3fmo_B          177 QTGKVIEQMGKFYPELKLAYAVRGNKLERGQ---KISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGH  253 (300)
T ss_dssp             HHHHHHHHHTTTSTTCCEEEESTTCCCCTTC---CCCCSEEEECHHHHHHHHTTTCCCCGGGCSEEEETTHHHHHHSTTH
T ss_pred             HHHHHHHHHHhhCCCcEEEEEeCCccHhhhh---cCCCCEEEECHHHHHHHHHhcCCCChhhceEEEEeCHHHHhhccCc
Confidence            9999999987654 57777777766533221   35679999999999998865 456678899999999999987 678


Q ss_pred             HHHHHHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEec
Q 017573          156 KDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVK  200 (369)
Q Consensus       156 ~~~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~  200 (369)
                      ...+..+...+++..|++++|||++.....+...++.+|..+...
T Consensus       254 ~~~~~~i~~~~~~~~q~i~~SAT~~~~v~~~a~~~l~~p~~i~~~  298 (300)
T 3fmo_B          254 QDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLK  298 (300)
T ss_dssp             HHHHHHHHTTSCTTCEEEEEESCCCHHHHHHHHHHSSSCEEEEEC
T ss_pred             HHHHHHHHHhCCCCCEEEEEeccCCHHHHHHHHHHCCCCeEEEec
Confidence            888999999999999999999999999999999999999887664

>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=100.00  E-value=1.9e-31  Score=241.65  Aligned_cols=319  Identities=18%  Similarity=0.204  Sum_probs=228.7

Q ss_pred             CCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCc
Q 017573           14 YGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGV   93 (369)
Q Consensus        14 ~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~   93 (369)
                      .|+ .|++.|.-..-.+.+|+  +..+.||+|||+++.++++-....+.   .+.+|+|+..|+.|-++++..+...+|+
T Consensus        72 lg~-r~~dvQligg~~L~~G~--iaEM~TGEGKTLva~lp~~lnAL~G~---~vhVvT~ndyLA~rdae~m~~l~~~Lgl  145 (822)
T 3jux_A           72 LGM-RPFDVQVMGGIALHEGK--VAEMKTGEGKTLAATMPIYLNALIGK---GVHLVTVNDYLARRDALWMGPVYLFLGL  145 (822)
T ss_dssp             TSC-CCCHHHHHHHHHHHTTC--EEECCTTSCHHHHTHHHHHHHHTTSS---CEEEEESSHHHHHHHHHHHHHHHHHTTC
T ss_pred             hCC-CCcHHHHHHHHHHhCCC--hhhccCCCCccHHHHHHHHHHHhcCC---ceEEEeccHHHHHhHHHHHHHHHHHhCC
Confidence            354 68888887777666655  99999999999999988874433333   7999999999999999999999999999


Q ss_pred             EEEEEECC--------------------------------------------------cchHHHHHHHccCCcEEEeccH
Q 017573           94 KVHACVGG--------------------------------------------------TSVREDQRILQAGVHVVVGTPG  123 (369)
Q Consensus        94 ~v~~~~~~--------------------------------------------------~~~~~~~~~~~~~~~iiv~t~~  123 (369)
                      ++.++...                                                  ......+...  .+||+++|..
T Consensus       146 svg~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~err~aY--~~DItYgTn~  223 (822)
T 3jux_A          146 RVGVINSLGKSYEVVWKNPDLARKAIEENWSVWPDGFNGEVLKEESMNKEAVEAFQVELKEITRKEAY--LCDVTYGTNN  223 (822)
T ss_dssp             CEEEEETTTEEEEEEESSHHHHHHHHHTTCCSSCTTCCSSSCCGGGSCHHHHTTTCEECCBCCHHHHH--HSSEEEEEHH
T ss_pred             EEEEEcCCCcccccccccchhhhhhhcccccccccccccccccccccccccchhccccCCHHHHHHHh--cCCCEEccCc
Confidence            99988872                                                  1111111111  3799999998


Q ss_pred             HH-HHHHHcCC------CCCCCccEEEEechhHhh-ccC---------------cHHHHHHHHhhCC-------------
Q 017573          124 RV-FDMLRRQS------LRPDYIKMFVLDEADEML-SRG---------------FKDQIYDIFQLLP-------------  167 (369)
Q Consensus       124 ~l-~~~~~~~~------~~~~~~~~viiDE~H~~~-~~~---------------~~~~~~~~~~~~~-------------  167 (369)
                      .| +..++.+-      .....+.+.|+||++.+. +..               .......+...+.             
T Consensus       224 EfgFDYLRDnm~~~~~~~vqR~~~~aIVDEvDSiLIDeArtPLiISg~~~~~~~~y~~~~~~v~~l~~~~dy~vdek~~~  303 (822)
T 3jux_A          224 EFGFDYLRDNLVLDYNDKVQRGHFYAIVDEADSVLIDEARTPLIISGPSKESPSVYRRFAQIAKKFVKDKDFTVDEKART  303 (822)
T ss_dssp             HHHHHHHHHTSCSSTTSCCCCCCCEEEEETHHHHHTTGGGSCEEEECCCCSCHHHHHHHHHHTTSSCBTTTEEECCSSSC
T ss_pred             chhhHhHHhhccCCHHHhccCCCCeEEEecccceeecCCCCCceeeCCCCCccHHHHHHHHHHHhcCcCCcEEEEcccCe
Confidence            88 45554431      123457899999999865 100               0011111111000             


Q ss_pred             --------------------------------------------------------------------------------
Q 017573          168 --------------------------------------------------------------------------------  167 (369)
Q Consensus       168 --------------------------------------------------------------------------------  167 (369)
                                                                                                      
T Consensus       304 v~lTe~G~~~~E~~l~i~nly~~~n~~l~~~i~~AL~A~~l~~~d~dYiV~dg~V~iVDe~TGR~m~grr~s~GLHQaiE  383 (822)
T 3jux_A          304 IILTEEGVAKAEKIIGVENLYDPGNVSLLYHLINALKALHLFKKDVDYVVMNGEVIIVDEFTGRLLPGRRYSGGLHQAIE  383 (822)
T ss_dssp             EEECHHHHHHHHHHHTCSCTTSGGGHHHHHHHHHHHHHHHHSTTTSSEEEETTEEEECSSSSCSCCCSCCCGGGHHHHHH
T ss_pred             EEECHHHHHHHHHHhCCccccchhhhHHHHHHHHHHHHHHHHcCCCcEEEECCEEEEEECCCCcCCCCCcCchHHHHHHH
Confidence                                                                                            


Q ss_pred             ------------------------ccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCccccccceeEEEEEccchhhhH
Q 017573          168 ------------------------AKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKL  223 (369)
Q Consensus       168 ------------------------~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  223 (369)
                                              --.++.+||||......++ ...++..+.....  ..+...+............+.
T Consensus       384 aKEgv~i~~e~~tla~IT~Qn~Fr~Y~kL~GMTGTa~te~~Ef-~~iY~l~vv~IPt--nkp~~R~d~~d~vy~t~~eK~  460 (822)
T 3jux_A          384 AKEGVPIKEESITYATITFQNYFRMYEKLAGMTGTAKTEESEF-VQVYGMEVVVIPT--HKPMIRKDHDDLVFRTQKEKY  460 (822)
T ss_dssp             HHHSSCCCCCCCEEEEECHHHHHTTSSEEEEEESSCGGGHHHH-HHHSCCCEEECCC--SSCCCCEECCCEEESSHHHHH
T ss_pred             HHcCCCCCCCcchhHHHHHHHHHHHhhHHeEECCCCchHHHHH-HHHhCCeEEEECC--CCCcceeecCcEEEecHHHHH
Confidence                                    0056899999998766554 4444444333322  222222222112223445577


Q ss_pred             HHHHHHHHhc--cCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCC
Q 017573          224 ETLCDLYETL--AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDV  301 (369)
Q Consensus       224 ~~l~~~~~~~--~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~  301 (369)
                      ..+...+...  .+.++||||++++.++.+++.|.+.|+++..+||+....++..+.+.++.|  .|+|||+++++|+|+
T Consensus       461 ~al~~~I~~~~~~gqpVLVFt~S~e~sE~Ls~~L~~~Gi~~~vLhgkq~~rE~~ii~~ag~~g--~VtVATdmAgRGtDI  538 (822)
T 3jux_A          461 EKIVEEIEKRYKKGQPVLVGTTSIEKSELLSSMLKKKGIPHQVLNAKYHEKEAEIVAKAGQKG--MVTIATNMAGRGTDI  538 (822)
T ss_dssp             HHHHHHHHHHHHHTCCEEEEESSHHHHHHHHHHHHTTTCCCEEECSCHHHHHHHHHHHHHSTT--CEEEEETTTTTTCCC
T ss_pred             HHHHHHHHHHhhCCCCEEEEECCHHHHHHHHHHHHHCCCCEEEeeCCchHHHHHHHHhCCCCC--eEEEEcchhhCCcCc
Confidence            7777766543  467999999999999999999999999999999996666666566666655  599999999999999


Q ss_pred             C--------CCcEEEEecCCCCccchhhhhcccccCCCceeEEEEeccccHH
Q 017573          302 Q--------QVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDER  345 (369)
Q Consensus       302 ~--------~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~  345 (369)
                      +        +..+||.++.|.+...|.|++||+||.|++|.+++|++..|.-
T Consensus       539 ~lg~~V~~~GglhVInte~Pes~r~y~qriGRTGRqG~~G~a~~fvsleD~l  590 (822)
T 3jux_A          539 KLGPGVAELGGLCIIGTERHESRRIDNQLRGRAGRQGDPGESIFFLSLEDDL  590 (822)
T ss_dssp             CCCTTTTTTTSCEEEESSCCSSHHHHHHHHTTSSCSSCCCEEEEEEETTSHH
T ss_pred             cCCcchhhcCCCEEEecCCCCCHHHHHHhhCccccCCCCeeEEEEechhHHH
Confidence            8        6679999999999999999999999999999999999988743

>3dkp_A Probable ATP-dependent RNA helicase DDX52; DEAD, ADP, structural genomics, structural GEN consortium, SGC, rRNA, ATP-binding, hydrolase; HET: ADP; 2.10A {Homo sapiens}

Probab=100.00  E-value=1.5e-32  Score=228.59  Aligned_cols=202  Identities=26%  Similarity=0.446  Sum_probs=167.8

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhc-cCCCccEEEEcCCHHHHHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY-GLVQCQALVLAPTRELAQQ   79 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~-~~~~~~~liv~P~~~l~~q   79 (369)
                      ++|++.+.+++.++||..|+++|.++++.+.+++++++.+|||+|||++++++++..+.. ...+.+++|++|+++|+.|
T Consensus        34 ~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~~~~~~~~~lil~Pt~~L~~q  113 (245)
T 3dkp_A           34 YKINSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMQLKQPANKGFRALIISPTRELASQ  113 (245)
T ss_dssp             HCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHCSCCSSSCCEEEECSSHHHHHH
T ss_pred             cCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHhhcccCCceEEEEeCCHHHHHH
Confidence            379999999999999999999999999999999999999999999999999999988764 2344589999999999999


Q ss_pred             HHHHHHHhccccCcEEEEEECCcchHHH-HHHHccCCcEEEeccHHHHHHHHcC--CCCCCCccEEEEechhHhhc---c
Q 017573           80 IEKVMRALGDYLGVKVHACVGGTSVRED-QRILQAGVHVVVGTPGRVFDMLRRQ--SLRPDYIKMFVLDEADEMLS---R  153 (369)
Q Consensus        80 ~~~~~~~~~~~~~~~v~~~~~~~~~~~~-~~~~~~~~~iiv~t~~~l~~~~~~~--~~~~~~~~~viiDE~H~~~~---~  153 (369)
                      +.+.+.++....+..+....++...... ......+++|+|+||+.+...+...  .....+++++|+||+|++.+   .
T Consensus       114 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~~~~~~~~lViDEah~~~~~~~~  193 (245)
T 3dkp_A          114 IHRELIKISEGTGFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPPGIDLASVEWLVVDESDKLFEDGKT  193 (245)
T ss_dssp             HHHHHHHHTTTSCCCEECCCHHHHHHTTTSTTSCCCCCEEEECHHHHHHHHHSSSCSCCCTTCCEEEESSHHHHHHHC--
T ss_pred             HHHHHHHHhcccCceEEEEecCccHHHHhhhhhcCCCCEEEECHHHHHHHHHhCCCCcccccCcEEEEeChHHhcccccc
Confidence            9999999988778777766654432221 1122356799999999999988876  45677899999999999987   4


Q ss_pred             CcHHHHHHHHhhC-CccCcEEEEEeeCChhHHHHHHHhcCCCEEEEecCc
Q 017573          154 GFKDQIYDIFQLL-PAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRD  202 (369)
Q Consensus       154 ~~~~~~~~~~~~~-~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~~~  202 (369)
                      ++...+..++..+ ++..|++++|||++.+...+...++.++..+.....
T Consensus       194 ~~~~~~~~i~~~~~~~~~~~~~~SAT~~~~v~~~~~~~l~~p~~i~~~~~  243 (245)
T 3dkp_A          194 GFRDQLASIFLACTSHKVRRAMFSATFAYDVEQWCKLNLDNVISVSIGAR  243 (245)
T ss_dssp             CHHHHHHHHHHHCCCTTCEEEEEESSCCHHHHHHHHHHSSSCEEEEECC-
T ss_pred             cHHHHHHHHHHhcCCCCcEEEEEeccCCHHHHHHHHHhCCCCEEEEeCCC
Confidence            6777788877665 457899999999999999999999999988876543

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19

Probab=99.96  E-value=2.1e-28  Score=190.21  Aligned_cols=162  Identities=68%  Similarity=1.049  Sum_probs=147.3

Q ss_pred             ceeEEEEEccchhhhHHHHHHHHHhccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCc
Q 017573          208 GIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSR  287 (369)
Q Consensus       208 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~  287 (369)
                      .+.+.+........+.+.+.+++.....+++||||++.+.++.+++.|...+..+..+||+++..+|..+++.|++|+.+
T Consensus         3 ~i~~~~~~~~~~~~K~~~l~~ll~~~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~   82 (165)
T 1fuk_A            3 GIKQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSR   82 (165)
T ss_dssp             -CEEEEEEEESGGGHHHHHHHHHHHTTCSCEEEEESSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCS
T ss_pred             CcEEEEEECCcchhHHHHHHHHHHhCCCCCEEEEECCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHHcCCCE
Confidence            46677777776666999999999988889999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEecCCcCCCCCCCCcEEEEecCCCCccchhhhhcccccCCCceeEEEEeccccHHHHHHHHHHhccccccCCcchhh
Q 017573          288 VLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPSNVAD  367 (369)
Q Consensus       288 vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  367 (369)
                      |||+|+++++|+|+|++++||++++|++..+|.|++||+||.|+.|.+++++++.+...+..++++++..+++++.++.+
T Consensus        83 vlv~T~~~~~G~d~~~~~~Vi~~~~p~~~~~~~qr~GR~gR~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  162 (165)
T 1fuk_A           83 ILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELEKFYSTQIEELPSDIAT  162 (165)
T ss_dssp             EEEEEGGGTTTCCCCSCSEEEESSCCSSGGGGGGSSCSCC-----CEEEEEEETTTHHHHHHHHHHSSCCCEECCSCCTT
T ss_pred             EEEEcChhhcCCCcccCCEEEEeCCCCCHHHHHHHhcccccCCCCceEEEEEcchHHHHHHHHHHHHccCccccCccHHh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999988876


Q ss_pred             cC
Q 017573          368 LL  369 (369)
Q Consensus       368 ~~  369 (369)
                      ++
T Consensus       163 ~~  164 (165)
T 1fuk_A          163 LL  164 (165)
T ss_dssp             TT
T ss_pred             hc
Confidence            54

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=99.96  E-value=6.5e-27  Score=216.05  Aligned_cols=131  Identities=22%  Similarity=0.231  Sum_probs=110.3

Q ss_pred             hCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccC
Q 017573           13 AYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLG   92 (369)
Q Consensus        13 ~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~   92 (369)
                      ..|+ .|++.|..+++.+.+|+  +.++.||+|||+++.++++.....+   ..++|++|++.|+.|.++++..++..++
T Consensus        75 ~lG~-~Pt~VQ~~~ip~LlqG~--IaeakTGeGKTLvf~Lp~~L~aL~G---~qv~VvTPTreLA~Qdae~m~~l~~~lG  148 (997)
T 2ipc_A           75 YLGM-RHFDVQLIGGAVLHEGK--IAEMKTGEGKTLVATLAVALNALTG---KGVHVVTVNDYLARRDAEWMGPVYRGLG  148 (997)
T ss_dssp             HTCC-CCCHHHHHHHHHHHTTS--EEECCSTHHHHHHHHHHHHHHHTTC---SCCEEEESSHHHHHHHHHHHHHHHHTTT
T ss_pred             HhCC-CCcHHHHhhcccccCCc--eeeccCCCchHHHHHHHHHHHHHhC---CCEEEEeCCHHHHHHHHHHHHHHHHhcC
Confidence            3688 99999999999999998  9999999999999999885443333   3799999999999999999999999999


Q ss_pred             cEEEEEECCcchHHHHHHHccCCcEEEeccHHH-HHHHHcCC------CCCC---CccEEEEechhHhh
Q 017573           93 VKVHACVGGTSVREDQRILQAGVHVVVGTPGRV-FDMLRRQS------LRPD---YIKMFVLDEADEML  151 (369)
Q Consensus        93 ~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l-~~~~~~~~------~~~~---~~~~viiDE~H~~~  151 (369)
                      +++..+.|+........  ...++|+|+||..| +.++...-      ....   .++++|+||+|.+.
T Consensus       149 Lsv~~i~Gg~~~~~r~~--ay~~DIvyGTpgrlgfDyLrd~m~~~~~~l~~r~d~~l~~lIIDEaDsmL  215 (997)
T 2ipc_A          149 LSVGVIQHASTPAERRK--AYLADVTYVTNSELGFDYLRDNMAISPDQLVLRHDHPLHYAIIDEVDSIL  215 (997)
T ss_dssp             CCEEECCTTCCHHHHHH--HHTSSEEEEEHHHHHHHHHHHTSCSSTTTCCSCSSSSSCEEEETTHHHHT
T ss_pred             CeEEEEeCCCCHHHHHH--HcCCCEEEECchhhhhHHHHHhhhcchhhcccccCCCcceEEEechHHHH
Confidence            99999999887544333  34589999999999 77777652      3455   78999999999976

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}

Probab=99.96  E-value=3e-27  Score=183.14  Aligned_cols=158  Identities=41%  Similarity=0.635  Sum_probs=146.1

Q ss_pred             ccccceeEEEEEccchhhhHHHHHHHHHhccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhc
Q 017573          204 LTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRS  283 (369)
Q Consensus       204 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~  283 (369)
                      .....+.+.+..... ..+...+.+++.....+++||||++.+.++.+++.|...+..+..+||+++..+|..+++.|++
T Consensus         5 ~~~~~i~~~~~~~~~-~~K~~~L~~ll~~~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~hg~~~~~~r~~~~~~f~~   83 (163)
T 2hjv_A            5 LTTRNIEHAVIQVRE-ENKFSLLKDVLMTENPDSCIIFCRTKEHVNQLTDELDDLGYPCDKIHGGMIQEDRFDVMNEFKR   83 (163)
T ss_dssp             -CCCCEEEEEEECCG-GGHHHHHHHHHHHHCCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHT
T ss_pred             cCcccceEEEEECCh-HHHHHHHHHHHHhcCCCcEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHHc
Confidence            345567788777764 5688899999988888899999999999999999999999999999999999999999999999


Q ss_pred             CCCcEEEEecCCcCCCCCCCCcEEEEecCCCCccchhhhhcccccCCCceeEEEEeccccHHHHHHHHHHhccccccCC
Q 017573          284 GSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELP  362 (369)
Q Consensus       284 ~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  362 (369)
                      |+.+|||+|+++++|+|+|++++||++++|++..+|.|++||+||.|+.|.+++++.+.+...++.+++.++..+++++
T Consensus        84 g~~~vlv~T~~~~~Gld~~~~~~Vi~~~~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~  162 (163)
T 2hjv_A           84 GEYRYLVATDVAARGIDIENISLVINYDLPLEKESYVHRTGRTGRAGNKGKAISFVTAFEKRFLADIEEYIGFEIQKIE  162 (163)
T ss_dssp             TSCSEEEECGGGTTTCCCSCCSEEEESSCCSSHHHHHHHTTTSSCTTCCEEEEEEECGGGHHHHHHHHHHHTSCCEECC
T ss_pred             CCCeEEEECChhhcCCchhcCCEEEEeCCCCCHHHHHHhccccCcCCCCceEEEEecHHHHHHHHHHHHHHCCCcCccC
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999988877654

>2rb4_A ATP-dependent RNA helicase DDX25; rossmann fold, structural genomics, structural consortium, SGC, alternative initiation, ATP-binding, devel protein; 2.80A {Homo sapiens}

Probab=99.95  E-value=2.1e-27  Score=186.45  Aligned_cols=160  Identities=45%  Similarity=0.814  Sum_probs=146.5

Q ss_pred             cccceeEEEEEccchhhhHHHHHHHHHhccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcC
Q 017573          205 TLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSG  284 (369)
Q Consensus       205 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~  284 (369)
                      .+..+.+.+..++....+...+..++.....+++||||++.+.++.+++.|...+..+..+||+++..+|..+++.|++|
T Consensus         4 ~~~~i~q~~~~~~~~~~K~~~L~~ll~~~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~R~~~~~~f~~g   83 (175)
T 2rb4_A            4 TLNNIRQYYVLCEHRKDKYQALCNIYGSITIGQAIIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTVEQRASIIQRFRDG   83 (175)
T ss_dssp             CBCCEEEEEEECSSHHHHHHHHHHHHTTSCCSEEEEECSCHHHHHHHHHHHHTTTCCEEEECSSCCHHHHHHHHHHHHTT
T ss_pred             ccCCceEEEEEcCChHhHHHHHHHHHHhCCCCCEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHHcC
Confidence            45678899998888777999999999888888999999999999999999999999999999999999999999999999


Q ss_pred             CCcEEEEecCCcCCCCCCCCcEEEEecCC------CCccchhhhhcccccCCCceeEEEEeccccHHHHHHHHHHhcccc
Q 017573          285 SSRVLITTDLLARGIDVQQVSLVINYDLP------TQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVI  358 (369)
Q Consensus       285 ~~~vli~t~~~~~G~d~~~~~~vi~~~~~------~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  358 (369)
                      +.+|||+|+++++|+|+|.+++||++++|      .+..+|.||+||+||.|+.|.+++++++.+...+..+.+.++..+
T Consensus        84 ~~~vLvaT~~~~~Gid~~~~~~Vi~~d~p~~~~~~~~~~~~~qr~GR~gR~g~~g~~~~~~~~~~~~~~~~i~~~~~~~~  163 (175)
T 2rb4_A           84 KEKVLITTNVCARGIDVKQVTIVVNFDLPVKQGEEPDYETYLHRIGRTGRFGKKGLAFNMIEVDELPSLMKIQDHFNSSI  163 (175)
T ss_dssp             SCSEEEECCSCCTTTCCTTEEEEEESSCCC--CCSCCHHHHHHHHCBC----CCEEEEEEECGGGHHHHHHHHHHHTCCC
T ss_pred             CCeEEEEecchhcCCCcccCCEEEEeCCCCCccccCCHHHHHHHhcccccCCCCceEEEEEccchHHHHHHHHHHhcCcc
Confidence            99999999999999999999999999999      889999999999999999999999999999999999999999988


Q ss_pred             ccCCcc
Q 017573          359 EELPSN  364 (369)
Q Consensus       359 ~~~~~~  364 (369)
                      ++++.+
T Consensus       164 ~~~~~~  169 (175)
T 2rb4_A          164 KQLNAE  169 (175)
T ss_dssp             EEECSS
T ss_pred             cccCCc
Confidence            877644

>1c4o_A DNA nucleotide excision repair enzyme UVRB; uvrabc, helicase, hypertherm protein, replication; HET: DNA BOG; 1.50A {Thermus thermophilus} SCOP: c.37.1.19 c.37.1.19 PDB: 1d2m_A*

Probab=99.95  E-value=5.8e-27  Score=219.46  Aligned_cols=117  Identities=26%  Similarity=0.363  Sum_probs=108.3

Q ss_pred             cCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecC-
Q 017573          234 AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDL-  312 (369)
Q Consensus       234 ~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~-  312 (369)
                      .+.++||||++...++.+++.|...+..+..+||+++..+|.++++.|++|+.+|||+|+.+++|+|+|++++||+++. 
T Consensus       438 ~~~~vlVf~~t~~~ae~L~~~L~~~gi~~~~lh~~~~~~~R~~~~~~f~~g~~~VLvaT~~l~~GlDip~v~lVI~~d~d  517 (664)
T 1c4o_A          438 RGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLREGLDIPEVSLVAILDAD  517 (664)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESCCCCTTCCCTTEEEEEETTTT
T ss_pred             cCCEEEEEECCHHHHHHHHHHHHhcCCCceeecCCCCHHHHHHHHHHhhcCCceEEEccChhhcCccCCCCCEEEEeCCc
Confidence            4579999999999999999999999999999999999999999999999999999999999999999999999999997 


Q ss_pred             ----CCCccchhhhhcccccCCCceeEEEEeccccHHHHHHHH
Q 017573          313 ----PTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQ  351 (369)
Q Consensus       313 ----~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~  351 (369)
                          |.+..+|.|++||+||.+ .|.+++++++.+....+.+.
T Consensus       518 ~~G~p~s~~~~iQr~GRagR~~-~G~~i~~~~~~~~~~~~~i~  559 (664)
T 1c4o_A          518 KEGFLRSERSLIQTIGRAARNA-RGEVWLYADRVSEAMQRAIE  559 (664)
T ss_dssp             SCSGGGSHHHHHHHHGGGTTST-TCEEEEECSSCCHHHHHHHH
T ss_pred             ccCCCCCHHHHHHHHCccCcCC-CCEEEEEEcCCCHHHHHHHH
Confidence                889999999999999984 79999999988776554443

>1t5i_A C_terminal domain of A probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; 1.90A {Homo sapiens} SCOP: c.37.1.19

Probab=99.95  E-value=3e-27  Score=184.51  Aligned_cols=160  Identities=36%  Similarity=0.682  Sum_probs=144.3

Q ss_pred             ccceeEEEEEccchhhhHHHHHHHHHhccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCC
Q 017573          206 LEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGS  285 (369)
Q Consensus       206 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~  285 (369)
                      +..+.+++..... ..+...+.+++.....+++||||++.+.++.+++.|...+..+..+||+++..+|..+++.|++|+
T Consensus         3 ~~~i~q~~~~~~~-~~K~~~L~~ll~~~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~hg~~~~~~r~~~~~~f~~g~   81 (172)
T 1t5i_A            3 LHGLQQYYVKLKD-NEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQ   81 (172)
T ss_dssp             --CCEEEEEECCG-GGHHHHHHHHHHHSCCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTS
T ss_pred             cCCeEEEEEECCh-HHHHHHHHHHHHhCCCCcEEEEECCHHHHHHHHHHHHhcCCCEEEEECCCCHHHHHHHHHHHHCCC
Confidence            3456777777665 568899999999888889999999999999999999999999999999999999999999999999


Q ss_pred             CcEEEEecCCcCCCCCCCCcEEEEecCCCCccchhhhhcccccCCCceeEEEEeccc-cHHHHHHHHHHhccccccCCcc
Q 017573          286 SRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRD-DERMLFDIQKFYNVVIEELPSN  364 (369)
Q Consensus       286 ~~vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~  364 (369)
                      .+|||+|+++++|+|+|++++||++++|++...|.|++||+||.|+.|.+++++++. +...++.+.+.+...+++++.+
T Consensus        82 ~~vLvaT~~~~~Gldi~~~~~Vi~~d~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~  161 (172)
T 1t5i_A           82 RRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDE  161 (172)
T ss_dssp             CSEEEESSCCSTTCCGGGCSEEEESSCCSSHHHHHHHHHHHTGGGCCCEEEEEECSHHHHHHHHHHHHHHCCCEEECC--
T ss_pred             CcEEEECCchhcCcchhhCCEEEEECCCCCHHHHHHHhcccccCCCCcEEEEEEcChhHHHHHHHHHHHHhcchhhCChh
Confidence            999999999999999999999999999999999999999999999999999999876 5678899999999999999877


Q ss_pred             hh
Q 017573          365 VA  366 (369)
Q Consensus       365 ~~  366 (369)
                      +.
T Consensus       162 ~~  163 (172)
T 1t5i_A          162 ID  163 (172)
T ss_dssp             --
T ss_pred             hc
Confidence            64

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}

Probab=99.95  E-value=1.8e-27  Score=188.56  Aligned_cols=178  Identities=28%  Similarity=0.446  Sum_probs=144.3

Q ss_pred             HhcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHHHhccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCC
Q 017573          189 KFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGD  268 (369)
Q Consensus       189 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~  268 (369)
                      .++.+|..+.+.........+.+.+..... ..+...+.+++... .+++||||++.+.++.+++.|...+..+..+||+
T Consensus        10 ~~~~~p~~i~v~~~~~~~~~i~q~~~~~~~-~~K~~~L~~~l~~~-~~~~lVF~~~~~~~~~l~~~L~~~g~~~~~lhg~   87 (191)
T 2p6n_A           10 GVDLGTENLYFQSMGAASLDVIQEVEYVKE-EAKMVYLLECLQKT-PPPVLIFAEKKADVDAIHEYLLLKGVEAVAIHGG   87 (191)
T ss_dssp             ------------------CCSEEEEEECCG-GGHHHHHHHHHTTS-CSCEEEECSCHHHHHHHHHHHHHHTCCEEEECTT
T ss_pred             cccCCCEEEEECCCCCCCcCceEEEEEcCh-HHHHHHHHHHHHhC-CCCEEEEECCHHHHHHHHHHHHHcCCcEEEEeCC
Confidence            445566666666666667788888877665 46888888888765 4689999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCCCCccchhhhhcccccCCCceeEEEEeccc-cHHHH
Q 017573          269 MDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRD-DERML  347 (369)
Q Consensus       269 ~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~-~~~~~  347 (369)
                      ++..+|.++++.|++|+.+|||+|+++++|+|+|++++||++++|++..+|.|++||+||.|+.|.+++++++. +...+
T Consensus        88 ~~~~~R~~~l~~F~~g~~~vLvaT~~~~~Gldi~~v~~VI~~d~p~~~~~~~qr~GR~gR~g~~g~~i~l~~~~~~~~~~  167 (191)
T 2p6n_A           88 KDQEERTKAIEAFREGKKDVLVATDVASKGLDFPAIQHVINYDMPEEIENYVHRIGRTGCSGNTGIATTFINKACDESVL  167 (191)
T ss_dssp             SCHHHHHHHHHHHHHTSCSEEEECHHHHTTCCCCCCSEEEESSCCSSHHHHHHHHTTSCC---CCEEEEEECTTSCHHHH
T ss_pred             CCHHHHHHHHHHHhcCCCEEEEEcCchhcCCCcccCCEEEEeCCCCCHHHHHHHhCccccCCCCcEEEEEEcCchhHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999976 78888


Q ss_pred             HHHHHHhccccccCCcchhhc
Q 017573          348 FDIQKFYNVVIEELPSNVADL  368 (369)
Q Consensus       348 ~~~~~~~~~~~~~~~~~~~~~  368 (369)
                      ..+.+.++....++|++|.++
T Consensus       168 ~~l~~~l~~~~~~~p~~l~~~  188 (191)
T 2p6n_A          168 MDLKALLLEAKQKVPPVLQVL  188 (191)
T ss_dssp             HHHHHHHHHTTCCCCHHHHST
T ss_pred             HHHHHHHHHccCcCCHHHHhh
Confidence            999999999999999888764

>2jgn_A DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosphorylation, nucleotide-binding, hydrolase, RNA-binding, ATP-binding, DNA-binding, nuclear protein; 1.91A {Homo sapiens}

Probab=99.95  E-value=2.3e-27  Score=187.17  Aligned_cols=165  Identities=35%  Similarity=0.537  Sum_probs=137.5

Q ss_pred             cccccceeEEEEEccchhhhHHHHHHHHHhc-cCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHH
Q 017573          203 ELTLEGIKQFYVNVEKEEWKLETLCDLYETL-AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREF  281 (369)
Q Consensus       203 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f  281 (369)
                      ......+.+.+..+.. ..+...+.+++... ..+++||||++.+.++.+++.|+..+..+..+||+++..+|.++++.|
T Consensus        14 ~~~~~~i~q~~~~v~~-~~K~~~L~~ll~~~~~~~k~lVF~~~~~~~~~l~~~L~~~g~~~~~lhg~~~~~~r~~~~~~f   92 (185)
T 2jgn_A           14 GSTSENITQKVVWVEE-SDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQF   92 (185)
T ss_dssp             --CCTTEEEEEEECCG-GGHHHHHHHHHHHC-CCSCEEEEESCHHHHHHHHHHHHHTTCCEEEEC--------CHHHHHH
T ss_pred             CCCCCCceEEEEEeCc-HHHHHHHHHHHHhcCCCCeEEEEECCHHHHHHHHHHHHHcCCceEEEeCCCCHHHHHHHHHHH
Confidence            3446678888887765 45888888888876 567999999999999999999999999999999999999999999999


Q ss_pred             hcCCCcEEEEecCCcCCCCCCCCcEEEEecCCCCccchhhhhcccccCCCceeEEEEeccccHHHHHHHHHHhccccccC
Q 017573          282 RSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEEL  361 (369)
Q Consensus       282 ~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  361 (369)
                      ++|+.+|||+|+++++|+|+|++++||++++|++..+|.|++||++|.|+.|.+++++++.+...++.+.+.++....++
T Consensus        93 ~~g~~~vLvaT~~~~~Gldi~~~~~VI~~d~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~l~~~l~~~~~~~  172 (185)
T 2jgn_A           93 RSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINITKDLLDLLVEAKQEV  172 (185)
T ss_dssp             HHTSSSEEEEEC------CCCSBSEEEESSCCSSHHHHHHHHTTBCCTTSCEEEEEEECGGGGGGHHHHHHHHHHTTCCC
T ss_pred             HcCCCeEEEEcChhhcCCCcccCCEEEEeCCCCCHHHHHHHccccCCCCCCcEEEEEEchhhHHHHHHHHHHHHhccCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             Ccchhhc
Q 017573          362 PSNVADL  368 (369)
Q Consensus       362 ~~~~~~~  368 (369)
                      ++++.++
T Consensus       173 ~~~l~~~  179 (185)
T 2jgn_A          173 PSWLENM  179 (185)
T ss_dssp             CHHHHHH
T ss_pred             CHHHHHH
Confidence            9888654

>2d7d_A Uvrabc system protein B; helicase, protein-DNA-ADP ternary complex, hydrolase/DNA complex; HET: ADP; 2.10A {Bacillus subtilis} PDB: 2nmv_A* 2fdc_A* 1t5l_A 3uwx_B 1d9z_A* 1d9x_A 2d7d_B* 2nmv_B*

Probab=99.95  E-value=5.5e-25  Score=206.03  Aligned_cols=116  Identities=26%  Similarity=0.377  Sum_probs=108.0

Q ss_pred             cCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecC-
Q 017573          234 AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDL-  312 (369)
Q Consensus       234 ~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~-  312 (369)
                      .+.++||||++...++.+++.|...+.++..+||+++..+|.++++.|++|+.+|||+|+.+++|+|+|++++||+++. 
T Consensus       444 ~~~~vlVf~~t~~~ae~L~~~L~~~gi~~~~lh~~~~~~~R~~~l~~f~~g~~~VLVaT~~l~~GlDip~v~lVi~~d~d  523 (661)
T 2d7d_A          444 RNERVLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDAD  523 (661)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHHTSCSEEEESCCCSTTCCCTTEEEEEETTTT
T ss_pred             cCCeEEEEECCHHHHHHHHHHHHhcCCCeEEEeCCCCHHHHHHHHHHHhcCCeEEEEecchhhCCcccCCCCEEEEeCcc
Confidence            4569999999999999999999999999999999999999999999999999999999999999999999999999997 


Q ss_pred             ----CCCccchhhhhcccccCCCceeEEEEeccccHHHHHHH
Q 017573          313 ----PTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDI  350 (369)
Q Consensus       313 ----~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~  350 (369)
                          |.+...|.|++||+||. ..|.+++++++.+......+
T Consensus       524 ~~G~p~s~~~~iQr~GRagR~-~~G~~i~~~~~~~~~~~~~i  564 (661)
T 2d7d_A          524 KEGFLRSERSLIQTIGRAARN-AEGRVIMYADKITKSMEIAI  564 (661)
T ss_dssp             CCTTTTSHHHHHHHHHTTTTS-TTCEEEEECSSCCHHHHHHH
T ss_pred             cccCCCCHHHHHHHhCcccCC-CCCEEEEEEeCCCHHHHHHH
Confidence                88999999999999998 78999999998876655443

>3eaq_A Heat resistant RNA dependent ATPase; DEAD box RNA helicase, dimer, ATP-binding, helicase, hydrolase, nucleotide-binding; 2.30A {Thermus thermophilus} PDB: 3ear_A 3eas_A

Probab=99.94  E-value=1.1e-25  Score=181.75  Aligned_cols=144  Identities=31%  Similarity=0.552  Sum_probs=135.6

Q ss_pred             hhhhHHHHHHHHHhccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCC
Q 017573          219 EEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARG  298 (369)
Q Consensus       219 ~~~~~~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G  298 (369)
                      ...+.+.+.+++.....+++||||++.+.++.+++.|...+..+..+||+++..+|.++++.|++|..+|||+|+++++|
T Consensus        15 ~~~k~~~l~~ll~~~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~r~~~~~~f~~g~~~vlvaT~~~~~G   94 (212)
T 3eaq_A           15 VRGRLEVLSDLLYVASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGEVRVLVATDVAARG   94 (212)
T ss_dssp             TTSHHHHHHHHHHHHCCSCEEEECSSHHHHHHHHHHHHHHTCCEEEECSSSCHHHHHHHHHHHHSSSCCEEEECTTTTCS
T ss_pred             HHHHHHHHHHHHHhCCCCeEEEEeCCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHHCCCCeEEEecChhhcC
Confidence            35688999999988888999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCcEEEEecCCCCccchhhhhcccccCCCceeEEEEeccccHHHHHHHHHHhccccccCC
Q 017573          299 IDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELP  362 (369)
Q Consensus       299 ~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  362 (369)
                      +|+|++++||++++|++...|.||+||+||.|+.|.+++++++.+...++.+.+.++..+.+++
T Consensus        95 idi~~v~~Vi~~~~p~~~~~~~qr~GR~gR~g~~g~~~~l~~~~~~~~~~~i~~~~~~~~~~~~  158 (212)
T 3eaq_A           95 LDIPQVDLVVHYRLPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRERRDVEALERAVGRRFKRVN  158 (212)
T ss_dssp             SSCCCBSEEEESSCCSSHHHHHHHHTTBCCCC--BEEEEEECGGGHHHHHHHHHHHSSCCEECC
T ss_pred             CCCccCcEEEECCCCcCHHHHHHHhcccCCCCCCCeEEEEEchhHHHHHHHHHHHhcCcCeecC
Confidence            9999999999999999999999999999999999999999999999999999999998887665

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus}

Probab=99.93  E-value=1.2e-24  Score=183.51  Aligned_cols=153  Identities=31%  Similarity=0.520  Sum_probs=137.5

Q ss_pred             eeEEEEEccchhhhHHHHHHHHHhccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcE
Q 017573          209 IKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRV  288 (369)
Q Consensus       209 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~v  288 (369)
                      +.++++.... ..+.+.+.+++.....+++||||++++.++.+++.|...+..+..+||++++.+|..+++.|++|..+|
T Consensus         3 v~~~~i~~~~-~~K~~~L~~ll~~~~~~~~LVF~~t~~~~~~l~~~L~~~g~~~~~lhg~l~~~~r~~~~~~f~~g~~~v   81 (300)
T 3i32_A            3 YEEEAVPAPV-RGRLEVLSDLLYVASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQGERERVMGAFRQGEVRV   81 (300)
T ss_dssp             SEEEEEECCS-SSHHHHHHHHHHHHCCSSEEEECSSHHHHHHHHHHHHTTTCCEEEECSCCCTHHHHHHHHHHHHTSCCE
T ss_pred             eEEEEEECCH-HHHHHHHHHHHHhcCCCCEEEEECCHHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHhhcCCceE
Confidence            3455555554 558899999998888899999999999999999999999999999999999999999999999999999


Q ss_pred             EEEecCCcCCCCCCCCcEEEEecCCCCccchhhhhcccccCCCceeEEEEeccccHHHHHHHHHHhccccccCC
Q 017573          289 LITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELP  362 (369)
Q Consensus       289 li~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  362 (369)
                      ||+|+++++|+|+|++++||+++.|++...|.|++||+||.|+.|.+++++++.+...++.+.+.++..+.+++
T Consensus        82 LVaT~va~~Gidi~~v~~VI~~d~p~s~~~y~Qr~GRagR~g~~G~~i~l~~~~e~~~~~~ie~~~~~~~~~~~  155 (300)
T 3i32_A           82 LVATDVAARGLDIPQVDLVVHYRMPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRERRDVEALERAVGRRFKRVN  155 (300)
T ss_dssp             EEECSTTTCSTTCCCCSEEEESSCCSSTTHHHHHHTCCC-----CEEEEEECSSTHHHHHHHHHHHTCCCEECC
T ss_pred             EEEechhhcCccccceeEEEEcCCCCCHHHHHHHccCcCcCCCCceEEEEeChHHHHHHHHHHHHhCCcceEeC
Confidence            99999999999999999999999999999999999999999999999999999999999999999998887665

>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H RNA-binding helicase, innate immunity, IFIH1, S genomics; 1.60A {Homo sapiens}

Probab=99.93  E-value=9.5e-26  Score=184.00  Aligned_cols=164  Identities=15%  Similarity=0.112  Sum_probs=116.4

Q ss_pred             CCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccC---CCccEEEEcCCHHHHHH-HHHHHHHhcc
Q 017573           14 YGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGL---VQCQALVLAPTRELAQQ-IEKVMRALGD   89 (369)
Q Consensus        14 ~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~---~~~~~liv~P~~~l~~q-~~~~~~~~~~   89 (369)
                      .+...|+++|.++++.+.+++++++.+|||+|||++++.++...+....   .+.+++|++|+++|+.| +.+.+.++..
T Consensus        29 ~~~~~l~~~Q~~~i~~~~~~~~~li~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~~lil~p~~~L~~q~~~~~~~~~~~  108 (216)
T 3b6e_A           29 EPELQLRPYQMEVAQPALEGKNIIICLPTGSGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEFQPFLK  108 (216)
T ss_dssp             SCCCCCCHHHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHHHHHHHHTTCCCCEEEEESSHHHHHHHHHHTHHHHHT
T ss_pred             cCCCCchHHHHHHHHHHhcCCCEEEEcCCCCCHHHHHHHHHHHHHhhcccccCCCcEEEEECHHHHHHHHHHHHHHHHhc
Confidence            4556899999999999999999999999999999999988887664321   23489999999999999 7788888765


Q ss_pred             ccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCC------CCCCCccEEEEechhHhhccCcHHHHH-HH
Q 017573           90 YLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQS------LRPDYIKMFVLDEADEMLSRGFKDQIY-DI  162 (369)
Q Consensus        90 ~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~------~~~~~~~~viiDE~H~~~~~~~~~~~~-~~  162 (369)
                      . ++.+....++.............++|+|+||+.+...+....      .....++++|+||+|++....+...+. .+
T Consensus       109 ~-~~~v~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~~~~~~~iIiDEah~~~~~~~~~~~~~~~  187 (216)
T 3b6e_A          109 K-WYRVIGLSGDTQLKISFPEVVKSCDIIISTAQILENSLLNLENGEDAGVQLSDFSLIIIDECHHTNKEAVYNNIMRHY  187 (216)
T ss_dssp             T-TSCEEECCC---CCCCHHHHHHHCSEEEEEHHHHHHHHHC-------CCCGGGCSEEEETTC-------CHHHHHHHH
T ss_pred             c-CceEEEEeCCcccchhHHhhccCCCEEEECHHHHHHHHhccCcccccccchhcccEEEEECchhhccCCcHHHHHHHH
Confidence            4 667777777655433332333458999999999998887653      445678999999999997665444432 22


Q ss_pred             HhhC-------------CccCcEEEEEee
Q 017573          163 FQLL-------------PAKVQVGVFSAT  178 (369)
Q Consensus       163 ~~~~-------------~~~~~~i~~saT  178 (369)
                      ....             .+..+++++|||
T Consensus       188 ~~~~~~~~~~~~~~~~~~~~~~~l~lSAT  216 (216)
T 3b6e_A          188 LMQKLKNNRLKKENKPVIPLPQILGLTAS  216 (216)
T ss_dssp             HHHHHHHHHHHHTTCCCCCCCEEEEEECC
T ss_pred             HHHhcccccccccccCCCCcceEEEeecC
Confidence            2211             146789999998

>2yjt_D ATP-dependent RNA helicase SRMB, regulator of ribonuclease activity A; hydrolase inhibitor-hydrolase complex, DEAD box RNA helicase; 2.90A {Escherichia coli}

Probab=99.87  E-value=5e-27  Score=183.21  Aligned_cols=154  Identities=34%  Similarity=0.564  Sum_probs=140.1

Q ss_pred             eeEEEEEccchhhhHHHHHHHHHhccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcE
Q 017573          209 IKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRV  288 (369)
Q Consensus       209 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~v  288 (369)
                      +.+.+...+....+...+.+++.....+++||||++.+.++.+++.|...+..+..+||+++..+|..+++.|++|+.+|
T Consensus         4 i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~iVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~r~~~~~~f~~g~~~v   83 (170)
T 2yjt_D            4 IHQWYYRADDLEHKTALLVHLLKQPEATRSIVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGRVNV   83 (170)
Confidence            44555555554567888888888777789999999999999999999999999999999999999999999999999999


Q ss_pred             EEEecCCcCCCCCCCCcEEEEecCCCCccchhhhhcccccCCCceeEEEEeccccHHHHHHHHHHhccccccCC
Q 017573          289 LITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELP  362 (369)
Q Consensus       289 li~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  362 (369)
                      ||+|+++++|+|+|++++||++++|++...|.|++||+||.|+.|.+++++++.+...+..+.++++..+++.+
T Consensus        84 LvaT~~~~~Gid~~~~~~Vi~~~~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  157 (170)
T 2yjt_D           84 LVATDVAARGIDIPDVSHVFNFDMPRSGDTYLHRIGRTARAGRKGTAISLVEAHDHLLLGKVGRYIEEPIKARV  157 (170)
Confidence            99999999999999999999999999999999999999999999999999999999999999999888776543

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=99.92  E-value=2.3e-24  Score=198.09  Aligned_cols=103  Identities=11%  Similarity=0.176  Sum_probs=67.1

Q ss_pred             cCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEE--EecCCcCCCCCCC----CcEE
Q 017573          234 AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLI--TTDLLARGIDVQQ----VSLV  307 (369)
Q Consensus       234 ~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli--~t~~~~~G~d~~~----~~~v  307 (369)
                      ..++++||++|...++.+++.+..  .. ....+..  .++.++++.|+++. .|++  +|..+.+|+|+|+    ++.|
T Consensus       383 ~~g~~lvff~S~~~~~~v~~~l~~--~~-~~~q~~~--~~~~~~l~~f~~~~-~il~~V~~~~~~EGiD~~~~~~~~~~V  456 (540)
T 2vl7_A          383 SSKSVLVFFPSYEMLESVRIHLSG--IP-VIEENKK--TRHEEVLELMKTGK-YLVMLVMRAKESEGVEFREKENLFESL  456 (540)
T ss_dssp             CSSEEEEEESCHHHHHHHHTTCTT--SC-EEESTTT--CCHHHHHHHHHTSC-CEEEEEC---------------CEEEE
T ss_pred             CCCCEEEEeCCHHHHHHHHHHhcc--Cc-eEecCCC--CcHHHHHHHHhcCC-eEEEEEecCceecceecCCCcccccEE
Confidence            456899999999999999988865  22 3445543  46788999998864 5777  6799999999997    7899


Q ss_pred             EEecCCCCcc------------------------------chhhhhcccccCCCceeEEEEeccc
Q 017573          308 INYDLPTQPE------------------------------NYLHRIGRSGRFGRKGVAINFVTRD  342 (369)
Q Consensus       308 i~~~~~~~~~------------------------------~~~Q~~GR~~R~~~~~~~~~~~~~~  342 (369)
                      |+.+.|....                              .+.|.+||+.|..++--++++.++.
T Consensus       457 ii~~lPf~~~~d~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~Q~~GR~iR~~~D~g~v~llD~R  521 (540)
T 2vl7_A          457 VLAGLPYPNVSDDMVRKRIERLSKLTGKDEDSIIHDLTAIVIKQTIGRAFRDPNDYVKIYLCDSR  521 (540)
T ss_dssp             EEESCCCCCTTSHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHCCSTTCCCEEEEESGG
T ss_pred             EEECCCCCCCCCHHHHHHHHHHHHhhCCChhHHHHHHHHHHHHHHhCCcccCCCccEEEEEEccc
Confidence            9999875322                              3579999999986664455566544

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=99.90  E-value=2.1e-21  Score=179.25  Aligned_cols=310  Identities=17%  Similarity=0.148  Sum_probs=193.9

Q ss_pred             CCcHhhhhhhhcc----ccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCc
Q 017573           18 KPSAIQQRGIVPF----CKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGV   93 (369)
Q Consensus        18 ~~~~~Q~~~~~~~----~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~   93 (369)
                      ++||+|.++...+    ..++++++++|||+|||++++++++.   .   +.+++|++|+++|+.|+.+++..+....++
T Consensus         3 ~~r~~Q~~~~~~v~~~l~~~~~~~~~a~TGtGKT~~~l~p~l~---~---~~~v~i~~pt~~l~~q~~~~~~~l~~~~~~   76 (551)
T 3crv_A            3 KLRDWQEKLKDKVIEGLRNNFLVALNAPTGSGKTLFSLLVSLE---V---KPKVLFVVRTHNEFYPIYRDLTKIREKRNI   76 (551)
T ss_dssp             SCCHHHHHHHHHHHHHHHTTCEEEEECCTTSSHHHHHHHHHHH---H---CSEEEEEESSGGGHHHHHHHHTTCCCSSCC
T ss_pred             CCCHHHHHHHHHHHHHHHcCCcEEEECCCCccHHHHHHHHHHh---C---CCeEEEEcCCHHHHHHHHHHHHHHhhhcCc
Confidence            7999999988754    46899999999999999999999887   1   238999999999999999999888666677


Q ss_pred             EEEEEECCcch---------------------------------HHHH------------------HHHccCCcEEEecc
Q 017573           94 KVHACVGGTSV---------------------------------REDQ------------------RILQAGVHVVVGTP  122 (369)
Q Consensus        94 ~v~~~~~~~~~---------------------------------~~~~------------------~~~~~~~~iiv~t~  122 (369)
                      ++..+.|....                                 ....                  +.....++|+|+||
T Consensus        77 ~~~~l~gr~~~c~~~~~~~~~~~~~c~~c~~~~~~~~~g~~~~~~~~~~~~~~~G~~~~~Cpy~~ar~~~~~adIVV~~~  156 (551)
T 3crv_A           77 TFSFLVGKPSSCLYAEKGAESEDIPCKYCELKGSIVEVKTDDSPLSLVKKLKKDGLQDKFCPYYSLLNSLYKADVIALTY  156 (551)
T ss_dssp             CEEECCCHHHHCTTBCTTCCGGGCCGGGCTTTTCCCCCCCCSCHHHHHHHHHHHHHHHTCCHHHHHHHHGGGCSEEEEET
T ss_pred             cEEEEccccccCcCchhcCCCcccccCCCCCccccccccccCCHHHHHHHHHHcCCcCCcCccHHHHhhhhcCCEEEeCc
Confidence            77776653211                                 0000                  11234689999999


Q ss_pred             HHHHHHHHcCCCCC-CCccEEEEechhHhhccCc----------------------------------------------
Q 017573          123 GRVFDMLRRQSLRP-DYIKMFVLDEADEMLSRGF----------------------------------------------  155 (369)
Q Consensus       123 ~~l~~~~~~~~~~~-~~~~~viiDE~H~~~~~~~----------------------------------------------  155 (369)
                      ..++....+..+.. ....++|+||||++.+ ..                                              
T Consensus       157 ~~l~~~~~~~~~~~~~~~~~vIiDEAHnl~d-~~~~~s~~ls~~~l~~~~~~l~~~~~~~~l~~l~~~l~~~~~~~~~~~  235 (551)
T 3crv_A          157 PYFFIDRYREFIDIDLREYMIVIDEAHNLDK-VNELEERSLSEITIQMAIKQSKSEESRRILSKLLNQLREVVLPDEKYI  235 (551)
T ss_dssp             HHHHCHHHHTTSCCCSTTEEEEETTGGGGGG-GGGGGCEEEEHHHHHHHHHHCSCHHHHHHHHHHHHHHTTSCCSCSSCE
T ss_pred             hHhcCHHHHHhcCCCcCCeEEEEecccchHH-HHHhhceecCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccc
Confidence            99987654443322 3457899999998765 10                                              


Q ss_pred             ---------HHHHH----------------------------HHH----------------------------hhCCcc-
Q 017573          156 ---------KDQIY----------------------------DIF----------------------------QLLPAK-  169 (369)
Q Consensus       156 ---------~~~~~----------------------------~~~----------------------------~~~~~~-  169 (369)
                               ...+.                            .++                            +.+... 
T Consensus       236 ~~~~~~~~~~~~l~~l~~~l~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~~~~~~l~~~pl~~~~~l~~~~~~~  315 (551)
T 3crv_A          236 KVENVPKLSKEELEILADDYEDIRKDSLKQGKVNKIHIGSILRFFSLLSIGSFIPFSYSKRLVIKNPEISYYLNLLNDNE  315 (551)
T ss_dssp             ECSCCCCCCHHHHHHHHHHHHHHHHHHHHTTCBCCCHHHHHHHHHHHHHHSSCEEEEETTEEEEECCCTHHHHGGGGCTT
T ss_pred             ccccChHHHHHHHHHHHHHHHHHHHhhhhcCCcccchHHHHHHHHHHHhccCCeEeccCCEEEEEECCHHHHHHHHhccC
Confidence                     00000                            000                            001112 


Q ss_pred             CcEEEEEeeCChhHHHHHHHhcCC-CEEE---E-ecCccccccceeEEEEEc--cc--h---hhhHHHHHHHHHh---cc
Q 017573          170 VQVGVFSATMPPEALEITRKFMNK-PVRI---L-VKRDELTLEGIKQFYVNV--EK--E---EWKLETLCDLYET---LA  234 (369)
Q Consensus       170 ~~~i~~saT~~~~~~~~~~~~~~~-~~~~---~-~~~~~~~~~~~~~~~~~~--~~--~---~~~~~~l~~~~~~---~~  234 (369)
                      ..+|++|||+.+ ...+...+... +...   . ......  ..-...+...  +.  .   ....+.+.+.+..   ..
T Consensus       316 ~svIltSaTL~~-~~~~~~~lGl~~~~~~~~~~~~~~spf--~~~~~l~v~~~~~~~~~~r~~~~~~~l~~~i~~l~~~~  392 (551)
T 3crv_A          316 LSIILMSGTLPP-REYMEKVWGIKRNMLYLDVEREIQKRV--SGSYECYIGVDVTSKYDMRSDNMWKRYADYLLKIYFQA  392 (551)
T ss_dssp             CEEEEEESSCCC-HHHHHHTSCCCSCEEEEEHHHHTTSCC--SCEEEEEEECSCCCCTTTCCHHHHHHHHHHHHHHHHHC
T ss_pred             ceEEEEeeCCCc-HHHHHHHhCCCCccccccceeecCCcC--CCceEEEEeCCCCCccccCCHHHHHHHHHHHHHHHHhC
Confidence            578889999976 32333333222 2221   0 011111  1222223221  11  0   1112333333322   24


Q ss_pred             CCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEe--cCCcCCCCCC---C--CcEE
Q 017573          235 ITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITT--DLLARGIDVQ---Q--VSLV  307 (369)
Q Consensus       235 ~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t--~~~~~G~d~~---~--~~~v  307 (369)
                      ++.++||++|...++.+++.   .+..+..-..+++   +.+.++.|+.+.-.||+++  ..+.+|+|+|   +  ++.|
T Consensus       393 ~g~~lvlF~Sy~~l~~v~~~---~~~~v~~q~~~~~---~~~~~~~~~~~~~~vl~~v~gg~~~EGiD~~d~~g~~l~~v  466 (551)
T 3crv_A          393 KANVLVVFPSYEIMDRVMSR---ISLPKYVESEDSS---VEDLYSAISANNKVLIGSVGKGKLAEGIELRNNDRSLISDV  466 (551)
T ss_dssp             SSEEEEEESCHHHHHHHHTT---CCSSEEECCSSCC---HHHHHHHTTSSSSCEEEEESSCCSCCSSCCEETTEESEEEE
T ss_pred             CCCEEEEecCHHHHHHHHHh---cCCcEEEcCCCCC---HHHHHHHHHhcCCeEEEEEecceecccccccccCCcceeEE
Confidence            56899999999999999873   3333333222334   4557777854344799998  5999999999   3  7889


Q ss_pred             EEecCCCCc--------------------c----------chhhhhcccccCCCceeEEEEecccc
Q 017573          308 INYDLPTQP--------------------E----------NYLHRIGRSGRFGRKGVAINFVTRDD  343 (369)
Q Consensus       308 i~~~~~~~~--------------------~----------~~~Q~~GR~~R~~~~~~~~~~~~~~~  343 (369)
                      |+.+.|...                    -          .+.|.+||+.|..++.-++++.++.-
T Consensus       467 iI~~lPfp~~dp~~~ar~~~~~~~~g~~~~~~~y~~pa~~~l~Qa~GRlIR~~~D~G~v~llD~R~  532 (551)
T 3crv_A          467 VIVGIPYPPPDDYLKILAQRVSLKMNRENEEFLFKIPALVTIKQAIGRAIRDVNDKCNVWLLDKRF  532 (551)
T ss_dssp             EEESCCCCCCSHHHHHHHHHTTCCSSTTTHHHHTHHHHHHHHHHHHHTTCCSTTCEEEEEEESGGG
T ss_pred             EEEcCCCCCCCHHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHHHhccCccCCCccEEEEEeehhc
Confidence            988866411                    0          13699999999877755666666543

>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=99.90  E-value=6.2e-24  Score=180.02  Aligned_cols=154  Identities=17%  Similarity=0.095  Sum_probs=120.9

Q ss_pred             CCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEE
Q 017573           18 KPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHA   97 (369)
Q Consensus        18 ~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~   97 (369)
                      +|+++|.++++.+.++++.++++|||+|||.+++.++...+..+.  .++||++|+++|+.||.+++.++....+..+..
T Consensus       113 ~l~~~Q~~ai~~~l~~~~~ll~~~tGsGKT~~~~~~~~~~~~~~~--~~~lil~Pt~~L~~q~~~~l~~~~~~~~~~~~~  190 (282)
T 1rif_A          113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENYE--GKILIIVPTTALTTQMADDFVDYRLFSHAMIKK  190 (282)
T ss_dssp             CCCHHHHHHHHHHHHHSEEEECCCTTSCHHHHHHHHHHHHHHHCS--SEEEEECSSHHHHHHHHHHHHHHTSCCGGGEEE
T ss_pred             CccHHHHHHHHHHHhcCCeEEEcCCCCCcHHHHHHHHHHHHHcCC--CeEEEEECCHHHHHHHHHHHHHhcccccceEEE
Confidence            899999999999998889999999999999999887776655332  289999999999999999999987655566666


Q ss_pred             EECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEEe
Q 017573           98 CVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSA  177 (369)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~sa  177 (369)
                      +.++.....   ......+|+|+|++.+....   ......++++|+||||++.+    ..+..++..+....+++++||
T Consensus       191 ~~~~~~~~~---~~~~~~~I~v~T~~~l~~~~---~~~~~~~~~vIiDEaH~~~~----~~~~~il~~~~~~~~~l~lSA  260 (282)
T 1rif_A          191 IGGGASKDD---KYKNDAPVVVGTWQTVVKQP---KEWFSQFGMMMNDECHLATG----KSISSIISGLNNCMFKFGLSG  260 (282)
T ss_dssp             CSTTCSSTT---CCCTTCSEEEECHHHHTTSC---GGGGGGEEEEEEETGGGCCH----HHHHHHTTTCTTCCEEEEECS
T ss_pred             EeCCCcchh---hhccCCcEEEEchHHHHhhH---HHHHhhCCEEEEECCccCCc----ccHHHHHHHhhcCCeEEEEeC
Confidence            666654322   11245799999998875432   22345689999999999863    366677788877899999999


Q ss_pred             eCChhH
Q 017573          178 TMPPEA  183 (369)
Q Consensus       178 T~~~~~  183 (369)
                      ||+...
T Consensus       261 Tp~~~~  266 (282)
T 1rif_A          261 SLRDGK  266 (282)
T ss_dssp             SCCTTS
T ss_pred             CCCCcc
Confidence            997543

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=99.87  E-value=1.6e-20  Score=174.45  Aligned_cols=316  Identities=15%  Similarity=0.143  Sum_probs=186.7

Q ss_pred             CCCcHhhhhhhhcc----ccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccC
Q 017573           17 EKPSAIQQRGIVPF----CKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLG   92 (369)
Q Consensus        17 ~~~~~~Q~~~~~~~----~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~   92 (369)
                      .+||+.|.++...+    .++++++++||||+|||++++++++..+...  +.+++|++|++++..|..+++..+....+
T Consensus         2 ~~~R~~Q~~~~~~v~~~l~~~~~~~~~apTGtGKT~a~l~p~l~~~~~~--~~kvli~t~T~~l~~Qi~~el~~l~~~~~   79 (620)
T 4a15_A            2 YENRQYQVEAIDFLRSSLQKSYGVALESPTGSGKTIMALKSALQYSSER--KLKVLYLVRTNSQEEQVIKELRSLSSTMK   79 (620)
T ss_dssp             ---CHHHHHHHHHHHHHHHHSSEEEEECCTTSCHHHHHHHHHHHHHHHH--TCEEEEEESSHHHHHHHHHHHHHHHHHSC
T ss_pred             CCCCHHHHHHHHHHHHHHHcCCCEEEECCCCCCHHHHHHHHHHHhhhhc--CCeEEEECCCHHHHHHHHHHHHHHhhccC
Confidence            37899999998754    4689999999999999999999999887543  23899999999999999999988755444


Q ss_pred             cEEEEEECCcchHH------------------HH----------------------------------------------
Q 017573           93 VKVHACVGGTSVRE------------------DQ----------------------------------------------  108 (369)
Q Consensus        93 ~~v~~~~~~~~~~~------------------~~----------------------------------------------  108 (369)
                      +++..+.|..+..-                  .+                                              
T Consensus        80 ~~~~~l~gr~~lC~~~~~~~~~~~~~~~~~~~~C~~l~~~~~~~~~~~C~~~~~~~~~gd~~~~l~~~~~die~l~~~~~  159 (620)
T 4a15_A           80 IRAIPMQGRVNMCILYRMVDDLHEINAESLAKFCNMKKREVMAGNEAACPYFNFKIRSDETKRFLFDELPTAEEFYDYGE  159 (620)
T ss_dssp             CCEEECCCHHHHCSSHHHHCCCSSCCHHHHHHHHHHHHHHHHTTCTTSSTTCSGGGGCHHHHHHHHHHCCCHHHHHHHHH
T ss_pred             eEEEEEECCCcccccChhhhhcccchhhhHHHHHHHHHhccccCCCCCCCcccccCcccchhHHhccCCCCHHHHHHHhh
Confidence            55544433211000                  00                                              


Q ss_pred             ----------HHHccCCcEEEeccHHHHHHHHcC------CCCCCCccEEEEechhHhhcc-------------------
Q 017573          109 ----------RILQAGVHVVVGTPGRVFDMLRRQ------SLRPDYIKMFVLDEADEMLSR-------------------  153 (369)
Q Consensus       109 ----------~~~~~~~~iiv~t~~~l~~~~~~~------~~~~~~~~~viiDE~H~~~~~-------------------  153 (369)
                                +.....+||+|++|+.++....+.      ..... -.++|+||||++.+.                   
T Consensus       160 ~~~~CPy~~aR~~~~~ADvVV~ny~ylld~~~r~~~~~~~~i~p~-~~ivI~DEAHNL~d~a~~~~S~~ls~~~l~~~~~  238 (620)
T 4a15_A          160 RNNVCPYESMKAALPDADIVIAPYAYFLNRSVAEKFLSHWGVSRN-QIVIILDEAHNLPDIGRSIGSFRISVESLNRADR  238 (620)
T ss_dssp             HTTCCHHHHHHHHGGGCSEEEEEHHHHTCHHHHHHHHHHHTCCGG-GEEEEETTGGGHHHHHHHHHCEEEEHHHHHHHHH
T ss_pred             hcCCCccHHHHHHhhcCCEEEeCchhhcCHHHHHHHHHhhccCcC-CeEEEEECCCchHHHHHHhhcceeCHHHHHHHHH
Confidence                      001235899999998875433221      12222 369999999986530                   


Q ss_pred             -------Cc------H-HH-------HH------------------------------------------HHHh------
Q 017573          154 -------GF------K-DQ-------IY------------------------------------------DIFQ------  164 (369)
Q Consensus       154 -------~~------~-~~-------~~------------------------------------------~~~~------  164 (369)
                             ..      . +.       +.                                          .+..      
T Consensus       239 ~l~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~~  318 (620)
T 4a15_A          239 EAQAYGDPELSQKIHVSDLIEMIRSALQSMVSERCGKGDVRIRFQEFMEYMRIMNKRSEREIRSLLNYLYLFGEYVENEK  318 (620)
T ss_dssp             HHHHTTCCEEETTEEHHHHHHHHHHHHHHHHHHHCSSSCEEECTHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHhhcccccCCChHHHHHHHHHhhcccHHHHHHHHHHHHHHHHHHHhhc
Confidence                   00      0 00       00                                          0000      


Q ss_pred             --h--------------------CC------------------------------ccCcEEEEEeeCChhHHHHHHHhcC
Q 017573          165 --L--------------------LP------------------------------AKVQVGVFSATMPPEALEITRKFMN  192 (369)
Q Consensus       165 --~--------------------~~------------------------------~~~~~i~~saT~~~~~~~~~~~~~~  192 (369)
                        .                    ..                              ....+|++|||+.+ ...+...+..
T Consensus       319 ~~~~~~~~~~~~~~~~fl~~~~~~~~~~~~~~~~~~~~~~l~~~~l~~~~~l~~~~~~~~il~SaTL~p-~~~~~~~lGl  397 (620)
T 4a15_A          319 EKVGKVPFSYCSSVASRIIAFSDQDEEKYAAILSPEDGGYMQAACLDPSGILEVLKESKTIHMSGTLDP-FDFYSDITGF  397 (620)
T ss_dssp             HHTTSCCCCHHHHHHHHHHHHHTSCTTTEEEEEECGGGCEEEEEECCTHHHHGGGGGSEEEEEESSCCS-HHHHHHHHCC
T ss_pred             cccccccccHHHHHHHHHHHHhhcCCCCEEEEEEeCCCcEEEEEECCHHHHHHHHhCCeEEEEccCCCc-HHHHHHHhCC
Confidence              0                    00                              01245889999975 3333333322


Q ss_pred             CCEEEEecCccccccceeEEEEE-cc-----chhhh----HHHHHHHHHhccCCCeEEEeCCHhhHHHHHHHHhhCCCee
Q 017573          193 KPVRILVKRDELTLEGIKQFYVN-VE-----KEEWK----LETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTV  262 (369)
Q Consensus       193 ~~~~~~~~~~~~~~~~~~~~~~~-~~-----~~~~~----~~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~  262 (369)
                      ...... ........+...++.. .+     .....    .+.+..++.. .+++++||++|....+.+++.++..+  .
T Consensus       398 ~~~~~~-~~spf~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~i~~l~~~-~~g~~lvlF~Sy~~l~~v~~~l~~~~--~  473 (620)
T 4a15_A          398 EIPFKK-IGEIFPPENRYIAYYDGVSSKYDTLDEKELDRMATVIEDIILK-VKKNTIVYFPSYSLMDRVENRVSFEH--M  473 (620)
T ss_dssp             CCCEEE-CCCCSCGGGEEEEEECCC-------CHHHHHHHHHHHHHHHHH-HCSCEEEEESCHHHHHHHTSSCCSCC--E
T ss_pred             Cceeee-cCCCCCHHHeEEEEeCCCCCcCCCCCHHHHHHHHHHHHHHHHh-CCCCEEEEeCCHHHHHHHHHHHHhcc--h
Confidence            222222 2222223332222211 11     11111    2223333333 35789999999999999999887322  2


Q ss_pred             EEecCCCCHHHHHHHHHHHhcCCCcEEEEec--CCcCCCCCCC--CcEEEEecCCCCc----------------------
Q 017573          263 SATHGDMDQNTRDIIMREFRSGSSRVLITTD--LLARGIDVQQ--VSLVINYDLPTQP----------------------  316 (369)
Q Consensus       263 ~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~--~~~~G~d~~~--~~~vi~~~~~~~~----------------------  316 (369)
                      . ...+++..++..+++.|. ++-.||+++.  .+.+|+|+|+  ++.||+.+.|...                      
T Consensus       474 ~-~~q~~~~~~~~~ll~~f~-~~~~vL~~v~~gsf~EGiD~~g~~l~~viI~~lPfp~~~p~~~ar~~~~~~~~g~~~~~  551 (620)
T 4a15_A          474 K-EYRGIDQKELYSMLKKFR-RDHGTIFAVSGGRLSEGINFPGNELEMIILAGLPFPRPDAINRSLFDYYERKYGKGWEY  551 (620)
T ss_dssp             E-CCTTCCSHHHHHHHHHHT-TSCCEEEEETTSCC--------CCCCEEEESSCCCCCCCHHHHHHHHHHHHHHSCHHHH
T ss_pred             h-ccCCCChhHHHHHHHHhc-cCCcEEEEEecCceeccccCCCCceEEEEEEcCCCCCCCHHHHHHHHHHHHhhCCCchH
Confidence            2 344455678999999999 7778999984  8999999996  7889999877531                      


Q ss_pred             -------cchhhhhcccccCCCceeEEEEeccc
Q 017573          317 -------ENYLHRIGRSGRFGRKGVAINFVTRD  342 (369)
Q Consensus       317 -------~~~~Q~~GR~~R~~~~~~~~~~~~~~  342 (369)
                             ..+.|.+||+.|..++--+++++++.
T Consensus       552 ~y~~pa~~~l~Qa~GRlIR~~~D~G~v~llD~R  584 (620)
T 4a15_A          552 SVVYPTAIKIRQEIGRLIRSAEDTGACVILDKR  584 (620)
T ss_dssp             HTHHHHHHHHHHHHHTTCCSTTCCEEEEEECGG
T ss_pred             HhHHHHHHHHHHHhCccccCCCceEEEEEEccc
Confidence                   12379999999987665555565554

>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=99.87  E-value=2.7e-21  Score=158.72  Aligned_cols=139  Identities=17%  Similarity=0.180  Sum_probs=109.3

Q ss_pred             CCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcE-E
Q 017573           17 EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVK-V   95 (369)
Q Consensus        17 ~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~-v   95 (369)
                      ..|+++|.+++..+.+++++++++|||+|||.+++.++...      +.+++|++|+++|+.||.+.+.++    +.+ +
T Consensus        92 ~~l~~~Q~~ai~~~~~~~~~ll~~~tG~GKT~~a~~~~~~~------~~~~liv~P~~~L~~q~~~~~~~~----~~~~v  161 (237)
T 2fz4_A           92 ISLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINEL------STPTLIVVPTLALAEQWKERLGIF----GEEYV  161 (237)
T ss_dssp             CCCCHHHHHHHHHHTTTSEEEEEESSSTTHHHHHHHHHHHS------CSCEEEEESSHHHHHHHHHHHGGG----CGGGE
T ss_pred             CCcCHHHHHHHHHHHhCCCEEEEeCCCCCHHHHHHHHHHHc------CCCEEEEeCCHHHHHHHHHHHHhC----CCCeE
Confidence            37999999999999999999999999999999987776643      238999999999999999999884    566 7


Q ss_pred             EEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEE
Q 017573           96 HACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVF  175 (369)
Q Consensus        96 ~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~  175 (369)
                      ..+.++..         ...+|+|+|++.+.......   ...++++|+||+|++.+..+.    .+...++ ..+++++
T Consensus       162 ~~~~g~~~---------~~~~i~v~T~~~l~~~~~~~---~~~~~llIiDEaH~l~~~~~~----~i~~~~~-~~~~l~L  224 (237)
T 2fz4_A          162 GEFSGRIK---------ELKPLTVSTYDSAYVNAEKL---GNRFMLLIFDEVHHLPAESYV----QIAQMSI-APFRLGL  224 (237)
T ss_dssp             EEESSSCB---------CCCSEEEEEHHHHHHTHHHH---TTTCSEEEEECSSCCCTTTHH----HHHHTCC-CSEEEEE
T ss_pred             EEEeCCCC---------CcCCEEEEeHHHHHhhHHHh---cccCCEEEEECCccCCChHHH----HHHHhcc-CCEEEEE
Confidence            77766554         24689999999987655431   234799999999998766543    3445554 5678999


Q ss_pred             EeeCChh
Q 017573          176 SATMPPE  182 (369)
Q Consensus       176 saT~~~~  182 (369)
                      ||||...
T Consensus       225 SATp~r~  231 (237)
T 2fz4_A          225 TATFERE  231 (237)
T ss_dssp             EESCC--
T ss_pred             ecCCCCC
Confidence            9999754

>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=99.86  E-value=6.9e-21  Score=156.65  Aligned_cols=160  Identities=19%  Similarity=0.184  Sum_probs=117.1

Q ss_pred             CCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCC--CccEEEEcCCHHHHHHHHHHHHHhcc-cc
Q 017573           15 GFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLV--QCQALVLAPTRELAQQIEKVMRALGD-YL   91 (369)
Q Consensus        15 ~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~--~~~~liv~P~~~l~~q~~~~~~~~~~-~~   91 (369)
                      ....++++|.++++.+.+++++++.||||+|||..+..+++........  ..++++++|+++++.|..+.+.+... ..
T Consensus        58 ~~~p~~~~q~~~i~~i~~g~~~~i~g~TGsGKTt~~~~~~~~~~~~~~~~~~~~~l~~~p~~~la~q~~~~~~~~~~~~~  137 (235)
T 3llm_A           58 ELLPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDDFIQNDRAAECNIVVTQPRRISAVSVAERVAFERGEEP  137 (235)
T ss_dssp             HTSGGGGGHHHHHHHHHHCSEEEEECCTTSSHHHHHHHHHHHHHHHTTCGGGCEEEEEESSHHHHHHHHHHHHHTTTCCT
T ss_pred             hcCChHHHHHHHHHHHhcCCEEEEEeCCCCCcHHhHHHHHhcchhhcCCCCceEEEEeccchHHHHHHHHHHHHHhcccc
Confidence            3446899999999999999999999999999998877777765543322  33799999999999999998876543 22


Q ss_pred             CcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHh-hccCcH-HHHHHHHhhCCcc
Q 017573           92 GVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEM-LSRGFK-DQIYDIFQLLPAK  169 (369)
Q Consensus        92 ~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~-~~~~~~-~~~~~~~~~~~~~  169 (369)
                      +..+........     ......++|+|+|++.+.+.+..   ...+++++|+||+|+. .+.++. ..+..+.... +.
T Consensus       138 ~~~~g~~~~~~~-----~~~~~~~~Ivv~Tpg~l~~~l~~---~l~~~~~lVlDEah~~~~~~~~~~~~l~~i~~~~-~~  208 (235)
T 3llm_A          138 GKSCGYSVRFES-----ILPRPHASIMFCTVGVLLRKLEA---GIRGISHVIVDEIHERDINTDFLLVVLRDVVQAY-PE  208 (235)
T ss_dssp             TSSEEEEETTEE-----ECCCSSSEEEEEEHHHHHHHHHH---CCTTCCEEEECCTTSCCHHHHHHHHHHHHHHHHC-TT
T ss_pred             CceEEEeechhh-----ccCCCCCeEEEECHHHHHHHHHh---hhcCCcEEEEECCccCCcchHHHHHHHHHHHhhC-CC
Confidence            333433222111     00113578999999999988876   3677899999999984 444444 4555555555 47


Q ss_pred             CcEEEEEeeCChhH
Q 017573          170 VQVGVFSATMPPEA  183 (369)
Q Consensus       170 ~~~i~~saT~~~~~  183 (369)
                      .|++++|||++.+.
T Consensus       209 ~~~il~SAT~~~~~  222 (235)
T 3llm_A          209 VRIVLMSATIDTSM  222 (235)
T ss_dssp             SEEEEEECSSCCHH
T ss_pred             CeEEEEecCCCHHH
Confidence            88999999998654

>1z5z_A Helicase of the SNF2/RAD54 family; hydrolase, recombination, hydrolase-recombination complex; 2.00A {Sulfolobus solfataricus} SCOP: c.37.1.19

Probab=99.79  E-value=5.9e-19  Score=147.16  Aligned_cols=125  Identities=16%  Similarity=0.227  Sum_probs=97.5

Q ss_pred             hhhhHHHHHHHHHhc--cCCCeEEEeCCHhhHHHHHHHHhhC-CCeeEEecCCCCHHHHHHHHHHHhcC-CCc-EEEEec
Q 017573          219 EEWKLETLCDLYETL--AITQSVIFVNTRRKVDWLTDKMRSR-DHTVSATHGDMDQNTRDIIMREFRSG-SSR-VLITTD  293 (369)
Q Consensus       219 ~~~~~~~l~~~~~~~--~~~k~lv~~~~~~~~~~~~~~l~~~-~~~~~~~~~~~~~~~r~~~~~~f~~~-~~~-vli~t~  293 (369)
                      ...|...+.+++...  .+.|+|||++....+..+.+.|... +..+..++|+++..+|.++++.|+++ +.+ +|++|.
T Consensus        94 ~s~K~~~L~~ll~~~~~~~~kvlIFs~~~~~~~~l~~~L~~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~v~L~st~  173 (271)
T 1z5z_A           94 RSGKMIRTMEIIEEALDEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVK  173 (271)
T ss_dssp             TCHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHHHCSCCCEECTTSCHHHHHHHHHHHHHCTTCCEEEEECC
T ss_pred             cCHHHHHHHHHHHHHHhCCCeEEEEeccHHHHHHHHHHHHHhcCCcEEEEECCCCHHHHHHHHHHhcCCCCCCEEEEehh
Confidence            455788888888765  6789999999999999999999885 89999999999999999999999998 677 678999


Q ss_pred             CCcCCCCCCCCcEEEEecCCCCccchhhhhcccccCCCceeE--EEEecccc
Q 017573          294 LLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVA--INFVTRDD  343 (369)
Q Consensus       294 ~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~--~~~~~~~~  343 (369)
                      ++++|+|++.+++||++++|||+..+.|++||++|.|+.+.+  +.++..+.
T Consensus       174 ~~g~Glnl~~a~~VI~~d~~wnp~~~~Q~~gR~~R~Gq~~~v~v~~li~~~T  225 (271)
T 1z5z_A          174 AGGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVGT  225 (271)
T ss_dssp             TTCCCCCCTTCSEEEECSCCSCTTTC--------------CCEEEEEEETTS
T ss_pred             hhcCCcCcccCCEEEEECCCCChhHHHHHHHhccccCCCCceEEEEEeeCCC
Confidence            999999999999999999999999999999999999987654  55555553

>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=98.91  E-value=4e-09  Score=98.16  Aligned_cols=160  Identities=19%  Similarity=0.194  Sum_probs=91.9

Q ss_pred             HHHHHHHhC-CCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHH--HHHHHHhhhccCCCccEEEEcCCHHHHHHHHH
Q 017573            6 NLLRGIYAY-GFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATF--CSGILQQLDYGLVQCQALVLAPTRELAQQIEK   82 (369)
Q Consensus         6 ~i~~~l~~~-~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~--~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~   82 (369)
                      .+...|... +-....+.|++++..+..++.+++.|++|+|||.++  ++..+..+... .+.++++++||...+.++.+
T Consensus       136 ~~~~~l~~~~~~~~~~~~Q~~Ai~~~l~~~~~vi~G~pGTGKTt~l~~ll~~l~~~~~~-~~~~vll~APTg~AA~~L~e  214 (608)
T 1w36_D          136 LLAQTLDKLFPVSDEINWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQMADG-ERCRIRLAAPTGKAAARLTE  214 (608)
T ss_dssp             HHHHHHHTTCCCTTSCCHHHHHHHHHHTBSEEEEECCTTSTHHHHHHHHHHHHHHTCSS-CCCCEEEEBSSHHHHHHHHH
T ss_pred             HHHHHHHHHhccCCCCHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHHHhhhc-CCCeEEEEeCChhHHHHHHH
Confidence            344555543 222237899999999999999999999999999553  33333333212 23489999999999999988


Q ss_pred             HHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHH
Q 017573           83 VMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDI  162 (369)
Q Consensus        83 ~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~  162 (369)
                      .+......+++......+ ..  ...   ..-..++-.++...  .+.........++++|+||++++.    ...+..+
T Consensus       215 ~~~~~~~~l~l~~~~~~~-~~--~~~---~Tih~ll~~~~~~~--~~~~~~~~~l~~d~lIIDEAsml~----~~~~~~L  282 (608)
T 1w36_D          215 SLGKALRQLPLTDEQKKR-IP--EDA---STLHRLLGAQPGSQ--RLRHHAGNPLHLDVLVVDEASMID----LPMMSRL  282 (608)
T ss_dssp             HHTHHHHHSSCCSCCCCS-CS--CCC---BTTTSCC-------------CTTSCCSCSEEEECSGGGCB----HHHHHHH
T ss_pred             HHHHHHhcCCCCHHHHhc-cc--hhh---hhhHhhhccCCCch--HHHhccCCCCCCCEEEEechhhCC----HHHHHHH
Confidence            877654433321100000 00  000   00001111112111  011111222357999999999653    4566778


Q ss_pred             HhhCCccCcEEEEEee
Q 017573          163 FQLLPAKVQVGVFSAT  178 (369)
Q Consensus       163 ~~~~~~~~~~i~~saT  178 (369)
                      +..++...+++++.-.
T Consensus       283 l~~l~~~~~liLvGD~  298 (608)
T 1w36_D          283 IDALPDHARVIFLGDR  298 (608)
T ss_dssp             HHTCCTTCEEEEEECT
T ss_pred             HHhCCCCCEEEEEcch
Confidence            8888888888876655

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=98.74  E-value=1.2e-08  Score=96.01  Aligned_cols=68  Identities=24%  Similarity=0.241  Sum_probs=56.1

Q ss_pred             CCCcHhhhhhhhccccCC-cEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHh
Q 017573           17 EKPSAIQQRGIVPFCKGL-DVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRAL   87 (369)
Q Consensus        17 ~~~~~~Q~~~~~~~~~~~-~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~   87 (369)
                      ..+++.|.+|+..++..+ -.+|+||+|||||.+....+.+.+..+.   ++|+++||..-+.++.+.+...
T Consensus       188 ~~LN~~Q~~AV~~al~~~~~~lI~GPPGTGKT~ti~~~I~~l~~~~~---~ILv~a~TN~AvD~i~erL~~~  256 (646)
T 4b3f_X          188 TCLDTSQKEAVLFALSQKELAIIHGPPGTGKTTTVVEIILQAVKQGL---KVLCCAPSNIAVDNLVERLALC  256 (646)
T ss_dssp             TTCCHHHHHHHHHHHHCSSEEEEECCTTSCHHHHHHHHHHHHHHTTC---CEEEEESSHHHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHhcCCCceEEECCCCCCHHHHHHHHHHHHHhCCC---eEEEEcCchHHHHHHHHHHHhc
Confidence            458899999999987655 5799999999999887766666665543   8999999999999988888654

>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, HYD; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A*

Probab=98.72  E-value=9.7e-08  Score=87.98  Aligned_cols=128  Identities=20%  Similarity=0.225  Sum_probs=80.1

Q ss_pred             CCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEE
Q 017573           17 EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVH   96 (369)
Q Consensus        17 ~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~   96 (369)
                      ..+++.|++++..+..++.+++.||+|+|||.++. .++..+...  +.++++++|+...+..+.+...       ....
T Consensus       188 ~~L~~~Q~~Av~~~~~~~~~~I~G~pGTGKTt~i~-~l~~~l~~~--g~~Vl~~ApT~~Aa~~L~e~~~-------~~a~  257 (574)
T 3e1s_A          188 KGLSEEQASVLDQLAGHRLVVLTGGPGTGKSTTTK-AVADLAESL--GLEVGLCAPTGKAARRLGEVTG-------RTAS  257 (574)
T ss_dssp             TTCCHHHHHHHHHHTTCSEEEEECCTTSCHHHHHH-HHHHHHHHT--TCCEEEEESSHHHHHHHHHHHT-------SCEE
T ss_pred             CCCCHHHHHHHHHHHhCCEEEEEcCCCCCHHHHHH-HHHHHHHhc--CCeEEEecCcHHHHHHhHhhhc-------ccHH
Confidence            36889999999999999999999999999997643 334343332  2389999999888776655431       1111


Q ss_pred             EEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEE
Q 017573           97 ACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFS  176 (369)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~s  176 (369)
                      .++         +.+.....           .+.........++++|+||++++.    ...+..++..++...+++++.
T Consensus       258 Tih---------~ll~~~~~-----------~~~~~~~~~~~~dvlIIDEasml~----~~~~~~Ll~~~~~~~~lilvG  313 (574)
T 3e1s_A          258 TVH---------RLLGYGPQ-----------GFRHNHLEPAPYDLLIVDEVSMMG----DALMLSLLAAVPPGARVLLVG  313 (574)
T ss_dssp             EHH---------HHTTEETT-----------EESCSSSSCCSCSEEEECCGGGCC----HHHHHHHHTTSCTTCEEEEEE
T ss_pred             HHH---------HHHcCCcc-----------hhhhhhcccccCCEEEEcCccCCC----HHHHHHHHHhCcCCCEEEEEe
Confidence            100         00000000           011111223347999999999863    345667777777777766654


Q ss_pred             ee
Q 017573          177 AT  178 (369)
Q Consensus       177 aT  178 (369)
                      -+
T Consensus       314 D~  315 (574)
T 3e1s_A          314 DT  315 (574)
T ss_dssp             CT
T ss_pred             cc
Confidence            33

>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD, hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A* 2gk7_A 2xzo_A* 2xzp_A

Probab=98.68  E-value=1.9e-07  Score=87.45  Aligned_cols=70  Identities=19%  Similarity=0.146  Sum_probs=55.1

Q ss_pred             CCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHh
Q 017573           16 FEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRAL   87 (369)
Q Consensus        16 ~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~   87 (369)
                      ...+++.|.+++..+..+...+|+||+|+|||.+....+......  .+.++++++|+..-+.++.+.+.+.
T Consensus       178 ~~~ln~~Q~~av~~~l~~~~~li~GppGTGKT~~~~~~i~~l~~~--~~~~ilv~a~tn~A~~~l~~~l~~~  247 (624)
T 2gk6_A          178 LPDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQ--GNGPVLVCAPSNIAVDQLTEKIHQT  247 (624)
T ss_dssp             SCCCCHHHHHHHHHHHTCSEEEEECCTTSCHHHHHHHHHHHHHTS--SSCCEEEEESSHHHHHHHHHHHHTT
T ss_pred             cCCCCHHHHHHHHHHhcCCCeEEECCCCCCHHHHHHHHHHHHHHc--CCCeEEEEeCcHHHHHHHHHHHHhc
Confidence            346889999999998888889999999999998765444433321  2338999999999999988887654

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=98.65  E-value=2.8e-07  Score=88.21  Aligned_cols=69  Identities=20%  Similarity=0.219  Sum_probs=55.4

Q ss_pred             CCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHh
Q 017573           17 EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRAL   87 (369)
Q Consensus        17 ~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~   87 (369)
                      ..+++.|.+|+..+..+.-.+|+||+|+|||.++...+...+..  .+.++++++|+..-+.++.+.+.+.
T Consensus       359 ~~Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~~i~~~i~~l~~~--~~~~ILv~a~tn~A~d~l~~rL~~~  427 (802)
T 2xzl_A          359 AQLNSSQSNAVSHVLQRPLSLIQGPPGTGKTVTSATIVYHLSKI--HKDRILVCAPSNVAVDHLAAKLRDL  427 (802)
T ss_dssp             CCCCHHHHHHHHHHTTCSEEEEECSTTSSHHHHHHHHHHHHHHH--HCCCEEEEESSHHHHHHHHHHHHHT
T ss_pred             ccCCHHHHHHHHHHhcCCCEEEECCCCCCHHHHHHHHHHHHHhC--CCCeEEEEcCcHHHHHHHHHHHHhh
Confidence            46789999999999888889999999999998765544433332  1238999999999999999888765

>3upu_A ATP-dependent DNA helicase DDA; RECA-like domain, SH3 domain, PIN-tower interface, coupling hydrolysis to DNA unwinding, ssDNA; 3.30A {Enterobacteria phage T4}

Probab=98.64  E-value=1.6e-07  Score=84.75  Aligned_cols=71  Identities=20%  Similarity=0.149  Sum_probs=50.9

Q ss_pred             HhCCCCCCcHhhhhhhhccccC-----CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHH
Q 017573           12 YAYGFEKPSAIQQRGIVPFCKG-----LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVM   84 (369)
Q Consensus        12 ~~~~~~~~~~~Q~~~~~~~~~~-----~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~   84 (369)
                      .-+.|..|++-|++++..+...     +.++|.|++|+|||.++. .++..+..... ..+++++|+...+..+.+.+
T Consensus        19 ~p~~~~~Ln~~Q~~av~~~~~~i~~~~~~~li~G~aGTGKT~ll~-~~~~~l~~~~~-~~il~~a~T~~Aa~~l~~~~   94 (459)
T 3upu_A           19 SHMTFDDLTEGQKNAFNIVMKAIKEKKHHVTINGPAGTGATTLTK-FIIEALISTGE-TGIILAAPTHAAKKILSKLS   94 (459)
T ss_dssp             --CCSSCCCHHHHHHHHHHHHHHHSSSCEEEEECCTTSCHHHHHH-HHHHHHHHTTC-CCEEEEESSHHHHHHHHHHH
T ss_pred             CCCccccCCHHHHHHHHHHHHHHhcCCCEEEEEeCCCCCHHHHHH-HHHHHHHhcCC-ceEEEecCcHHHHHHHHhhh
Confidence            3457889999999999977542     489999999999997654 44444433222 26999999988776665544

>2wjy_A Regulator of nonsense transcripts 1; nonsense mediated decay, zinc-finger, ATP-binding, metal-BIN UPF2, UPF1, helicase, hydrolase; 2.50A {Homo sapiens} PDB: 2wjv_A 2iyk_A

Probab=98.57  E-value=4.6e-07  Score=86.59  Aligned_cols=69  Identities=20%  Similarity=0.166  Sum_probs=54.2

Q ss_pred             CCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHh
Q 017573           17 EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRAL   87 (369)
Q Consensus        17 ~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~   87 (369)
                      ..+++.|.+|+..+..+.-.+|+||+|+|||.+....+. .+... .+.++++++|+..-+.++.+.+.+.
T Consensus       355 ~~Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~ti~~~i~-~l~~~-~~~~ilv~a~tn~A~~~l~~~l~~~  423 (800)
T 2wjy_A          355 PDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVY-HLARQ-GNGPVLVCAPSNIAVDQLTEKIHQT  423 (800)
T ss_dssp             CCCCHHHHHHHHHHHTSSEEEEECCTTSCHHHHHHHHHH-HHHTT-CSSCEEEEESSHHHHHHHHHHHHTT
T ss_pred             cCCCHHHHHHHHHhccCCeEEEEcCCCCCHHHHHHHHHH-HHHHc-CCCcEEEEcCcHHHHHHHHHHHHHh
Confidence            457899999999988888899999999999987654443 33321 2238999999999999888887654

>3lfu_A DNA helicase II; SF1 helicase, ATP-binding, DNA damage, DNA REP replication, DNA-binding, hydrolase, nucleotide-B SOS response; HET: DNA; 1.80A {Escherichia coli} PDB: 2is6_A* 2is2_A* 2is1_A* 2is4_A*

Probab=98.51  E-value=3.7e-05  Score=72.67  Aligned_cols=70  Identities=14%  Similarity=0.184  Sum_probs=57.7

Q ss_pred             CCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhcc-CCCccEEEEcCCHHHHHHHHHHHHHhc
Q 017573           17 EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYG-LVQCQALVLAPTRELAQQIEKVMRALG   88 (369)
Q Consensus        17 ~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~-~~~~~~liv~P~~~l~~q~~~~~~~~~   88 (369)
                      ..+++-|++++..  .++.++|.|++|||||.+.+.-+...+..+ ....+++++++++..+.++.+.+.+..
T Consensus         8 ~~Ln~~Q~~av~~--~~~~~lV~a~aGsGKT~~l~~ri~~l~~~~~~~~~~iL~ltft~~aa~e~~~rl~~~~   78 (647)
T 3lfu_A            8 DSLNDKQREAVAA--PRSNLLVLAGAGSGKTRVLVHRIAWLMSVENCSPYSIMAVTFTNKAAAEMRHRIGQLM   78 (647)
T ss_dssp             TTCCHHHHHHHTC--CSSCEEEEECTTSCHHHHHHHHHHHHHHTSCCCGGGEEEEESSHHHHHHHHHHHHHHH
T ss_pred             hcCCHHHHHHHhC--CCCCEEEEECCCCCHHHHHHHHHHHHHHhCCCChhhEEEEeccHHHHHHHHHHHHHHh
Confidence            5789999999984  367899999999999998877777666543 233489999999999999999988764

>3hgt_A HDA1 complex subunit 3; RECA-like domain, SWI2/SNF2 helical domain, chromatin regulator, coiled coil, nucleus, repressor, transcription; 2.20A {Saccharomyces cerevisiae} PDB: 3hgq_A

Probab=98.25  E-value=1.9e-05  Score=66.07  Aligned_cols=124  Identities=14%  Similarity=0.099  Sum_probs=90.1

Q ss_pred             hhhhHHHHHHHHHhc--cCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCc
Q 017573          219 EEWKLETLCDLYETL--AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLA  296 (369)
Q Consensus       219 ~~~~~~~l~~~~~~~--~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~  296 (369)
                      .+.|+..+..++...  .+.+++||++..+...-+.+++...++++..+.|.....+ .+.    .++...+.+.|...+
T Consensus       107 ~SGKf~~L~~LL~~l~~~~~kVLIfsq~t~~LDilE~~l~~~~~~y~RlDG~~~~~~-~k~----~~~~~~i~Lltsag~  181 (328)
T 3hgt_A          107 NSGKFSVLRDLINLVQEYETETAIVCRPGRTMDLLEALLLGNKVHIKRYDGHSIKSA-AAA----NDFSCTVHLFSSEGI  181 (328)
T ss_dssp             TCHHHHHHHHHHHHHTTSCEEEEEEECSTHHHHHHHHHHTTSSCEEEESSSCCC------------CCSEEEEEEESSCC
T ss_pred             cCccHHHHHHHHHHHHhCCCEEEEEECChhHHHHHHHHHhcCCCceEeCCCCchhhh-hhc----ccCCceEEEEECCCC
Confidence            355788888877655  3459999999999999999999999999999999854432 211    234555666677666


Q ss_pred             CCCC-----CCCCcEEEEecCCCCccch-hhhhcccccCC----CceeEEEEeccccHHHH
Q 017573          297 RGID-----VQQVSLVINYDLPTQPENY-LHRIGRSGRFG----RKGVAINFVTRDDERML  347 (369)
Q Consensus       297 ~G~d-----~~~~~~vi~~~~~~~~~~~-~Q~~GR~~R~~----~~~~~~~~~~~~~~~~~  347 (369)
                      .|+|     ...++.||.+|+.|++..= +|++-|+.|.+    +.-.++.+++.+..+..
T Consensus       182 ~gin~~~~nl~~aD~VI~~DsdwNp~~d~iQa~~r~~R~~~gq~k~v~V~RLvt~~TiEh~  242 (328)
T 3hgt_A          182 NFTKYPIKSKARFDMLICLDTTVDTSQKDIQYLLQYKRERKGLERYAPIVRLVAINSIDHC  242 (328)
T ss_dssp             CTTTSCCCCCSCCSEEEECSTTCCTTSHHHHHHHCCC---------CCEEEEEETTSHHHH
T ss_pred             CCcCcccccCCCCCEEEEECCCCCCCChHHHHHHHHhhhccCCCCcceEEEEeCCCCHHHH
Confidence            6776     6789999999999999885 99999988873    45678888887766543

>2o0j_A Terminase, DNA packaging protein GP17; nucleotide-binding fold, hydrolase; HET: DNA ADP; 1.80A {Enterobacteria phage T4} PDB: 2o0h_A* 2o0k_A*

Probab=97.85  E-value=4.7e-05  Score=66.10  Aligned_cols=71  Identities=8%  Similarity=0.020  Sum_probs=54.8

Q ss_pred             CCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhcc
Q 017573           18 KPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGD   89 (369)
Q Consensus        18 ~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~   89 (369)
                      .|.|+|+..+..+...+.+++..+-+.|||.++...++..+... .+..++++.|+..-+..+.+.+..+..
T Consensus       163 ~L~p~Qk~il~~l~~~R~~vi~~sRq~GKT~l~a~~~l~~a~~~-~g~~v~~vA~t~~qA~~vf~~i~~mi~  233 (385)
T 2o0j_A          163 QLRDYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCFN-KDKAVGILAHKGSMSAEVLDRTKQAIE  233 (385)
T ss_dssp             CCCHHHHHHHHHHHHSSEEEEEECSSSCHHHHHHHHHHHHHHSS-SSCEEEEEESSHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHhhccCcEEEEEEcCcCChhHHHHHHHHHHHHhC-CCCeEEEEeCCHHHHHHHHHHHHHHHH
Confidence            78999999998775567789999999999987766555433332 334799999999988877777766543

>3cpe_A Terminase, DNA packaging protein GP17; large terminase, alternative initiation, ATP-binding, DNA- binding, hydrolase, nuclease; HET: DNA; 2.80A {Bacteriophage T4} PDB: 3ezk_A*

Probab=97.76  E-value=0.00022  Score=66.23  Aligned_cols=73  Identities=10%  Similarity=0.036  Sum_probs=56.7

Q ss_pred             CCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhcccc
Q 017573           18 KPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYL   91 (369)
Q Consensus        18 ~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~   91 (369)
                      .|+|+|+..+..+-..+..++..+-|.|||.+....++..+...+ +..++++.|+...+....+.+..+....
T Consensus       163 ~l~p~Q~~i~~~l~~~r~~~i~~~Rq~GKS~~~a~~~l~~~~~~~-~~~i~~va~t~~qA~~~~~~i~~~i~~~  235 (592)
T 3cpe_A          163 QLRDYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCFNK-DKAVGILAHKGSMSAEVLDRTKQAIELL  235 (592)
T ss_dssp             CCCHHHHHHHHHHHHCSEEEEEECSSSCHHHHHHHHHHHHHHTSS-SCEEEEEESSHHHHHHHHHHHHHHHTTS
T ss_pred             cCCHHHHHHHHhhccccEEEEEEcCccChHHHHHHHHHHHHHhCC-CCeEEEEECCHHHHHHHHHHHHHHHHhC
Confidence            689999999987755677999999999999876655554444332 3489999999999988888777765443

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A*

Probab=97.67  E-value=0.00017  Score=55.95  Aligned_cols=32  Identities=22%  Similarity=0.312  Sum_probs=24.8

Q ss_pred             cHhhhhhhhccc---------cCCcEEEEcCCCChhhHHHH
Q 017573           20 SAIQQRGIVPFC---------KGLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        20 ~~~Q~~~~~~~~---------~~~~~li~~~tG~GKT~~~~   51 (369)
                      .+.|++++..+.         .++.+++.||+|+|||..+-
T Consensus        16 ~~~~~~~~~~~~~~~~~~~~~~g~~~~l~G~~G~GKTtL~~   56 (180)
T 3ec2_A           16 NVSQNRALLTIRVFVHNFNPEEGKGLTFVGSPGVGKTHLAV   56 (180)
T ss_dssp             SHHHHHHHHHHHHHHHSCCGGGCCEEEECCSSSSSHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHhccccCCCEEEEECCCCCCHHHHHH
Confidence            456777776654         36889999999999997653

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=97.66  E-value=0.00021  Score=62.84  Aligned_cols=108  Identities=19%  Similarity=0.189  Sum_probs=64.1

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHcc
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQA  113 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~  113 (369)
                      +-.++.|+.|+|||....-.    +..    .+.++++|+++++.++.+.+.+.    +.        .          .
T Consensus       162 ~v~~I~G~aGsGKTt~I~~~----~~~----~~~lVlTpT~~aa~~l~~kl~~~----~~--------~----------~  211 (446)
T 3vkw_A          162 KVVLVDGVPGCGKTKEILSR----VNF----EEDLILVPGRQAAEMIRRRANAS----GI--------I----------V  211 (446)
T ss_dssp             EEEEEEECTTSCHHHHHHHH----CCT----TTCEEEESCHHHHHHHHHHHTTT----SC--------C----------C
T ss_pred             cEEEEEcCCCCCHHHHHHHH----hcc----CCeEEEeCCHHHHHHHHHHhhhc----Cc--------c----------c
Confidence            44689999999999764222    211    27899999999998888877432    00        0          1


Q ss_pred             CCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEEee
Q 017573          114 GVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSAT  178 (369)
Q Consensus       114 ~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~saT  178 (369)
                      ....-+.|.++++..  ........++++|+||+-.+.    ...+..++...+. .+++++.-+
T Consensus       212 ~~~~~V~T~dsfL~~--~~~~~~~~~d~liiDE~sm~~----~~~l~~l~~~~~~-~~vilvGD~  269 (446)
T 3vkw_A          212 ATKDNVRTVDSFLMN--YGKGARCQFKRLFIDEGLMLH----TGCVNFLVEMSLC-DIAYVYGDT  269 (446)
T ss_dssp             CCTTTEEEHHHHHHT--TTSSCCCCCSEEEEETGGGSC----HHHHHHHHHHTTC-SEEEEEECT
T ss_pred             cccceEEEeHHhhcC--CCCCCCCcCCEEEEeCcccCC----HHHHHHHHHhCCC-CEEEEecCc
Confidence            123347777776531  111112236999999998652    2333344445443 555554443

>1uaa_A REP helicase, protein (ATP-dependent DNA helicase REP.); complex (helicase/DNA), DNA unwinding, hydrolase/DNA complex; HET: DNA; 3.00A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19

Probab=97.64  E-value=8.7e-05  Score=70.32  Aligned_cols=70  Identities=16%  Similarity=0.125  Sum_probs=57.4

Q ss_pred             CCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhc-cCCCccEEEEcCCHHHHHHHHHHHHHhcc
Q 017573           18 KPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY-GLVQCQALVLAPTRELAQQIEKVMRALGD   89 (369)
Q Consensus        18 ~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~-~~~~~~~liv~P~~~l~~q~~~~~~~~~~   89 (369)
                      .+++-|++++...  ++.++|.|+.|||||.+...-+...+.. +....++++|+.|+..+.++.+.+.+...
T Consensus         2 ~L~~~Q~~av~~~--~~~~lV~AgaGSGKT~~l~~ri~~ll~~~~~~~~~IL~lTfT~~Aa~em~~Rl~~~l~   72 (673)
T 1uaa_A            2 RLNPGQQQAVEFV--TGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVGQTLG   72 (673)
T ss_dssp             CCCHHHHHHHHCC--SSEEEECCCTTSCHHHHHHHHHHHHHHHHCCCGGGEEEEESSHHHHHHHHHHHHHHSC
T ss_pred             CCCHHHHHHHhCC--CCCEEEEeCCCCChHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHHcC
Confidence            5789999999863  6789999999999999887777766654 32334899999999999999999987654

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=97.64  E-value=0.00012  Score=56.97  Aligned_cols=39  Identities=18%  Similarity=0.024  Sum_probs=28.3

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCH
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTR   74 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~   74 (369)
                      ++-.++.+|+|+|||..++-.+......+.   +++++.|..
T Consensus         3 g~i~vi~G~~gsGKTT~ll~~~~~~~~~g~---~v~~~~~~~   41 (184)
T 2orw_A            3 GKLTVITGPMYSGKTTELLSFVEIYKLGKK---KVAVFKPKI   41 (184)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHHHHHTTC---EEEEEEEC-
T ss_pred             cEEEEEECCCCCCHHHHHHHHHHHHHHCCC---eEEEEeecc
Confidence            455789999999999887655555444443   788888874

>1xx6_A Thymidine kinase; NESG, northeast structural genomics consortium, protein STRU initiative, PSI, structural genomics, DNA synthesis; HET: ADP; 2.00A {Clostridium acetobutylicum} SCOP: c.37.1.24 g.39.1.14

Probab=97.62  E-value=0.00012  Score=57.04  Aligned_cols=39  Identities=15%  Similarity=0.084  Sum_probs=28.9

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCH
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTR   74 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~   74 (369)
                      ++-.++.+|+|+|||..++-.+.+....+.   +++++.|..
T Consensus         8 g~i~v~~G~mgsGKTT~ll~~a~r~~~~g~---kV~v~k~~~   46 (191)
T 1xx6_A            8 GWVEVIVGPMYSGKSEELIRRIRRAKIAKQ---KIQVFKPEI   46 (191)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHHTTC---CEEEEEEC-
T ss_pred             CEEEEEECCCCCcHHHHHHHHHHHHHHCCC---EEEEEEecc
Confidence            456789999999999887666555544444   899999874

>1a5t_A Delta prime, HOLB; zinc finger, DNA replication; 2.20A {Escherichia coli K12} SCOP: a.80.1.1 c.37.1.20 PDB: 1jr3_E* 1xxh_E* 1xxi_E* 3glf_E* 3glg_E* 3glh_E* 3gli_E*

Probab=97.60  E-value=0.00018  Score=61.85  Aligned_cols=38  Identities=16%  Similarity=0.068  Sum_probs=28.1

Q ss_pred             CcHhhhhhhhcccc----C---CcEEEEcCCCChhhHHHHHHHHH
Q 017573           19 PSAIQQRGIVPFCK----G---LDVIQQAQSGTGKTATFCSGILQ   56 (369)
Q Consensus        19 ~~~~Q~~~~~~~~~----~---~~~li~~~tG~GKT~~~~~~~~~   56 (369)
                      ++|+|.+++..+..    +   ...++.||+|+|||..+...+-.
T Consensus         3 ~~pw~~~~~~~l~~~i~~~~~~~a~L~~G~~G~GKt~~a~~la~~   47 (334)
T 1a5t_A            3 WYPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALSRY   47 (334)
T ss_dssp             CCGGGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCCchHHHHHHHHHHHHcCCcceeEEEECCCCchHHHHHHHHHHH
Confidence            57899998876653    3   24899999999999876544443

>1l8q_A Chromosomal replication initiator protein DNAA; AAA+, helix-turn-helix, nucleotide-binding, DNA binding, REP initiation, DNA binding protein; HET: ADP; 2.70A {Aquifex aeolicus} SCOP: a.4.12.2 c.37.1.20 PDB: 3r8f_A* 2hcb_A*

Probab=97.59  E-value=0.00056  Score=58.52  Aligned_cols=36  Identities=14%  Similarity=0.099  Sum_probs=23.1

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcC
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAP   72 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P   72 (369)
                      ..+++.||+|+|||..+- .+...+...  +..++++..
T Consensus        38 ~~lll~G~~GtGKT~la~-~i~~~~~~~--~~~~~~i~~   73 (324)
T 1l8q_A           38 NPIFIYGSVGTGKTHLLQ-AAGNEAKKR--GYRVIYSSA   73 (324)
T ss_dssp             SSEEEECSSSSSHHHHHH-HHHHHHHHT--TCCEEEEEH
T ss_pred             CeEEEECCCCCcHHHHHH-HHHHHHHHC--CCEEEEEEH
Confidence            579999999999997754 333333322  225666543

>2b8t_A Thymidine kinase; deoxyribonucleoside kinase, zinc-binding domain, TK1, UU-TK, transferase; HET: THM; 2.00A {Ureaplasma parvum} SCOP: c.37.1.24 g.39.1.14 PDB: 2uz3_A*

Probab=97.52  E-value=0.00028  Score=56.39  Aligned_cols=91  Identities=19%  Similarity=0.175  Sum_probs=53.7

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHc
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQ  112 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~  112 (369)
                      +.-.++.+++|+|||..++..+.+....+.   +++++.|...-  . .  ........++.                  
T Consensus        12 G~i~litG~mGsGKTT~ll~~~~r~~~~g~---kVli~~~~~d~--r-~--~~~i~srlG~~------------------   65 (223)
T 2b8t_A           12 GWIEFITGPMFAGKTAELIRRLHRLEYADV---KYLVFKPKIDT--R-S--IRNIQSRTGTS------------------   65 (223)
T ss_dssp             CEEEEEECSTTSCHHHHHHHHHHHHHHTTC---CEEEEEECCCG--G-G--CSSCCCCCCCS------------------
T ss_pred             cEEEEEECCCCCcHHHHHHHHHHHHHhcCC---EEEEEEeccCc--h-H--HHHHHHhcCCC------------------
Confidence            455788999999999887666665555444   78998876421  0 0  00111111110                  


Q ss_pred             cCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhh
Q 017573          113 AGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEML  151 (369)
Q Consensus       113 ~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~  151 (369)
                       ...+-+.+.+.+...+.... ....+++|++||++.+.
T Consensus        66 -~~~~~~~~~~~i~~~i~~~~-~~~~~dvViIDEaQ~l~  102 (223)
T 2b8t_A           66 -LPSVEVESAPEILNYIMSNS-FNDETKVIGIDEVQFFD  102 (223)
T ss_dssp             -SCCEEESSTHHHHHHHHSTT-SCTTCCEEEECSGGGSC
T ss_pred             -ccccccCCHHHHHHHHHHHh-hCCCCCEEEEecCccCc
Confidence             01233556666666665532 23347999999999753

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=97.51  E-value=8.7e-05  Score=55.48  Aligned_cols=29  Identities=14%  Similarity=0.039  Sum_probs=21.7

Q ss_pred             hhhhhhhccccCCcEEEEcCCCChhhHHHH
Q 017573           22 IQQRGIVPFCKGLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        22 ~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~   51 (369)
                      .+..++..+ .++.+++.+|+|+|||..+-
T Consensus        26 ~~~~~l~~~-~g~~~~l~G~~G~GKTtL~~   54 (149)
T 2kjq_A           26 ELVYVLRHK-HGQFIYVWGEEGAGKSHLLQ   54 (149)
T ss_dssp             HHHHHCCCC-CCSEEEEESSSTTTTCHHHH
T ss_pred             HHHHHHHhc-CCCEEEEECCCCCCHHHHHH
Confidence            344455555 67889999999999997643

>1pjr_A PCRA; DNA repair, DNA replication, SOS response, helicase, ATP- binding, DNA-binding; 2.50A {Geobacillus stearothermophilus} SCOP: c.37.1.19 c.37.1.19 PDB: 1qhg_A* 3pjr_A* 2pjr_A* 1qhh_B* 1qhh_D* 1qhh_A* 1qhh_C* 2pjr_B*

Probab=97.49  E-value=0.00027  Score=67.39  Aligned_cols=70  Identities=17%  Similarity=0.175  Sum_probs=57.3

Q ss_pred             CCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhc-cCCCccEEEEcCCHHHHHHHHHHHHHhc
Q 017573           17 EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY-GLVQCQALVLAPTRELAQQIEKVMRALG   88 (369)
Q Consensus        17 ~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~-~~~~~~~liv~P~~~l~~q~~~~~~~~~   88 (369)
                      ..+++-|++++...  ++.++|.|+.|||||.+...-+...+.. +....++|+++.|+..+.++.+.+.+..
T Consensus        10 ~~Ln~~Q~~av~~~--~g~~lV~AgAGSGKT~vL~~ri~~ll~~~~~~p~~IL~vTFTnkAA~Em~~Rl~~~l   80 (724)
T 1pjr_A           10 AHLNKEQQEAVRTT--EGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTNKAAREMRERVQSLL   80 (724)
T ss_dssp             TTSCHHHHHHHHCC--SSCEEEEECTTSCHHHHHHHHHHHHHHTTCCCGGGEEEEESSHHHHHHHHHHHHHHH
T ss_pred             hhCCHHHHHHHhCC--CCCEEEEEcCCCCHHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHHh
Confidence            57999999999863  5789999999999999887777766654 3233489999999999999998887753

>2j9r_A Thymidine kinase; TK1, DNK, lasso, transferase, ATP-binding, deoxyribonucleoside kinase, DNA synthesis, phosphate accept nucleotide-binding; HET: THM; 2.7A {Bacillus anthracis} PDB: 2ja1_A*

Probab=97.45  E-value=0.00017  Score=56.77  Aligned_cols=40  Identities=15%  Similarity=0.133  Sum_probs=29.6

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHH
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRE   75 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~   75 (369)
                      |+-.++.+++|+|||..++-.+.+....+.   +++++.|...
T Consensus        28 G~l~vitG~MgsGKTT~lL~~a~r~~~~g~---kVli~k~~~d   67 (214)
T 2j9r_A           28 GWIEVICGSMFSGKSEELIRRVRRTQFAKQ---HAIVFKPCID   67 (214)
T ss_dssp             CEEEEEECSTTSCHHHHHHHHHHHHHHTTC---CEEEEECC--
T ss_pred             CEEEEEECCCCCcHHHHHHHHHHHHHHCCC---EEEEEEeccC
Confidence            344578999999999887777766655554   8999999753

>2orv_A Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2'deoxythymidil))tetraphosphate, transferase; HET: 4TA; 2.30A {Homo sapiens} SCOP: c.37.1.24 g.39.1.14

Probab=97.40  E-value=0.00021  Score=56.78  Aligned_cols=39  Identities=13%  Similarity=0.083  Sum_probs=30.4

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCH
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTR   74 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~   74 (369)
                      ++-.++.+++|+|||..++-.+.++...+.   +++++-|..
T Consensus        19 g~l~v~~G~MgsGKTT~lL~~~~r~~~~g~---kvli~kp~~   57 (234)
T 2orv_A           19 GQIQVILGPMFSGKSTELMRRVRRFQIAQY---KCLVIKYAK   57 (234)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHHHHTTTC---CEEEEEETT
T ss_pred             eEEEEEECCCCCcHHHHHHHHHHHHHHCCC---eEEEEeecC
Confidence            455688999999999887777666655544   899999875

>3u4q_A ATP-dependent helicase/nuclease subunit A; helicase, nuclease, double strand DNA repair, protein-DNA CO hydrolase-DNA complex; HET: DNA; 2.80A {Bacillus subtilis} PDB: 3u44_A*

Probab=97.34  E-value=0.00044  Score=69.86  Aligned_cols=105  Identities=19%  Similarity=0.140  Sum_probs=72.1

Q ss_pred             CCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccC---CCccEEEEcCCHHHHHHHHHHHHHhccccCc
Q 017573           17 EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGL---VQCQALVLAPTRELAQQIEKVMRALGDYLGV   93 (369)
Q Consensus        17 ~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~---~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~   93 (369)
                      ..+++-|.+++..-  +++++|.|+.|||||.+.+--++..+..+.   ...+++++++|++.+..+.+.+.+.......
T Consensus         9 ~~~t~eQ~~~i~~~--~~~~~v~a~AGSGKT~vl~~ri~~ll~~~~~~~~~~~il~~Tft~~aa~e~~~ri~~~l~~~~~   86 (1232)
T 3u4q_A            9 STWTDDQWNAIVST--GQDILVAAAAGSGKTAVLVERMIRKITAEENPIDVDRLLVVTFTNASAAEMKHRIAEALEKELV   86 (1232)
T ss_dssp             -CCCHHHHHHHHCC--SSCEEEEECTTCCHHHHHHHHHHHHHSCSSSCCCGGGEEEECSSHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHhCC--CCCEEEEecCCCcHHHHHHHHHHHHHhcCCCCCCccceEEEeccHHHHHHHHHHHHHHHHHHhh
Confidence            47899999999764  889999999999999998777777776643   3348999999999999999888774321100


Q ss_pred             EEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHH
Q 017573           94 KVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDML  129 (369)
Q Consensus        94 ~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~  129 (369)
                      .    .++.  ....+....-..+-|+|.++|...+
T Consensus        87 ~----~~~~--~~~~~~~~~~~~~~i~T~hsf~~~~  116 (1232)
T 3u4q_A           87 Q----RPGS--LHIRRQLSLLNRASISTLHSFCLQV  116 (1232)
T ss_dssp             H----STTC--HHHHHHHHHTTTSEEECHHHHHHHH
T ss_pred             c----Ccch--HHHHHHHhccCCCeEEeHHHHHHHH
Confidence            0    0000  1111111222457889999986444

>2chg_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATPase, ATP-binding, nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus fulgidus}

Probab=97.26  E-value=0.0025  Score=50.84  Aligned_cols=38  Identities=16%  Similarity=0.268  Sum_probs=23.8

Q ss_pred             CccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEE
Q 017573          138 YIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFS  176 (369)
Q Consensus       138 ~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~s  176 (369)
                      ...++++||+|.+.... ...+..++...+....+++.|
T Consensus       102 ~~~vliiDe~~~l~~~~-~~~l~~~l~~~~~~~~~i~~~  139 (226)
T 2chg_A          102 PFKIIFLDEADALTADA-QAALRRTMEMYSKSCRFILSC  139 (226)
T ss_dssp             SCEEEEEETGGGSCHHH-HHHHHHHHHHTTTTEEEEEEE
T ss_pred             CceEEEEeChhhcCHHH-HHHHHHHHHhcCCCCeEEEEe
Confidence            35799999999875432 344555555555555555544

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=97.24  E-value=0.00079  Score=52.05  Aligned_cols=38  Identities=13%  Similarity=0.061  Sum_probs=29.1

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCC
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPT   73 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~   73 (369)
                      ++-.++.+|+|+|||.-.+-.+-+....+.   +++++.|.
T Consensus        20 g~l~fiyG~MgsGKTt~Ll~~i~n~~~~~~---kvl~~kp~   57 (195)
T 1w4r_A           20 GQIQVILGPMFSGKSTELMRRVRRFQIAQY---KCLVIKYA   57 (195)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHHHHHHHTTC---CEEEEEET
T ss_pred             eEEEEEECCCCCcHHHHHHHHHHHHHHcCC---eEEEEccc
Confidence            456799999999999776666665555443   89999887

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=97.16  E-value=0.0017  Score=48.15  Aligned_cols=20  Identities=20%  Similarity=0.230  Sum_probs=17.4

Q ss_pred             ccCCcEEEEcCCCChhhHHH
Q 017573           31 CKGLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        31 ~~~~~~li~~~tG~GKT~~~   50 (369)
                      ..+.++++.+|+|+|||..+
T Consensus        22 ~~~~~vll~G~~GtGKt~lA   41 (145)
T 3n70_A           22 ETDIAVWLYGAPGTGRMTGA   41 (145)
T ss_dssp             TCCSCEEEESSTTSSHHHHH
T ss_pred             CCCCCEEEECCCCCCHHHHH
Confidence            35688999999999999876

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=97.16  E-value=0.0021  Score=47.49  Aligned_cols=20  Identities=10%  Similarity=0.061  Sum_probs=17.0

Q ss_pred             ccCCcEEEEcCCCChhhHHH
Q 017573           31 CKGLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        31 ~~~~~~li~~~tG~GKT~~~   50 (369)
                      ..+.++++.+|+|+|||..+
T Consensus        25 ~~~~~vll~G~~GtGKt~lA   44 (143)
T 3co5_A           25 KRTSPVFLTGEAGSPFETVA   44 (143)
T ss_dssp             TCSSCEEEEEETTCCHHHHH
T ss_pred             CCCCcEEEECCCCccHHHHH
Confidence            34688999999999999765

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=97.15  E-value=0.0021  Score=56.23  Aligned_cols=19  Identities=32%  Similarity=0.314  Sum_probs=16.3

Q ss_pred             CCcEEEEcCCCChhhHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~   51 (369)
                      +..+++.||+|+|||..+-
T Consensus        44 ~~~vll~G~~G~GKT~l~~   62 (387)
T 2v1u_A           44 PSNALLYGLTGTGKTAVAR   62 (387)
T ss_dssp             CCCEEECBCTTSSHHHHHH
T ss_pred             CCcEEEECCCCCCHHHHHH
Confidence            4789999999999997754

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=97.14  E-value=0.0032  Score=53.11  Aligned_cols=25  Identities=8%  Similarity=0.038  Sum_probs=19.0

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhh
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQL   58 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~   58 (369)
                      +.++++.||+|+|||.++- .++..+
T Consensus        45 ~~~lli~GpPGTGKT~~v~-~v~~~L   69 (318)
T 3te6_A           45 NKLFYITNADDSTKFQLVN-DVMDEL   69 (318)
T ss_dssp             CCEEEEECCCSHHHHHHHH-HHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHH-HHHHHH
Confidence            5789999999999997753 444444

>1d2n_A N-ethylmaleimide-sensitive fusion protein; hexamerization domain, ATPase, transport; HET: ANP; 1.75A {Cricetulus griseus} SCOP: c.37.1.20 PDB: 1nsf_A*

Probab=97.14  E-value=0.004  Score=51.62  Aligned_cols=18  Identities=28%  Similarity=0.390  Sum_probs=15.7

Q ss_pred             CcEEEEcCCCChhhHHHH
Q 017573           34 LDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~   51 (369)
                      ..+++.||+|+|||..+-
T Consensus        65 ~~vLl~G~~GtGKT~la~   82 (272)
T 1d2n_A           65 VSVLLEGPPHSGKTALAA   82 (272)
T ss_dssp             EEEEEECSTTSSHHHHHH
T ss_pred             eEEEEECCCCCcHHHHHH
Confidence            579999999999998764

>3e2i_A Thymidine kinase; Zn-binding, ATP-binding, DNA synthesis, nucleotide-B transferase; HET: MSE; 2.01A {Staphylococcus aureus}

Probab=97.13  E-value=0.0011  Score=52.07  Aligned_cols=40  Identities=13%  Similarity=0.142  Sum_probs=27.8

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHH
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRE   75 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~   75 (369)
                      |.=.++.+|+|+|||..++..+.+....+.   +++++.|...
T Consensus        28 G~I~vitG~M~sGKTT~Llr~~~r~~~~g~---kvli~kp~~D   67 (219)
T 3e2i_A           28 GWIECITGSMFSGKSEELIRRLRRGIYAKQ---KVVVFKPAID   67 (219)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHHHHHHHTTC---CEEEEEEC--
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHHHHcCC---ceEEEEeccC
Confidence            344689999999999876666554444433   8999999753

>1g5t_A COB(I)alamin adenosyltransferase; P-loop protein, cobalamin biosynthesis, RECA fold; HET: ATP; 1.80A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1g5r_A* 1g64_A*

Probab=97.12  E-value=0.0038  Score=48.36  Aligned_cols=136  Identities=15%  Similarity=0.141  Sum_probs=71.9

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHH-HHHHHHHHHHhccccCcEEEEEECCcch--HH-HH
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTREL-AQQIEKVMRALGDYLGVKVHACVGGTSV--RE-DQ  108 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l-~~q~~~~~~~~~~~~~~~v~~~~~~~~~--~~-~~  108 (369)
                      ...+++..++|.|||.+++..++.++..+.   +++++--.+.- ...-.+.+..+    ++.......+...  .. ..
T Consensus        28 ~g~i~v~tG~GkGKTTaA~GlalRA~g~G~---rV~~vQF~Kg~~~~gE~~~l~~L----~v~~~~~g~gf~~~~~~~~~  100 (196)
T 1g5t_A           28 RGIIIVFTGNGKGKTTAAFGTAARAVGHGK---NVGVVQFIKGTWPNGERNLLEPH----GVEFQVMATGFTWETQNREA  100 (196)
T ss_dssp             CCCEEEEESSSSCHHHHHHHHHHHHHHTTC---CEEEEESSCCSSCCHHHHHHGGG----TCEEEECCTTCCCCGGGHHH
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHHCCC---eEEEEEeeCCCCCccHHHHHHhC----CcEEEEcccccccCCCCcHH
Confidence            468999999999999999999998888776   88888433210 00000111221    2222221111100  00 00


Q ss_pred             HHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccC--cHHHHHHHHhhCCccCcEEEEEeeCChhHHH
Q 017573          109 RILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRG--FKDQIYDIFQLLPAKVQVGVFSATMPPEALE  185 (369)
Q Consensus       109 ~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~--~~~~~~~~~~~~~~~~~~i~~saT~~~~~~~  185 (369)
                      ....        --..|......  +....+|+||+||+-.....+  ....+..++...+....+|+.+--+++.+.+
T Consensus       101 ~~~~--------a~~~l~~a~~~--l~~~~yDlvILDEi~~al~~g~l~~~ev~~~l~~Rp~~~~vIlTGr~ap~~l~e  169 (196)
T 1g5t_A          101 DTAA--------CMAVWQHGKRM--LADPLLDMVVLDELTYMVAYDYLPLEEVISALNARPGHQTVIITGRGCHRDILD  169 (196)
T ss_dssp             HHHH--------HHHHHHHHHHH--TTCTTCSEEEEETHHHHHHTTSSCHHHHHHHHHTSCTTCEEEEECSSCCHHHHH
T ss_pred             HHHH--------HHHHHHHHHHH--HhcCCCCEEEEeCCCccccCCCCCHHHHHHHHHhCcCCCEEEEECCCCcHHHHH
Confidence            0000        01122222222  223458999999997654333  3466777777777676666644445544433

>2z4s_A Chromosomal replication initiator protein DNAA; AAA+ ATPase, domain III (ATPase domain), ATP-binding, cytoplasm, DNA replication; HET: ADP; 3.00A {Thermotoga maritima} PDB: 2z4r_A*

Probab=97.09  E-value=0.0031  Score=56.28  Aligned_cols=38  Identities=13%  Similarity=0.069  Sum_probs=24.0

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcC
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAP   72 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P   72 (369)
                      ..+++.||+|+|||..+- ++...+.....+.+++++..
T Consensus       131 ~~lll~Gp~G~GKTtLa~-aia~~l~~~~~~~~v~~v~~  168 (440)
T 2z4s_A          131 NPLFIYGGVGLGKTHLLQ-SIGNYVVQNEPDLRVMYITS  168 (440)
T ss_dssp             CCEEEECSSSSSHHHHHH-HHHHHHHHHCCSSCEEEEEH
T ss_pred             CeEEEECCCCCCHHHHHH-HHHHHHHHhCCCCeEEEeeH
Confidence            579999999999997653 33334433222335666544

>2zpa_A Uncharacterized protein YPFI; RNA modification enzyme, RNA helicase, acetyltransferase, GCN5 acetyltransferase; HET: ACO ADP; 2.35A {Escherichia coli K12}

Probab=96.97  E-value=0.0015  Score=60.50  Aligned_cols=113  Identities=17%  Similarity=0.242  Sum_probs=72.2

Q ss_pred             CCcHhhhhhhhcccc--CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEE
Q 017573           18 KPSAIQQRGIVPFCK--GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKV   95 (369)
Q Consensus        18 ~~~~~Q~~~~~~~~~--~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v   95 (369)
                      .++.-|++++..+.+  ....++.|+-|.|||..+ ..++..+..     .+++.+|+..-+....+...+         
T Consensus       175 ~~T~dQ~~al~~~~~~~~~~~vlta~RGRGKSa~l-G~~~a~~~~-----~~~vtAP~~~a~~~l~~~~~~---------  239 (671)
T 2zpa_A          175 APQPEQQQLLKQLMTMPPGVAAVTAARGRGKSALA-GQLISRIAG-----RAIVTAPAKASTDVLAQFAGE---------  239 (671)
T ss_dssp             SCCHHHHHHHHHHTTCCSEEEEEEECTTSSHHHHH-HHHHHHSSS-----CEEEECSSCCSCHHHHHHHGG---------
T ss_pred             CCCHHHHHHHHHHHHhhhCeEEEecCCCCCHHHHH-HHHHHHHHh-----CcEEECCCHHHHHHHHHHhhC---------
Confidence            578899999988876  456799999999999554 333334321     578889998755543332211         


Q ss_pred             EEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEE
Q 017573           96 HACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVF  175 (369)
Q Consensus        96 ~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~  175 (369)
                                          .+-+..|+.+..   .    ....+++|||||=.+    ....+..++...+    .++|
T Consensus       240 --------------------~i~~~~Pd~~~~---~----~~~~dlliVDEAAaI----p~pll~~ll~~~~----~v~~  284 (671)
T 2zpa_A          240 --------------------KFRFIAPDALLA---S----DEQADWLVVDEAAAI----PAPLLHQLVSRFP----RTLL  284 (671)
T ss_dssp             --------------------GCCBCCHHHHHH---S----CCCCSEEEEETGGGS----CHHHHHHHHTTSS----EEEE
T ss_pred             --------------------CeEEeCchhhhh---C----cccCCEEEEEchhcC----CHHHHHHHHhhCC----eEEE
Confidence                                133445555431   1    123699999999976    3455556665443    5777


Q ss_pred             EeeCC
Q 017573          176 SATMP  180 (369)
Q Consensus       176 saT~~  180 (369)
                      |.|..
T Consensus       285 ~tTv~  289 (671)
T 2zpa_A          285 TTTVQ  289 (671)
T ss_dssp             EEEBS
T ss_pred             EecCC
Confidence            77864

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=96.90  E-value=0.0014  Score=55.57  Aligned_cols=19  Identities=32%  Similarity=0.358  Sum_probs=16.2

Q ss_pred             CCcEEEEcCCCChhhHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~   51 (369)
                      +.++++.||+|+|||..+-
T Consensus        67 ~~~vll~G~~GtGKT~la~   85 (309)
T 3syl_A           67 TLHMSFTGNPGTGKTTVAL   85 (309)
T ss_dssp             CCEEEEEECTTSSHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHH
Confidence            3579999999999998764

>3bos_A Putative DNA replication factor; P-loop containing nucleoside triphosphate hydrolases, struct genomics; HET: MSE CDP; 1.75A {Shewanella amazonensis} PDB: 3sc3_A

Probab=96.89  E-value=0.0019  Score=52.30  Aligned_cols=19  Identities=11%  Similarity=0.038  Sum_probs=16.6

Q ss_pred             CCcEEEEcCCCChhhHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~   51 (369)
                      +..+++.||+|+|||..+-
T Consensus        52 ~~~~ll~G~~G~GKT~la~   70 (242)
T 3bos_A           52 VQAIYLWGPVKSGRTHLIH   70 (242)
T ss_dssp             CSEEEEECSTTSSHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHH
Confidence            5789999999999997754

>2qby_B CDC6 homolog 3, cell division control protein 6 homolog 3; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=96.86  E-value=0.0044  Score=54.22  Aligned_cols=19  Identities=26%  Similarity=0.207  Sum_probs=16.0

Q ss_pred             CCcEEEEcCCCChhhHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~   51 (369)
                      ...+++.||+|+|||..+-
T Consensus        45 ~~~vll~G~~G~GKT~la~   63 (384)
T 2qby_B           45 KFSNLFLGLTGTGKTFVSK   63 (384)
T ss_dssp             CCEEEEEECTTSSHHHHHH
T ss_pred             CCcEEEECCCCCCHHHHHH
Confidence            3579999999999997753

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=96.82  E-value=0.0048  Score=48.54  Aligned_cols=19  Identities=21%  Similarity=0.275  Sum_probs=16.3

Q ss_pred             CcEEEEcCCCChhhHHHHH
Q 017573           34 LDVIQQAQSGTGKTATFCS   52 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~   52 (369)
                      +.+++.||+|+|||..+..
T Consensus        55 ~~~~l~G~~GtGKT~la~~   73 (202)
T 2w58_A           55 KGLYLHGSFGVGKTYLLAA   73 (202)
T ss_dssp             CEEEEECSTTSSHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHH
Confidence            7899999999999987543

>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=96.68  E-value=0.0044  Score=53.54  Aligned_cols=39  Identities=18%  Similarity=0.302  Sum_probs=24.7

Q ss_pred             CccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEEe
Q 017573          138 YIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSA  177 (369)
Q Consensus       138 ~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~sa  177 (369)
                      ..+++++||+|.+.... ...+...+...+....+++.+.
T Consensus       133 ~~~vliiDE~~~l~~~~-~~~Ll~~le~~~~~~~~il~~~  171 (353)
T 1sxj_D          133 PYKIIILDEADSMTADA-QSALRRTMETYSGVTRFCLICN  171 (353)
T ss_dssp             SCEEEEETTGGGSCHHH-HHHHHHHHHHTTTTEEEEEEES
T ss_pred             CceEEEEECCCccCHHH-HHHHHHHHHhcCCCceEEEEeC
Confidence            35799999999875432 3455556666555555555443

>3u61_B DNA polymerase accessory protein 44; AAA+, ATP hydrolase, clamp loader, sliding clamp, primer-TEM DNA, DNA binding protein-DNA complex; HET: DNA ADP 08T; 3.20A {Enterobacteria phage T4} PDB: 3u5z_B* 3u60_B*

Probab=96.68  E-value=0.0043  Score=52.90  Aligned_cols=37  Identities=14%  Similarity=0.169  Sum_probs=23.9

Q ss_pred             CccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEE
Q 017573          138 YIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGV  174 (369)
Q Consensus       138 ~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~  174 (369)
                      ..+++++||+|.+........+..++...+...++++
T Consensus       105 ~~~vliiDEi~~l~~~~~~~~L~~~le~~~~~~~iI~  141 (324)
T 3u61_B          105 RQKVIVIDEFDRSGLAESQRHLRSFMEAYSSNCSIII  141 (324)
T ss_dssp             CEEEEEEESCCCGGGHHHHHHHHHHHHHHGGGCEEEE
T ss_pred             CCeEEEEECCcccCcHHHHHHHHHHHHhCCCCcEEEE
Confidence            4689999999998622234555555555555565555

>3kl4_A SRP54, signal recognition 54 kDa protein; signal recognition particle, SRP, SRP54, FFH, signal sequenc peptide; 3.50A {Sulfolobus solfataricus} PDB: 1qzx_A 1qzw_A

Probab=96.65  E-value=0.018  Score=50.77  Aligned_cols=131  Identities=17%  Similarity=0.242  Sum_probs=67.4

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEc--CCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHH
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLA--PTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL  111 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~--P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~  111 (369)
                      .-+++.+++|+|||+.+...+......+   .+++++.  +.+.-+.   +++..+....++.+.......         
T Consensus        98 ~vI~lvG~~GsGKTTt~~kLA~~l~~~G---~kVllv~~D~~r~~a~---eqL~~~~~~~gv~~~~~~~~~---------  162 (433)
T 3kl4_A           98 FIIMLVGVQGSGKTTTAGKLAYFYKKRG---YKVGLVAADVYRPAAY---DQLLQLGNQIGVQVYGEPNNQ---------  162 (433)
T ss_dssp             EEEEECCCTTSCHHHHHHHHHHHHHHTT---CCEEEEEECCSCHHHH---HHHHHHHHTTTCCEECCTTCS---------
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHcC---CeEEEEecCccchhHH---HHHHHHHHhcCCceeeccccC---------
Confidence            4578899999999987654444333322   2676666  2332222   223333333344332211111         


Q ss_pred             ccCCcEEEeccHHH-HHHHHcCCCCCCCccEEEEechhHhh---ccCcHHHHHHHHhhCCccCcEEEEEeeCChhHHHHH
Q 017573          112 QAGVHVVVGTPGRV-FDMLRRQSLRPDYIKMFVLDEADEML---SRGFKDQIYDIFQLLPAKVQVGVFSATMPPEALEIT  187 (369)
Q Consensus       112 ~~~~~iiv~t~~~l-~~~~~~~~~~~~~~~~viiDE~H~~~---~~~~~~~~~~~~~~~~~~~~~i~~saT~~~~~~~~~  187 (369)
                               .|..+ ...+..  .....++++|+|++-+..   +......+..+.....+...++.++|+...+.....
T Consensus       163 ---------dp~~i~~~al~~--a~~~~~DvvIIDTaGr~~~~~d~~lm~el~~i~~~~~pd~vlLVlDa~~gq~a~~~a  231 (433)
T 3kl4_A          163 ---------NPIEIAKKGVDI--FVKNKMDIIIVDTAGRHGYGEETKLLEEMKEMYDVLKPDDVILVIDASIGQKAYDLA  231 (433)
T ss_dssp             ---------CHHHHHHHHHHH--TTTTTCSEEEEEECCCSSSCCTTHHHHHHHHHHHHHCCSEEEEEEEGGGGGGGHHHH
T ss_pred             ---------CHHHHHHHHHHH--HHhcCCCEEEEECCCCccccCCHHHHHHHHHHHHhhCCcceEEEEeCccchHHHHHH
Confidence                     11111 112222  122347999999997643   223445555666666556666778888765554444


Q ss_pred             HHh
Q 017573          188 RKF  190 (369)
Q Consensus       188 ~~~  190 (369)
                      ..+
T Consensus       232 ~~f  234 (433)
T 3kl4_A          232 SRF  234 (433)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            433

>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA replication initation factor, cell cycle control factor; HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11 c.37.1.20

Probab=96.55  E-value=0.0027  Score=55.66  Aligned_cols=35  Identities=17%  Similarity=0.207  Sum_probs=21.8

Q ss_pred             cEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEc
Q 017573           35 DVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLA   71 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~   71 (369)
                      .+++.||+|+|||..+- .+...+.... +..++++.
T Consensus        46 ~~li~G~~G~GKTtl~~-~l~~~~~~~~-~~~~~~i~   80 (389)
T 1fnn_A           46 RATLLGRPGTGKTVTLR-KLWELYKDKT-TARFVYIN   80 (389)
T ss_dssp             EEEEECCTTSSHHHHHH-HHHHHHTTSC-CCEEEEEE
T ss_pred             eEEEECCCCCCHHHHHH-HHHHHHhhhc-CeeEEEEe
Confidence            79999999999997753 3333333221 22455554

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=96.49  E-value=0.0074  Score=46.51  Aligned_cols=21  Identities=29%  Similarity=0.204  Sum_probs=17.0

Q ss_pred             CCcEEEEcCCCChhhHHHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFCSG   53 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~   53 (369)
                      ..++++.||+|+|||..+...
T Consensus        43 ~~~vll~G~~G~GKT~la~~~   63 (187)
T 2p65_A           43 KNNPILLGDPGVGKTAIVEGL   63 (187)
T ss_dssp             SCEEEEESCGGGCHHHHHHHH
T ss_pred             CCceEEECCCCCCHHHHHHHH
Confidence            467999999999999775433

>1iqp_A RFCS; clamp loader, extended AAA-ATPase domain, complex with ADP, replication; HET: ADP; 2.80A {Pyrococcus furiosus} SCOP: a.80.1.1 c.37.1.20

Probab=96.49  E-value=0.0075  Score=51.36  Aligned_cols=38  Identities=18%  Similarity=0.348  Sum_probs=23.9

Q ss_pred             CccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEE
Q 017573          138 YIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFS  176 (369)
Q Consensus       138 ~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~s  176 (369)
                      ...++++||+|.+.... ...+..++...+....+++.+
T Consensus       110 ~~~vliiDe~~~l~~~~-~~~L~~~le~~~~~~~~i~~~  147 (327)
T 1iqp_A          110 SFKIIFLDEADALTQDA-QQALRRTMEMFSSNVRFILSC  147 (327)
T ss_dssp             SCEEEEEETGGGSCHHH-HHHHHHHHHHTTTTEEEEEEE
T ss_pred             CCeEEEEeCCCcCCHHH-HHHHHHHHHhcCCCCeEEEEe
Confidence            35799999999875332 344555566555555555533

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=96.48  E-value=0.0068  Score=50.56  Aligned_cols=20  Identities=25%  Similarity=0.217  Sum_probs=16.9

Q ss_pred             cCCcEEEEcCCCChhhHHHH
Q 017573           32 KGLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~   51 (369)
                      ...++++.||+|+|||..+-
T Consensus        50 ~~~~~ll~G~~GtGKT~la~   69 (285)
T 3h4m_A           50 PPKGILLYGPPGTGKTLLAK   69 (285)
T ss_dssp             CCSEEEEESSSSSSHHHHHH
T ss_pred             CCCeEEEECCCCCcHHHHHH
Confidence            45789999999999997753

>3eie_A Vacuolar protein sorting-associated protein 4; AAA ATPase, ATP-binding cassette, ATP-binding, endosome, MEM nucleotide-binding; 2.70A {Saccharomyces cerevisiae} PDB: 3eih_A* 2rko_A 3mhv_C

Probab=96.42  E-value=0.014  Score=49.59  Aligned_cols=19  Identities=21%  Similarity=0.212  Sum_probs=16.3

Q ss_pred             CCcEEEEcCCCChhhHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~   51 (369)
                      .+++++.||+|+|||..+-
T Consensus        51 ~~~vLl~GppGtGKT~la~   69 (322)
T 3eie_A           51 TSGILLYGPPGTGKSYLAK   69 (322)
T ss_dssp             CCEEEEECSSSSCHHHHHH
T ss_pred             CCeEEEECCCCCcHHHHHH
Confidence            4679999999999997763

>3dm5_A SRP54, signal recognition 54 kDa protein; protein-RNA, signal recognition particle, SRP-GTPase, protein targeting, cytoplasm, GTP-binding; HET: GDP; 2.51A {Pyrococcus furiosus}

Probab=96.39  E-value=0.039  Score=48.71  Aligned_cols=57  Identities=23%  Similarity=0.152  Sum_probs=32.8

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEc--CCHHHHHHHHHHHHHhccccCcEEE
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLA--PTRELAQQIEKVMRALGDYLGVKVH   96 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~--P~~~l~~q~~~~~~~~~~~~~~~v~   96 (369)
                      .-+++.+++|+|||+++...+......+   .+++++.  |.+.-+   .+++..+....++.+.
T Consensus       101 ~vIlivG~~G~GKTTt~~kLA~~l~~~G---~kVllv~~D~~R~aa---~eqL~~~~~~~gvpv~  159 (443)
T 3dm5_A          101 TILLMVGIQGSGKTTTVAKLARYFQKRG---YKVGVVCSDTWRPGA---YHQLRQLLDRYHIEVF  159 (443)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHTTT---CCEEEEECCCSSTHH---HHHHHHHHGGGTCEEE
T ss_pred             eEEEEECcCCCCHHHHHHHHHHHHHHCC---CeEEEEeCCCcchhH---HHHHHHHHHhcCCcEE
Confidence            4579999999999988655444333322   2676666  333322   2334444444455553

>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=96.33  E-value=0.024  Score=49.39  Aligned_cols=19  Identities=32%  Similarity=0.345  Sum_probs=16.2

Q ss_pred             CCcEEEEcCCCChhhHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~   51 (369)
                      +..+++.||+|+|||..+-
T Consensus        45 ~~~vli~G~~G~GKTtl~~   63 (386)
T 2qby_A           45 PNNIFIYGLTGTGKTAVVK   63 (386)
T ss_dssp             CCCEEEEECTTSSHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHH
Confidence            4679999999999997653

>1sxj_E Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=96.30  E-value=0.017  Score=49.91  Aligned_cols=42  Identities=10%  Similarity=0.271  Sum_probs=27.9

Q ss_pred             CccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEEeeCC
Q 017573          138 YIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMP  180 (369)
Q Consensus       138 ~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~saT~~  180 (369)
                      ..+++|+||+|.+ +......+..++...++...+++.|..+.
T Consensus       134 ~~~vlilDE~~~L-~~~~~~~L~~~le~~~~~~~~Il~t~~~~  175 (354)
T 1sxj_E          134 RYKCVIINEANSL-TKDAQAALRRTMEKYSKNIRLIMVCDSMS  175 (354)
T ss_dssp             CCEEEEEECTTSS-CHHHHHHHHHHHHHSTTTEEEEEEESCSC
T ss_pred             CCeEEEEeCcccc-CHHHHHHHHHHHHhhcCCCEEEEEeCCHH
Confidence            4689999999984 34445666677776666665665554443

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=96.26  E-value=0.079  Score=42.81  Aligned_cols=51  Identities=22%  Similarity=0.176  Sum_probs=33.5

Q ss_pred             ccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHH
Q 017573           31 CKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMR   85 (369)
Q Consensus        31 ~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~   85 (369)
                      ..|.-+++.||+|+|||..++..+......+.   +++++..... ..+..+.+.
T Consensus        21 ~~G~~~~i~G~~GsGKTtl~~~~~~~~~~~~~---~v~~~~~e~~-~~~~~~~~~   71 (247)
T 2dr3_A           21 PERNVVLLSGGPGTGKTIFSQQFLWNGLKMGE---PGIYVALEEH-PVQVRQNMA   71 (247)
T ss_dssp             ETTCEEEEEECTTSSHHHHHHHHHHHHHHTTC---CEEEEESSSC-HHHHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHHHhcCC---eEEEEEccCC-HHHHHHHHH
Confidence            45678899999999999886655555544332   7888775432 344444444

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.14  E-value=0.01  Score=51.56  Aligned_cols=18  Identities=39%  Similarity=0.331  Sum_probs=16.4

Q ss_pred             CCcEEEEcCCCChhhHHH
Q 017573           33 GLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~   50 (369)
                      .+++++.||+|+|||+.+
T Consensus       182 prGvLL~GPPGTGKTllA  199 (405)
T 4b4t_J          182 PKGVILYGPPGTGKTLLA  199 (405)
T ss_dssp             CCCEEEESCSSSSHHHHH
T ss_pred             CCceEEeCCCCCCHHHHH
Confidence            589999999999999875

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=96.10  E-value=0.025  Score=49.57  Aligned_cols=19  Identities=21%  Similarity=0.209  Sum_probs=16.5

Q ss_pred             CCcEEEEcCCCChhhHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~   51 (369)
                      ..++++.||+|+|||..+-
T Consensus       148 ~~~vLL~GppGtGKT~la~  166 (389)
T 3vfd_A          148 ARGLLLFGPPGNGKTMLAK  166 (389)
T ss_dssp             CSEEEEESSTTSCHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHH
Confidence            4789999999999997763

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=96.10  E-value=0.018  Score=49.01  Aligned_cols=19  Identities=21%  Similarity=0.144  Sum_probs=16.4

Q ss_pred             CCcEEEEcCCCChhhHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~   51 (369)
                      .+.+++.||+|+|||..+-
T Consensus        45 ~~~iLL~GppGtGKT~la~   63 (322)
T 1xwi_A           45 WRGILLFGPPGTGKSYLAK   63 (322)
T ss_dssp             CSEEEEESSSSSCHHHHHH
T ss_pred             CceEEEECCCCccHHHHHH
Confidence            4789999999999997753

>3cf0_A Transitional endoplasmic reticulum ATPase; AAA, P97/VCP, ERAD, CDC48, ATP-binding, lipid-binding, nucle binding, nucleus, phosphoprotein, transport; HET: ADP; 3.00A {Mus musculus}

Probab=96.09  E-value=0.032  Score=46.95  Aligned_cols=20  Identities=25%  Similarity=0.189  Sum_probs=17.0

Q ss_pred             cCCcEEEEcCCCChhhHHHH
Q 017573           32 KGLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~   51 (369)
                      .++.+++.||+|+|||..+-
T Consensus        48 ~~~~vLL~Gp~GtGKT~la~   67 (301)
T 3cf0_A           48 PSKGVLFYGPPGCGKTLLAK   67 (301)
T ss_dssp             CCSEEEEECSSSSSHHHHHH
T ss_pred             CCceEEEECCCCcCHHHHHH
Confidence            46789999999999997753

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.05  E-value=0.011  Score=52.18  Aligned_cols=18  Identities=28%  Similarity=0.259  Sum_probs=16.3

Q ss_pred             CCcEEEEcCCCChhhHHH
Q 017573           33 GLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~   50 (369)
                      .+++++.||+|+|||+.+
T Consensus       215 prGvLLyGPPGTGKTllA  232 (434)
T 4b4t_M          215 PKGALMYGPPGTGKTLLA  232 (434)
T ss_dssp             CCEEEEESCTTSSHHHHH
T ss_pred             CCeeEEECcCCCCHHHHH
Confidence            589999999999999775

>1njg_A DNA polymerase III subunit gamma; rossman-like fold, AAA+ ATPase domains, sensor 1, sensor 2, transferase; HET: DNA; 2.20A {Escherichia coli} SCOP: c.37.1.20 PDB: 1njf_A*

Probab=96.01  E-value=0.038  Score=44.50  Aligned_cols=17  Identities=24%  Similarity=0.280  Sum_probs=14.7

Q ss_pred             cEEEEcCCCChhhHHHH
Q 017573           35 DVIQQAQSGTGKTATFC   51 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~   51 (369)
                      .+++.||+|+|||..+-
T Consensus        47 ~~ll~G~~G~GKT~l~~   63 (250)
T 1njg_A           47 AYLFSGTRGVGKTSIAR   63 (250)
T ss_dssp             EEEEECSTTSCHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            58999999999997653

>1sxj_B Activator 1 37 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=95.96  E-value=0.017  Score=49.04  Aligned_cols=37  Identities=22%  Similarity=0.359  Sum_probs=22.8

Q ss_pred             ccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEE
Q 017573          139 IKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFS  176 (369)
Q Consensus       139 ~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~s  176 (369)
                      ..++|+||+|.+.... ...+..++...+....+++.|
T Consensus       108 ~~viiiDe~~~l~~~~-~~~L~~~le~~~~~~~~il~~  144 (323)
T 1sxj_B          108 HKIVILDEADSMTAGA-QQALRRTMELYSNSTRFAFAC  144 (323)
T ss_dssp             CEEEEEESGGGSCHHH-HHTTHHHHHHTTTTEEEEEEE
T ss_pred             ceEEEEECcccCCHHH-HHHHHHHHhccCCCceEEEEe
Confidence            5799999999875332 334445555555555555544

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=95.94  E-value=0.023  Score=47.67  Aligned_cols=19  Identities=21%  Similarity=0.212  Sum_probs=16.5

Q ss_pred             CCcEEEEcCCCChhhHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~   51 (369)
                      .+.+++.||+|+|||..+-
T Consensus        54 ~~~vll~Gp~GtGKT~la~   72 (297)
T 3b9p_A           54 AKGLLLFGPPGNGKTLLAR   72 (297)
T ss_dssp             CSEEEEESSSSSCHHHHHH
T ss_pred             CCeEEEECcCCCCHHHHHH
Confidence            5789999999999997753

>2qp9_X Vacuolar protein sorting-associated protein 4; ATPase domain, beta domain, C-terminal helix, ATP-binding, E nucleotide-binding; 2.90A {Saccharomyces cerevisiae} PDB: 2qpa_A*

Probab=95.94  E-value=0.04  Score=47.55  Aligned_cols=19  Identities=21%  Similarity=0.212  Sum_probs=16.3

Q ss_pred             CCcEEEEcCCCChhhHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~   51 (369)
                      .+++++.||+|+|||..+-
T Consensus        84 ~~~iLL~GppGtGKT~la~  102 (355)
T 2qp9_X           84 TSGILLYGPPGTGKSYLAK  102 (355)
T ss_dssp             CCCEEEECSTTSCHHHHHH
T ss_pred             CceEEEECCCCCcHHHHHH
Confidence            3679999999999998764

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=95.91  E-value=0.025  Score=49.84  Aligned_cols=18  Identities=33%  Similarity=0.361  Sum_probs=16.2

Q ss_pred             CCcEEEEcCCCChhhHHH
Q 017573           33 GLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~   50 (369)
                      .+.+++.||+|+|||+.+
T Consensus       206 prGiLL~GPPGtGKT~la  223 (428)
T 4b4t_K          206 PRGVLLYGPPGTGKTMLV  223 (428)
T ss_dssp             CCEEEEESCTTTTHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            578999999999999875

>1jr3_A DNA polymerase III subunit gamma; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1xxh_B* 3glh_B* 3glf_B* 3gli_B* 3glg_B* 1xxi_B*

Probab=95.88  E-value=0.018  Score=50.12  Aligned_cols=36  Identities=14%  Similarity=0.299  Sum_probs=21.7

Q ss_pred             ccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEE
Q 017573          139 IKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVF  175 (369)
Q Consensus       139 ~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~  175 (369)
                      ..++|+||+|.+.... ...+...+...+....+++.
T Consensus       120 ~~vliiDe~~~l~~~~-~~~Ll~~le~~~~~~~~Il~  155 (373)
T 1jr3_A          120 FKVYLIDEVHMLSRHS-FNALLKTLEEPPEHVKFLLA  155 (373)
T ss_dssp             SEEEEEECGGGSCHHH-HHHHHHHHHSCCSSEEEEEE
T ss_pred             eEEEEEECcchhcHHH-HHHHHHHHhcCCCceEEEEE
Confidence            5799999999875332 34445555554444444443

>2qz4_A Paraplegin; AAA+, SPG7, protease, ADP, structural genomics, structural G consortium, SGC, ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.22A {Homo sapiens}

Probab=95.88  E-value=0.1  Score=42.60  Aligned_cols=19  Identities=21%  Similarity=0.136  Sum_probs=16.3

Q ss_pred             CCcEEEEcCCCChhhHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~   51 (369)
                      .+.+++.||+|+|||..+-
T Consensus        39 ~~~vll~G~~GtGKT~la~   57 (262)
T 2qz4_A           39 PKGALLLGPPGCGKTLLAK   57 (262)
T ss_dssp             CCEEEEESCTTSSHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHH
Confidence            4679999999999997753

>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=95.76  E-value=0.035  Score=46.72  Aligned_cols=38  Identities=8%  Similarity=0.183  Sum_probs=24.2

Q ss_pred             CccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEE
Q 017573          138 YIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFS  176 (369)
Q Consensus       138 ~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~s  176 (369)
                      ..+++|+||+|.+.... ...+.+.+..-++...+++.|
T Consensus        82 ~~kvviIdead~lt~~a-~naLLk~LEep~~~t~fIl~t  119 (305)
T 2gno_A           82 TRKYVIVHDCERMTQQA-ANAFLKALEEPPEYAVIVLNT  119 (305)
T ss_dssp             SSEEEEETTGGGBCHHH-HHHTHHHHHSCCTTEEEEEEE
T ss_pred             CceEEEeccHHHhCHHH-HHHHHHHHhCCCCCeEEEEEE
Confidence            46899999999985433 344555556555555555444

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=95.68  E-value=0.024  Score=49.59  Aligned_cols=18  Identities=39%  Similarity=0.331  Sum_probs=16.3

Q ss_pred             CCcEEEEcCCCChhhHHH
Q 017573           33 GLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~   50 (369)
                      .+.+++.||+|+|||+.+
T Consensus       216 prGvLLyGPPGTGKTlLA  233 (437)
T 4b4t_I          216 PKGVILYGAPGTGKTLLA  233 (437)
T ss_dssp             CSEEEEESSTTTTHHHHH
T ss_pred             CCCCceECCCCchHHHHH
Confidence            588999999999999875

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=95.64  E-value=0.019  Score=50.73  Aligned_cols=18  Identities=33%  Similarity=0.309  Sum_probs=16.4

Q ss_pred             CCcEEEEcCCCChhhHHH
Q 017573           33 GLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~   50 (369)
                      .+.+++.||+|+|||+.+
T Consensus       215 prGvLL~GPPGtGKTllA  232 (437)
T 4b4t_L          215 PKGVLLYGPPGTGKTLLA  232 (437)
T ss_dssp             CCEEEEESCTTSSHHHHH
T ss_pred             CCeEEEECCCCCcHHHHH
Confidence            589999999999999875

>3hu3_A Transitional endoplasmic reticulum ATPase; VCP, transport protein; HET: AGS; 2.20A {Homo sapiens} PDB: 3hu2_A* 3hu1_A* 1e32_A* 1s3s_A*

Probab=95.58  E-value=0.063  Score=48.40  Aligned_cols=42  Identities=24%  Similarity=0.390  Sum_probs=27.7

Q ss_pred             cEEEEechhHhhccC----------cHHHHHHHHhhCCccCcEEEEEeeCCh
Q 017573          140 KMFVLDEADEMLSRG----------FKDQIYDIFQLLPAKVQVGVFSATMPP  181 (369)
Q Consensus       140 ~~viiDE~H~~~~~~----------~~~~~~~~~~~~~~~~~~i~~saT~~~  181 (369)
                      +++++||+|.+....          ....+...+........++++.||-.+
T Consensus       299 ~iLfLDEId~l~~~~~~~~~~~~~~~~~~LL~~ld~~~~~~~v~vIaaTn~~  350 (489)
T 3hu3_A          299 AIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRP  350 (489)
T ss_dssp             EEEEEESHHHHCBCTTSCCCHHHHHHHHHHHHHHHHSCTTSCEEEEEEESCG
T ss_pred             cEEEecchhhhccccccccchHHHHHHHHHHHHhhccccCCceEEEEecCCc
Confidence            689999999886421          123444555555556667777888654

>2zan_A Vacuolar protein sorting-associating protein 4B; SKD1, VPS4B, AAA ATPase, ATP-binding, coiled coil, membrane, nucleotide-binding, phosphorylation; HET: ATP; 3.00A {Mus musculus} PDB: 2zam_A* 2zao_A* 2jqh_A 2jqk_A 1wr0_A 2jq9_A 2k3w_A 1yxr_A

Probab=95.55  E-value=0.077  Score=47.29  Aligned_cols=19  Identities=21%  Similarity=0.144  Sum_probs=16.3

Q ss_pred             CCcEEEEcCCCChhhHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~   51 (369)
                      .+.+++.||+|+|||..+-
T Consensus       167 ~~~vLL~GppGtGKT~lA~  185 (444)
T 2zan_A          167 WRGILLFGPPGTGKSYLAK  185 (444)
T ss_dssp             CSEEEEECSTTSSHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHH
Confidence            4789999999999997763

>2chq_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATP ATP-binding, nucleotide-binding; HET: ANP; 3.5A {Archaeoglobus fulgidus} PDB: 2chv_A

Probab=95.47  E-value=0.016  Score=49.03  Aligned_cols=17  Identities=41%  Similarity=0.515  Sum_probs=14.9

Q ss_pred             cEEEEcCCCChhhHHHH
Q 017573           35 DVIQQAQSGTGKTATFC   51 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~   51 (369)
                      ++++.||+|+|||..+-
T Consensus        40 ~~ll~G~~G~GKt~la~   56 (319)
T 2chq_A           40 HLLFSGPPGTGKTATAI   56 (319)
T ss_dssp             CEEEESSSSSSHHHHHH
T ss_pred             eEEEECcCCcCHHHHHH
Confidence            59999999999997753

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=95.45  E-value=0.01  Score=52.95  Aligned_cols=18  Identities=33%  Similarity=0.298  Sum_probs=15.3

Q ss_pred             CcEEEEcCCCChhhHHHH
Q 017573           34 LDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~   51 (369)
                      .+++++||+|+|||..+-
T Consensus        51 ~~vLL~GppGtGKTtlAr   68 (447)
T 3pvs_A           51 HSMILWGPPGTGKTTLAE   68 (447)
T ss_dssp             CEEEEECSTTSSHHHHHH
T ss_pred             cEEEEECCCCCcHHHHHH
Confidence            468999999999997753

>1sxj_C Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=95.45  E-value=0.048  Score=46.74  Aligned_cols=38  Identities=21%  Similarity=0.369  Sum_probs=25.2

Q ss_pred             CccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEE
Q 017573          138 YIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFS  176 (369)
Q Consensus       138 ~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~s  176 (369)
                      ..+++|+||+|.+... ....+..++...+....+++.+
T Consensus       110 ~~~viiiDe~~~l~~~-~~~~L~~~le~~~~~~~~il~~  147 (340)
T 1sxj_C          110 GFKLIILDEADAMTNA-AQNALRRVIERYTKNTRFCVLA  147 (340)
T ss_dssp             SCEEEEETTGGGSCHH-HHHHHHHHHHHTTTTEEEEEEE
T ss_pred             CceEEEEeCCCCCCHH-HHHHHHHHHhcCCCCeEEEEEe
Confidence            3689999999987543 2455666666666566555443

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=95.41  E-value=0.035  Score=49.10  Aligned_cols=19  Identities=26%  Similarity=0.291  Sum_probs=16.7

Q ss_pred             cCCcEEEEcCCCChhhHHH
Q 017573           32 KGLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~   50 (369)
                      ..+.+|+.||+|+|||+.+
T Consensus       242 pprGILLyGPPGTGKTlLA  260 (467)
T 4b4t_H          242 PPKGILLYGPPGTGKTLCA  260 (467)
T ss_dssp             CCSEEEECSCTTSSHHHHH
T ss_pred             CCCceEeeCCCCCcHHHHH
Confidence            3589999999999999775

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=95.30  E-value=0.087  Score=46.99  Aligned_cols=41  Identities=17%  Similarity=-0.054  Sum_probs=28.4

Q ss_pred             ccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCC
Q 017573           31 CKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPT   73 (369)
Q Consensus        31 ~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~   73 (369)
                      ..|.-+++.|++|+|||..++..+.+.....  +.+++|+..-
T Consensus       198 ~~G~l~ii~G~pg~GKT~lal~ia~~~a~~~--g~~vl~~slE  238 (444)
T 2q6t_A          198 GPGSLNIIAARPAMGKTAFALTIAQNAALKE--GVGVGIYSLE  238 (444)
T ss_dssp             CTTCEEEEEECTTSCHHHHHHHHHHHHHHTT--CCCEEEEESS
T ss_pred             CCCcEEEEEeCCCCCHHHHHHHHHHHHHHhC--CCeEEEEECC
Confidence            3456789999999999987766666554321  2268887653

>3hjh_A Transcription-repair-coupling factor; MFD, mutation frequency decline, ATP-binding, DNA DAMA repair, DNA-binding, helicase, hydrolase; 1.95A {Escherichia coli} PDB: 2b2n_A* 4dfc_A

Probab=95.29  E-value=0.12  Score=46.32  Aligned_cols=76  Identities=14%  Similarity=0.078  Sum_probs=53.2

Q ss_pred             HHHHHHHHHhccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCC
Q 017573          223 LETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQ  302 (369)
Q Consensus       223 ~~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~  302 (369)
                      ...+..+++. .+.++++.+.+...++.+.+.|...+......... .         .+.  .-.+.++...+..|+-+|
T Consensus       371 ~~~L~~~~~~-~~~rVvi~a~s~~r~erL~~~L~~~~i~~~~~~~~-~---------~~~--~g~v~i~~g~L~~GF~~p  437 (483)
T 3hjh_A          371 LDALRKFLET-FDGPVVFSVESEGRREALGELLARIKIAPQRIMRL-D---------EAS--DRGRYLMIGAAEHGFVDT  437 (483)
T ss_dssp             THHHHHHHHH-CCSCEEEEESCSSTTTTTHHHHGGGTCCCEECSCG-G---------GCC--TTCEEEEESCCCSCEEET
T ss_pred             HHHHHHHHHh-CCCeEEEEeCChHHHHHHHHHHHHcCCCceecCch-h---------hcC--CCcEEEEEcccccCcccC
Confidence            3455555543 24689999999999999999999887765443221 1         112  234778888899999999


Q ss_pred             CCcEEEEec
Q 017573          303 QVSLVINYD  311 (369)
Q Consensus       303 ~~~~vi~~~  311 (369)
                      ....+++.+
T Consensus       438 ~~klaVITE  446 (483)
T 3hjh_A          438 VRNLALICE  446 (483)
T ss_dssp             TTTEEEEEH
T ss_pred             CCCEEEEEc
Confidence            888887754

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=95.29  E-value=0.094  Score=46.91  Aligned_cols=42  Identities=17%  Similarity=0.069  Sum_probs=29.0

Q ss_pred             cccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCC
Q 017573           30 FCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPT   73 (369)
Q Consensus        30 ~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~   73 (369)
                      +..|.-+++.|++|+|||..++..+.+.....  +.+++|+..-
T Consensus       200 l~~G~liiI~G~pG~GKTtl~l~ia~~~~~~~--g~~Vl~~s~E  241 (454)
T 2r6a_A          200 FQRSDLIIVAARPSVGKTAFALNIAQNVATKT--NENVAIFSLE  241 (454)
T ss_dssp             BCTTCEEEEECCTTSCHHHHHHHHHHHHHHHS--SCCEEEEESS
T ss_pred             CCCCCEEEEECCCCCCHHHHHHHHHHHHHHhC--CCcEEEEECC
Confidence            34567789999999999987766655554322  2268887743

>1w5s_A Origin recognition complex subunit 2 ORC2; replication, CDC6, DNA replication initiation, DNA BIND protein, AAA+ ATPase; HET: ADP; 2.4A {Aeropyrum pernix} SCOP: a.4.5.11 c.37.1.20 PDB: 1w5t_A*

Probab=95.27  E-value=0.035  Score=48.88  Aligned_cols=18  Identities=28%  Similarity=0.362  Sum_probs=14.8

Q ss_pred             CcEEE--EcCCCChhhHHHH
Q 017573           34 LDVIQ--QAQSGTGKTATFC   51 (369)
Q Consensus        34 ~~~li--~~~tG~GKT~~~~   51 (369)
                      ..+++  .||+|+|||..+-
T Consensus        51 ~~~li~i~G~~G~GKT~L~~   70 (412)
T 1w5s_A           51 VNMIYGSIGRVGIGKTTLAK   70 (412)
T ss_dssp             EEEEEECTTCCSSSHHHHHH
T ss_pred             CEEEEeCcCcCCCCHHHHHH
Confidence            46788  8999999997654

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=95.21  E-value=0.069  Score=45.65  Aligned_cols=18  Identities=22%  Similarity=0.263  Sum_probs=15.8

Q ss_pred             CcEEEEcCCCChhhHHHH
Q 017573           34 LDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~   51 (369)
                      .++++.||+|+|||..+-
T Consensus        56 ~~vll~G~~GtGKT~la~   73 (338)
T 3pfi_A           56 DHILFSGPAGLGKTTLAN   73 (338)
T ss_dssp             CCEEEECSTTSSHHHHHH
T ss_pred             CeEEEECcCCCCHHHHHH
Confidence            589999999999998753

>3io5_A Recombination and repair protein; storage dimer, inactive conformation, RECA like core domain, binding, DNA damage, DNA recombination; 2.40A {Enterobacteria phage T4}

Probab=94.95  E-value=0.026  Score=47.19  Aligned_cols=42  Identities=10%  Similarity=-0.080  Sum_probs=30.5

Q ss_pred             cEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHH
Q 017573           35 DVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELA   77 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~   77 (369)
                      .+++.+|+|+|||..++..+.+....+ .+.+++|+..-.++.
T Consensus        30 iteI~G~pGsGKTtL~Lq~~~~~~~~g-~g~~vlyId~E~s~~   71 (333)
T 3io5_A           30 LLILAGPSKSFKSNFGLTMVSSYMRQY-PDAVCLFYDSEFGIT   71 (333)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHHHHHC-TTCEEEEEESSCCCC
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHhcC-CCceEEEEeccchhh
Confidence            579999999999988777766655432 123899988765553

>1n0w_A DNA repair protein RAD51 homolog 1; DNA repair, homologous recombination, breast cancer susceptibility, RECA-like ATPase, protein complex; HET: DNA MSE; 1.70A {Homo sapiens} SCOP: c.37.1.11

Probab=94.88  E-value=0.22  Score=40.08  Aligned_cols=44  Identities=14%  Similarity=-0.108  Sum_probs=27.5

Q ss_pred             cccCCcEEEEcCCCChhhHHHHHHHHHhhhcc---CCCccEEEEcCC
Q 017573           30 FCKGLDVIQQAQSGTGKTATFCSGILQQLDYG---LVQCQALVLAPT   73 (369)
Q Consensus        30 ~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~---~~~~~~liv~P~   73 (369)
                      +..|.-+.+.+|+|+|||..+...+...+...   ..+..++++...
T Consensus        21 i~~G~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~g~~~~~~~~i~~~   67 (243)
T 1n0w_A           21 IETGSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTE   67 (243)
T ss_dssp             EETTSEEEEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESS
T ss_pred             CcCCeEEEEECCCCCcHHHHHHHHHHHHhCchhcCCCCCeEEEEECC
Confidence            34567889999999999987655554322211   012267776543

>2ce7_A Cell division protein FTSH; metalloprotease; HET: ADP; 2.44A {Thermotoga maritima} SCOP: a.269.1.1 c.37.1.20 PDB: 2cea_A* 3kds_E*

Probab=94.77  E-value=0.051  Score=48.66  Aligned_cols=18  Identities=28%  Similarity=0.307  Sum_probs=15.7

Q ss_pred             CCcEEEEcCCCChhhHHH
Q 017573           33 GLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~   50 (369)
                      .+.+++.+|+|+|||..+
T Consensus        49 p~gvLL~GppGtGKT~La   66 (476)
T 2ce7_A           49 PKGILLVGPPGTGKTLLA   66 (476)
T ss_dssp             CSEEEEECCTTSSHHHHH
T ss_pred             CCeEEEECCCCCCHHHHH
Confidence            367999999999999775

>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=94.50  E-value=0.19  Score=48.01  Aligned_cols=80  Identities=20%  Similarity=0.187  Sum_probs=65.3

Q ss_pred             cCCCeEEEeCCHhhHHHHHHHHh----hCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEec-CCcCCCCCCCCcEEE
Q 017573          234 AITQSVIFVNTRRKVDWLTDKMR----SRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTD-LLARGIDVQQVSLVI  308 (369)
Q Consensus       234 ~~~k~lv~~~~~~~~~~~~~~l~----~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~-~~~~G~d~~~~~~vi  308 (369)
                      .+.++++.+|++.-+...++.+.    ..+.++..++|+++..++...++...+|+.+|+|+|. .+...+++.++..||
T Consensus       416 ~g~qvlvlaPtr~La~Q~~~~l~~~~~~~gi~v~~l~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~~~~~~~l~lVV  495 (780)
T 1gm5_A          416 AGFQTAFMVPTSILAIQHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQEDVHFKNLGLVI  495 (780)
T ss_dssp             HTSCEEEECSCHHHHHHHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHHCCCCSCCCEEE
T ss_pred             cCCeEEEEeCcHHHHHHHHHHHHHHhhhcCceEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhhhhhccCCceEE
Confidence            35689999999988776666554    3478999999999999999999999999999999998 344457778888888


Q ss_pred             EecCC
Q 017573          309 NYDLP  313 (369)
Q Consensus       309 ~~~~~  313 (369)
                      +-+..
T Consensus       496 IDEaH  500 (780)
T 1gm5_A          496 IDEQH  500 (780)
T ss_dssp             EESCC
T ss_pred             ecccc
Confidence            76654

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=93.93  E-value=0.061  Score=45.33  Aligned_cols=36  Identities=14%  Similarity=0.144  Sum_probs=24.0

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhh-hccCCCccEEEEc
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQL-DYGLVQCQALVLA   71 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~-~~~~~~~~~liv~   71 (369)
                      ++++++.||+|+|||..+...+.... ..+.   +++++.
T Consensus       152 ~~~lll~G~~GtGKT~La~aia~~~~~~~g~---~v~~~~  188 (308)
T 2qgz_A          152 QKGLYLYGDMGIGKSYLLAAMAHELSEKKGV---STTLLH  188 (308)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHHHHHSCC---CEEEEE
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHHhcCC---cEEEEE
Confidence            57899999999999987654444333 3322   555554

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=93.92  E-value=0.1  Score=49.77  Aligned_cols=18  Identities=28%  Similarity=0.314  Sum_probs=16.1

Q ss_pred             CCcEEEEcCCCChhhHHH
Q 017573           33 GLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~   50 (369)
                      .+.+++.+|+|+|||+.+
T Consensus       238 p~GILL~GPPGTGKT~LA  255 (806)
T 3cf2_A          238 PRGILLYGPPGTGKTLIA  255 (806)
T ss_dssp             CCEEEEECCTTSCHHHHH
T ss_pred             CCeEEEECCCCCCHHHHH
Confidence            478999999999999775

>1ls1_A Signal recognition particle protein; FFH, SRP54, SRP, GTPase, ultrahigh resolution, protein transport; 1.10A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 1jpn_B* 1jpj_A* 1ry1_U* 2j45_A* 1o87_A* 2c04_A* 2j46_A* 1rj9_B* 2c03_A* 2j7p_A* 1okk_A* 2cnw_A* 1ng1_A* 2xkv_A 3ng1_A 1ffh_A 2ng1_A*

Probab=93.87  E-value=1.5  Score=36.56  Aligned_cols=37  Identities=24%  Similarity=0.148  Sum_probs=22.9

Q ss_pred             cCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEc
Q 017573           32 KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLA   71 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~   71 (369)
                      .++-+.+.++.|+|||..+...+......+   .+++++-
T Consensus        97 ~~~~i~i~g~~G~GKTT~~~~la~~~~~~~---~~v~l~~  133 (295)
T 1ls1_A           97 DRNLWFLVGLQGSGKTTTAAKLALYYKGKG---RRPLLVA  133 (295)
T ss_dssp             SSEEEEEECCTTTTHHHHHHHHHHHHHHTT---CCEEEEE
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHcC---CeEEEec
Confidence            455677889999999976544333222222   2666655

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=93.75  E-value=0.18  Score=48.24  Aligned_cols=18  Identities=28%  Similarity=0.272  Sum_probs=15.9

Q ss_pred             CCcEEEEcCCCChhhHHH
Q 017573           33 GLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~   50 (369)
                      .+.+++.+|+|+|||+.+
T Consensus       511 ~~gvLl~GPPGtGKT~lA  528 (806)
T 3cf2_A          511 SKGVLFYGPPGCGKTLLA  528 (806)
T ss_dssp             CSCCEEESSTTSSHHHHH
T ss_pred             CceEEEecCCCCCchHHH
Confidence            478999999999999765

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=93.45  E-value=0.43  Score=41.96  Aligned_cols=80  Identities=10%  Similarity=0.184  Sum_probs=64.3

Q ss_pred             ccCCCeEEEeCCHhhHHHHHHHHhh---CCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCc----CCCCCCCCc
Q 017573          233 LAITQSVIFVNTRRKVDWLTDKMRS---RDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLA----RGIDVQQVS  305 (369)
Q Consensus       233 ~~~~k~lv~~~~~~~~~~~~~~l~~---~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~----~G~d~~~~~  305 (369)
                      ..+.++++.+|++.-+..+++.+++   .+.++..++|+.+..++....+.+..|+.+|+|+|+..-    .-++...++
T Consensus        62 ~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~l~~~~~~Iiv~Tp~~l~~~l~~~~~~~~~  141 (414)
T 3oiy_A           62 RKGKKSALVFPTVTLVKQTLERLQKLADEKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREKLSQKRFD  141 (414)
T ss_dssp             TTTCCEEEEESSHHHHHHHHHHHHHHCCSSCCEEECCTTSCHHHHHHHHHHHHHTCCSEEEEEHHHHHHCHHHHTTCCCS
T ss_pred             cCCCEEEEEECCHHHHHHHHHHHHHHccCCceEEEEECCCChhhHHHHHHHhhcCCCCEEEECHHHHHHHHHHhcccccc
Confidence            3557899999999999999998888   577999999999998888888999999899999997221    114445777


Q ss_pred             EEEEecC
Q 017573          306 LVINYDL  312 (369)
Q Consensus       306 ~vi~~~~  312 (369)
                      .+|+-+.
T Consensus       142 ~iViDEa  148 (414)
T 3oiy_A          142 FVFVDDV  148 (414)
T ss_dssp             EEEESCH
T ss_pred             EEEEeCh
Confidence            8876554

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=93.31  E-value=0.18  Score=48.31  Aligned_cols=17  Identities=29%  Similarity=0.302  Sum_probs=15.0

Q ss_pred             cEEEEcCCCChhhHHHH
Q 017573           35 DVIQQAQSGTGKTATFC   51 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~   51 (369)
                      ++++.||+|+|||..+-
T Consensus       523 ~~Ll~Gp~GtGKT~lA~  539 (758)
T 3pxi_A          523 SFIFLGPTGVGKTELAR  539 (758)
T ss_dssp             EEEEESCTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            59999999999998764

>2fna_A Conserved hypothetical protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE ADP; 2.00A {Sulfolobus solfataricus} SCOP: a.4.5.11 c.37.1.20

Probab=93.31  E-value=2.8  Score=35.54  Aligned_cols=29  Identities=10%  Similarity=0.026  Sum_probs=19.9

Q ss_pred             hhhhhhhccccCCcEEEEcCCCChhhHHHH
Q 017573           22 IQQRGIVPFCKGLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        22 ~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~   51 (369)
                      -+.+.+.. .....++|.||.|+|||..+.
T Consensus        20 ~el~~L~~-l~~~~v~i~G~~G~GKT~L~~   48 (357)
T 2fna_A           20 KEIEKLKG-LRAPITLVLGLRRTGKSSIIK   48 (357)
T ss_dssp             HHHHHHHH-TCSSEEEEEESTTSSHHHHHH
T ss_pred             HHHHHHHH-hcCCcEEEECCCCCCHHHHHH
Confidence            33344444 333689999999999997653

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=93.06  E-value=0.085  Score=42.73  Aligned_cols=51  Identities=20%  Similarity=0.204  Sum_probs=32.1

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRA   86 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~   86 (369)
                      |.-+++.|++|+|||..++-.+.+.+.....  +++|++-.. -..+..+.+..
T Consensus        30 G~l~~i~G~pG~GKT~l~l~~~~~~~~~~~~--~v~~~s~E~-~~~~~~~~~~~   80 (251)
T 2zts_A           30 GTTVLLTGGTGTGKTTFAAQFIYKGAEEYGE--PGVFVTLEE-RARDLRREMAS   80 (251)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHHHHHHHHCC--CEEEEESSS-CHHHHHHHHHT
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHHhcCC--CceeecccC-CHHHHHHHHHH
Confidence            4668999999999998776666554433221  677776432 23444444443

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=91.97  E-value=0.17  Score=42.68  Aligned_cols=52  Identities=15%  Similarity=-0.035  Sum_probs=33.8

Q ss_pred             cccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHH
Q 017573           30 FCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMR   85 (369)
Q Consensus        30 ~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~   85 (369)
                      +..|.-+++.|++|+|||..++..+.+....+   .+++|++.- .-..|+..++.
T Consensus        65 l~~G~l~li~G~pG~GKTtl~l~ia~~~a~~g---~~vl~~slE-~s~~~l~~R~~  116 (315)
T 3bh0_A           65 YKRRNFVLIAARPSMGKTAFALKQAKNMSDND---DVVNLHSLE-MGKKENIKRLI  116 (315)
T ss_dssp             BCTTCEEEEECCTTSSHHHHHHHHHHHHHTTT---CEEEEEESS-SCHHHHHHHHH
T ss_pred             CCCCcEEEEEeCCCCCHHHHHHHHHHHHHHcC---CeEEEEECC-CCHHHHHHHHH
Confidence            44567799999999999987766666555443   278887743 23344444443

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=91.97  E-value=0.17  Score=40.34  Aligned_cols=40  Identities=23%  Similarity=0.225  Sum_probs=26.5

Q ss_pred             cccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcC
Q 017573           30 FCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAP   72 (369)
Q Consensus        30 ~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P   72 (369)
                      +..|.-+++.+|+|+|||..+...+......+.   +++++..
T Consensus        20 i~~G~~~~i~G~~GsGKTtl~~~l~~~~~~~~~---~v~~~~~   59 (235)
T 2w0m_A           20 IPQGFFIALTGEPGTGKTIFSLHFIAKGLRDGD---PCIYVTT   59 (235)
T ss_dssp             EETTCEEEEECSTTSSHHHHHHHHHHHHHHHTC---CEEEEES
T ss_pred             CcCCCEEEEEcCCCCCHHHHHHHHHHHHHHCCC---eEEEEEc
Confidence            455678899999999999765444433333222   6777654

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=91.57  E-value=0.24  Score=48.20  Aligned_cols=20  Identities=25%  Similarity=0.280  Sum_probs=16.4

Q ss_pred             CCcEEEEcCCCChhhHHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFCS   52 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~   52 (369)
                      ..++++.||+|+|||..+-.
T Consensus       191 ~~~vlL~G~pG~GKT~la~~  210 (854)
T 1qvr_A          191 KNNPVLIGEPGVGKTAIVEG  210 (854)
T ss_dssp             CCCCEEEECTTSCHHHHHHH
T ss_pred             CCceEEEcCCCCCHHHHHHH
Confidence            35799999999999977543

>1w36_B RECB, exodeoxyribonuclease V beta chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 c.52.1.24 PDB: 3k70_B*

Probab=91.54  E-value=0.39  Score=48.56  Aligned_cols=55  Identities=25%  Similarity=0.171  Sum_probs=43.4

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHhhhcc---------CCCccEEEEcCCHHHHHHHHHHHHHhc
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQLDYG---------LVQCQALVLAPTRELAQQIEKVMRALG   88 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~~~~~---------~~~~~~liv~P~~~l~~q~~~~~~~~~   88 (369)
                      +..+|.|+.|||||.+...-++..+...         -.-.++|+|+=|++-+.++.+++++..
T Consensus        17 g~~lV~AsAGSGKT~~L~~r~lrLll~~g~~~~~~~~~~~~~ILvvTFT~aAA~EMr~RI~~~L   80 (1180)
T 1w36_B           17 GERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLVVTFTEAATAELRGRIRSNI   80 (1180)
T ss_dssp             SCEEEECCTTSCHHHHHHHHHHHHHTTCSSSSSCSSCCCGGGEEEEESCHHHHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCHHHHHHHHHHHHHhcCCcccccCCCCCHHHEEEEeccHHHHHHHHHHHHHHH
Confidence            4569999999999999887777777531         122379999999999999988887643

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=91.50  E-value=0.21  Score=39.54  Aligned_cols=28  Identities=32%  Similarity=0.396  Sum_probs=21.8

Q ss_pred             cEEEEcCCCChhhHHHHHHHHHhhhccC
Q 017573           35 DVIQQAQSGTGKTATFCSGILQQLDYGL   62 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~~~~~~~~~~~~   62 (369)
                      ++++.++.|+|||..++..+......+.
T Consensus         8 ~I~~~~kgGvGKTt~a~~la~~l~~~G~   35 (228)
T 2r8r_A            8 KVFLGAAPGVGKTYAMLQAAHAQLRQGV   35 (228)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHHHHHTTC
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHCCC
Confidence            5899999999999987766666555543

>3u4q_B ATP-dependent helicase/deoxyribonuclease subunit; helicase, nuclease, double strand DNA repair, protein-DNA CO hydrolase-DNA complex; HET: DNA; 2.80A {Bacillus subtilis} PDB: 3u44_B*

Probab=91.46  E-value=0.15  Score=51.51  Aligned_cols=50  Identities=20%  Similarity=0.234  Sum_probs=36.4

Q ss_pred             EEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHH
Q 017573           36 VIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRA   86 (369)
Q Consensus        36 ~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~   86 (369)
                      -+|.|+.|||||.+++--+...+..+..+.+++++||... .-++.+.+.+
T Consensus         4 ~lV~agAGSGKT~~l~~ri~~ll~~~~~~~~il~lVP~q~-TFt~~~rl~~   53 (1166)
T 3u4q_B            4 EFLVGRSGSGKTKLIINSIQDELRRAPFGKPIIFLVPDQM-TFLMEYELAK   53 (1166)
T ss_dssp             EEEEECTTSSHHHHHHHHHHHHHHHCTTSSCEEEECCGGG-HHHHHHHHTC
T ss_pred             EEEEeCCCCChHHHHHHHHHHHHHhCCCCCcEEEEecCcc-cHHHHHHHHH
Confidence            3789999999999988888777766555458999999753 3334444443

>2ffh_A Protein (FFH); SRP54, signal recognition particle, GTPase, M domain, RNA-binding, signal sequence-binding, helix-turn-helix, protein targeting; 3.20A {Thermus aquaticus} SCOP: a.24.13.1 a.36.1.1 c.37.1.10 PDB: 2iy3_A

Probab=91.33  E-value=3.5  Score=36.25  Aligned_cols=36  Identities=22%  Similarity=0.077  Sum_probs=22.9

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEc
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLA   71 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~   71 (369)
                      ++-+.+.++.|+|||+.+...+......   +.+++++.
T Consensus        98 ~~vi~i~G~~GsGKTT~~~~LA~~l~~~---g~~Vllvd  133 (425)
T 2ffh_A           98 RNLWFLVGLQGSGKTTTAAKLALYYKGK---GRRPLLVA  133 (425)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHHHHHTT---TCCEEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHc---CCeEEEee
Confidence            4457788999999998765444333222   22666665

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}

Probab=91.26  E-value=2  Score=31.90  Aligned_cols=72  Identities=14%  Similarity=0.277  Sum_probs=52.0

Q ss_pred             cEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHH----ccCCcEEEeccHHHHHHHHcCCCCCCCccE
Q 017573           66 QALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL----QAGVHVVVGTPGRVFDMLRRQSLRPDYIKM  141 (369)
Q Consensus        66 ~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~----~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~  141 (369)
                      ++||.|+++..+..+.+.+.+.    +..+..++++.........+    .+...|+|+|.     . ...+++...+++
T Consensus        37 ~~lVF~~~~~~~~~l~~~L~~~----~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vlv~T~-----~-~~~Gld~~~~~~  106 (163)
T 2hjv_A           37 SCIIFCRTKEHVNQLTDELDDL----GYPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVATD-----V-AARGIDIENISL  106 (163)
T ss_dssp             SEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECG-----G-GTTTCCCSCCSE
T ss_pred             cEEEEECCHHHHHHHHHHHHHc----CCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEECC-----h-hhcCCchhcCCE
Confidence            8999999999999888888775    67888899887655544332    35678999992     2 233566666777


Q ss_pred             EEEech
Q 017573          142 FVLDEA  147 (369)
Q Consensus       142 viiDE~  147 (369)
                      ||.-+.
T Consensus       107 Vi~~~~  112 (163)
T 2hjv_A          107 VINYDL  112 (163)
T ss_dssp             EEESSC
T ss_pred             EEEeCC
Confidence            776443

>1u94_A RECA protein, recombinase A; homologous recombination, ATPase, DNA repair, DNA binding protein; 1.90A {Escherichia coli} SCOP: c.37.1.11 d.48.1.1 PDB: 1u98_A 1u99_A 1xms_A* 1xmv_A* 2rec_A 2reb_A 1n03_A* 1rea_A 1aa3_A

Probab=91.26  E-value=0.22  Score=42.73  Aligned_cols=40  Identities=18%  Similarity=0.073  Sum_probs=29.4

Q ss_pred             cCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCH
Q 017573           32 KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTR   74 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~   74 (369)
                      .+.-+++.+++|+|||..++..+.+....+.   +++|+..-.
T Consensus        62 ~G~ii~I~G~pGsGKTtLal~la~~~~~~g~---~vlyid~E~  101 (356)
T 1u94_A           62 MGRIVEIYGPESSGKTTLTLQVIAAAQREGK---TCAFIDAEH  101 (356)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHHHHHHTTC---CEEEEESSC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHCCC---eEEEEeCCC
Confidence            3466899999999999888766665554433   788887643

>2zr9_A Protein RECA, recombinase A; recombination, RECA mutants, DNA-repair, ATP-binding, DNA DA recombination, DNA repair, DNA-binding; HET: DTP; 2.50A {Mycobacterium smegmatis str} PDB: 2zr0_A* 2zra_A* 2zrb_A 2zrm_A* 1ubc_A* 1ubf_A* 1ubg_A* 1ube_A* 2g88_A* 2odw_A* 2oe2_A 2oep_A* 2oes_A 2ofo_A 2zr7_A 2odn_A* 2zrn_A 2zro_A* 2zrp_A* 2zre_A* ...

Probab=91.19  E-value=0.22  Score=42.73  Aligned_cols=39  Identities=15%  Similarity=0.116  Sum_probs=28.4

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCH
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTR   74 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~   74 (369)
                      |.-+++.+|+|+|||..++..+......+.   +++|+....
T Consensus        61 G~iv~I~G~pGsGKTtLal~la~~~~~~g~---~vlyi~~E~   99 (349)
T 2zr9_A           61 GRVIEIYGPESSGKTTVALHAVANAQAAGG---IAAFIDAEH   99 (349)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHHHHTTC---CEEEEESSC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhCCC---eEEEEECCC
Confidence            466899999999999887666655554432   788887543

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=91.02  E-value=0.18  Score=45.61  Aligned_cols=37  Identities=16%  Similarity=0.168  Sum_probs=24.1

Q ss_pred             Hhhhhhhhc-cccCCcEEEEcCCCChhhHHHHHHHHHhh
Q 017573           21 AIQQRGIVP-FCKGLDVIQQAQSGTGKTATFCSGILQQL   58 (369)
Q Consensus        21 ~~Q~~~~~~-~~~~~~~li~~~tG~GKT~~~~~~~~~~~   58 (369)
                      +.+.+.+.. +..+..+++.||||||||+.. .+++..+
T Consensus       247 ~~~l~~l~~~v~~g~~i~I~GptGSGKTTlL-~aL~~~i  284 (511)
T 2oap_1          247 SGVLAYLWLAIEHKFSAIVVGETASGKTTTL-NAIMMFI  284 (511)
T ss_dssp             HHHHHHHHHHHHTTCCEEEEESTTSSHHHHH-HHHGGGS
T ss_pred             HHHHHHHHHHHhCCCEEEEECCCCCCHHHHH-HHHHhhC
Confidence            333334433 346788999999999999653 3444444

>2z43_A DNA repair and recombination protein RADA; archaea, filament, DNA binding, molecular SWI RECA, DMC1; HET: DNA; 1.93A {Sulfolobus solfataricus} PDB: 2bke_A* 2dfl_A* 2zub_A* 2zuc_A* 2zud_A*

Probab=90.98  E-value=0.31  Score=41.33  Aligned_cols=54  Identities=17%  Similarity=0.086  Sum_probs=32.6

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhc---cCCCccEEEEcCCHHH-HHHHHHHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDY---GLVQCQALVLAPTREL-AQQIEKVMRA   86 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~---~~~~~~~liv~P~~~l-~~q~~~~~~~   86 (369)
                      |.-+++.||+|+|||..++..+.+....   +..+.+++|+.--..+ ..+..+.+..
T Consensus       107 G~i~~i~G~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~~e~~~~~~~l~~~~~~  164 (324)
T 2z43_A          107 RTMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEGTFRWERIENMAKA  164 (324)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSCCCHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHHHHHHHH
Confidence            4668999999999998776665554322   1113378888765432 3334433433

>3hws_A ATP-dependent CLP protease ATP-binding subunit CL; CLPXP, AAA+ molecular machine, hexamer, asymmetric,, ATP-BIN chaperone, metal-binding; HET: ADP; 3.25A {Escherichia coli} PDB: 3hte_A

Probab=90.94  E-value=0.26  Score=42.60  Aligned_cols=20  Identities=20%  Similarity=0.247  Sum_probs=17.0

Q ss_pred             cCCcEEEEcCCCChhhHHHH
Q 017573           32 KGLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~   51 (369)
                      ...++++.||+|+|||.++-
T Consensus        50 ~~~~vll~GppGtGKT~la~   69 (363)
T 3hws_A           50 GKSNILLIGPTGSGKTLLAE   69 (363)
T ss_dssp             CCCCEEEECCTTSSHHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHHH
Confidence            45789999999999998763

>1e9r_A Conjugal transfer protein TRWB; coupling protein, bacterial conjugation, F1-ATPase-like quaternary structure, ring helicases; 2.4A {Escherichia coli} SCOP: c.37.1.11 PDB: 1e9s_A 1gki_A* 1gl7_A* 1gl6_A*

Probab=90.77  E-value=0.27  Score=43.72  Aligned_cols=44  Identities=16%  Similarity=0.274  Sum_probs=29.8

Q ss_pred             cCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHH
Q 017573           32 KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQ   78 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~   78 (369)
                      ...+++|.|+||+|||..+-..+.+.+..+.   .++|+=|..+...
T Consensus        52 ~~~h~~i~G~tGsGKs~~~~~li~~~~~~g~---~viv~Dpkge~~~   95 (437)
T 1e9r_A           52 EPRHLLVNGATGTGKSVLLRELAYTGLLRGD---RMVIVDPNGDMLS   95 (437)
T ss_dssp             GGGCEEEEECTTSSHHHHHHHHHHHHHHTTC---EEEEEEETTHHHH
T ss_pred             CcceEEEECCCCCCHHHHHHHHHHHHHHCCC---cEEEEeCCCchhH
Confidence            3589999999999999875333333333332   6777778766643

>3hr8_A Protein RECA; alpha and beta proteins (A/B, A+B), ATP-binding, cytoplasm, damage, DNA recombination, DNA repair, DNA-binding; 1.95A {Thermotoga maritima}

Probab=90.77  E-value=0.2  Score=42.99  Aligned_cols=41  Identities=24%  Similarity=0.185  Sum_probs=28.0

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHH
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTREL   76 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l   76 (369)
                      |.-++|.+|+|+|||..++..+......+.   +++|+..-..+
T Consensus        61 G~i~~I~GppGsGKSTLal~la~~~~~~gg---~VlyId~E~s~  101 (356)
T 3hr8_A           61 GRIVEIFGQESSGKTTLALHAIAEAQKMGG---VAAFIDAEHAL  101 (356)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHHHHHTTC---CEEEEESSCCC
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHhcCC---eEEEEeccccc
Confidence            355799999999999876655554433332   78888765443

>1sky_E F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alpha3BETA3 SUBC F1-ATPase, hydrolase; 3.20A {Bacillus SP} SCOP: a.69.1.1 b.49.1.1 c.37.1.11

Probab=90.72  E-value=2.9  Score=37.18  Aligned_cols=27  Identities=26%  Similarity=0.246  Sum_probs=20.7

Q ss_pred             cccCCcEEEEcCCCChhhHHHHHHHHH
Q 017573           30 FCKGLDVIQQAQSGTGKTATFCSGILQ   56 (369)
Q Consensus        30 ~~~~~~~li~~~tG~GKT~~~~~~~~~   56 (369)
                      +.+|+..++.++.|+|||..+...+.+
T Consensus       148 i~kGq~~~i~G~sGvGKTtL~~~l~~~  174 (473)
T 1sky_E          148 YIKGGKIGLFGGAGVGKTVLIQELIHN  174 (473)
T ss_dssp             EETTCEEEEECCSSSCHHHHHHHHHHH
T ss_pred             hccCCEEEEECCCCCCccHHHHHHHhh
Confidence            346889999999999999776544443

>1ofh_A ATP-dependent HSL protease ATP-binding subunit HSLU; chaperone, hydrolase, ATP-binding; HET: ADP; 2.5A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1ofi_A*

Probab=90.66  E-value=0.27  Score=41.15  Aligned_cols=19  Identities=21%  Similarity=0.302  Sum_probs=16.5

Q ss_pred             CCcEEEEcCCCChhhHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~   51 (369)
                      ..++++.||+|+|||..+-
T Consensus        50 ~~~vll~G~~GtGKT~la~   68 (310)
T 1ofh_A           50 PKNILMIGPTGVGKTEIAR   68 (310)
T ss_dssp             CCCEEEECCTTSSHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHH
Confidence            5789999999999997753

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19

Probab=90.61  E-value=2.1  Score=31.84  Aligned_cols=73  Identities=14%  Similarity=0.252  Sum_probs=51.9

Q ss_pred             ccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHH----ccCCcEEEeccHHHHHHHHcCCCCCCCcc
Q 017573           65 CQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL----QAGVHVVVGTPGRVFDMLRRQSLRPDYIK  140 (369)
Q Consensus        65 ~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~----~~~~~iiv~t~~~l~~~~~~~~~~~~~~~  140 (369)
                      .++||.|+++..+....+.+.+.    +..+..++++.........+    .+...|+|+|.     . ...+++...++
T Consensus        31 ~~~lVF~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-----~-~~~G~d~~~~~  100 (165)
T 1fuk_A           31 TQAVIFCNTRRKVEELTTKLRND----KFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTD-----L-LARGIDVQQVS  100 (165)
T ss_dssp             SCEEEEESSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEG-----G-GTTTCCCCSCS
T ss_pred             CCEEEEECCHHHHHHHHHHHHHc----CCCEEEEECCCCHHHHHHHHHHHHcCCCEEEEEcC-----h-hhcCCCcccCC
Confidence            38999999999999888888764    67788889887755544332    35678999992     2 23456666677


Q ss_pred             EEEEech
Q 017573          141 MFVLDEA  147 (369)
Q Consensus       141 ~viiDE~  147 (369)
                      +||.-+.
T Consensus       101 ~Vi~~~~  107 (165)
T 1fuk_A          101 LVINYDL  107 (165)
T ss_dssp             EEEESSC
T ss_pred             EEEEeCC
Confidence            7766443

>2r2a_A Uncharacterized protein; zonular occludens toxin, structural genomics, APC84050.2, PS protein structure initiative; HET: MSE; 1.82A {Neisseria meningitidis MC58}

Probab=90.57  E-value=0.24  Score=38.62  Aligned_cols=22  Identities=23%  Similarity=0.370  Sum_probs=17.3

Q ss_pred             EEEEcCCCChhhHHHHHHHHHh
Q 017573           36 VIQQAQSGTGKTATFCSGILQQ   57 (369)
Q Consensus        36 ~li~~~tG~GKT~~~~~~~~~~   57 (369)
                      .++.|++|||||..+...+...
T Consensus         8 ~l~tG~pGsGKT~~a~~~~~~~   29 (199)
T 2r2a_A            8 CLITGTPGSGKTLKMVSMMAND   29 (199)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHC
T ss_pred             EEEEeCCCCCHHHHHHHHHHHH
Confidence            5899999999998876555443

>2bjv_A PSP operon transcriptional activator; AAA, transcription activation, gene regulation, sigma54 activator, enhancer binding protein, PSPF; 1.7A {Escherichia coli} PDB: 2bjw_A 2c96_A* 2c98_A* 2c99_A* 2c9c_A* 2vii_A*

Probab=90.57  E-value=0.33  Score=39.70  Aligned_cols=19  Identities=26%  Similarity=0.253  Sum_probs=16.6

Q ss_pred             cCCcEEEEcCCCChhhHHH
Q 017573           32 KGLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~   50 (369)
                      .+..+++.||+|+|||..+
T Consensus        28 ~~~~vll~G~~GtGKt~la   46 (265)
T 2bjv_A           28 LDKPVLIIGERGTGKELIA   46 (265)
T ss_dssp             SCSCEEEECCTTSCHHHHH
T ss_pred             CCCCEEEECCCCCcHHHHH
Confidence            4678999999999999765

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=90.41  E-value=0.28  Score=43.66  Aligned_cols=40  Identities=18%  Similarity=-0.027  Sum_probs=29.7

Q ss_pred             ccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCC
Q 017573           31 CKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPT   73 (369)
Q Consensus        31 ~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~   73 (369)
                      ..|.-+++.|++|+|||..++-.+.+....+   .+++|++.-
T Consensus       195 ~~G~liiIaG~pG~GKTtlal~ia~~~a~~g---~~vl~fSlE  234 (444)
T 3bgw_A          195 KRRNFVLIAARPSMGKTAFALKQAKNMSDND---DVVNLHSLE  234 (444)
T ss_dssp             CSSCEEEEEECSSSSHHHHHHHHHHHHHHTT---CEEEEECSS
T ss_pred             CCCcEEEEEeCCCCChHHHHHHHHHHHHHcC---CEEEEEECC
Confidence            3456789999999999988777766665543   278887643

>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=90.38  E-value=1.5  Score=33.13  Aligned_cols=70  Identities=20%  Similarity=0.247  Sum_probs=51.1

Q ss_pred             ccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHH----ccCCcEEEeccHHHHHHHHcCCCCCCCcc
Q 017573           65 CQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL----QAGVHVVVGTPGRVFDMLRRQSLRPDYIK  140 (369)
Q Consensus        65 ~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~----~~~~~iiv~t~~~l~~~~~~~~~~~~~~~  140 (369)
                      .++||.|+++..+..+.+.+.+.    +..+..++++.........+    .+..+|+|+|.      ....+++...++
T Consensus        35 ~~~lVF~~~~~~~~~l~~~L~~~----~~~~~~~~g~~~~~~R~~~~~~f~~g~~~vLvaT~------~~~~Gid~~~~~  104 (175)
T 2rb4_A           35 GQAIIFCQTRRNAKWLTVEMIQD----GHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTN------VCARGIDVKQVT  104 (175)
T ss_dssp             SEEEEECSCHHHHHHHHHHHHTT----TCCEEEECSSCCHHHHHHHHHHHHTTSCSEEEECC------SCCTTTCCTTEE
T ss_pred             CCEEEEECCHHHHHHHHHHHHHc----CCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEec------chhcCCCcccCC
Confidence            38999999999998888887764    67888899887765544332    35788999993      223456666677


Q ss_pred             EEEE
Q 017573          141 MFVL  144 (369)
Q Consensus       141 ~vii  144 (369)
                      +||.
T Consensus       105 ~Vi~  108 (175)
T 2rb4_A          105 IVVN  108 (175)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            7774

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=90.37  E-value=0.22  Score=39.12  Aligned_cols=32  Identities=19%  Similarity=0.080  Sum_probs=26.6

Q ss_pred             CcHhhhhhhhccccCCcEEEEcCCCChhhHHH
Q 017573           19 PSAIQQRGIVPFCKGLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        19 ~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~   50 (369)
                      -+..|..+++.+..|+-+.+.+|.|+|||+.+
T Consensus         8 k~~g~~~~l~~i~~Ge~~~liG~nGsGKSTLl   39 (208)
T 3b85_A            8 KTLGQKHYVDAIDTNTIVFGLGPAGSGKTYLA   39 (208)
T ss_dssp             CSHHHHHHHHHHHHCSEEEEECCTTSSTTHHH
T ss_pred             CCHhHHHHHHhccCCCEEEEECCCCCCHHHHH
Confidence            34457788888888999999999999999653

>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=90.37  E-value=1.2  Score=41.30  Aligned_cols=122  Identities=8%  Similarity=0.072  Sum_probs=80.7

Q ss_pred             CCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHH--hcCCCcEEEEecC-Cc----------CCCCC
Q 017573          235 ITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREF--RSGSSRVLITTDL-LA----------RGIDV  301 (369)
Q Consensus       235 ~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f--~~~~~~vli~t~~-~~----------~G~d~  301 (369)
                      .+.+||.+|.+..++...+.|.+.+..+..++|+.+..++..+...+  ..+..+|+++|+. +.          ...+.
T Consensus        84 ~g~~lVisP~~~L~~q~~~~l~~~gi~~~~l~~~~~~~~~~~~~~~l~~~~~~~~Ilv~Tpe~L~~~~~~~~~l~~~~~~  163 (591)
T 2v1x_A           84 DGFTLVICPLISLMEDQLMVLKQLGISATMLNASSSKEHVKWVHAEMVNKNSELKLIYVTPEKIAKSKMFMSRLEKAYEA  163 (591)
T ss_dssp             SSEEEEECSCHHHHHHHHHHHHHHTCCEEECCSSCCHHHHHHHHHHHHCTTCCCCEEEECHHHHHSCHHHHHHHHHHHHT
T ss_pred             CCcEEEEeCHHHHHHHHHHHHHhcCCcEEEEeCCCCHHHHHHHHHHhhcccCCCCEEEEChhHhhccHHHHHHHHhhhhc
Confidence            46899999999999999999999899999999999999988888888  4678899999982 21          11223


Q ss_pred             CCCcEEEEecCC----CC--ccchhhhhcccccCCCceeEEEEeccccHHHHHHHHHHhcc
Q 017573          302 QQVSLVINYDLP----TQ--PENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNV  356 (369)
Q Consensus       302 ~~~~~vi~~~~~----~~--~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~  356 (369)
                      ..++.+|+-+..    |.  ...-...++...+.......+.+...........+.+.+..
T Consensus       164 ~~i~~iViDEAH~is~~g~dfr~~~~~l~~l~~~~~~~~ii~lSAT~~~~v~~~i~~~l~~  224 (591)
T 2v1x_A          164 RRFTRIAVDEVHCCSQWGHDFRPDYKALGILKRQFPNASLIGLTATATNHVLTDAQKILCI  224 (591)
T ss_dssp             TCEEEEEEETGGGGSTTCTTCCGGGGGGGHHHHHCTTSEEEEEESSCCHHHHHHHHHHTTC
T ss_pred             cCCcEEEEECcccccccccccHHHHHHHHHHHHhCCCCcEEEEecCCCHHHHHHHHHHhCC
Confidence            456666654321    11  12222333433332223445555555566666666666654

>2qmh_A HPR kinase/phosphorylase; V267F mutation, ATP-binding, carbohydrate metabolism, magnesium, metal-binding, multifunctional enzyme; 2.60A {Lactobacillus casei} PDB: 1jb1_A 1kkl_A 1kkm_A*

Probab=90.33  E-value=0.15  Score=39.47  Aligned_cols=20  Identities=40%  Similarity=0.552  Sum_probs=16.7

Q ss_pred             cCCcEEEEcCCCChhhHHHH
Q 017573           32 KGLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~   51 (369)
                      .++.+++.+|||+|||..++
T Consensus        33 ~g~~ilI~GpsGsGKStLA~   52 (205)
T 2qmh_A           33 YGLGVLITGDSGVGKSETAL   52 (205)
T ss_dssp             TTEEEEEECCCTTTTHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHH
Confidence            46778999999999997654

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=90.32  E-value=0.15  Score=39.74  Aligned_cols=17  Identities=18%  Similarity=-0.003  Sum_probs=14.8

Q ss_pred             CcEEEEcCCCChhhHHH
Q 017573           34 LDVIQQAQSGTGKTATF   50 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~   50 (369)
                      ..+++.+|+|+|||..+
T Consensus        59 n~ili~GPPGtGKTt~a   75 (212)
T 1tue_A           59 NCLVFCGPANTGKSYFG   75 (212)
T ss_dssp             SEEEEESCGGGCHHHHH
T ss_pred             cEEEEECCCCCCHHHHH
Confidence            45899999999999775

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=90.31  E-value=0.2  Score=38.41  Aligned_cols=19  Identities=26%  Similarity=0.288  Sum_probs=16.1

Q ss_pred             CCcEEEEcCCCChhhHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~   51 (369)
                      ...+++.||+|+|||..+-
T Consensus        43 ~~~~ll~G~~G~GKT~l~~   61 (195)
T 1jbk_A           43 KNNPVLIGEPGVGKTAIVE   61 (195)
T ss_dssp             SCEEEEECCTTSCHHHHHH
T ss_pred             CCceEEECCCCCCHHHHHH
Confidence            3679999999999997754

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}

Probab=90.14  E-value=4.1  Score=31.21  Aligned_cols=71  Identities=21%  Similarity=0.288  Sum_probs=51.6

Q ss_pred             cEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHH----ccCCcEEEeccHHHHHHHHcCCCCCCCccE
Q 017573           66 QALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL----QAGVHVVVGTPGRVFDMLRRQSLRPDYIKM  141 (369)
Q Consensus        66 ~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~----~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~  141 (369)
                      ++||.|+++.-+..+.+.+.+.    ++.+..++|+.........+    .+...|+|+|     ..+. .+++...++.
T Consensus        56 ~~lVF~~~~~~~~~l~~~L~~~----g~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT-----~~~~-~Gldi~~v~~  125 (191)
T 2p6n_A           56 PVLIFAEKKADVDAIHEYLLLK----GVEAVAIHGGKDQEERTKAIEAFREGKKDVLVAT-----DVAS-KGLDFPAIQH  125 (191)
T ss_dssp             CEEEECSCHHHHHHHHHHHHHH----TCCEEEECTTSCHHHHHHHHHHHHHTSCSEEEEC-----HHHH-TTCCCCCCSE
T ss_pred             CEEEEECCHHHHHHHHHHHHHc----CCcEEEEeCCCCHHHHHHHHHHHhcCCCEEEEEc-----Cchh-cCCCcccCCE
Confidence            8999999999999888888765    67888899887655544332    3578899999     3333 3466666777


Q ss_pred             EEEec
Q 017573          142 FVLDE  146 (369)
Q Consensus       142 viiDE  146 (369)
                      ||.-+
T Consensus       126 VI~~d  130 (191)
T 2p6n_A          126 VINYD  130 (191)
T ss_dssp             EEESS
T ss_pred             EEEeC
Confidence            77633

>1xp8_A RECA protein, recombinase A; recombination, radioresistance, DNA-repair, ATPase, DNA-BIND protein, DNA binding protein; HET: AGS; 2.50A {Deinococcus radiodurans} SCOP: c.37.1.11 d.48.1.1

Probab=90.09  E-value=0.31  Score=42.01  Aligned_cols=40  Identities=15%  Similarity=0.040  Sum_probs=28.9

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHH
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRE   75 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~   75 (369)
                      +.-++|.+++|+|||..++..+.+....+.   +++|+..-..
T Consensus        74 G~li~I~G~pGsGKTtlal~la~~~~~~g~---~vlyi~~E~s  113 (366)
T 1xp8_A           74 GRITEIYGPESGGKTTLALAIVAQAQKAGG---TCAFIDAEHA  113 (366)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHHHHTTC---CEEEEESSCC
T ss_pred             CcEEEEEcCCCCChHHHHHHHHHHHHHCCC---eEEEEECCCC
Confidence            466899999999999887766665544332   7888876543

>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=90.07  E-value=1.5  Score=44.08  Aligned_cols=78  Identities=19%  Similarity=0.228  Sum_probs=63.1

Q ss_pred             cCCCeEEEeCCHhhHHHHHHHHhh----CCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEec-CCcCCCCCCCCcEEE
Q 017573          234 AITQSVIFVNTRRKVDWLTDKMRS----RDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTD-LLARGIDVQQVSLVI  308 (369)
Q Consensus       234 ~~~k~lv~~~~~~~~~~~~~~l~~----~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~-~~~~G~d~~~~~~vi  308 (369)
                      .+.+++|.+|+...+...++.+.+    .+.++..+++..+..++...++...+|+.+|+|+|. .+...+.+.++..||
T Consensus       651 ~g~~vlvlvPt~~La~Q~~~~~~~~~~~~~i~v~~l~~~~~~~~~~~~~~~l~~g~~dIvV~T~~ll~~~~~~~~l~lvI  730 (1151)
T 2eyq_A          651 NHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQSDVKFKDLGLLI  730 (1151)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHHSCCCCSSEEEEE
T ss_pred             hCCeEEEEechHHHHHHHHHHHHHHhhcCCCeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhCCccccccceEE
Confidence            456899999999888777766653    357889999999999999999999999999999996 555557777787777


Q ss_pred             Eec
Q 017573          309 NYD  311 (369)
Q Consensus       309 ~~~  311 (369)
                      +-.
T Consensus       731 iDE  733 (1151)
T 2eyq_A          731 VDE  733 (1151)
T ss_dssp             EES
T ss_pred             Eec
Confidence            544

>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=90.02  E-value=2.2  Score=34.31  Aligned_cols=75  Identities=11%  Similarity=0.254  Sum_probs=52.7

Q ss_pred             cCCCeEEEeCCHhhHHHHHHHHhhC----CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecC-C------cCCCCCC
Q 017573          234 AITQSVIFVNTRRKVDWLTDKMRSR----DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDL-L------ARGIDVQ  302 (369)
Q Consensus       234 ~~~k~lv~~~~~~~~~~~~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~-~------~~G~d~~  302 (369)
                      ...++++.++++..+..+++.+++.    +..+..++|+.+.......+    .+..+|+|+|+. +      ..++++.
T Consensus       110 ~~~~~lil~Ptr~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~----~~~~~I~v~Tp~~l~~~l~~~~~~~l~  185 (249)
T 3ber_A          110 QRLFALVLTPTRELAFQISEQFEALGSSIGVQSAVIVGGIDSMSQSLAL----AKKPHIIIATPGRLIDHLENTKGFNLR  185 (249)
T ss_dssp             CSSCEEEECSSHHHHHHHHHHHHHHHGGGTCCEEEECTTSCHHHHHHHH----HTCCSEEEECHHHHHHHHHHSTTCCCT
T ss_pred             CCceEEEEeCCHHHHHHHHHHHHHHhccCCeeEEEEECCCChHHHHHHh----cCCCCEEEECHHHHHHHHHcCCCcCcc
Confidence            3457999999999888877766554    67888899987765543332    246789999962 1      1346777


Q ss_pred             CCcEEEEecC
Q 017573          303 QVSLVINYDL  312 (369)
Q Consensus       303 ~~~~vi~~~~  312 (369)
                      .++.+|+-+.
T Consensus       186 ~~~~lViDEa  195 (249)
T 3ber_A          186 ALKYLVMDEA  195 (249)
T ss_dssp             TCCEEEECSH
T ss_pred             ccCEEEEcCh
Confidence            7888876543

>4ag6_A VIRB4 ATPase, type IV secretory pathway VIRB4 components-like P; hydrolase, type IV secretion, conjugation; 2.35A {Thermoanaerobacter pseudethanolicus} PDB: 4ag5_A

Probab=89.99  E-value=0.39  Score=41.95  Aligned_cols=41  Identities=22%  Similarity=0.296  Sum_probs=28.8

Q ss_pred             cCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHH
Q 017573           32 KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRE   75 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~   75 (369)
                      .+.+++|.+++|+|||..+-..+......   +.+++++=|..+
T Consensus        34 ~~~~~~i~G~~G~GKs~~~~~~~~~~~~~---~~~~~~~D~~~~   74 (392)
T 4ag6_A           34 TNSNWTILAKPGAGKSFTAKMLLLREYMQ---GSRVIIIDPERE   74 (392)
T ss_dssp             CCCCEEEECCTTSSHHHHHHHHHHHHHTT---TCCEEEEESSCC
T ss_pred             ccCceEEEcCCCCCHHHHHHHHHHHHHHC---CCEEEEEeCCcC
Confidence            57899999999999997754444433332   237888777654

>2cvh_A DNA repair and recombination protein RADB; filament formation, homologous recombination, ATPase domain, hyperthermophIle; HET: DNA; 2.20A {Thermococcus kodakarensis} PDB: 2cvf_A*

Probab=89.98  E-value=0.32  Score=38.37  Aligned_cols=38  Identities=18%  Similarity=0.105  Sum_probs=25.9

Q ss_pred             cccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCC
Q 017573           30 FCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPT   73 (369)
Q Consensus        30 ~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~   73 (369)
                      +..|.-+++.+|+|+|||..+...+.   ..+   .+++++...
T Consensus        17 i~~G~~~~i~G~~GsGKTtl~~~l~~---~~~---~~v~~i~~~   54 (220)
T 2cvh_A           17 FAPGVLTQVYGPYASGKTTLALQTGL---LSG---KKVAYVDTE   54 (220)
T ss_dssp             BCTTSEEEEECSTTSSHHHHHHHHHH---HHC---SEEEEEESS
T ss_pred             CcCCEEEEEECCCCCCHHHHHHHHHH---HcC---CcEEEEECC
Confidence            44567789999999999977654444   222   267777643

>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=89.98  E-value=0.91  Score=35.72  Aligned_cols=74  Identities=8%  Similarity=0.222  Sum_probs=53.6

Q ss_pred             CCeEEEeCCHhhHHHHHHHHhhC-----CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecC-C-----cCCCCCCCC
Q 017573          236 TQSVIFVNTRRKVDWLTDKMRSR-----DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDL-L-----ARGIDVQQV  304 (369)
Q Consensus       236 ~k~lv~~~~~~~~~~~~~~l~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~-~-----~~G~d~~~~  304 (369)
                      .++++.+++++.+..+++.+++.     +..+..++|+.+.....+.   +..+..+|+|+|+. +     ...+++..+
T Consensus        83 ~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~---~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~  159 (220)
T 1t6n_A           83 VSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEV---LKKNCPHIVVGTPGRILALARNKSLNLKHI  159 (220)
T ss_dssp             CCEEEECSCHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHH---HHHSCCSEEEECHHHHHHHHHTTSSCCTTC
T ss_pred             EEEEEEeCCHHHHHHHHHHHHHHHhhCCCceEEEEeCCCChHHHHHH---HhcCCCCEEEeCHHHHHHHHHhCCCCcccC
Confidence            48999999999988887777654     6788899998876654433   34566789999962 1     233567778


Q ss_pred             cEEEEecC
Q 017573          305 SLVINYDL  312 (369)
Q Consensus       305 ~~vi~~~~  312 (369)
                      +.+|+-+.
T Consensus       160 ~~lViDEa  167 (220)
T 1t6n_A          160 KHFILDEC  167 (220)
T ss_dssp             CEEEEESH
T ss_pred             CEEEEcCH
Confidence            88886554

>2i1q_A DNA repair and recombination protein RADA; ATPase, recombinase, ATP complex, calcium stimulation, RECA, DMC1; HET: DNA ANP; 1.90A {Methanococcus voltae} SCOP: a.60.4.1 c.37.1.11 PDB: 1xu4_A* 2b21_A* 2fpk_A* 2fpl_A* 2fpm_A* 1t4g_A* 3fyh_A* 2f1j_A* 2f1i_A* 2f1h_A* 3ntu_A* 3ewa_A* 3ew9_A* 3etl_A* 4dc9_A* 2gdj_A*

Probab=89.85  E-value=0.41  Score=40.49  Aligned_cols=54  Identities=11%  Similarity=0.060  Sum_probs=32.4

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhcc---------CCC----ccEEEEcCCHHH-HHHHHHHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDYG---------LVQ----CQALVLAPTREL-AQQIEKVMRA   86 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~~---------~~~----~~~liv~P~~~l-~~q~~~~~~~   86 (369)
                      +.-+++.+++|+|||..++..+.+.....         ..+    .+++|+.--..+ ..+..+.+..
T Consensus        98 g~i~~i~G~~gsGKT~la~~la~~~~l~~~~~~~~~~~~~gg~~~~~v~yi~~e~~~~~~~l~~~~~~  165 (322)
T 2i1q_A           98 QSVTEFAGVFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRPERIMQMAEH  165 (322)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHHTTCGGGEECCTTTSCTTTTSSEEEEEEESSSCCCHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHhccccccccccccccCCCCCceEEEEECCCCCCHHHHHHHHHH
Confidence            35589999999999988766655432111         111    478888765432 3444444443

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=89.85  E-value=0.35  Score=41.11  Aligned_cols=52  Identities=27%  Similarity=0.242  Sum_probs=33.8

Q ss_pred             ccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHH
Q 017573           29 PFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVM   84 (369)
Q Consensus        29 ~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~   84 (369)
                      -+..|.-+++.|++|+|||..++..+.+....+   .+++|++.-. -..|+..++
T Consensus        42 Gl~~G~LiiIaG~pG~GKTt~al~ia~~~a~~g---~~Vl~fSlEm-s~~ql~~Rl   93 (338)
T 4a1f_A           42 GFNKGSLVIIGARPSMGKTSLMMNMVLSALNDD---RGVAVFSLEM-SAEQLALRA   93 (338)
T ss_dssp             SBCTTCEEEEEECTTSCHHHHHHHHHHHHHHTT---CEEEEEESSS-CHHHHHHHH
T ss_pred             CCCCCcEEEEEeCCCCCHHHHHHHHHHHHHHcC---CeEEEEeCCC-CHHHHHHHH
Confidence            344567799999999999988776666555433   2788876532 233444433

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=89.83  E-value=0.21  Score=38.91  Aligned_cols=21  Identities=19%  Similarity=0.105  Sum_probs=17.2

Q ss_pred             ccCCcEEEEcCCCChhhHHHH
Q 017573           31 CKGLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        31 ~~~~~~li~~~tG~GKT~~~~   51 (369)
                      ..++.+++.|++|+|||..+-
T Consensus        23 ~~~~~i~l~G~~GsGKsTl~~   43 (199)
T 3vaa_A           23 NAMVRIFLTGYMGAGKTTLGK   43 (199)
T ss_dssp             -CCCEEEEECCTTSCHHHHHH
T ss_pred             CCCCEEEEEcCCCCCHHHHHH
Confidence            356789999999999998763

>2l82_A Designed protein OR32; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, de novo protein; NMR {Artificial gene}

Probab=89.78  E-value=2.3  Score=28.48  Aligned_cols=112  Identities=14%  Similarity=0.189  Sum_probs=66.8

Q ss_pred             EEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecC--CcCCC-----CCCCCcEEEEec
Q 017573          239 VIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDL--LARGI-----DVQQVSLVINYD  311 (369)
Q Consensus       239 lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~--~~~G~-----d~~~~~~vi~~~  311 (369)
                      ++|.+..+-...+.+.+++.|..+..++++.+...|.+-++.|.....++--.-+.  ..+.+     -.|.++.|++..
T Consensus         6 vvfssdpeilkeivreikrqgvrvvllysdqdekrrrerleefekqgvdvrtvedkedfrenireiwerypqldvvvivt   85 (162)
T 2l82_A            6 VVFSSDPEILKEIVREIKRQGVRVVLLYSDQDEKRRRERLEEFEKQGVDVRTVEDKEDFRENIREIWERYPQLDVVVIVT   85 (162)
T ss_dssp             EEEESCHHHHHHHHHHHHHTTCEEEEEECCSCHHHHHHHHHHHHTTTCEEEECCSHHHHHHHHHHHHHHCTTCCEEEEEE
T ss_pred             EEecCCHHHHHHHHHHHHhCCeEEEEEecCchHHHHHHHHHHHHHcCCceeeeccHHHHHHHHHHHHHhCCCCcEEEEEe
Confidence            57788888889999999999999999999999999999999997644433222110  00000     136677776654


Q ss_pred             CCC--CccchhhhhcccccCCCceeEEEEeccccHHHHHHHHHHhc
Q 017573          312 LPT--QPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYN  355 (369)
Q Consensus       312 ~~~--~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~  355 (369)
                      ...  -..+|+...   .-  ..-.+++.+.+.|....+..++-+.
T Consensus        86 tddkewikdfieea---ke--rgvevfvvynnkdddrrkeaqqefr  126 (162)
T 2l82_A           86 TDDKEWIKDFIEEA---KE--RGVEVFVVYNNKDDDRRKEAQQEFR  126 (162)
T ss_dssp             CCCHHHHHHHHHHH---HH--TTCEEEEEEECSCHHHHHHHHHHHC
T ss_pred             cCcHHHHHHHHHHH---Hh--cCcEEEEEecCCCchhHHHHHHHhh
Confidence            321  011222211   11  1135666666666555555544443

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=89.71  E-value=0.98  Score=45.19  Aligned_cols=79  Identities=10%  Similarity=0.208  Sum_probs=64.2

Q ss_pred             cCCCeEEEeCCHhhHHHHHHHHhh---CCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecC-CcC---CCCCCCCcE
Q 017573          234 AITQSVIFVNTRRKVDWLTDKMRS---RDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDL-LAR---GIDVQQVSL  306 (369)
Q Consensus       234 ~~~k~lv~~~~~~~~~~~~~~l~~---~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~-~~~---G~d~~~~~~  306 (369)
                      .+.++||.+|++.-+..+++.+++   .+..+..++|+.+..++...++.+.+|+.+|+|+|+. +..   -++...++.
T Consensus       120 ~~~~~Lil~PtreLa~Q~~~~l~~l~~~~i~v~~l~Gg~~~~er~~~~~~l~~g~~~IlV~Tp~rL~~~l~~l~~~~l~~  199 (1104)
T 4ddu_A          120 KGKKSALVFPTVTLVKQTLERLQKLADEKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREKLSQKRFDF  199 (1104)
T ss_dssp             TTCCEEEEESSHHHHHHHHHHHHTTSCTTSCEEEECTTCCTTHHHHHHHHHHTSCCSEEEEEHHHHHHSHHHHHTSCCSE
T ss_pred             cCCeEEEEechHHHHHHHHHHHHHhhCCCCeEEEEeCCCCHHHHHHHHHHHhCCCCCEEEECHHHHHHHHHhhcccCcCE
Confidence            456899999999999999999988   4678999999999988888999999999999999972 211   134567888


Q ss_pred             EEEecC
Q 017573          307 VINYDL  312 (369)
Q Consensus       307 vi~~~~  312 (369)
                      +|+-+.
T Consensus       200 lViDEa  205 (1104)
T 4ddu_A          200 VFVDDV  205 (1104)
T ss_dssp             EEESCH
T ss_pred             EEEeCC
Confidence            886554

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=89.53  E-value=0.25  Score=38.63  Aligned_cols=22  Identities=18%  Similarity=0.234  Sum_probs=18.4

Q ss_pred             ccccCCcEEEEcCCCChhhHHH
Q 017573           29 PFCKGLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        29 ~~~~~~~~li~~~tG~GKT~~~   50 (369)
                      ++..++-+++.||+|+|||..+
T Consensus         8 ~~~~~~~i~l~G~sGsGKsTl~   29 (204)
T 2qor_A            8 HMARIPPLVVCGPSGVGKGTLI   29 (204)
T ss_dssp             -CCCCCCEEEECCTTSCHHHHH
T ss_pred             ccccCCEEEEECCCCCCHHHHH
Confidence            4567888999999999999765

>3iij_A Coilin-interacting nuclear ATPase protein; alpha and beta proteins (A/B), protein binding, transferase, phosphotransferase; HET: ADP; 1.76A {Homo sapiens} SCOP: c.37.1.1 PDB: 3iik_A 3iil_A* 3iim_A* 1rkb_A

Probab=89.41  E-value=0.27  Score=37.46  Aligned_cols=21  Identities=19%  Similarity=0.127  Sum_probs=17.6

Q ss_pred             ccCCcEEEEcCCCChhhHHHH
Q 017573           31 CKGLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        31 ~~~~~~li~~~tG~GKT~~~~   51 (369)
                      ..++.+++.|++|+|||..+-
T Consensus         9 ~~~~~i~i~G~~GsGKst~~~   29 (180)
T 3iij_A            9 MLLPNILLTGTPGVGKTTLGK   29 (180)
T ss_dssp             CCCCCEEEECSTTSSHHHHHH
T ss_pred             ccCCeEEEEeCCCCCHHHHHH
Confidence            356789999999999998753

>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=89.33  E-value=2.6  Score=32.93  Aligned_cols=69  Identities=29%  Similarity=0.398  Sum_probs=51.4

Q ss_pred             cEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHH----ccCCcEEEeccHHHHHHHHcCCCCCCCccE
Q 017573           66 QALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL----QAGVHVVVGTPGRVFDMLRRQSLRPDYIKM  141 (369)
Q Consensus        66 ~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~----~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~  141 (369)
                      ++||.|+++.-++...+.+.+.    +..+..++|+.........+    .+..+|+|+|     .. ...+++...+++
T Consensus        33 ~~lVF~~~~~~~~~l~~~L~~~----~~~~~~lhg~~~~~~r~~~~~~f~~g~~~vlvaT-----~~-~~~Gidi~~v~~  102 (212)
T 3eaq_A           33 RAMVFTRTKAETEEIAQGLLRL----GHPAQALHGDLSQGERERVLGAFRQGEVRVLVAT-----DV-AARGLDIPQVDL  102 (212)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHH----TCCEEEECSSSCHHHHHHHHHHHHSSSCCEEEEC-----TT-TTCSSSCCCBSE
T ss_pred             eEEEEeCCHHHHHHHHHHHHHc----CCCEEEEECCCCHHHHHHHHHHHHCCCCeEEEec-----Ch-hhcCCCCccCcE
Confidence            8999999999999888888765    77888999987765554333    3567899999     22 334566777787


Q ss_pred             EEE
Q 017573          142 FVL  144 (369)
Q Consensus       142 vii  144 (369)
                      ||.
T Consensus       103 Vi~  105 (212)
T 3eaq_A          103 VVH  105 (212)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            774

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=89.12  E-value=0.19  Score=42.81  Aligned_cols=24  Identities=21%  Similarity=0.448  Sum_probs=19.3

Q ss_pred             hccccCCcEEEEcCCCChhhHHHH
Q 017573           28 VPFCKGLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        28 ~~~~~~~~~li~~~tG~GKT~~~~   51 (369)
                      ..+..++++++.||+|+|||..+-
T Consensus        41 ~~l~~~~~vll~G~pGtGKT~la~   64 (331)
T 2r44_A           41 IGICTGGHILLEGVPGLAKTLSVN   64 (331)
T ss_dssp             HHHHHTCCEEEESCCCHHHHHHHH
T ss_pred             HHHHcCCeEEEECCCCCcHHHHHH
Confidence            334567899999999999997653

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=89.00  E-value=0.24  Score=41.31  Aligned_cols=19  Identities=21%  Similarity=0.050  Sum_probs=15.8

Q ss_pred             CCcEEEEcCCCChhhHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~   51 (369)
                      ...+++.||+|+|||..+-
T Consensus        36 p~~lLl~GppGtGKT~la~   54 (293)
T 3t15_A           36 PLILGIWGGKGQGKSFQCE   54 (293)
T ss_dssp             CSEEEEEECTTSCHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHH
Confidence            3578999999999997753

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=88.96  E-value=0.26  Score=37.71  Aligned_cols=19  Identities=21%  Similarity=0.149  Sum_probs=16.3

Q ss_pred             CCcEEEEcCCCChhhHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~   51 (369)
                      .+.+++.|++|+|||.++-
T Consensus         5 ~~~i~l~G~~GsGKst~a~   23 (185)
T 3trf_A            5 LTNIYLIGLMGAGKTSVGS   23 (185)
T ss_dssp             CCEEEEECSTTSSHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHH
Confidence            4678999999999998764

>1p9r_A General secretion pathway protein E; bacterial type II secretion system cytoplasmic protein - GSPE, putative ATPase/ ATP binding protein; 2.50A {Vibrio cholerae} SCOP: c.37.1.11 PDB: 1p9w_A*

Probab=88.95  E-value=0.44  Score=41.88  Aligned_cols=47  Identities=19%  Similarity=0.244  Sum_probs=27.9

Q ss_pred             Hhhhhhhhccc--cCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEE
Q 017573           21 AIQQRGIVPFC--KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVL   70 (369)
Q Consensus        21 ~~Q~~~~~~~~--~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv   70 (369)
                      +-+..++..+.  .+..++|.+|||||||+.. .+++..+...  ..+++++
T Consensus       153 ~~~~~~L~~l~~~~ggii~I~GpnGSGKTTlL-~allg~l~~~--~g~I~~~  201 (418)
T 1p9r_A          153 AHNHDNFRRLIKRPHGIILVTGPTGSGKSTTL-YAGLQELNSS--ERNILTV  201 (418)
T ss_dssp             HHHHHHHHHHHTSSSEEEEEECSTTSCHHHHH-HHHHHHHCCT--TSCEEEE
T ss_pred             HHHHHHHHHHHHhcCCeEEEECCCCCCHHHHH-HHHHhhcCCC--CCEEEEe
Confidence            34555555544  3456899999999999653 3444444332  2255554

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=88.68  E-value=0.22  Score=42.11  Aligned_cols=19  Identities=21%  Similarity=0.232  Sum_probs=15.9

Q ss_pred             CcEEEEcCCCChhhHHHHH
Q 017573           34 LDVIQQAQSGTGKTATFCS   52 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~   52 (369)
                      +-++|.||||+|||..+..
T Consensus        41 ~lIvI~GPTgsGKTtLa~~   59 (339)
T 3a8t_A           41 KLLVLMGATGTGKSRLSID   59 (339)
T ss_dssp             EEEEEECSTTSSHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHH
Confidence            4689999999999977643

>1qhx_A CPT, protein (chloramphenicol phosphotransferase); kinase, antibiotic resistance, phosphorylation, mononucleoti binding fold; HET: ATP; 2.50A {Streptomyces venezuelae} SCOP: c.37.1.3 PDB: 1grr_A* 1grq_A 1qhs_A* 1qhn_A* 1qhy_A*

Probab=88.68  E-value=0.21  Score=37.92  Aligned_cols=18  Identities=22%  Similarity=0.259  Sum_probs=15.4

Q ss_pred             CCcEEEEcCCCChhhHHH
Q 017573           33 GLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~   50 (369)
                      +.-+++.|++|||||.++
T Consensus         3 ~~~i~l~G~~GsGKST~a   20 (178)
T 1qhx_A            3 TRMIILNGGSSAGKSGIV   20 (178)
T ss_dssp             CCEEEEECCTTSSHHHHH
T ss_pred             ceEEEEECCCCCCHHHHH
Confidence            456899999999999875

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=88.60  E-value=0.4  Score=43.26  Aligned_cols=27  Identities=15%  Similarity=0.148  Sum_probs=21.1

Q ss_pred             hhhhhccccCCcEEEEcCCCChhhHHH
Q 017573           24 QRGIVPFCKGLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        24 ~~~~~~~~~~~~~li~~~tG~GKT~~~   50 (369)
                      ..+...+..+.++++.||+|+|||..+
T Consensus        32 ~~l~~al~~~~~VLL~GpPGtGKT~LA   58 (500)
T 3nbx_X           32 RLCLLAALSGESVFLLGPPGIAKSLIA   58 (500)
T ss_dssp             HHHHHHHHHTCEEEEECCSSSSHHHHH
T ss_pred             HHHHHHHhcCCeeEeecCchHHHHHHH
Confidence            334445566899999999999999765

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=88.48  E-value=0.24  Score=40.47  Aligned_cols=21  Identities=24%  Similarity=0.298  Sum_probs=17.7

Q ss_pred             cccCCcEEEEcCCCChhhHHH
Q 017573           30 FCKGLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        30 ~~~~~~~li~~~tG~GKT~~~   50 (369)
                      +..|+-+.+.+|+|||||...
T Consensus        22 i~~g~~v~i~Gp~GsGKSTll   42 (261)
T 2eyu_A           22 HRKMGLILVTGPTGSGKSTTI   42 (261)
T ss_dssp             GCSSEEEEEECSTTCSHHHHH
T ss_pred             hCCCCEEEEECCCCccHHHHH
Confidence            556788999999999999653

>2ewv_A Twitching motility protein PILT; pilus retraction motor, ATPase, hexameric PILT, protein TRAN; HET: ADP; 2.80A {Aquifex aeolicus} PDB: 2eww_A* 2gsz_A*

Probab=88.35  E-value=0.36  Score=41.80  Aligned_cols=29  Identities=17%  Similarity=0.343  Sum_probs=20.2

Q ss_pred             cccCCcEEEEcCCCChhhHHHHHHHHHhhh
Q 017573           30 FCKGLDVIQQAQSGTGKTATFCSGILQQLD   59 (369)
Q Consensus        30 ~~~~~~~li~~~tG~GKT~~~~~~~~~~~~   59 (369)
                      +..++.+++.+|||||||... ..++..+.
T Consensus       133 ~~~g~~i~ivG~~GsGKTTll-~~l~~~~~  161 (372)
T 2ewv_A          133 HRKMGLILVTGPTGSGKSTTI-ASMIDYIN  161 (372)
T ss_dssp             TSSSEEEEEECSSSSSHHHHH-HHHHHHHH
T ss_pred             hcCCCEEEEECCCCCCHHHHH-HHHHhhcC
Confidence            345678999999999999664 33443433

>3lw7_A Adenylate kinase related protein (ADKA-like); AMP, PSI, MCSG, structural genomics, midwest center for structural genomics; HET: AMP; 2.30A {Sulfolobus solfataricus} PDB: 3h0k_A

Probab=88.35  E-value=0.21  Score=37.68  Aligned_cols=17  Identities=18%  Similarity=0.259  Sum_probs=14.4

Q ss_pred             cEEEEcCCCChhhHHHH
Q 017573           35 DVIQQAQSGTGKTATFC   51 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~   51 (369)
                      -+++.|++|||||..+-
T Consensus         3 ~I~l~G~~GsGKsT~a~   19 (179)
T 3lw7_A            3 VILITGMPGSGKSEFAK   19 (179)
T ss_dssp             EEEEECCTTSCHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            47899999999998763

>2px0_A Flagellar biosynthesis protein FLHF; SRP GTPase, flagellum, protein transport, biosynthetic protein; HET: GNP; 3.00A {Bacillus subtilis} PDB: 2px3_A* 3syn_A*

Probab=88.35  E-value=0.52  Score=39.33  Aligned_cols=37  Identities=14%  Similarity=0.118  Sum_probs=23.6

Q ss_pred             cCCcEEEEcCCCChhhHHHHHHHHHhhh-ccCCCccEEEEc
Q 017573           32 KGLDVIQQAQSGTGKTATFCSGILQQLD-YGLVQCQALVLA   71 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~~~~~~~~~-~~~~~~~~liv~   71 (369)
                      .++-+.+.+++|+|||..+...+..... .+   .+++++.
T Consensus       104 ~g~vi~lvG~~GsGKTTl~~~LA~~l~~~~G---~~V~lv~  141 (296)
T 2px0_A          104 HSKYIVLFGSTGAGKTTTLAKLAAISMLEKH---KKIAFIT  141 (296)
T ss_dssp             CSSEEEEEESTTSSHHHHHHHHHHHHHHTTC---CCEEEEE
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHhcC---CEEEEEe
Confidence            3567899999999999876544433322 22   2566654

>1v5w_A DMC1, meiotic recombination protein DMC1/LIM15 homolog; DNA-binding protein, ring protein, octamer, AAA ATPase; 3.20A {Homo sapiens} SCOP: c.37.1.11 PDB: 2zjb_A

Probab=88.33  E-value=0.47  Score=40.56  Aligned_cols=42  Identities=12%  Similarity=-0.071  Sum_probs=27.8

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhcc---CCCccEEEEcCCH
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDYG---LVQCQALVLAPTR   74 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~~---~~~~~~liv~P~~   74 (369)
                      |.-+++.||+|+|||..++..+.+.....   ..+.+++|+....
T Consensus       122 G~i~~I~G~~GsGKTtla~~la~~~~~~~~~gg~~~~vlyi~~E~  166 (343)
T 1v5w_A          122 MAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTEN  166 (343)
T ss_dssp             SEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCeEEEEECCC
Confidence            35579999999999987766555433211   1233788887654

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=88.16  E-value=0.33  Score=37.04  Aligned_cols=19  Identities=11%  Similarity=0.148  Sum_probs=16.0

Q ss_pred             cCCcEEEEcCCCChhhHHH
Q 017573           32 KGLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~   50 (369)
                      .|+-+.+.||+|+|||..+
T Consensus         4 ~g~~i~i~GpsGsGKSTL~   22 (180)
T 1kgd_A            4 MRKTLVLLGAHGVGRRHIK   22 (180)
T ss_dssp             CCCEEEEECCTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4667899999999999764

>3jvv_A Twitching mobility protein; hexameric P-loop ATPase, secretion ATPase, ATP-binding, FIMB nucleotide-binding, transport; HET: ACP CIT; 2.60A {Pseudomonas aeruginosa} PDB: 3jvu_A*

Probab=88.06  E-value=0.38  Score=41.31  Aligned_cols=28  Identities=25%  Similarity=0.395  Sum_probs=19.6

Q ss_pred             cCCcEEEEcCCCChhhHHHHHHHHHhhhc
Q 017573           32 KGLDVIQQAQSGTGKTATFCSGILQQLDY   60 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~~~~~~~~~~   60 (369)
                      .+..+++.||||||||... -.++..+..
T Consensus       122 ~~g~i~I~GptGSGKTTlL-~~l~g~~~~  149 (356)
T 3jvv_A          122 PRGLVLVTGPTGSGKSTTL-AAMLDYLNN  149 (356)
T ss_dssp             SSEEEEEECSTTSCHHHHH-HHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH-HHHHhcccC
Confidence            4567899999999999653 344444443

>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=87.94  E-value=6.2  Score=36.12  Aligned_cols=100  Identities=9%  Similarity=0.081  Sum_probs=65.8

Q ss_pred             CCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHH----HccCCc
Q 017573           41 QSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRI----LQAGVH  116 (369)
Q Consensus        41 ~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~----~~~~~~  116 (369)
                      +....+....+..+...+.....+.++||.|+++.-+..+++.+.+.... +..+..++++.........    ..+..+
T Consensus       316 ~~~~~~~~~~~~~l~~~~~~~~~~~~~iVF~~s~~~~~~l~~~L~~~~~~-~~~v~~~h~~~~~~~R~~~~~~f~~g~~~  394 (563)
T 3i5x_A          316 EKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKK-DLPILEFHGKITQNKRTSLVKRFKKDESG  394 (563)
T ss_dssp             SSTTHHHHHHHHHHHHHHHHTTTCCEEEEECSCHHHHHHHHHHHHHHHTT-TSCEEEESTTSCHHHHHHHHHHHHHCSSE
T ss_pred             chhHhhHHHHHHHHHHHHhhcCCCCcEEEEcCcHHHHHHHHHHHHHhccC-CceEEEecCCCCHHHHHHHHHHHhcCCCC
Confidence            33344444444444444444344458999999999999999988876432 6778888888776554433    235788


Q ss_pred             EEEeccHHHHHHHHcCCCCCCCccEEEEech
Q 017573          117 VVVGTPGRVFDMLRRQSLRPDYIKMFVLDEA  147 (369)
Q Consensus       117 iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~  147 (369)
                      |+|+|.      ....+++...+++||.-..
T Consensus       395 vLvaT~------~~~~GiDip~v~~VI~~~~  419 (563)
T 3i5x_A          395 ILVCTD------VGARGMDFPNVHEVLQIGV  419 (563)
T ss_dssp             EEEECG------GGTSSCCCTTCCEEEEESC
T ss_pred             EEEEcc------hhhcCCCcccCCEEEEECC
Confidence            999993      3344677777888775543

>1zp6_A Hypothetical protein ATU3015; alpha-beta protein., structural genomics, PSI, protein struc initiative; 3.20A {Agrobacterium tumefaciens str} SCOP: c.37.1.25

Probab=87.88  E-value=0.26  Score=37.88  Aligned_cols=21  Identities=19%  Similarity=0.241  Sum_probs=17.3

Q ss_pred             cccCCcEEEEcCCCChhhHHH
Q 017573           30 FCKGLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        30 ~~~~~~~li~~~tG~GKT~~~   50 (369)
                      +..|.-+.+.||+|+|||+.+
T Consensus         6 i~~g~~i~l~G~~GsGKSTl~   26 (191)
T 1zp6_A            6 DLGGNILLLSGHPGSGKSTIA   26 (191)
T ss_dssp             CCTTEEEEEEECTTSCHHHHH
T ss_pred             CCCCeEEEEECCCCCCHHHHH
Confidence            445677899999999999764

>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=87.85  E-value=1.4  Score=40.09  Aligned_cols=121  Identities=11%  Similarity=0.048  Sum_probs=79.7

Q ss_pred             CCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecC-Cc-C----CCCCCCCcEEE
Q 017573          235 ITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDL-LA-R----GIDVQQVSLVI  308 (369)
Q Consensus       235 ~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~-~~-~----G~d~~~~~~vi  308 (369)
                      .+++||.+|.+.-+....+.|+..+..+..+++..+..++.........|..+++++|+- +. .    .++...++.+|
T Consensus        65 ~g~~lvi~P~~aL~~q~~~~l~~~gi~~~~l~~~~~~~~~~~~~~~~~~~~~~ilv~Tpe~l~~~~~~~~l~~~~~~~vV  144 (523)
T 1oyw_A           65 NGLTVVVSPLISLMKDQVDQLQANGVAAACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDNFLEHLAHWNPVLLA  144 (523)
T ss_dssp             SSEEEEECSCHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHHTCCSEEEECHHHHTSTTHHHHHTTSCEEEEE
T ss_pred             CCCEEEECChHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhChHHHHHHhhCCCCEEE
Confidence            468999999999999999999999999999999999999888899999999999999972 21 1    12334555666


Q ss_pred             EecCC----CC--ccchhhhhcccccCCCceeEEEEeccccHHHHHHHHHHhc
Q 017573          309 NYDLP----TQ--PENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYN  355 (369)
Q Consensus       309 ~~~~~----~~--~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~  355 (369)
                      +-+..    |.  .......+++..+.-.....+.+...........+.+.+.
T Consensus       145 iDEaH~i~~~g~~fr~~~~~l~~l~~~~~~~~~i~lSAT~~~~~~~~i~~~l~  197 (523)
T 1oyw_A          145 VDEAHCISQWGHDFRPEYAALGQLRQRFPTLPFMALTATADDTTRQDIVRLLG  197 (523)
T ss_dssp             ESSGGGGCTTSSCCCHHHHGGGGHHHHCTTSCEEEEESCCCHHHHHHHHHHHT
T ss_pred             EeCccccCcCCCccHHHHHHHHHHHHhCCCCCEEEEeCCCCHHHHHHHHHHhC
Confidence            54321    11  1111233444332222234454555555555555665554

>3tau_A Guanylate kinase, GMP kinase; structural genomics, center for structural genomics of infec diseases, csgid, putative guanylate kinase; HET: MSE; 2.05A {Listeria monocytogenes}

Probab=87.71  E-value=0.35  Score=37.93  Aligned_cols=19  Identities=32%  Similarity=0.515  Sum_probs=16.1

Q ss_pred             cCCcEEEEcCCCChhhHHH
Q 017573           32 KGLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~   50 (369)
                      .|+-+++.||+|+|||..+
T Consensus         7 ~g~~i~l~GpsGsGKsTl~   25 (208)
T 3tau_A            7 RGLLIVLSGPSGVGKGTVR   25 (208)
T ss_dssp             CCCEEEEECCTTSCHHHHH
T ss_pred             CCcEEEEECcCCCCHHHHH
Confidence            4667899999999999765

>2ius_A DNA translocase FTSK; nucleotide-binding, chromosome partition, ATP-binding, DNA- binding, cell division, transmembrane, inner membrane; HET: DNA; 2.7A {Escherichia coli} PDB: 2j5p_A*

Probab=87.58  E-value=0.77  Score=41.40  Aligned_cols=28  Identities=21%  Similarity=0.300  Sum_probs=20.4

Q ss_pred             ccCCcEEEEcCCCChhhHHHHHHHHHhh
Q 017573           31 CKGLDVIQQAQSGTGKTATFCSGILQQL   58 (369)
Q Consensus        31 ~~~~~~li~~~tG~GKT~~~~~~~~~~~   58 (369)
                      .++.+++|.++||||||.+.-..+...+
T Consensus       165 ~~~pHlLIaG~TGSGKSt~L~~li~sLl  192 (512)
T 2ius_A          165 AKMPHLLVAGTTGSGASVGVNAMILSML  192 (512)
T ss_dssp             GGSCSEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             ccCceEEEECCCCCCHHHHHHHHHHHHH
Confidence            3467899999999999977544444333

>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=87.56  E-value=1.9  Score=32.94  Aligned_cols=88  Identities=17%  Similarity=0.207  Sum_probs=49.2

Q ss_pred             CChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHH----HHHccCCcEE
Q 017573           43 GTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQ----RILQAGVHVV  118 (369)
Q Consensus        43 G~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~----~~~~~~~~ii  118 (369)
                      ...|-.. +.-++....   .+.++||.|+++.-+..+.+.+...    +..+..++|+.+.....    ....+...|+
T Consensus        29 ~~~K~~~-L~~ll~~~~---~~~k~lVF~~~~~~~~~l~~~L~~~----g~~~~~lhg~~~~~~r~~~~~~f~~g~~~vL  100 (185)
T 2jgn_A           29 ESDKRSF-LLDLLNATG---KDSLTLVFVETKKGADSLEDFLYHE----GYACTSIHGDRSQRDREEALHQFRSGKSPIL  100 (185)
T ss_dssp             GGGHHHH-HHHHHHHC----CCSCEEEEESCHHHHHHHHHHHHHT----TCCEEEEC--------CHHHHHHHHTSSSEE
T ss_pred             cHHHHHH-HHHHHHhcC---CCCeEEEEECCHHHHHHHHHHHHHc----CCceEEEeCCCCHHHHHHHHHHHHcCCCeEE
Confidence            3466543 334443322   2348999999999999888888764    67788888766543332    2234577899


Q ss_pred             EeccHHHHHHHHcCCCCCCCccEEEE
Q 017573          119 VGTPGRVFDMLRRQSLRPDYIKMFVL  144 (369)
Q Consensus       119 v~t~~~l~~~~~~~~~~~~~~~~vii  144 (369)
                      |+|. .    + ..+++...+++||.
T Consensus       101 vaT~-~----~-~~Gldi~~~~~VI~  120 (185)
T 2jgn_A          101 VATA-V----A-ARGLDISNVKHVIN  120 (185)
T ss_dssp             EEEC------------CCCSBSEEEE
T ss_pred             EEcC-h----h-hcCCCcccCCEEEE
Confidence            9992 2    2 22345556677765

>1cr0_A DNA primase/helicase; RECA-type protein fold, transferase; HET: DNA; 2.30A {Enterobacteria phage T7} SCOP: c.37.1.11 PDB: 1cr1_A* 1cr2_A* 1cr4_A* 1e0j_A* 1e0k_A*

Probab=87.52  E-value=0.65  Score=38.65  Aligned_cols=42  Identities=17%  Similarity=-0.021  Sum_probs=26.8

Q ss_pred             ccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcC
Q 017573           29 PFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAP   72 (369)
Q Consensus        29 ~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P   72 (369)
                      .+..|.-+++.||+|+|||..+...+.......  +.+++++..
T Consensus        31 ~l~~G~~~~i~G~~G~GKTTl~~~ia~~~~~~~--G~~v~~~~~   72 (296)
T 1cr0_A           31 GARGGEVIMVTSGSGMGKSTFVRQQALQWGTAM--GKKVGLAML   72 (296)
T ss_dssp             SBCTTCEEEEEESTTSSHHHHHHHHHHHHHHTS--CCCEEEEES
T ss_pred             CCCCCeEEEEEeCCCCCHHHHHHHHHHHHHHHc--CCeEEEEeC
Confidence            345678899999999999976544443332221  225766654

>1nlf_A Regulatory protein REPA; replicative DNA helicase structural changes, replication; 1.95A {Escherichia coli} SCOP: c.37.1.11 PDB: 1g8y_A 1olo_A

Probab=87.50  E-value=1  Score=37.02  Aligned_cols=46  Identities=15%  Similarity=0.068  Sum_probs=29.5

Q ss_pred             hccccCCcEEEEcCCCChhhHHHHHHHHHhhhccC--------CCccEEEEcCCH
Q 017573           28 VPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGL--------VQCQALVLAPTR   74 (369)
Q Consensus        28 ~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~--------~~~~~liv~P~~   74 (369)
                      .-+..|.-+++.+|+|+|||..+...+. .+..+.        ...+++++....
T Consensus        25 ggl~~G~i~~i~G~~GsGKTtl~~~l~~-~~~~g~~~~g~~~~~~~~v~~~~~e~   78 (279)
T 1nlf_A           25 PNMVAGTVGALVSPGGAGKSMLALQLAA-QIAGGPDLLEVGELPTGPVIYLPAED   78 (279)
T ss_dssp             TTEETTSEEEEEESTTSSHHHHHHHHHH-HHHTCCCTTCCCCCCCCCEEEEESSS
T ss_pred             CCccCCCEEEEEcCCCCCHHHHHHHHHH-HHhcCCCcCCCccCCCccEEEEECCC
Confidence            3455678899999999999977655444 333320        022677776543

>1u0j_A DNA replication protein; AAA+ protein, P-loop atpases, helicase; HET: DNA ADP; 2.10A {Adeno-associated virus - 2} SCOP: c.37.1.20 PDB: 1s9h_A

Probab=87.48  E-value=0.35  Score=39.43  Aligned_cols=17  Identities=24%  Similarity=0.120  Sum_probs=15.0

Q ss_pred             cEEEEcCCCChhhHHHH
Q 017573           35 DVIQQAQSGTGKTATFC   51 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~   51 (369)
                      .+++.||+|+|||..+.
T Consensus       106 ~~~l~GppgtGKt~~a~  122 (267)
T 1u0j_A          106 TIWLFGPATTGKTNIAE  122 (267)
T ss_dssp             EEEEECSTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            58999999999998764

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=87.37  E-value=0.33  Score=39.48  Aligned_cols=18  Identities=33%  Similarity=0.324  Sum_probs=15.7

Q ss_pred             CCcEEEEcCCCChhhHHH
Q 017573           33 GLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~   50 (369)
                      .+.+++.||+|+|||..+
T Consensus        45 ~~~vll~G~~GtGKT~la   62 (257)
T 1lv7_A           45 PKGVLMVGPPGTGKTLLA   62 (257)
T ss_dssp             CCEEEEECCTTSCHHHHH
T ss_pred             CCeEEEECcCCCCHHHHH
Confidence            467999999999999765

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=87.32  E-value=0.39  Score=37.34  Aligned_cols=19  Identities=26%  Similarity=0.384  Sum_probs=15.1

Q ss_pred             cCCcEEEEcCCCChhhHHH
Q 017573           32 KGLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~   50 (369)
                      .++-+.+.||+|+|||...
T Consensus         3 ~g~~i~lvGpsGaGKSTLl   21 (198)
T 1lvg_A            3 GPRPVVLSGPSGAGKSTLL   21 (198)
T ss_dssp             --CCEEEECCTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4678999999999999764

>1q57_A DNA primase/helicase; dntpase, DNA replication, transferase; HET: DNA; 3.45A {Enterobacteria phage T7} SCOP: c.37.1.11 e.13.1.2

Probab=87.31  E-value=0.49  Score=42.91  Aligned_cols=52  Identities=10%  Similarity=-0.085  Sum_probs=33.8

Q ss_pred             cccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHH
Q 017573           30 FCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVM   84 (369)
Q Consensus        30 ~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~   84 (369)
                      +..|.-++|.|++|+|||..++..+.+.....  +.+++|+.--. -..|+..++
T Consensus       239 l~~G~l~li~G~pG~GKT~lal~~a~~~a~~~--g~~vl~~s~E~-s~~~l~~r~  290 (503)
T 1q57_A          239 ARGGEVIMVTSGSGMVMSTFVRQQALQWGTAM--GKKVGLAMLEE-SVEETAEDL  290 (503)
T ss_dssp             CCTTCEEEEEESSCHHHHHHHHHHHHHHTTTS--CCCEEEEESSS-CHHHHHHHH
T ss_pred             cCCCeEEEEeecCCCCchHHHHHHHHHHHHhc--CCcEEEEeccC-CHHHHHHHH
Confidence            34567789999999999988776666655431  22788876532 234444443

>3exa_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.30A {Bacillus halodurans} PDB: 2qgn_A

Probab=87.29  E-value=0.34  Score=40.53  Aligned_cols=19  Identities=26%  Similarity=0.101  Sum_probs=15.3

Q ss_pred             CcEEEEcCCCChhhHHHHH
Q 017573           34 LDVIQQAQSGTGKTATFCS   52 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~   52 (369)
                      +-++|.||||+|||..+..
T Consensus         4 ~~i~i~GptgsGKt~la~~   22 (322)
T 3exa_A            4 KLVAIVGPTAVGKTKTSVM   22 (322)
T ss_dssp             EEEEEECCTTSCHHHHHHH
T ss_pred             cEEEEECCCcCCHHHHHHH
Confidence            3478999999999977643

>1y63_A LMAJ004144AAA protein; structural genomics, protein structure initiative, PSI, SGPP structural genomics of pathogenic protozoa consortium; HET: ADP; 1.70A {Leishmania major} SCOP: c.37.1.1

Probab=87.27  E-value=0.39  Score=36.76  Aligned_cols=19  Identities=37%  Similarity=0.690  Sum_probs=16.5

Q ss_pred             cCCcEEEEcCCCChhhHHH
Q 017573           32 KGLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~   50 (369)
                      .+..+++.|++|||||.++
T Consensus         9 ~~~~I~l~G~~GsGKSTv~   27 (184)
T 1y63_A            9 KGINILITGTPGTGKTSMA   27 (184)
T ss_dssp             SSCEEEEECSTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4567999999999999876

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=87.22  E-value=0.38  Score=41.53  Aligned_cols=18  Identities=44%  Similarity=0.468  Sum_probs=15.8

Q ss_pred             CcEEEEcCCCChhhHHHH
Q 017573           34 LDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~   51 (369)
                      +.+++.||+|+|||..+-
T Consensus        71 ~~vLl~GppGtGKT~la~   88 (368)
T 3uk6_A           71 RAVLIAGQPGTGKTAIAM   88 (368)
T ss_dssp             CEEEEEESTTSSHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHH
Confidence            579999999999998754

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=87.19  E-value=0.44  Score=35.88  Aligned_cols=18  Identities=17%  Similarity=0.226  Sum_probs=15.6

Q ss_pred             CCcEEEEcCCCChhhHHH
Q 017573           33 GLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~   50 (369)
                      +..+.+.|++|||||..+
T Consensus         4 ~~~i~l~G~~GsGKSTl~   21 (173)
T 1kag_A            4 KRNIFLVGPMGAGKSTIG   21 (173)
T ss_dssp             CCCEEEECCTTSCHHHHH
T ss_pred             CCeEEEECCCCCCHHHHH
Confidence            467899999999999765

>3foz_A TRNA delta(2)-isopentenylpyrophosphate transferas; nucleoside modification, isopentenyl-tRNA transferase, transferase-RNA complex; 2.50A {Escherichia coli k-12} PDB: 2zxu_A* 2zm5_A

Probab=87.05  E-value=0.36  Score=40.31  Aligned_cols=18  Identities=22%  Similarity=0.283  Sum_probs=14.9

Q ss_pred             cEEEEcCCCChhhHHHHH
Q 017573           35 DVIQQAQSGTGKTATFCS   52 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~~   52 (369)
                      -++|.||||+|||..+..
T Consensus        12 ~i~i~GptgsGKt~la~~   29 (316)
T 3foz_A           12 AIFLMGPTASGKTALAIE   29 (316)
T ss_dssp             EEEEECCTTSCHHHHHHH
T ss_pred             EEEEECCCccCHHHHHHH
Confidence            478999999999977643

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=87.02  E-value=0.36  Score=39.25  Aligned_cols=17  Identities=18%  Similarity=0.051  Sum_probs=14.3

Q ss_pred             cEEEEcCCCChhhHHHH
Q 017573           35 DVIQQAQSGTGKTATFC   51 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~   51 (369)
                      -+++.||+|||||..+.
T Consensus         3 li~I~G~~GSGKSTla~   19 (253)
T 2ze6_A            3 LHLIYGPTCSGKTDMAI   19 (253)
T ss_dssp             EEEEECCTTSSHHHHHH
T ss_pred             EEEEECCCCcCHHHHHH
Confidence            36899999999998764

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=87.00  E-value=0.56  Score=39.30  Aligned_cols=18  Identities=22%  Similarity=0.171  Sum_probs=15.4

Q ss_pred             CcEEEEcCCCChhhHHHH
Q 017573           34 LDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~   51 (369)
                      ..+++.||+|+|||..+-
T Consensus        48 ~~~ll~G~~GtGKt~la~   65 (311)
T 4fcw_A           48 GSFLFLGPTGVGKTELAK   65 (311)
T ss_dssp             EEEEEESCSSSSHHHHHH
T ss_pred             eEEEEECCCCcCHHHHHH
Confidence            468999999999997763

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=86.95  E-value=0.41  Score=37.26  Aligned_cols=20  Identities=35%  Similarity=0.448  Sum_probs=16.9

Q ss_pred             ccCCcEEEEcCCCChhhHHH
Q 017573           31 CKGLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        31 ~~~~~~li~~~tG~GKT~~~   50 (369)
                      ..|.-+.+.||+|||||..+
T Consensus         4 ~~g~~i~l~G~~GsGKSTl~   23 (207)
T 2j41_A            4 EKGLLIVLSGPSGVGKGTVR   23 (207)
T ss_dssp             CCCCEEEEECSTTSCHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHH
Confidence            45677899999999999765

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=86.87  E-value=0.56  Score=39.28  Aligned_cols=19  Identities=32%  Similarity=0.412  Sum_probs=16.6

Q ss_pred             cCCcEEEEcCCCChhhHHH
Q 017573           32 KGLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~   50 (369)
                      ....+++.||+|+|||..+
T Consensus        24 ~~~~vLi~Ge~GtGKt~lA   42 (304)
T 1ojl_A           24 SDATVLIHGDSGTGKELVA   42 (304)
T ss_dssp             TTSCEEEESCTTSCHHHHH
T ss_pred             CCCcEEEECCCCchHHHHH
Confidence            4578999999999999775

>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=86.83  E-value=3.5  Score=31.80  Aligned_cols=117  Identities=11%  Similarity=0.085  Sum_probs=65.7

Q ss_pred             CCCeEEEeCCHhhHHHHHHHHhhC-----CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecC-----CcC-CCCCCC
Q 017573          235 ITQSVIFVNTRRKVDWLTDKMRSR-----DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDL-----LAR-GIDVQQ  303 (369)
Q Consensus       235 ~~k~lv~~~~~~~~~~~~~~l~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~-----~~~-G~d~~~  303 (369)
                      ..++++.+|++..+..+.+.+.+.     +..+..++|+.+..+....   + .+..+|+|+|+.     +.. .+++..
T Consensus        71 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~---~-~~~~~i~v~T~~~l~~~~~~~~~~~~~  146 (206)
T 1vec_A           71 NIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMR---L-DDTVHVVIATPGRILDLIKKGVAKVDH  146 (206)
T ss_dssp             SCCEEEECSCHHHHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHH---T-TSCCSEEEECHHHHHHHHHTTCSCCTT
T ss_pred             CeeEEEEeCcHHHHHHHHHHHHHHHhhcCCceEEEEeCCccHHHHHHh---c-CCCCCEEEeCHHHHHHHHHcCCcCccc
Confidence            457999999999888877776543     5678888888766543222   2 346789999961     222 245667


Q ss_pred             CcEEEEecCCC-CccchhhhhcccccC-CCceeEEEEeccccHHHHHHHHHHhc
Q 017573          304 VSLVINYDLPT-QPENYLHRIGRSGRF-GRKGVAINFVTRDDERMLFDIQKFYN  355 (369)
Q Consensus       304 ~~~vi~~~~~~-~~~~~~Q~~GR~~R~-~~~~~~~~~~~~~~~~~~~~~~~~~~  355 (369)
                      ++.+|+-+... ....+...+.+..+. .+....+.+...-..+..+-+.+++.
T Consensus       147 ~~~lViDEah~~~~~~~~~~l~~i~~~~~~~~~~l~~SAT~~~~~~~~~~~~l~  200 (206)
T 1vec_A          147 VQMIVLDEADKLLSQDFVQIMEDIILTLPKNRQILLYSATFPLSVQKFMNSHLE  200 (206)
T ss_dssp             CCEEEEETHHHHTSTTTHHHHHHHHHHSCTTCEEEEEESCCCHHHHHHHHHHCS
T ss_pred             CCEEEEEChHHhHhhCcHHHHHHHHHhCCccceEEEEEeeCCHHHHHHHHHHcC
Confidence            88887654321 111233333333222 12234444444444444444555554

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=86.70  E-value=0.43  Score=37.10  Aligned_cols=20  Identities=40%  Similarity=0.353  Sum_probs=16.7

Q ss_pred             ccCCcEEEEcCCCChhhHHH
Q 017573           31 CKGLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        31 ~~~~~~li~~~tG~GKT~~~   50 (369)
                      ..|.-+.+.||+|+|||+.+
T Consensus         5 ~~g~ii~l~Gp~GsGKSTl~   24 (205)
T 3tr0_A            5 NKANLFIISAPSGAGKTSLV   24 (205)
T ss_dssp             CCCCEEEEECCTTSCHHHHH
T ss_pred             CCCcEEEEECcCCCCHHHHH
Confidence            35677899999999999764

>2vhj_A Ntpase P4, P4; non- hydrolysable ATP analogue, hydrolase, virus dsRNA, molecular motor, packaging ATPase, hexameric helicase; HET: ADP; 1.80A {Pseudomonas phage PHI12} PDB: 2vhq_A* 1w44_A* 1w46_A* 1w47_A* 1w48_A* 1w49_A* 1w4a_A* 1w4b_A* 1w4c_A 2vht_A* 2vhu_A* 2vhc_A*

Probab=86.58  E-value=0.25  Score=41.46  Aligned_cols=25  Identities=20%  Similarity=0.031  Sum_probs=18.9

Q ss_pred             cCCcEEEEcCCCChhhHHHHHHHHH
Q 017573           32 KGLDVIQQAQSGTGKTATFCSGILQ   56 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~~~~~~   56 (369)
                      .+..+++.+|+|+|||..++..+.+
T Consensus       122 ~gsviLI~GpPGsGKTtLAlqlA~~  146 (331)
T 2vhj_A          122 ASGMVIVTGKGNSGKTPLVHALGEA  146 (331)
T ss_dssp             ESEEEEEECSCSSSHHHHHHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHh
Confidence            3455799999999999877655443

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=86.57  E-value=0.38  Score=41.50  Aligned_cols=21  Identities=19%  Similarity=0.306  Sum_probs=17.6

Q ss_pred             cccCCcEEEEcCCCChhhHHH
Q 017573           30 FCKGLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        30 ~~~~~~~li~~~tG~GKT~~~   50 (369)
                      +..|+.+.+.+|+|+|||..+
T Consensus       172 i~~G~~i~ivG~sGsGKSTll  192 (361)
T 2gza_A          172 VQLERVIVVAGETGSGKTTLM  192 (361)
T ss_dssp             HHTTCCEEEEESSSSCHHHHH
T ss_pred             HhcCCEEEEECCCCCCHHHHH
Confidence            346889999999999999653

>2l8b_A Protein TRAI, DNA helicase I; RECD, hydrolase; NMR {Escherichia coli}

Probab=86.53  E-value=0.64  Score=35.26  Aligned_cols=58  Identities=10%  Similarity=0.067  Sum_probs=40.9

Q ss_pred             cHhhhhhhhccccC--CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHH
Q 017573           20 SAIQQRGIVPFCKG--LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQ   79 (369)
Q Consensus        20 ~~~Q~~~~~~~~~~--~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q   79 (369)
                      .+-|..++..+...  +-.++.++-|++|+...+..++......  +..+.+++|+..-...
T Consensus        36 ~~~~~~a~~~l~~s~~~~~iv~g~ggs~~~~~~~a~L~~~a~~~--Gr~V~vLAp~~~s~~~   95 (189)
T 2l8b_A           36 TAGYSDAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQ--GREVQIIAADRRSQMN   95 (189)
T ss_dssp             HHHHHHHHHHHHHHSCCEECCBCSSCSHHHHHHHHHHHHHHHHT--TCCEEEECSTTHHHHH
T ss_pred             CccchhHHHHHhccCCceEEEecccchHHHHHHHHHHHHHHHhc--CeEEEEEcCchHHHHH
Confidence            35688888888754  4578999999999987554544443332  3389999999765443

>2c9o_A RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-binding, chromatin regulator, growth regulation, hydrolase, nuclear protein, DNA recombination; HET: ADP; 2.2A {Homo sapiens} PDB: 2xsz_A*

Probab=86.49  E-value=0.43  Score=42.65  Aligned_cols=19  Identities=42%  Similarity=0.490  Sum_probs=16.4

Q ss_pred             CCcEEEEcCCCChhhHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~   51 (369)
                      ++++++.||+|+|||..+-
T Consensus        63 ~~~iLl~GppGtGKT~la~   81 (456)
T 2c9o_A           63 GRAVLLAGPPGTGKTALAL   81 (456)
T ss_dssp             TCEEEEECCTTSSHHHHHH
T ss_pred             CCeEEEECCCcCCHHHHHH
Confidence            3689999999999998764

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=86.48  E-value=0.66  Score=48.91  Aligned_cols=42  Identities=19%  Similarity=0.101  Sum_probs=32.2

Q ss_pred             cCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHH
Q 017573           32 KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTREL   76 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l   76 (369)
                      .++.+++.+|+|+|||..+...+.+....+.   +++++.....+
T Consensus      1426 ~g~~vll~GppGtGKT~LA~ala~ea~~~G~---~v~Fi~~e~~~ 1467 (2050)
T 3cmu_A         1426 MGRIVEIYGPESSGKTTLTLQVIAAAQREGK---TCAFIDAEHAL 1467 (2050)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHHHTTTC---CEEEECTTSCC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHcCC---cEEEEEccccc
Confidence            3688999999999999888777766655444   78888876443

>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=86.31  E-value=3.3  Score=31.09  Aligned_cols=72  Identities=8%  Similarity=0.098  Sum_probs=51.2

Q ss_pred             cEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHH----ccCCcEEEeccHHHHHHHHcCCCCCCCccE
Q 017573           66 QALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL----QAGVHVVVGTPGRVFDMLRRQSLRPDYIKM  141 (369)
Q Consensus        66 ~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~----~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~  141 (369)
                      ++||.|+++..+..+.+.+.+.    +..+..++++.........+    .+...|+|+|.     . ...+++...+++
T Consensus        33 ~~lVF~~~~~~~~~l~~~L~~~----~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vLvaT~-----~-~~~Gldi~~~~~  102 (172)
T 1t5i_A           33 QVVIFVKSVQRCIALAQLLVEQ----NFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATN-----L-FGRGMDIERVNI  102 (172)
T ss_dssp             SEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEESS-----C-CSTTCCGGGCSE
T ss_pred             cEEEEECCHHHHHHHHHHHHhc----CCCEEEEECCCCHHHHHHHHHHHHCCCCcEEEECC-----c-hhcCcchhhCCE
Confidence            8999999999999888888775    67888889887655543332    35788999993     1 233455555677


Q ss_pred             EEEech
Q 017573          142 FVLDEA  147 (369)
Q Consensus       142 viiDE~  147 (369)
                      ||.-+.
T Consensus       103 Vi~~d~  108 (172)
T 1t5i_A          103 AFNYDM  108 (172)
T ss_dssp             EEESSC
T ss_pred             EEEECC
Confidence            765443

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=86.25  E-value=8.9  Score=35.29  Aligned_cols=97  Identities=9%  Similarity=0.090  Sum_probs=63.8

Q ss_pred             hhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHH----HccCCcEEEe
Q 017573           45 GKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRI----LQAGVHVVVG  120 (369)
Q Consensus        45 GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~----~~~~~~iiv~  120 (369)
                      .+....+..+...+.....+.++||.|+++.-++.+++.+.+.... +..+..++++.........    ..+..+|+|+
T Consensus       269 ~~~~~~~~~l~~~~~~~~~~~~~iVF~~t~~~~~~l~~~L~~~~~~-~~~v~~~hg~~~~~~R~~~~~~F~~g~~~vLVa  347 (579)
T 3sqw_A          269 NSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKK-DLPILEFHGKITQNKRTSLVKRFKKDESGILVC  347 (579)
T ss_dssp             HHHHHHHHHHHHHHHHTTTCCEEEEECSSHHHHHHHHHHHHHHHTT-TSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEE
T ss_pred             hhHHHHHHHHHHHHhhcCCCCcEEEECCcHHHHHHHHHHHHHhhcC-CCcEEEecCCCCHHHHHHHHHHhhcCCCeEEEE
Confidence            3333333344444443334448999999999999999988876432 6778888888776554333    2457889999


Q ss_pred             ccHHHHHHHHcCCCCCCCccEEEEechh
Q 017573          121 TPGRVFDMLRRQSLRPDYIKMFVLDEAD  148 (369)
Q Consensus       121 t~~~l~~~~~~~~~~~~~~~~viiDE~H  148 (369)
                      |.     . ...+++...+++||.-..-
T Consensus       348 T~-----~-~~~GiDip~v~~VI~~~~p  369 (579)
T 3sqw_A          348 TD-----V-GARGMDFPNVHEVLQIGVP  369 (579)
T ss_dssp             CG-----G-GTSSCCCTTCCEEEEESCC
T ss_pred             cc-----h-hhcCCCcccCCEEEEcCCC
Confidence            93     3 3345777778887765543

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=86.19  E-value=0.32  Score=37.19  Aligned_cols=19  Identities=32%  Similarity=0.403  Sum_probs=15.8

Q ss_pred             CCcEEEEcCCCChhhHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~   51 (369)
                      +..+++.|++|||||+.+-
T Consensus         4 g~~I~l~G~~GsGKST~~~   22 (186)
T 3cm0_A            4 GQAVIFLGPPGAGKGTQAS   22 (186)
T ss_dssp             EEEEEEECCTTSCHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHH
Confidence            4568999999999998753

>1c9k_A COBU, adenosylcobinamide kinase; alpha/beta structure rossmann fold P-loop, transferase; HET: 5GP; 2.20A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1cbu_A

Probab=86.15  E-value=0.5  Score=36.00  Aligned_cols=44  Identities=16%  Similarity=0.188  Sum_probs=24.9

Q ss_pred             EEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHH
Q 017573           36 VIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRA   86 (369)
Q Consensus        36 ~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~   86 (369)
                      ++|.+++|||||..+...+.     .  +.+++|+......-.++.+.+..
T Consensus         2 ilV~Gg~~SGKS~~A~~la~-----~--~~~~~yiaT~~~~d~e~~~rI~~   45 (180)
T 1c9k_A            2 ILVTGGARSGKSRHAEALIG-----D--APQVLYIATSQILDDEMAARIQH   45 (180)
T ss_dssp             EEEEECTTSSHHHHHHHHHC-----S--CSSEEEEECCCC------CHHHH
T ss_pred             EEEECCCCCcHHHHHHHHHh-----c--CCCeEEEecCCCCCHHHHHHHHH
Confidence            68999999999976643321     1  22678888765444444444443

>3kb2_A SPBC2 prophage-derived uncharacterized protein YORR; alpha-beta protein., structural genomics, PSI-2, protein structure initiative; HET: G3D; 2.20A {Bacillus subtilis} SCOP: c.37.1.1 PDB: 2axp_A*

Probab=86.14  E-value=0.44  Score=35.77  Aligned_cols=17  Identities=12%  Similarity=-0.001  Sum_probs=14.4

Q ss_pred             cEEEEcCCCChhhHHHH
Q 017573           35 DVIQQAQSGTGKTATFC   51 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~   51 (369)
                      .+++.|++|+|||+++-
T Consensus         3 ~i~l~G~~GsGKsT~~~   19 (173)
T 3kb2_A            3 LIILEGPDCCFKSTVAA   19 (173)
T ss_dssp             EEEEECSSSSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            47899999999998753

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=86.07  E-value=4.1  Score=36.73  Aligned_cols=35  Identities=17%  Similarity=0.188  Sum_probs=23.5

Q ss_pred             cEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcC
Q 017573           35 DVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAP   72 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P   72 (369)
                      .+.+.+++|+|||..+...+......+   .+++++..
T Consensus       103 vI~ivG~~GvGKTTl~~kLA~~l~~~G---~kVllVd~  137 (504)
T 2j37_W          103 VIMFVGLQGSGKTTTCSKLAYYYQRKG---WKTCLICA  137 (504)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHTT---CCEEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhCC---CeEEEEec
Confidence            578899999999987654444333222   26777765

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=86.00  E-value=1  Score=49.70  Aligned_cols=69  Identities=16%  Similarity=0.163  Sum_probs=40.7

Q ss_pred             HHHHHHHHhCCCCCCcHhhhhhhhccc----cCCcEEEEcCCCChhhHHHHHHHHHhhhc-cCCCccEEEEcCCHH
Q 017573            5 ENLLRGIYAYGFEKPSAIQQRGIVPFC----KGLDVIQQAQSGTGKTATFCSGILQQLDY-GLVQCQALVLAPTRE   75 (369)
Q Consensus         5 ~~i~~~l~~~~~~~~~~~Q~~~~~~~~----~~~~~li~~~tG~GKT~~~~~~~~~~~~~-~~~~~~~liv~P~~~   75 (369)
                      +.|.....+.|+ ++.+.+..=+-++.    ....+++.||||+|||.++-.. ..++.. ........++-|..-
T Consensus       875 ~ai~~~~~~~~L-~~~~~~v~KviQLye~~~vRhGvmlVGp~gsGKTt~~~~L-~~al~~l~~~~~~~~~iNPKai  948 (3245)
T 3vkg_A          875 KKIQEIAKQRHL-VTKQEWVEKILQLHQILNINHGVMMVGPSGGGKTTSWEVY-LEAIEQVDNIKSEAHVMDPKAI  948 (3245)
T ss_dssp             HHHHHHHHHTTC-CCCHHHHHHHHHHHHHHTTCSEEEEECSSSSSHHHHHHHH-HHHHTTTTTCEEEEEEECTTTS
T ss_pred             HHHHHHHHHcCC-ccCHHHHHHHHHHHHHHHheeeEEEECCCCCCHHHHHHHH-HHHHHHhhCCCceEEEECCCCC
Confidence            445666677776 66666654443443    4678999999999999875322 222221 111224556667543

>2r62_A Cell division protease FTSH homolog; ATPase domain, ATP-binding, cell CELL division, hydrolase, membrane, metal-binding; 3.30A {Helicobacter pylori} PDB: 2r65_A*

Probab=85.97  E-value=0.3  Score=39.98  Aligned_cols=19  Identities=32%  Similarity=0.247  Sum_probs=16.2

Q ss_pred             CCcEEEEcCCCChhhHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~   51 (369)
                      .+.+++.||+|+|||..+-
T Consensus        44 ~~~vll~G~~GtGKT~la~   62 (268)
T 2r62_A           44 PKGVLLVGPPGTGKTLLAK   62 (268)
T ss_dssp             CSCCCCBCSSCSSHHHHHH
T ss_pred             CceEEEECCCCCcHHHHHH
Confidence            4679999999999997764

>1um8_A ATP-dependent CLP protease ATP-binding subunit CL; CLPP binding loop, chaperone; HET: ADP; 2.60A {Helicobacter pylori} SCOP: c.37.1.20

Probab=85.95  E-value=0.48  Score=41.08  Aligned_cols=19  Identities=21%  Similarity=0.302  Sum_probs=16.3

Q ss_pred             CCcEEEEcCCCChhhHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~   51 (369)
                      ..++++.||+|+|||..+-
T Consensus        72 ~~~ill~Gp~GtGKT~la~   90 (376)
T 1um8_A           72 KSNILLIGPTGSGKTLMAQ   90 (376)
T ss_dssp             CCCEEEECCTTSSHHHHHH
T ss_pred             CCCEEEECCCCCCHHHHHH
Confidence            4689999999999997763

>1vma_A Cell division protein FTSY; TM0570, structural genomics, JCS protein structure initiative, PSI, joint center for structu genomics; HET: CIT; 1.60A {Thermotoga maritima} SCOP: a.24.13.1 c.37.1.10

Probab=85.91  E-value=0.76  Score=38.47  Aligned_cols=36  Identities=19%  Similarity=0.141  Sum_probs=22.5

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEc
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLA   71 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~   71 (369)
                      ++-+.+.+++|+|||+.+...+......   +.+++++.
T Consensus       104 ~~vi~ivG~~GsGKTTl~~~LA~~l~~~---g~kV~lv~  139 (306)
T 1vma_A          104 PFVIMVVGVNGTGKTTSCGKLAKMFVDE---GKSVVLAA  139 (306)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHHT---TCCEEEEE
T ss_pred             CeEEEEEcCCCChHHHHHHHHHHHHHhc---CCEEEEEc
Confidence            3457899999999997764443322222   22666654

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=85.87  E-value=0.47  Score=35.95  Aligned_cols=16  Identities=19%  Similarity=0.271  Sum_probs=14.0

Q ss_pred             cEEEEcCCCChhhHHH
Q 017573           35 DVIQQAQSGTGKTATF   50 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~   50 (369)
                      -+++.|++|||||..+
T Consensus         4 ~I~i~G~~GsGKST~a   19 (181)
T 1ly1_A            4 IILTIGCPGSGKSTWA   19 (181)
T ss_dssp             EEEEECCTTSSHHHHH
T ss_pred             EEEEecCCCCCHHHHH
Confidence            4789999999999875

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=85.85  E-value=0.48  Score=35.51  Aligned_cols=18  Identities=17%  Similarity=0.209  Sum_probs=15.9

Q ss_pred             CcEEEEcCCCChhhHHHH
Q 017573           34 LDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~   51 (369)
                      +++++.+++|||||.++-
T Consensus         8 ~~i~l~G~~GsGKSTva~   25 (168)
T 1zuh_A            8 QHLVLIGFMGSGKSSLAQ   25 (168)
T ss_dssp             CEEEEESCTTSSHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHH
Confidence            678999999999998763

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=85.84  E-value=0.32  Score=36.78  Aligned_cols=21  Identities=24%  Similarity=0.161  Sum_probs=17.1

Q ss_pred             cccCCcEEEEcCCCChhhHHH
Q 017573           30 FCKGLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        30 ~~~~~~~li~~~tG~GKT~~~   50 (369)
                      +.+|.-+.+.||.|||||..+
T Consensus         6 i~~gei~~l~G~nGsGKSTl~   26 (171)
T 4gp7_A            6 IPELSLVVLIGSSGSGKSTFA   26 (171)
T ss_dssp             EESSEEEEEECCTTSCHHHHH
T ss_pred             CCCCEEEEEECCCCCCHHHHH
Confidence            345677899999999999764

>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=85.54  E-value=1.4  Score=34.96  Aligned_cols=73  Identities=11%  Similarity=0.074  Sum_probs=51.6

Q ss_pred             cCCCeEEEeCCHhhHHHHHHHHhhC-----CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecC-C-----cCCCCCC
Q 017573          234 AITQSVIFVNTRRKVDWLTDKMRSR-----DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDL-L-----ARGIDVQ  302 (369)
Q Consensus       234 ~~~k~lv~~~~~~~~~~~~~~l~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~-~-----~~G~d~~  302 (369)
                      ...++++.+++++.+..+++.+++.     +..+..++|+.+...+...+     ...+|+|+|+. +     ...+++.
T Consensus        91 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~-----~~~~Iiv~Tp~~l~~~~~~~~~~~~  165 (230)
T 2oxc_A           91 LSTQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRL-----KKCHIAVGSPGRIKQLIELDYLNPG  165 (230)
T ss_dssp             CSCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEECTTSCHHHHHHHT-----TSCSEEEECHHHHHHHHHTTSSCGG
T ss_pred             CCceEEEEeCCHHHHHHHHHHHHHHhcccCCceEEEEeCCCCHHHHHHhc-----cCCCEEEECHHHHHHHHhcCCcccc
Confidence            3468999999999998888877654     56788899988766554432     25789999972 1     1235666


Q ss_pred             CCcEEEEec
Q 017573          303 QVSLVINYD  311 (369)
Q Consensus       303 ~~~~vi~~~  311 (369)
                      .++.+|+-+
T Consensus       166 ~~~~lViDE  174 (230)
T 2oxc_A          166 SIRLFILDE  174 (230)
T ss_dssp             GCCEEEESS
T ss_pred             cCCEEEeCC
Confidence            777777654

>3ney_A 55 kDa erythrocyte membrane protein; structural genomics consortium, SGC, 55 kDa erythrocyte MEMB protein; 2.26A {Homo sapiens} SCOP: c.37.1.0

Probab=85.35  E-value=0.58  Score=36.26  Aligned_cols=19  Identities=16%  Similarity=0.219  Sum_probs=16.3

Q ss_pred             cCCcEEEEcCCCChhhHHH
Q 017573           32 KGLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~   50 (369)
                      .++-+++.||+|+|||...
T Consensus        18 ~g~~ivl~GPSGaGKsTL~   36 (197)
T 3ney_A           18 GRKTLVLIGASGVGRSHIK   36 (197)
T ss_dssp             SCCEEEEECCTTSSHHHHH
T ss_pred             CCCEEEEECcCCCCHHHHH
Confidence            5677899999999999764

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=85.35  E-value=0.48  Score=39.87  Aligned_cols=19  Identities=16%  Similarity=0.184  Sum_probs=15.6

Q ss_pred             CcEEEEcCCCChhhHHHHH
Q 017573           34 LDVIQQAQSGTGKTATFCS   52 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~   52 (369)
                      +.+++.||||+|||..+..
T Consensus         6 ~~i~i~GptGsGKTtla~~   24 (323)
T 3crm_A            6 PAIFLMGPTAAGKTDLAMA   24 (323)
T ss_dssp             EEEEEECCTTSCHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHH
Confidence            3589999999999987643

>1kht_A Adenylate kinase; phosphotransferase, signaling protein, transferase; HET: AMP; 2.50A {Methanococcus voltae} SCOP: c.37.1.1 PDB: 3h86_B* 1ki9_A

Probab=85.31  E-value=0.55  Score=35.98  Aligned_cols=19  Identities=21%  Similarity=0.221  Sum_probs=15.8

Q ss_pred             CCcEEEEcCCCChhhHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~   51 (369)
                      +..+++.|++|||||+.+-
T Consensus         3 ~~~I~i~G~~GsGKsT~~~   21 (192)
T 1kht_A            3 NKVVVVTGVPGVGSTTSSQ   21 (192)
T ss_dssp             CCEEEEECCTTSCHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHH
Confidence            4568999999999998753

>4akg_A Glutathione S-transferase class-MU 26 kDa isozyme heavy chain cytoplasmic; motor protein, AAA+ protein, ASCE protein, P-loop ntpase; HET: ATP ADP; 3.30A {Schistosoma japonicum} PDB: 4ai6_A* 4akh_A* 4aki_A* 3qmz_A

Probab=85.27  E-value=1  Score=49.11  Aligned_cols=45  Identities=24%  Similarity=0.127  Sum_probs=30.1

Q ss_pred             HHHHHHHhCCCCCCcHhhhhhh----hccccCCcEEEEcCCCChhhHHHH
Q 017573            6 NLLRGIYAYGFEKPSAIQQRGI----VPFCKGLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus         6 ~i~~~l~~~~~~~~~~~Q~~~~----~~~~~~~~~li~~~tG~GKT~~~~   51 (369)
                      .+...+.+.++ ++.+.+..-+    +.+.....+++.||||+|||.++-
T Consensus       893 ~i~~~~~~~~l-~~~~~~~~K~~ql~e~~~~r~gvmlvGptgsGKTt~~~  941 (2695)
T 4akg_A          893 CLKDAGQRSGF-SMSEEFLKKCMQFYYMQKTQQALILVGKAGCGKTATWK  941 (2695)
T ss_dssp             HHHHHHHHHTC-CCCHHHHHHHHHHHHHHHHCSEEEEECSTTSSHHHHHH
T ss_pred             HHHHHHHHcCC-cccHHHHHHHHHHHHHHHhcceEEEECCCCCCHHHHHH
Confidence            45555666666 4566553333    333456889999999999998753

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=85.23  E-value=0.86  Score=38.47  Aligned_cols=36  Identities=22%  Similarity=0.197  Sum_probs=22.9

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEc
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLA   71 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~   71 (369)
                      ++-+.+.++.|+|||+.+...+......+   .+++++.
T Consensus       105 ~~vI~ivG~~G~GKTT~~~~LA~~l~~~g---~kVllid  140 (320)
T 1zu4_A          105 LNIFMLVGVNGTGKTTSLAKMANYYAELG---YKVLIAA  140 (320)
T ss_dssp             CEEEEEESSTTSSHHHHHHHHHHHHHHTT---CCEEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHCC---CeEEEEe
Confidence            45578899999999977644443322222   2666664

>2iut_A DNA translocase FTSK; nucleotide-binding, chromosome partition, ATP-binding, DNA- cell division, DNA translocation, KOPS, membrane; HET: DNA SAP; 2.25A {Pseudomonas aeruginosa} PDB: 2iuu_A*

Probab=85.22  E-value=1.2  Score=40.72  Aligned_cols=42  Identities=17%  Similarity=0.269  Sum_probs=27.1

Q ss_pred             cCCcEEEEcCCCChhhHHHHHHHHHhhhcc-CCCccEEEEcCC
Q 017573           32 KGLDVIQQAQSGTGKTATFCSGILQQLDYG-LVQCQALVLAPT   73 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~~~~~~~~~~~-~~~~~~liv~P~   73 (369)
                      +..+++|.+.||||||.+.-..++..+... +...+++++=|.
T Consensus       213 k~pHlLIaG~TGSGKS~~L~tlI~sLl~~~sP~ev~lilIDpK  255 (574)
T 2iut_A          213 KMPHLLVAGTTGSGKSVGVNAMLLSILFKSTPSEARLIMIDPK  255 (574)
T ss_dssp             GSCCEEEECCTTSSHHHHHHHHHHHHHTTCCTTTEEEEEECSS
T ss_pred             hCCeeEEECCCCCCHHHHHHHHHHHHHHhCCCcceEEEEeCCC
Confidence            457899999999999987655555544332 223345555454

>3d8b_A Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, structural genomics consortium, ATP- hydrolase, magnesium, metal-binding, nucleotide-binding; HET: ADP; 2.00A {Homo sapiens}

Probab=85.18  E-value=0.57  Score=40.31  Aligned_cols=19  Identities=26%  Similarity=0.184  Sum_probs=16.4

Q ss_pred             CCcEEEEcCCCChhhHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~   51 (369)
                      .+.+++.||+|+|||..+-
T Consensus       117 ~~~vLl~GppGtGKT~la~  135 (357)
T 3d8b_A          117 PKGILLFGPPGTGKTLIGK  135 (357)
T ss_dssp             CSEEEEESSTTSSHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHH
Confidence            4789999999999998763

>3bs4_A Uncharacterized protein PH0321; structural genomics, unknown function, PSI-2, protein struct initiative; 1.60A {Pyrococcus horikoshii}

Probab=85.10  E-value=1.1  Score=36.46  Aligned_cols=51  Identities=10%  Similarity=0.082  Sum_probs=34.3

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHh
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRAL   87 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~   87 (369)
                      +..+++.+++|+|||..++..+.+.+..+.   +++|++-. +-..++.+.+..+
T Consensus        21 gs~~li~g~p~~~~~~l~~qfl~~g~~~Ge---~~~~~~~~-e~~~~l~~~~~~~   71 (260)
T 3bs4_A           21 SLILIHEEDASSRGKDILFYILSRKLKSDN---LVGMFSIS-YPLQLIIRILSRF   71 (260)
T ss_dssp             CEEEEEECSGGGCHHHHHHHHHHHHHHTTC---EEEEEECS-SCHHHHHHHHHHT
T ss_pred             CcEEEEEeCCCccHHHHHHHHHHHHHHCCC---cEEEEEEe-CCHHHHHHHHHHc
Confidence            456788878888888666666676666655   78887754 3445555666655

>2v54_A DTMP kinase, thymidylate kinase; nucleotide biosynthesis, ATP-binding, nucleotide-binding, poxvirus, transferase; HET: TYD POP; 2.4A {Vaccinia virus copenhagen} PDB: 2w0s_A*

Probab=85.06  E-value=0.59  Score=36.27  Aligned_cols=20  Identities=20%  Similarity=0.341  Sum_probs=16.6

Q ss_pred             cCCcEEEEcCCCChhhHHHH
Q 017573           32 KGLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~   51 (369)
                      .+..+++.|++|||||+.+-
T Consensus         3 ~~~~I~l~G~~GsGKsT~~~   22 (204)
T 2v54_A            3 RGALIVFEGLDKSGKTTQCM   22 (204)
T ss_dssp             CCCEEEEECCTTSSHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHH
Confidence            45678999999999998753

>3umf_A Adenylate kinase; rossmann fold, transferase; 2.05A {Schistosoma mansoni}

Probab=85.01  E-value=0.58  Score=36.94  Aligned_cols=21  Identities=19%  Similarity=0.219  Sum_probs=16.5

Q ss_pred             ccCCcEEEEcCCCChhhHHHH
Q 017573           31 CKGLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        31 ~~~~~~li~~~tG~GKT~~~~   51 (369)
                      .+.+-+++.+|+||||++.+-
T Consensus        27 ~k~kiI~llGpPGsGKgTqa~   47 (217)
T 3umf_A           27 AKAKVIFVLGGPGSGKGTQCE   47 (217)
T ss_dssp             TSCEEEEEECCTTCCHHHHHH
T ss_pred             cCCcEEEEECCCCCCHHHHHH
Confidence            344567889999999998764

>2pt7_A CAG-ALFA; ATPase, protein-protein complex, type IV secretion, hydrolas binding complex; 2.40A {Helicobacter pylori} SCOP: c.37.1.11 PDB: 1nly_A* 1nlz_A 1opx_A* 1g6o_A

Probab=84.96  E-value=0.38  Score=40.86  Aligned_cols=19  Identities=37%  Similarity=0.504  Sum_probs=16.8

Q ss_pred             ccCCcEEEEcCCCChhhHH
Q 017573           31 CKGLDVIQQAQSGTGKTAT   49 (369)
Q Consensus        31 ~~~~~~li~~~tG~GKT~~   49 (369)
                      ..++.+.+.+|+|||||..
T Consensus       169 ~~g~~v~i~G~~GsGKTTl  187 (330)
T 2pt7_A          169 AIGKNVIVCGGTGSGKTTY  187 (330)
T ss_dssp             HHTCCEEEEESTTSCHHHH
T ss_pred             cCCCEEEEECCCCCCHHHH
Confidence            4688999999999999964

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=84.93  E-value=5.9  Score=34.44  Aligned_cols=71  Identities=20%  Similarity=0.269  Sum_probs=52.1

Q ss_pred             CccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHH----ccCCcEEEeccHHHHHHHHcCCCCCCCc
Q 017573           64 QCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL----QAGVHVVVGTPGRVFDMLRRQSLRPDYI  139 (369)
Q Consensus        64 ~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~----~~~~~iiv~t~~~l~~~~~~~~~~~~~~  139 (369)
                      +.++||.|+++.-++.+.+.+.+.    +..+..++++..........    .+..+|+|+|     ..+. .+++...+
T Consensus       276 ~~~~lVf~~~~~~~~~l~~~L~~~----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlvaT-----~~~~-~Gidip~v  345 (417)
T 2i4i_A          276 DSLTLVFVETKKGADSLEDFLYHE----GYACTSIHGDRSQRDREEALHQFRSGKSPILVAT-----AVAA-RGLDISNV  345 (417)
T ss_dssp             TCEEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHHTSSCEEEEC-----HHHH-TTSCCCCE
T ss_pred             CCeEEEEECCHHHHHHHHHHHHHC----CCCeeEecCCCCHHHHHHHHHHHHcCCCCEEEEC-----Chhh-cCCCcccC
Confidence            348999999999999888888774    67888899887765544332    3577899999     3333 35677777


Q ss_pred             cEEEE
Q 017573          140 KMFVL  144 (369)
Q Consensus       140 ~~vii  144 (369)
                      ++||.
T Consensus       346 ~~Vi~  350 (417)
T 2i4i_A          346 KHVIN  350 (417)
T ss_dssp             EEEEE
T ss_pred             CEEEE
Confidence            77765

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=84.84  E-value=1  Score=34.40  Aligned_cols=20  Identities=35%  Similarity=0.444  Sum_probs=16.4

Q ss_pred             cCCcEEEEcCCCChhhHHHH
Q 017573           32 KGLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~   51 (369)
                      .+..+++.|++|+|||..+-
T Consensus        12 ~~~~i~l~G~~GsGKsT~~~   31 (186)
T 2yvu_A           12 KGIVVWLTGLPGSGKTTIAT   31 (186)
T ss_dssp             CCEEEEEECCTTSSHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHH
Confidence            35668999999999998754

>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=84.80  E-value=4.4  Score=31.18  Aligned_cols=74  Identities=12%  Similarity=0.156  Sum_probs=51.3

Q ss_pred             CCCeEEEeCCHhhHHHHHHHHhhC--CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecC-----Cc-CCCCCCCCcE
Q 017573          235 ITQSVIFVNTRRKVDWLTDKMRSR--DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDL-----LA-RGIDVQQVSL  306 (369)
Q Consensus       235 ~~k~lv~~~~~~~~~~~~~~l~~~--~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~-----~~-~G~d~~~~~~  306 (369)
                      ..++++.+|++..+..+++.+++.  +..+..++|+.+.......+.    ...+|+|+|+.     +. ..+++..++.
T Consensus        72 ~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~i~v~T~~~l~~~~~~~~~~~~~~~~  147 (207)
T 2gxq_A           72 KPRALVLTPTRELALQVASELTAVAPHLKVVAVYGGTGYGKQKEALL----RGADAVVATPGRALDYLRQGVLDLSRVEV  147 (207)
T ss_dssp             CCSEEEECSSHHHHHHHHHHHHHHCTTSCEEEECSSSCSHHHHHHHH----HCCSEEEECHHHHHHHHHHTSSCCTTCSE
T ss_pred             CCcEEEEECCHHHHHHHHHHHHHHhhcceEEEEECCCChHHHHHHhh----CCCCEEEECHHHHHHHHHcCCcchhhceE
Confidence            458999999999999888888765  356778888776554433332    24679999961     11 2356677888


Q ss_pred             EEEecC
Q 017573          307 VINYDL  312 (369)
Q Consensus       307 vi~~~~  312 (369)
                      +|+-+.
T Consensus       148 iViDEa  153 (207)
T 2gxq_A          148 AVLDEA  153 (207)
T ss_dssp             EEEESH
T ss_pred             EEEECh
Confidence            876543

>2qt1_A Nicotinamide riboside kinase 1; non-protein kinase, NAD+, NRK1, nicotinic acid riboside kinase activity, NAD biosynthesis; HET: NNR; 1.32A {Homo sapiens} PDB: 2qsy_A* 2qsz_A* 2qt0_A* 2p0e_A* 2qg6_A* 2ql6_A*

Probab=84.80  E-value=0.47  Score=37.04  Aligned_cols=25  Identities=16%  Similarity=-0.000  Sum_probs=19.3

Q ss_pred             hhhccccCCcEEEEcCCCChhhHHH
Q 017573           26 GIVPFCKGLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        26 ~~~~~~~~~~~li~~~tG~GKT~~~   50 (369)
                      .++.+..+.-+.+.|++|+|||..+
T Consensus        14 ~~~~~~~~~~i~i~G~~GsGKSTl~   38 (207)
T 2qt1_A           14 LVPRGSKTFIIGISGVTNSGKTTLA   38 (207)
T ss_dssp             CCCCSCCCEEEEEEESTTSSHHHHH
T ss_pred             ccccCCCCeEEEEECCCCCCHHHHH
Confidence            3445555677899999999999765

>1s96_A Guanylate kinase, GMP kinase; E.coli, dimer, SAD, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.1 PDB: 2an9_A* 2anb_A* 2anc_A 2f3r_A* 2f3t_A*

Probab=84.79  E-value=0.47  Score=37.58  Aligned_cols=22  Identities=32%  Similarity=0.442  Sum_probs=16.7

Q ss_pred             ccccCCcEEEEcCCCChhhHHH
Q 017573           29 PFCKGLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        29 ~~~~~~~~li~~~tG~GKT~~~   50 (369)
                      ++..|+-+.+.||.|+|||...
T Consensus        12 ~~~~G~ii~l~GpsGsGKSTLl   33 (219)
T 1s96_A           12 HMAQGTLYIVSAPSGAGKSSLI   33 (219)
T ss_dssp             ---CCCEEEEECCTTSCHHHHH
T ss_pred             cCCCCcEEEEECCCCCCHHHHH
Confidence            4566788999999999999653

>1knq_A Gluconate kinase; ALFA/beta structure, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.17 PDB: 1ko1_A 1ko4_A 1ko5_A* 1ko8_A* 1kof_A*

Probab=84.75  E-value=0.38  Score=36.35  Aligned_cols=18  Identities=28%  Similarity=0.242  Sum_probs=15.5

Q ss_pred             CCcEEEEcCCCChhhHHH
Q 017573           33 GLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~   50 (369)
                      +..+.+.|++|+|||..+
T Consensus         8 g~~i~l~G~~GsGKSTl~   25 (175)
T 1knq_A            8 HHIYVLMGVSGSGKSAVA   25 (175)
T ss_dssp             SEEEEEECSTTSCHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHH
Confidence            556899999999999765

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=84.43  E-value=0.6  Score=35.95  Aligned_cols=21  Identities=19%  Similarity=0.115  Sum_probs=17.2

Q ss_pred             ccCCcEEEEcCCCChhhHHHH
Q 017573           31 CKGLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        31 ~~~~~~li~~~tG~GKT~~~~   51 (369)
                      ..+..+++.|++|||||.++-
T Consensus         7 ~~~~~I~l~G~~GsGKsT~~~   27 (196)
T 2c95_A            7 KKTNIIFVVGGPGSGKGTQCE   27 (196)
T ss_dssp             TTSCEEEEEECTTSSHHHHHH
T ss_pred             cCCCEEEEECCCCCCHHHHHH
Confidence            345679999999999998763

>2rhm_A Putative kinase; P-loop containing nucleoside triphosphate hydrolases fold, S genomics, joint center for structural genomics, JCSG; HET: MSE; 1.70A {Chloroflexus aurantiacus}

Probab=84.42  E-value=0.52  Score=36.20  Aligned_cols=19  Identities=26%  Similarity=0.183  Sum_probs=15.8

Q ss_pred             CCcEEEEcCCCChhhHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~   51 (369)
                      +..+++.|++|+|||..+-
T Consensus         5 ~~~I~l~G~~GsGKST~~~   23 (193)
T 2rhm_A            5 PALIIVTGHPATGKTTLSQ   23 (193)
T ss_dssp             CEEEEEEESTTSSHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHH
Confidence            4568999999999998753

>2v3c_C SRP54, signal recognition 54 kDa protein; nucleotide-binding, signal recognition particle, GTP-binding, RNA-binding; 2.50A {Methanocaldococcus jannaschii} PDB: 3ndb_B

Probab=84.41  E-value=0.91  Score=40.10  Aligned_cols=36  Identities=22%  Similarity=0.206  Sum_probs=24.8

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcC
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAP   72 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P   72 (369)
                      ..+++.+++|+|||..+...+......+.   +++++..
T Consensus       100 ~vI~ivG~~GvGKTTla~~La~~l~~~G~---kVllv~~  135 (432)
T 2v3c_C          100 NVILLVGIQGSGKTTTAAKLARYIQKRGL---KPALIAA  135 (432)
T ss_dssp             CCEEEECCSSSSTTHHHHHHHHHHHHHHC---CEEEECC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHcCC---eEEEEec
Confidence            46889999999999876555444433333   6777763

>3ice_A Transcription termination factor RHO; transcription, ATPase, hexamer, helicase, RNA, RECA, OB fold ATP-binding, hydrolase; HET: MSE ADP SPD; 2.80A {Escherichia coli k-12} PDB: 1pv4_A 1pvo_A* 1xpo_A* 1xpr_A* 1xpu_A* 2ht1_A

Probab=84.29  E-value=1.1  Score=38.75  Aligned_cols=23  Identities=26%  Similarity=0.322  Sum_probs=19.2

Q ss_pred             ccccCCcEEEEcCCCChhhHHHH
Q 017573           29 PFCKGLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        29 ~~~~~~~~li~~~tG~GKT~~~~   51 (369)
                      .+..|+.+.+.+|+|+|||..+.
T Consensus       170 pi~rGQr~~IvG~sG~GKTtLl~  192 (422)
T 3ice_A          170 PIGRGQRGLIVAPPKAGKTMLLQ  192 (422)
T ss_dssp             CCBTTCEEEEECCSSSSHHHHHH
T ss_pred             eecCCcEEEEecCCCCChhHHHH
Confidence            34568999999999999997653

>1ixz_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 2.20A {Thermus thermophilus} SCOP: c.37.1.20 PDB: 1iy0_A* 1iy1_A*

Probab=84.19  E-value=0.62  Score=37.75  Aligned_cols=17  Identities=29%  Similarity=0.321  Sum_probs=14.7

Q ss_pred             CcEEEEcCCCChhhHHH
Q 017573           34 LDVIQQAQSGTGKTATF   50 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~   50 (369)
                      +++++.+|+|+|||..+
T Consensus        50 ~g~ll~G~~G~GKTtl~   66 (254)
T 1ixz_A           50 KGVLLVGPPGVGKTHLA   66 (254)
T ss_dssp             SEEEEECCTTSSHHHHH
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            45999999999999764

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=84.10  E-value=0.6  Score=39.61  Aligned_cols=18  Identities=17%  Similarity=0.185  Sum_probs=15.2

Q ss_pred             cEEEEcCCCChhhHHHHH
Q 017573           35 DVIQQAQSGTGKTATFCS   52 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~~   52 (369)
                      -++|.||||||||..+..
T Consensus         9 lI~I~GptgSGKTtla~~   26 (340)
T 3d3q_A            9 LIVIVGPTASGKTELSIE   26 (340)
T ss_dssp             EEEEECSTTSSHHHHHHH
T ss_pred             eEEEECCCcCcHHHHHHH
Confidence            578999999999987643

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=83.98  E-value=0.7  Score=35.86  Aligned_cols=19  Identities=32%  Similarity=0.349  Sum_probs=16.2

Q ss_pred             cCCcEEEEcCCCChhhHHH
Q 017573           32 KGLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~   50 (369)
                      .+..+.+.||+|+|||..+
T Consensus        28 ~g~~i~l~G~~GsGKSTl~   46 (200)
T 4eun_A           28 PTRHVVVMGVSGSGKTTIA   46 (200)
T ss_dssp             CCCEEEEECCTTSCHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHH
Confidence            4577899999999999765

>1ex7_A Guanylate kinase; substrate-induced FIT, domain movement, GMP, ATP, substrate specificity, X-RAY diffraction, transferase; HET: 5GP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1ex6_A* 1gky_A* 3sqk_A 4f4j_A

Probab=83.97  E-value=0.59  Score=35.87  Aligned_cols=17  Identities=29%  Similarity=0.507  Sum_probs=14.4

Q ss_pred             CcEEEEcCCCChhhHHH
Q 017573           34 LDVIQQAQSGTGKTATF   50 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~   50 (369)
                      +-+++.||.|+|||...
T Consensus         2 RpIVi~GPSG~GK~Tl~   18 (186)
T 1ex7_A            2 RPIVISGPSGTGKSTLL   18 (186)
T ss_dssp             CCEEEECCTTSSHHHHH
T ss_pred             CEEEEECCCCCCHHHHH
Confidence            45899999999999754

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=83.88  E-value=0.78  Score=36.23  Aligned_cols=21  Identities=19%  Similarity=0.226  Sum_probs=16.5

Q ss_pred             cccCCcEEEEcCCCChhhHHH
Q 017573           30 FCKGLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        30 ~~~~~~~li~~~tG~GKT~~~   50 (369)
                      +..|+-+.+.||+|+|||..+
T Consensus        20 i~~G~~~~lvGpsGsGKSTLl   40 (218)
T 1z6g_A           20 MNNIYPLVICGPSGVGKGTLI   40 (218)
T ss_dssp             --CCCCEEEECSTTSSHHHHH
T ss_pred             cCCCCEEEEECCCCCCHHHHH
Confidence            346788999999999999654

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=83.85  E-value=0.73  Score=34.79  Aligned_cols=17  Identities=18%  Similarity=0.288  Sum_probs=14.8

Q ss_pred             cEEEEcCCCChhhHHHH
Q 017573           35 DVIQQAQSGTGKTATFC   51 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~   51 (369)
                      .+++.+++|||||.++-
T Consensus         6 ~i~i~G~~GsGKsTla~   22 (175)
T 1via_A            6 NIVFIGFMGSGKSTLAR   22 (175)
T ss_dssp             CEEEECCTTSCHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHH
Confidence            68999999999998763

>3sr0_A Adenylate kinase; phosphoryl transfer analogue, ALF4, transferase (phosphotran phosphoryl transfer, nucleotide-binding; HET: ADP AMP; 1.56A {Aquifex aeolicus} PDB: 2rh5_A 2rgx_A*

Probab=83.59  E-value=0.8  Score=35.81  Aligned_cols=16  Identities=19%  Similarity=0.268  Sum_probs=13.8

Q ss_pred             EEEEcCCCChhhHHHH
Q 017573           36 VIQQAQSGTGKTATFC   51 (369)
Q Consensus        36 ~li~~~tG~GKT~~~~   51 (369)
                      +++.||+||||++.+-
T Consensus         3 Iil~GpPGsGKgTqa~   18 (206)
T 3sr0_A            3 LVFLGPPGAGKGTQAK   18 (206)
T ss_dssp             EEEECSTTSSHHHHHH
T ss_pred             EEEECCCCCCHHHHHH
Confidence            6889999999998764

>3l0o_A Transcription termination factor RHO; helicase, RHO factor, RNA capture mechanism, ATP-binding, hydrolase, nucleotide-binding, RN binding; 2.35A {Thermotoga maritima}

Probab=83.49  E-value=1.2  Score=38.54  Aligned_cols=29  Identities=24%  Similarity=0.271  Sum_probs=22.0

Q ss_pred             cccCCcEEEEcCCCChhhHHHHHHHHHhhh
Q 017573           30 FCKGLDVIQQAQSGTGKTATFCSGILQQLD   59 (369)
Q Consensus        30 ~~~~~~~li~~~tG~GKT~~~~~~~~~~~~   59 (369)
                      +-+|+..+|.++.|+|||..+ ..+.+.+.
T Consensus       172 igrGQR~lIfg~~g~GKT~Ll-~~Ia~~i~  200 (427)
T 3l0o_A          172 IGKGQRGMIVAPPKAGKTTIL-KEIANGIA  200 (427)
T ss_dssp             CBTTCEEEEEECTTCCHHHHH-HHHHHHHH
T ss_pred             ccCCceEEEecCCCCChhHHH-HHHHHHHh
Confidence            446899999999999999776 34444444

>2cdn_A Adenylate kinase; phosphoryl transfer, associative mechanism, ATP-binding, nucleotide biosynthesis, nucleotide-binding, transferase; HET: ADP; 1.9A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1p4s_A

Probab=83.03  E-value=0.83  Score=35.40  Aligned_cols=19  Identities=21%  Similarity=0.335  Sum_probs=15.7

Q ss_pred             CCcEEEEcCCCChhhHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~   51 (369)
                      +..+++.|++|||||..+-
T Consensus        20 ~~~I~l~G~~GsGKST~a~   38 (201)
T 2cdn_A           20 HMRVLLLGPPGAGKGTQAV   38 (201)
T ss_dssp             CCEEEEECCTTSSHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHH
Confidence            3468999999999998753

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=82.96  E-value=1.1  Score=47.19  Aligned_cols=41  Identities=17%  Similarity=0.058  Sum_probs=33.4

Q ss_pred             cccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCC
Q 017573           30 FCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPT   73 (369)
Q Consensus        30 ~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~   73 (369)
                      +..+.++++.+|+|+|||..+...+.+....+.   +++|+.-.
T Consensus      1078 i~~g~~vll~G~~GtGKT~la~~~~~ea~k~Ge---~~~Fit~e 1118 (2050)
T 3cmu_A         1078 LPMGRIVEIYGPESSGKTTLTLQVIAAAQREGK---TCAFIDAE 1118 (2050)
T ss_dssp             EETTSEEEEECCTTSSHHHHHHHHHHHHHTTTC---CEEEECTT
T ss_pred             cCCCcEEEEECCCCCCHHHHHHHHHHHHHHcCC---eEEEEEcc
Confidence            446788999999999999998888887776654   78888754

>1hqc_A RUVB; extended AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ADE; 3.20A {Thermus thermophilus} SCOP: a.4.5.11 c.37.1.20 PDB: 1ixs_B* 1ixr_C*

Probab=82.86  E-value=0.68  Score=39.02  Aligned_cols=18  Identities=22%  Similarity=0.224  Sum_probs=15.8

Q ss_pred             CcEEEEcCCCChhhHHHH
Q 017573           34 LDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~   51 (369)
                      ..+++.||+|+|||..+-
T Consensus        39 ~~vll~G~~GtGKT~la~   56 (324)
T 1hqc_A           39 EHLLLFGPPGLGKTTLAH   56 (324)
T ss_dssp             CCCEEECCTTCCCHHHHH
T ss_pred             CcEEEECCCCCCHHHHHH
Confidence            689999999999997753

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=82.84  E-value=0.53  Score=39.08  Aligned_cols=18  Identities=28%  Similarity=0.361  Sum_probs=15.2

Q ss_pred             CcEEEEcCCCChhhHHHH
Q 017573           34 LDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~   51 (369)
                      .-+++.||+|||||..+-
T Consensus        34 ~livl~G~sGsGKSTla~   51 (287)
T 1gvn_B           34 TAFLLGGQPGSGKTSLRS   51 (287)
T ss_dssp             EEEEEECCTTSCTHHHHH
T ss_pred             eEEEEECCCCCCHHHHHH
Confidence            458999999999997753

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=82.82  E-value=0.76  Score=35.68  Aligned_cols=17  Identities=24%  Similarity=0.321  Sum_probs=15.1

Q ss_pred             CcEEEEcCCCChhhHHH
Q 017573           34 LDVIQQAQSGTGKTATF   50 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~   50 (369)
                      .-+++.|++|||||..+
T Consensus        19 ~~I~l~G~~GsGKSTla   35 (202)
T 3t61_A           19 GSIVVMGVSGSGKSSVG   35 (202)
T ss_dssp             SCEEEECSTTSCHHHHH
T ss_pred             eEEEEECCCCCCHHHHH
Confidence            57899999999999775

>1in4_A RUVB, holliday junction DNA helicase RUVB; AAA+-class ATPase, winged-helix domain, ATP hydrolysis, walker A, walker B, sensor 1, sensor 2; HET: ADP; 1.60A {Thermotoga maritima} SCOP: a.4.5.11 c.37.1.20 PDB: 1in5_A* 1in6_A* 1in8_A* 1in7_A* 1j7k_A*

Probab=82.79  E-value=0.78  Score=39.02  Aligned_cols=17  Identities=29%  Similarity=0.317  Sum_probs=15.2

Q ss_pred             CcEEEEcCCCChhhHHH
Q 017573           34 LDVIQQAQSGTGKTATF   50 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~   50 (369)
                      ..+++.||+|+|||..+
T Consensus        52 ~~~ll~Gp~G~GKTTLa   68 (334)
T 1in4_A           52 DHVLLAGPPGLGKTTLA   68 (334)
T ss_dssp             CCEEEESSTTSSHHHHH
T ss_pred             CeEEEECCCCCcHHHHH
Confidence            67999999999999765

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=82.77  E-value=0.88  Score=35.72  Aligned_cols=17  Identities=18%  Similarity=0.321  Sum_probs=14.4

Q ss_pred             cEEEEcCCCChhhHHHH
Q 017573           35 DVIQQAQSGTGKTATFC   51 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~   51 (369)
                      .+++.|++|||||+.+-
T Consensus         2 ~I~l~G~~GsGKsT~a~   18 (216)
T 3fb4_A            2 NIVLMGLPGAGKGTQAE   18 (216)
T ss_dssp             EEEEECSTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            37899999999998763

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=82.71  E-value=0.77  Score=37.77  Aligned_cols=17  Identities=29%  Similarity=0.347  Sum_probs=14.8

Q ss_pred             CcEEEEcCCCChhhHHH
Q 017573           34 LDVIQQAQSGTGKTATF   50 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~   50 (369)
                      +++++.||+|+|||..+
T Consensus        45 ~GvlL~Gp~GtGKTtLa   61 (274)
T 2x8a_A           45 AGVLLAGPPGCGKTLLA   61 (274)
T ss_dssp             SEEEEESSTTSCHHHHH
T ss_pred             CeEEEECCCCCcHHHHH
Confidence            55999999999999764

>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=82.63  E-value=6.3  Score=31.38  Aligned_cols=73  Identities=8%  Similarity=0.099  Sum_probs=51.8

Q ss_pred             CCCeEEEeCCHhhHHHHHHHHhh----CCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEec-----CCc-CCCCCCCC
Q 017573          235 ITQSVIFVNTRRKVDWLTDKMRS----RDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTD-----LLA-RGIDVQQV  304 (369)
Q Consensus       235 ~~k~lv~~~~~~~~~~~~~~l~~----~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~-----~~~-~G~d~~~~  304 (369)
                      ..++++.+|+++.+..+.+.+++    .+..+..++|+.+.......+..    ..+|+|+|+     .+. ..+++..+
T Consensus       102 ~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~----~~~I~v~Tp~~l~~~l~~~~~~~~~~  177 (242)
T 3fe2_A          102 GPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIRDLER----GVEICIATPGRLIDFLECGKTNLRRT  177 (242)
T ss_dssp             CCSEEEECSSHHHHHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHH----CCSEEEECHHHHHHHHHHTSCCCTTC
T ss_pred             CCEEEEEeCcHHHHHHHHHHHHHHHhhcCceEEEEECCCChHHHHHHhcC----CCCEEEECHHHHHHHHHcCCCCcccc
Confidence            45799999999988877666654    37788899998887765544432    468999996     111 23567778


Q ss_pred             cEEEEec
Q 017573          305 SLVINYD  311 (369)
Q Consensus       305 ~~vi~~~  311 (369)
                      +.+|+-+
T Consensus       178 ~~lViDE  184 (242)
T 3fe2_A          178 TYLVLDE  184 (242)
T ss_dssp             CEEEETT
T ss_pred             cEEEEeC
Confidence            8887654

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=82.57  E-value=0.86  Score=35.58  Aligned_cols=21  Identities=19%  Similarity=0.191  Sum_probs=17.4

Q ss_pred             ccCCcEEEEcCCCChhhHHHH
Q 017573           31 CKGLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        31 ~~~~~~li~~~tG~GKT~~~~   51 (369)
                      ..+..+++.|++|||||+.+-
T Consensus         8 ~~~~~I~l~G~~GsGKST~~~   28 (212)
T 2wwf_A            8 KKGKFIVFEGLDRSGKSTQSK   28 (212)
T ss_dssp             BCSCEEEEEESTTSSHHHHHH
T ss_pred             hcCCEEEEEcCCCCCHHHHHH
Confidence            456779999999999998763

>1aky_A Adenylate kinase; ATP:AMP phosphotransferase, myokinase, transferase (phosphotransferase); HET: AP5; 1.63A {Saccharomyces cerevisiae} SCOP: c.37.1.1 g.41.2.1 PDB: 2aky_A* 3aky_A* 1dvr_A*

Probab=82.57  E-value=0.85  Score=35.97  Aligned_cols=19  Identities=16%  Similarity=0.281  Sum_probs=15.8

Q ss_pred             CCcEEEEcCCCChhhHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~   51 (369)
                      +..+++.|++|||||+.+-
T Consensus         4 ~~~I~l~G~~GsGKsT~a~   22 (220)
T 1aky_A            4 SIRMVLIGPPGAGKGTQAP   22 (220)
T ss_dssp             CCEEEEECCTTSSHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHH
Confidence            4568999999999998763

>2iyv_A Shikimate kinase, SK; transferase, aromatic amino acid biosynthesis, P-loop kinase, metal- binding, shikimate pathway; HET: ADP; 1.35A {Mycobacterium tuberculosis} SCOP: c.37.1.2 PDB: 2iyr_A* 2iyq_A* 2iyt_A 2iyu_A* 2iys_A* 2iyw_A* 2iyx_A* 2iyy_A* 2iyz_A* 2g1k_A* 1l4y_A* 1u8a_A* 1we2_A* 1zyu_A* 2dfn_A* 2dft_A* 2g1j_A 1l4u_A* 3baf_A*

Probab=82.50  E-value=0.95  Score=34.43  Aligned_cols=18  Identities=17%  Similarity=0.180  Sum_probs=15.1

Q ss_pred             CcEEEEcCCCChhhHHHH
Q 017573           34 LDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~   51 (369)
                      ..+++.+++|||||.++-
T Consensus         3 ~~I~l~G~~GsGKsT~a~   20 (184)
T 2iyv_A            3 PKAVLVGLPGSGKSTIGR   20 (184)
T ss_dssp             CSEEEECSTTSSHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHH
Confidence            358999999999998763

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=82.49  E-value=0.89  Score=35.93  Aligned_cols=19  Identities=21%  Similarity=0.270  Sum_probs=16.0

Q ss_pred             CCcEEEEcCCCChhhHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~   51 (369)
                      ...+++.|++|||||..+-
T Consensus         5 ~~~I~l~G~~GsGKsT~~~   23 (222)
T 1zak_A            5 PLKVMISGAPASGKGTQCE   23 (222)
T ss_dssp             SCCEEEEESTTSSHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHH
Confidence            3578999999999998763

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=82.47  E-value=1.4  Score=38.99  Aligned_cols=35  Identities=20%  Similarity=0.114  Sum_probs=24.1

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHhhhc-cCCCccEEEEc
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQLDY-GLVQCQALVLA   71 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~~~~-~~~~~~~liv~   71 (369)
                      +.+++.++.|+|||+++...+...... +.   +++++.
T Consensus       101 ~vI~ivG~~GvGKTT~a~~LA~~l~~~~G~---kVllvd  136 (433)
T 2xxa_A          101 AVVLMAGLQGAGKTTSVGKLGKFLREKHKK---KVLVVS  136 (433)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHHTSCC---CEEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHhcCC---eEEEEe
Confidence            357788999999998876555544433 32   677665

>3dl0_A Adenylate kinase; phosphotransferase, zinc coordination, ATP-binding, binding, nucleotide biosynthesis, nucleotide-binding, trans; HET: AP5; 1.58A {Bacillus subtilis} PDB: 1p3j_A* 2ori_A* 2eu8_A* 2oo7_A* 2p3s_A* 2qaj_A* 2osb_A* 3dkv_A* 1zin_A* 1zio_A* 1zip_A* 1s3g_A*

Probab=82.41  E-value=0.76  Score=36.11  Aligned_cols=17  Identities=18%  Similarity=0.239  Sum_probs=14.4

Q ss_pred             cEEEEcCCCChhhHHHH
Q 017573           35 DVIQQAQSGTGKTATFC   51 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~   51 (369)
                      .+++.|++|||||+.+-
T Consensus         2 ~I~l~G~~GsGKsT~a~   18 (216)
T 3dl0_A            2 NLVLMGLPGAGKGTQGE   18 (216)
T ss_dssp             EEEEECSTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            47899999999998763

>3cmw_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 2.80A {Escherichia coli} PDB: 3cmt_A* 3cmx_A* 3cmv_A*

Probab=82.34  E-value=1.3  Score=46.13  Aligned_cols=43  Identities=16%  Similarity=0.060  Sum_probs=33.1

Q ss_pred             cccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHH
Q 017573           30 FCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRE   75 (369)
Q Consensus        30 ~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~   75 (369)
                      +..+..+++.+|+|+|||..++..+.+.+..+.   +++|+.-...
T Consensus        31 i~~G~i~lI~G~pGsGKT~LAlqla~~~~~~G~---~vlYI~te~~   73 (1706)
T 3cmw_A           31 LPMGRIVEIYGPESSGKTTLTLQVIAAAQREGK---TCAFIDAEHA   73 (1706)
T ss_dssp             EETTSEEEEECSTTSSHHHHHHHHHHHHHHTTC---CEEEECTTSC
T ss_pred             cCCCeEEEEECCCCCCHHHHHHHHHHHHhhCCC---ceEEEEecCc
Confidence            344688999999999999888777776665543   7899886543

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=82.32  E-value=1.3  Score=36.91  Aligned_cols=37  Identities=22%  Similarity=0.300  Sum_probs=22.8

Q ss_pred             cCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEc
Q 017573           32 KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLA   71 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~   71 (369)
                      .+.-+.+.+|+|+|||+.+-. +...+...  ++++.+..
T Consensus        99 ~g~vi~lvG~nGsGKTTll~~-Lag~l~~~--~g~V~l~g  135 (302)
T 3b9q_A           99 KPAVIMIVGVNGGGKTTSLGK-LAHRLKNE--GTKVLMAA  135 (302)
T ss_dssp             SCEEEEEECCTTSCHHHHHHH-HHHHHHHT--TCCEEEEC
T ss_pred             CCcEEEEEcCCCCCHHHHHHH-HHHHHHHc--CCeEEEEe
Confidence            455678999999999976432 22233222  22677665

>1e6c_A Shikimate kinase; phosphoryl transfer, ADP, shikimate pathway, P-loop protein, transferase; 1.8A {Erwinia chrysanthemi} SCOP: c.37.1.2 PDB: 1shk_A 2shk_A*

Probab=82.31  E-value=0.92  Score=34.03  Aligned_cols=18  Identities=17%  Similarity=0.098  Sum_probs=15.1

Q ss_pred             CcEEEEcCCCChhhHHHH
Q 017573           34 LDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~   51 (369)
                      +.+++.+++|||||.++-
T Consensus         3 ~~I~l~G~~GsGKsT~a~   20 (173)
T 1e6c_A            3 EPIFMVGARGCGMTTVGR   20 (173)
T ss_dssp             CCEEEESCTTSSHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHH
Confidence            358999999999998763

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=82.25  E-value=0.73  Score=35.94  Aligned_cols=19  Identities=21%  Similarity=0.398  Sum_probs=15.9

Q ss_pred             CCcEEEEcCCCChhhHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~   51 (369)
                      +..+++.|++|||||..+-
T Consensus         4 ~~~I~i~G~~GsGKsT~~~   22 (213)
T 2plr_A            4 GVLIAFEGIDGSGKSSQAT   22 (213)
T ss_dssp             CEEEEEECCTTSSHHHHHH
T ss_pred             CeEEEEEcCCCCCHHHHHH
Confidence            4568999999999998753

>3uie_A Adenylyl-sulfate kinase 1, chloroplastic; rossmann fold, transferase-transferase complex; HET: ADX ANP; 1.79A {Arabidopsis thaliana} SCOP: c.37.1.0 PDB: 4fxp_A*

Probab=82.21  E-value=0.75  Score=35.68  Aligned_cols=20  Identities=30%  Similarity=0.340  Sum_probs=16.6

Q ss_pred             ccCCcEEEEcCCCChhhHHH
Q 017573           31 CKGLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        31 ~~~~~~li~~~tG~GKT~~~   50 (369)
                      ..+.-+.+.||+|+|||..+
T Consensus        23 ~~g~~i~l~G~sGsGKSTl~   42 (200)
T 3uie_A           23 QKGCVIWVTGLSGSGKSTLA   42 (200)
T ss_dssp             SCCEEEEEECSTTSSHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHH
Confidence            34677899999999999765

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=82.21  E-value=0.78  Score=35.13  Aligned_cols=17  Identities=24%  Similarity=0.304  Sum_probs=14.3

Q ss_pred             cEEEEcCCCChhhHHHH
Q 017573           35 DVIQQAQSGTGKTATFC   51 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~   51 (369)
                      .+++.|++|+|||+.+-
T Consensus         3 ~I~i~G~~GsGKsT~~~   19 (194)
T 1nks_A            3 IGIVTGIPGVGKSTVLA   19 (194)
T ss_dssp             EEEEEECTTSCHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            47899999999997753

>3eph_A TRNA isopentenyltransferase; transferase, alternative initiation, ATP-binding, cytoplasm, mitochondrion, nucleotide-binding, nucleus; 2.95A {Saccharomyces cerevisiae} PDB: 3epj_A 3epk_A* 3epl_A*

Probab=82.17  E-value=0.73  Score=40.06  Aligned_cols=19  Identities=16%  Similarity=0.204  Sum_probs=15.1

Q ss_pred             cEEEEcCCCChhhHHHHHH
Q 017573           35 DVIQQAQSGTGKTATFCSG   53 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~~~   53 (369)
                      -++|.||||+|||..+...
T Consensus         4 ~i~i~GptgsGKttla~~L   22 (409)
T 3eph_A            4 VIVIAGTTGVGKSQLSIQL   22 (409)
T ss_dssp             EEEEEECSSSSHHHHHHHH
T ss_pred             EEEEECcchhhHHHHHHHH
Confidence            4689999999999776433

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=82.08  E-value=0.66  Score=36.95  Aligned_cols=21  Identities=29%  Similarity=0.366  Sum_probs=13.5

Q ss_pred             cccCCcEEEEcCCCChhhHHH
Q 017573           30 FCKGLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        30 ~~~~~~~li~~~tG~GKT~~~   50 (369)
                      +..|+-+.+.||+|+|||..+
T Consensus        24 v~~G~ii~l~Gp~GsGKSTl~   44 (231)
T 3lnc_A           24 KSVGVILVLSSPSGCGKTTVA   44 (231)
T ss_dssp             EECCCEEEEECSCC----CHH
T ss_pred             cCCCCEEEEECCCCCCHHHHH
Confidence            446778899999999999764

>3tqf_A HPR(Ser) kinase; transferase, hydrolase; 2.80A {Coxiella burnetii}

Probab=81.93  E-value=0.78  Score=34.60  Aligned_cols=23  Identities=17%  Similarity=0.235  Sum_probs=18.6

Q ss_pred             cCCcEEEEcCCCChhhHHHHHHH
Q 017573           32 KGLDVIQQAQSGTGKTATFCSGI   54 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~~~~   54 (369)
                      .++.+++.++.|+|||..++..+
T Consensus        15 ~G~gvli~G~SGaGKStlal~L~   37 (181)
T 3tqf_A           15 DKMGVLITGEANIGKSELSLALI   37 (181)
T ss_dssp             TTEEEEEEESSSSSHHHHHHHHH
T ss_pred             CCEEEEEEcCCCCCHHHHHHHHH
Confidence            56889999999999997765443

>1rj9_A FTSY, signal recognition protein; SRP-GTPase domain, heterodimer, nucleotide twinning, protein complex, protein transport; HET: GCP; 1.90A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 2q9c_A* 2q9b_A* 2q9a_A* 1okk_D* 2xkv_D 2iyl_D* 2cnw_D* 2j7p_D*

Probab=81.89  E-value=1.7  Score=36.34  Aligned_cols=37  Identities=24%  Similarity=0.239  Sum_probs=22.4

Q ss_pred             cCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEc
Q 017573           32 KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLA   71 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~   71 (369)
                      .+.-+.+.+|+|+|||+.+-. +...+...  ++++++..
T Consensus       101 ~g~vi~lvG~nGsGKTTll~~-Lagll~~~--~g~V~l~g  137 (304)
T 1rj9_A          101 KGRVVLVVGVNGVGKTTTIAK-LGRYYQNL--GKKVMFCA  137 (304)
T ss_dssp             SSSEEEEECSTTSSHHHHHHH-HHHHHHTT--TCCEEEEC
T ss_pred             CCeEEEEECCCCCcHHHHHHH-HHHHHHhc--CCEEEEEe
Confidence            356688999999999976432 22222222  22666655

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=81.75  E-value=0.87  Score=34.90  Aligned_cols=19  Identities=26%  Similarity=0.298  Sum_probs=15.5

Q ss_pred             CCcEEEEcCCCChhhHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~   51 (369)
                      +..+++.|++|||||..+-
T Consensus         3 ~~~I~l~G~~GsGKsT~a~   21 (196)
T 1tev_A            3 PLVVFVLGGPGAGKGTQCA   21 (196)
T ss_dssp             CEEEEEECCTTSSHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHH
Confidence            3458899999999998763

>1znw_A Guanylate kinase, GMP kinase; ATP:GMP-phosphotransferase, TR; 2.10A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1znx_A* 1zny_A* 1znz_A* 1s4q_A 1z8f_A

Probab=81.70  E-value=0.98  Score=35.25  Aligned_cols=22  Identities=27%  Similarity=0.391  Sum_probs=16.8

Q ss_pred             ccccCCcEEEEcCCCChhhHHH
Q 017573           29 PFCKGLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        29 ~~~~~~~~li~~~tG~GKT~~~   50 (369)
                      .+.+|+-+.+.+|.|+|||..+
T Consensus        16 ~i~~Gei~~l~GpnGsGKSTLl   37 (207)
T 1znw_A           16 PAAVGRVVVLSGPSAVGKSTVV   37 (207)
T ss_dssp             ---CCCEEEEECSTTSSHHHHH
T ss_pred             CCCCCCEEEEECCCCCCHHHHH
Confidence            5667888999999999999653

>1g8p_A Magnesium-chelatase 38 kDa subunit; parallel beta sheet, P-loop, rossman fold, AAA+, photosynthesis, metal transport; 2.10A {Rhodobacter capsulatus} SCOP: c.37.1.20 PDB: 2x31_G

Probab=81.64  E-value=0.59  Score=39.89  Aligned_cols=19  Identities=26%  Similarity=0.247  Sum_probs=16.2

Q ss_pred             CCcEEEEcCCCChhhHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~   51 (369)
                      ..++++.||+|+|||..+-
T Consensus        45 ~~~vLl~G~~GtGKT~la~   63 (350)
T 1g8p_A           45 IGGVLVFGDRGTGKSTAVR   63 (350)
T ss_dssp             GCCEEEECCGGGCTTHHHH
T ss_pred             CceEEEECCCCccHHHHHH
Confidence            4679999999999997753

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=81.63  E-value=0.88  Score=36.10  Aligned_cols=18  Identities=22%  Similarity=0.278  Sum_probs=15.6

Q ss_pred             CCcEEEEcCCCChhhHHH
Q 017573           33 GLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~   50 (369)
                      ...+++.|++|||||..+
T Consensus         7 ~~~I~l~G~~GsGKsT~a   24 (227)
T 1zd8_A            7 LLRAVIMGAPGSGKGTVS   24 (227)
T ss_dssp             CCEEEEEECTTSSHHHHH
T ss_pred             CcEEEEECCCCCCHHHHH
Confidence            456899999999999875

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=81.53  E-value=0.86  Score=37.51  Aligned_cols=17  Identities=29%  Similarity=0.321  Sum_probs=14.7

Q ss_pred             CcEEEEcCCCChhhHHH
Q 017573           34 LDVIQQAQSGTGKTATF   50 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~   50 (369)
                      +.+++.+|+|+|||..+
T Consensus        74 ~gvll~Gp~GtGKTtl~   90 (278)
T 1iy2_A           74 KGVLLVGPPGVGKTHLA   90 (278)
T ss_dssp             CEEEEECCTTSSHHHHH
T ss_pred             CeEEEECCCcChHHHHH
Confidence            45999999999999764

>1xjc_A MOBB protein homolog; structural genomics, midwest center for structural GEN PSI, protein structure initiative, MCSG; 2.10A {Geobacillus stearothermophilus} SCOP: c.37.1.10

Probab=81.53  E-value=2  Score=32.29  Aligned_cols=24  Identities=13%  Similarity=-0.092  Sum_probs=16.7

Q ss_pred             cEEEEcCCCChhhHHHHHHHHHhhh
Q 017573           35 DVIQQAQSGTGKTATFCSGILQQLD   59 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~~~~~~~~~   59 (369)
                      -+.+.++.|+|||..+. .++..+.
T Consensus         6 ~i~i~G~sGsGKTTl~~-~L~~~l~   29 (169)
T 1xjc_A            6 VWQVVGYKHSGKTTLME-KWVAAAV   29 (169)
T ss_dssp             EEEEECCTTSSHHHHHH-HHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH-HHHHhhH
Confidence            46889999999997643 3444443

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus}

Probab=81.41  E-value=5.3  Score=33.24  Aligned_cols=72  Identities=25%  Similarity=0.340  Sum_probs=52.0

Q ss_pred             cEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHH----ccCCcEEEeccHHHHHHHHcCCCCCCCccE
Q 017573           66 QALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL----QAGVHVVVGTPGRVFDMLRRQSLRPDYIKM  141 (369)
Q Consensus        66 ~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~----~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~  141 (369)
                      ++||.|+++.-++.+.+.+.+.    ++.+..++|+.........+    .+..+|+|+|.     . ...+++...+++
T Consensus        30 ~~LVF~~t~~~~~~l~~~L~~~----g~~~~~lhg~l~~~~r~~~~~~f~~g~~~vLVaT~-----v-a~~Gidi~~v~~   99 (300)
T 3i32_A           30 RAMVFTRTKAETEEIAQGLLRL----GHPAQALHGDMSQGERERVMGAFRQGEVRVLVATD-----V-AARGLDIPQVDL   99 (300)
T ss_dssp             SEEEECSSHHHHHHHHHHHHTT----TCCEEEECSCCCTHHHHHHHHHHHHTSCCEEEECS-----T-TTCSTTCCCCSE
T ss_pred             CEEEEECCHHHHHHHHHHHHhC----CCCEEEEeCCCCHHHHHHHHHHhhcCCceEEEEec-----h-hhcCccccceeE
Confidence            8999999999888888777654    77889999987765544333    35788999992     2 334566777787


Q ss_pred             EEEech
Q 017573          142 FVLDEA  147 (369)
Q Consensus       142 viiDE~  147 (369)
                      ||.=+.
T Consensus       100 VI~~d~  105 (300)
T 3i32_A          100 VVHYRM  105 (300)
T ss_dssp             EEESSC
T ss_pred             EEEcCC
Confidence            775443

>1qf9_A UMP/CMP kinase, protein (uridylmonophosphate/cytidylmonophosphate kinase); nucleoside monophosphate kinase, NMP kinase; HET: ADP C5P; 1.70A {Dictyostelium discoideum} SCOP: c.37.1.1 PDB: 1uke_A* 2ukd_A* 3ukd_A* 4ukd_A* 5ukd_A*

Probab=81.35  E-value=0.88  Score=34.81  Aligned_cols=18  Identities=22%  Similarity=0.231  Sum_probs=15.0

Q ss_pred             CcEEEEcCCCChhhHHHH
Q 017573           34 LDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~   51 (369)
                      ..+++.|++|||||.++-
T Consensus         7 ~~I~l~G~~GsGKsT~~~   24 (194)
T 1qf9_A            7 NVVFVLGGPGSGKGTQCA   24 (194)
T ss_dssp             EEEEEEESTTSSHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHH
Confidence            358899999999998753

>1pzn_A RAD51, DNA repair and recombination protein RAD51, RADA; heptameric ring, heptamer, ring, oligomer, RAD51 polymerizat motif; HET: DNA; 2.85A {Pyrococcus furiosus} SCOP: a.60.4.1 c.37.1.11

Probab=81.35  E-value=1.2  Score=38.03  Aligned_cols=41  Identities=12%  Similarity=-0.042  Sum_probs=24.8

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhc---cCCCccEEEEcCC
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDY---GLVQCQALVLAPT   73 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~---~~~~~~~liv~P~   73 (369)
                      |.-+.+.+|+|+|||..+...+......   +..+.+++++.-.
T Consensus       131 G~i~~I~G~~GsGKTTL~~~l~~~~~~~~~~Gg~~G~vi~i~~e  174 (349)
T 1pzn_A          131 QAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTE  174 (349)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEESS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhccchhcCCCCCeEEEEeCC
Confidence            4567999999999997765444432111   1112366777643

>3tlx_A Adenylate kinase 2; structural genomics, structural genomics consortium, SGC, RO fold, transferase, ATP binding, phosphorylation; HET: ADP ATP AMP; 2.75A {Plasmodium falciparum}

Probab=81.30  E-value=0.77  Score=36.98  Aligned_cols=20  Identities=20%  Similarity=0.124  Sum_probs=16.5

Q ss_pred             cCCcEEEEcCCCChhhHHHH
Q 017573           32 KGLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~   51 (369)
                      ....+++.||+|||||+.+-
T Consensus        28 ~~~~I~l~G~~GsGKsT~a~   47 (243)
T 3tlx_A           28 PDGRYIFLGAPGSGKGTQSL   47 (243)
T ss_dssp             CCEEEEEECCTTSSHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHH
Confidence            34568999999999998763

>3nwn_A Kinesin-like protein KIF9; motor domain, ADP, structural genomics, structural consortium, SGC, contractIle protein; HET: ADP; 2.00A {Homo sapiens}

Probab=81.22  E-value=0.77  Score=39.33  Aligned_cols=23  Identities=30%  Similarity=0.463  Sum_probs=17.4

Q ss_pred             hccccCCc--EEEEcCCCChhhHHH
Q 017573           28 VPFCKGLD--VIQQAQSGTGKTATF   50 (369)
Q Consensus        28 ~~~~~~~~--~li~~~tG~GKT~~~   50 (369)
                      +.+++|.+  ++..|.||||||.++
T Consensus        98 ~~~l~G~N~tifAYGQTGSGKTyTM  122 (359)
T 3nwn_A           98 SQALDGYNGTIMCYGQTGAGKTYTM  122 (359)
T ss_dssp             HHHHTTCCEEEEEEESTTSSHHHHH
T ss_pred             HHHhCCCCEEEEEeCCCCCCccEEe
Confidence            33445655  688899999999875

>4a74_A DNA repair and recombination protein RADA; hydrolase, recombinase; HET: DNA ANP; 1.48A {Pyrococcus furiosus} PDB: 4a6x_A* 4a6p_A* 4a7o_A*

Probab=81.20  E-value=0.78  Score=36.35  Aligned_cols=24  Identities=17%  Similarity=-0.038  Sum_probs=18.6

Q ss_pred             cccCCcEEEEcCCCChhhHHHHHH
Q 017573           30 FCKGLDVIQQAQSGTGKTATFCSG   53 (369)
Q Consensus        30 ~~~~~~~li~~~tG~GKT~~~~~~   53 (369)
                      +..|+-+.+.+|+|+|||..+...
T Consensus        22 i~~G~~~~l~G~nGsGKSTll~~l   45 (231)
T 4a74_A           22 IETQAITEVFGEFGSGKTQLAHTL   45 (231)
T ss_dssp             EESSEEEEEEESTTSSHHHHHHHH
T ss_pred             CCCCcEEEEECCCCCCHHHHHHHH
Confidence            445677899999999999765433

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=81.08  E-value=0.61  Score=35.46  Aligned_cols=19  Identities=26%  Similarity=0.158  Sum_probs=11.9

Q ss_pred             CCcEEEEcCCCChhhHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~   51 (369)
                      +..+++.|++|||||..+-
T Consensus         5 ~~~I~l~G~~GsGKST~a~   23 (183)
T 2vli_A            5 SPIIWINGPFGVGKTHTAH   23 (183)
T ss_dssp             CCEEEEECCC----CHHHH
T ss_pred             CeEEEEECCCCCCHHHHHH
Confidence            4568999999999998763

>1ak2_A Adenylate kinase isoenzyme-2; nucleoside monophosphate kinase, phosphotransferase; 1.92A {Bos taurus} SCOP: c.37.1.1 g.41.2.1 PDB: 2ak2_A 2c9y_A*

Probab=80.94  E-value=1  Score=35.86  Aligned_cols=19  Identities=21%  Similarity=0.350  Sum_probs=16.1

Q ss_pred             CCcEEEEcCCCChhhHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~   51 (369)
                      ...+++.|++|||||..+-
T Consensus        16 ~~~I~l~G~~GsGKsT~a~   34 (233)
T 1ak2_A           16 GVRAVLLGPPGAGKGTQAP   34 (233)
T ss_dssp             CCEEEEECCTTSSHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHH
Confidence            4579999999999998764

>3lda_A DNA repair protein RAD51; DNA binding protein, ATP-binding, DNA damage, DNA recombinat repair, nucleotide-binding; HET: DNA; 2.50A {Saccharomyces cerevisiae} PDB: 1szp_A*

Probab=80.86  E-value=1.8  Score=37.82  Aligned_cols=41  Identities=15%  Similarity=-0.033  Sum_probs=26.2

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhc---cCCCccEEEEcCC
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDY---GLVQCQALVLAPT   73 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~---~~~~~~~liv~P~   73 (369)
                      |.-+.|.+|+|+|||..+...++.....   +..+.+++|+.-.
T Consensus       178 Gei~~I~G~sGsGKTTLl~~la~~~~~p~~~Gg~~~~viyid~E  221 (400)
T 3lda_A          178 GSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTE  221 (400)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESS
T ss_pred             CcEEEEEcCCCCChHHHHHHHHHHhccCcccCCCCCcEEEEeCC
Confidence            4668999999999997765444433321   1123368887654

>1nn5_A Similar to deoxythymidylate kinase (thymidylate K; P-loop, D4TMP, transferase; HET: 2DT ANP; 1.50A {Homo sapiens} SCOP: c.37.1.1 PDB: 1e2e_A* 1e2d_A* 1e2g_A* 1e2q_A* 1e99_A* 1e9a_A* 1e9b_A* 1nmx_A* 1nmz_A* 1nn0_A* 1nn1_A* 1e2f_A* 1nn3_A* 2xx3_A* 1e9c_A* 1e9d_A* 1e9e_A* 1e98_A* 1nmy_A* 1e9f_A*

Probab=80.69  E-value=1  Score=35.13  Aligned_cols=20  Identities=15%  Similarity=0.275  Sum_probs=16.8

Q ss_pred             cCCcEEEEcCCCChhhHHHH
Q 017573           32 KGLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~   51 (369)
                      .+..+++.|++|||||..+-
T Consensus         8 ~~~~I~l~G~~GsGKsT~~~   27 (215)
T 1nn5_A            8 RGALIVLEGVDRAGKSTQSR   27 (215)
T ss_dssp             CCCEEEEEESTTSSHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHH
Confidence            45678999999999998764

>2bdt_A BH3686; alpha-beta protein, structural genomics, PSI, protein struct initiative, northeast structural genomics consortium, NESG, function; 2.40A {Bacillus halodurans} SCOP: c.37.1.25

Probab=80.65  E-value=1  Score=34.44  Aligned_cols=16  Identities=31%  Similarity=0.389  Sum_probs=13.7

Q ss_pred             cEEEEcCCCChhhHHH
Q 017573           35 DVIQQAQSGTGKTATF   50 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~   50 (369)
                      -+.+.+|+|+|||+.+
T Consensus         4 ii~l~G~~GaGKSTl~   19 (189)
T 2bdt_A            4 LYIITGPAGVGKSTTC   19 (189)
T ss_dssp             EEEEECSTTSSHHHHH
T ss_pred             EEEEECCCCCcHHHHH
Confidence            4689999999999765

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=80.64  E-value=0.95  Score=34.86  Aligned_cols=19  Identities=21%  Similarity=0.214  Sum_probs=16.2

Q ss_pred             cCCcEEEEcCCCChhhHHH
Q 017573           32 KGLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~   50 (369)
                      .+..+++.|++|||||..+
T Consensus        11 ~~~~I~l~G~~GsGKsT~a   29 (199)
T 2bwj_A           11 KCKIIFIIGGPGSGKGTQC   29 (199)
T ss_dssp             HSCEEEEEECTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            3567899999999999875

>1g41_A Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dependent proteolysis, chaperone; HET: ADP; 2.30A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1g3i_A* 1im2_A* 1kyi_A* 1g4a_E* 1g4b_E 1yyf_A* 1do0_A* 1do2_A* 1e94_E* 1hqy_E* 1ht1_E* 1ht2_E*

Probab=80.57  E-value=1  Score=39.79  Aligned_cols=18  Identities=22%  Similarity=0.359  Sum_probs=16.0

Q ss_pred             CCcEEEEcCCCChhhHHH
Q 017573           33 GLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~   50 (369)
                      .+++++.+|+|+|||..+
T Consensus        50 ~~~iLl~GppGtGKT~la   67 (444)
T 1g41_A           50 PKNILMIGPTGVGKTEIA   67 (444)
T ss_dssp             CCCEEEECCTTSSHHHHH
T ss_pred             CceEEEEcCCCCCHHHHH
Confidence            478999999999999775

>1f9v_A Kinesin-like protein KAR3; kinesin-related protein, motor protein, microtubinding proteinbule, contractIle protein; HET: ADP; 1.30A {Saccharomyces cerevisiae} SCOP: c.37.1.9 PDB: 1f9t_A* 1f9w_A* 1f9u_A* 3kar_A*

Probab=80.54  E-value=1.2  Score=38.05  Aligned_cols=26  Identities=27%  Similarity=0.388  Sum_probs=19.4

Q ss_pred             hhhccccCCc--EEEEcCCCChhhHHHH
Q 017573           26 GIVPFCKGLD--VIQQAQSGTGKTATFC   51 (369)
Q Consensus        26 ~~~~~~~~~~--~li~~~tG~GKT~~~~   51 (369)
                      +++.+++|.+  ++..|.||||||.++.
T Consensus        76 lv~~~l~G~n~tifAYGqTGSGKTyTM~  103 (347)
T 1f9v_A           76 LVQSSLDGYNVCIFAYGQTGSGKTFTML  103 (347)
T ss_dssp             HHGGGGGTCCEEEEEECCTTSSHHHHHH
T ss_pred             HHHHhcCCceeEEEEECCCCCCCcEecc
Confidence            3445567766  5778999999998863

>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA replication, MCM complex, AAA+ Pro ATP-binding, DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}

Probab=80.53  E-value=0.92  Score=42.00  Aligned_cols=16  Identities=19%  Similarity=0.414  Sum_probs=14.6

Q ss_pred             cEEEEcCCCChhhHHH
Q 017573           35 DVIQQAQSGTGKTATF   50 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~   50 (369)
                      ++++.||+|+|||..+
T Consensus       329 ~vLL~GppGtGKT~LA  344 (595)
T 3f9v_A          329 HILIIGDPGTAKSQML  344 (595)
T ss_dssp             CEEEEESSCCTHHHHH
T ss_pred             ceEEECCCchHHHHHH
Confidence            8999999999999764

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=80.51  E-value=1.1  Score=36.29  Aligned_cols=18  Identities=28%  Similarity=0.309  Sum_probs=16.7

Q ss_pred             CCcEEEEcCCCChhhHHH
Q 017573           33 GLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~   50 (369)
                      ++.+.+.+++|+|||.++
T Consensus        48 g~~i~l~G~~GsGKSTl~   65 (250)
T 3nwj_A           48 GRSMYLVGMMGSGKTTVG   65 (250)
T ss_dssp             TCCEEEECSTTSCHHHHH
T ss_pred             CCEEEEECCCCCCHHHHH
Confidence            899999999999999775

>1e4v_A Adenylate kinase; transferase(phosphotransferase); HET: AP5; 1.85A {Escherichia coli} SCOP: c.37.1.1 g.41.2.1 PDB: 1e4y_A* 1ake_A* 1ank_A* 2eck_A* 3hpq_A* 4ake_A 3hpr_A*

Probab=80.37  E-value=0.94  Score=35.55  Aligned_cols=17  Identities=18%  Similarity=0.124  Sum_probs=14.4

Q ss_pred             cEEEEcCCCChhhHHHH
Q 017573           35 DVIQQAQSGTGKTATFC   51 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~   51 (369)
                      .+++.|++|||||+.+-
T Consensus         2 ~I~l~G~~GsGKsT~a~   18 (214)
T 1e4v_A            2 RIILLGAPVAGKGTQAQ   18 (214)
T ss_dssp             EEEEEESTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            47899999999998763

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=80.18  E-value=1.1  Score=34.76  Aligned_cols=17  Identities=18%  Similarity=0.276  Sum_probs=14.2

Q ss_pred             cEEEEcCCCChhhHHHH
Q 017573           35 DVIQQAQSGTGKTATFC   51 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~   51 (369)
                      .+++.|++|||||+.+-
T Consensus         2 ~I~i~G~~GsGKsT~~~   18 (205)
T 2jaq_A            2 KIAIFGTVGAGKSTISA   18 (205)
T ss_dssp             EEEEECCTTSCHHHHHH
T ss_pred             EEEEECCCccCHHHHHH
Confidence            36899999999997753

>1j8m_F SRP54, signal recognition 54 kDa protein; signaling protein; 2.00A {Acidianus ambivalens} SCOP: a.24.13.1 c.37.1.10 PDB: 1j8y_F

Probab=80.11  E-value=1.8  Score=36.04  Aligned_cols=36  Identities=19%  Similarity=0.108  Sum_probs=22.7

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEc
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLA   71 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~   71 (369)
                      ++-+.+.+++|+|||..+...+......+   .+++++.
T Consensus        98 ~~vi~i~G~~G~GKTT~~~~la~~~~~~g---~~v~l~~  133 (297)
T 1j8m_F           98 PYVIMLVGVQGTGKTTTAGKLAYFYKKKG---FKVGLVG  133 (297)
T ss_dssp             SEEEEEECSSCSSTTHHHHHHHHHHHHTT---CCEEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHCC---CeEEEEe
Confidence            34577889999999977654443332222   2666665

>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=80.06  E-value=3.7  Score=32.66  Aligned_cols=75  Identities=15%  Similarity=0.248  Sum_probs=44.8

Q ss_pred             cCCCeEEEeCCHhhHHHHHHHHhhC----CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEec-----CCcC-CCCCCC
Q 017573          234 AITQSVIFVNTRRKVDWLTDKMRSR----DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTD-----LLAR-GIDVQQ  303 (369)
Q Consensus       234 ~~~k~lv~~~~~~~~~~~~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~-----~~~~-G~d~~~  303 (369)
                      ...++++.++++..+..+++.+++.    +..+..+.|+.+...   ..+.+..+..+|+|+|+     .+.. .++...
T Consensus        97 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~---~~~~l~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~  173 (237)
T 3bor_A           97 KETQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRN---EMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKW  173 (237)
T ss_dssp             CSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECC----------------CCCSEEEECHHHHHHHHHTTSSCSTT
T ss_pred             CCceEEEEECcHHHHHHHHHHHHHHhhhcCceEEEEECCCchHH---HHHHHhcCCCCEEEECHHHHHHHHHhCCcCccc
Confidence            3458999999999988888877654    456666777654332   23344556688999994     2222 356667


Q ss_pred             CcEEEEec
Q 017573          304 VSLVINYD  311 (369)
Q Consensus       304 ~~~vi~~~  311 (369)
                      ++.+|+-+
T Consensus       174 ~~~lViDE  181 (237)
T 3bor_A          174 IKMFVLDE  181 (237)
T ss_dssp             CCEEEEES
T ss_pred             CcEEEECC
Confidence            88887654

>1sxj_A Activator 1 95 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=80.02  E-value=1.1  Score=40.82  Aligned_cols=39  Identities=13%  Similarity=0.094  Sum_probs=23.9

Q ss_pred             ccEEEEechhHhhccC--cHHHHHHHHhhCCccCcEEEEEeeC
Q 017573          139 IKMFVLDEADEMLSRG--FKDQIYDIFQLLPAKVQVGVFSATM  179 (369)
Q Consensus       139 ~~~viiDE~H~~~~~~--~~~~~~~~~~~~~~~~~~i~~saT~  179 (369)
                      ..++++||+|.+....  ....+..++...  ...+++++++.
T Consensus       149 ~~vliIDEid~l~~~~~~~l~~L~~~l~~~--~~~iIli~~~~  189 (516)
T 1sxj_A          149 HFVIIMDEVDGMSGGDRGGVGQLAQFCRKT--STPLILICNER  189 (516)
T ss_dssp             SEEEEECSGGGCCTTSTTHHHHHHHHHHHC--SSCEEEEESCT
T ss_pred             CeEEEEECCCccchhhHHHHHHHHHHHHhc--CCCEEEEEcCC
Confidence            5799999999986432  123444444432  34577777664

---

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	369
d1hv8a1	208	c.37.1.19 (A:3-210) Putative DEAD box RNA helicase	1e-50
d2j0sa1	222	c.37.1.19 (A:22-243) Probable ATP-dependent RNA he	4e-50
d2g9na1	218	c.37.1.19 (A:21-238) Initiation factor 4a {Human (	1e-49
d1fuka_	162	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	3e-46
d1qdea_	212	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	3e-46
d2j0sa2	168	c.37.1.19 (A:244-411) Probable ATP-dependent RNA h	1e-45
d1t6na_	207	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	7e-43
d1wrba1	238	c.37.1.19 (A:164-401) putative ATP-dependent RNA h	6e-42
d1veca_	206	c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Huma	3e-40
d2rb4a1	168	c.37.1.19 (A:307-474) ATP-dependent RNA helicase D	5e-39
d1s2ma1	206	c.37.1.19 (A:46-251) Putative ATP-dependent RNA he	9e-39
d1s2ma2	171	c.37.1.19 (A:252-422) Putative ATP-dependent RNA h	9e-35
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	1e-33
d1a1va2	299	c.37.1.14 (A:326-624) HCV helicase domain {Human h	4e-33
d1hv8a2	155	c.37.1.19 (A:211-365) Putative DEAD box RNA helica	2e-32
d1q0ua_	209	c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR	6e-30
d1wp9a2	286	c.37.1.19 (A:201-486) putative ATP-dependent RNA h	1e-26
d1gkub2	248	c.37.1.16 (B:251-498) Helicase-like "domain" of re	2e-26
d1t5ia_	168	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	5e-26
d1gkub1	237	c.37.1.16 (B:1-250) Helicase-like "domain" of reve	2e-23
d1oywa2	206	c.37.1.19 (A:1-206) RecQ helicase domain {Escheric	3e-20
d1oywa3	200	c.37.1.19 (A:207-406) RecQ helicase domain {Escher	5e-20
d1jr6a_	138	c.37.1.14 (A:) HCV helicase domain {Human hepatiti	7e-20
d2p6ra3	202	c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus	1e-18
d2fwra1	200	c.37.1.19 (A:257-456) DNA repair protein RAD25 {Ar	2e-18
d1wp9a1	200	c.37.1.19 (A:1-200) putative ATP-dependent RNA hel	3e-15
d1t5la2	181	c.37.1.19 (A:415-595) Nucleotide excision repair e	1e-14
d1c4oa2	174	c.37.1.19 (A:410-583) Nucleotide excision repair e	2e-13
d2p6ra4	201	c.37.1.19 (A:203-403) Hel308 helicase {Archaeoglob	7e-10
d1z3ix1	346	c.37.1.19 (X:390-735) Rad54-like, Rad54L {Zebra fi	6e-06
d2eyqa5	211	c.37.1.19 (A:779-989) Transcription-repair couplin	6e-05
d1tf5a4	175	c.37.1.19 (A:396-570) Translocation ATPase SecA, n	7e-04
d1yksa2	299	c.37.1.14 (A:325-623) YFV helicase domain {Yellow	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 =  166 bits (422), Expect = 1e-50
 Identities = 70/201 (34%), Positives = 114/201 (56%), Gaps = 3/201 (1%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKG-LDVIQQAQSGTGKTATFCSGILQQLD 59
           + L +N+L  I   GFEKP+ IQ + I  F     +++ QA++G+GKTA+F   +++ ++
Sbjct: 9   LNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVN 68

Query: 60  YGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVV 119
                 +A++L PTRELA Q+   + +L     +K+    GG ++    + L+   ++VV
Sbjct: 69  EN-NGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALK-NANIVV 126

Query: 120 GTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATM 179
           GTPGR+ D + R +L    +K F+LDEADEML+ GF   +  I        ++ +FSATM
Sbjct: 127 GTPGRILDHINRGTLNLKNVKYFILDEADEMLNMGFIKDVEKILNACNKDKRILLFSATM 186

Query: 180 PPEALEITRKFMNKPVRILVK 200
           P E L + +K+M     I  K
Sbjct: 187 PREILNLAKKYMGDYSFIKAK 207

>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 =  165 bits (418), Expect = 4e-50
 Identities = 134/201 (66%), Positives = 159/201 (79%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
           MGL+E+LLRGIYAYGFEKPSAIQQR I    KG DVI Q+QSGTGKTATF   +LQ LD 
Sbjct: 22  MGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDI 81

Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG 120
            + + QAL+LAPTRELA QI+K + ALGDY+ V+ HAC+GGT+V ED R L  G HVV G
Sbjct: 82  QVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAG 141

Query: 121 TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMP 180
           TPGRVFDM+RR+SLR   IKM VLDEADEML++GFK+QIYD+++ LP   QV + SAT+P
Sbjct: 142 TPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLP 201

Query: 181 PEALEITRKFMNKPVRILVKR 201
            E LE+T KFM  P+RILVKR
Sbjct: 202 HEILEMTNKFMTDPIRILVKR 222

>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 =  163 bits (414), Expect = 1e-49
 Identities = 141/202 (69%), Positives = 162/202 (80%), Gaps = 1/202 (0%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
           M L E+LLRGIYAYGFEKPSAIQQR I+P  KG DVI QAQSGTGKTATF   ILQQ++ 
Sbjct: 17  MNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIEL 76

Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGV-HVVV 119
            L   QALVLAPTRELAQQI+KV+ ALGDY+G   HAC+GGT+VR + + LQ    H++V
Sbjct: 77  DLKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIV 136

Query: 120 GTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATM 179
           GTPGRVFDML R+ L P YIKMFVLDEADEMLSRGFKDQIYDIFQ L +  QV + SATM
Sbjct: 137 GTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVVLLSATM 196

Query: 180 PPEALEITRKFMNKPVRILVKR 201
           P + LE+T+KFM  P+RILVK+
Sbjct: 197 PSDVLEVTKKFMRDPIRILVKK 218

>d1fuka_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 162

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  153 bits (387), Expect = 3e-46
 Identities = 109/161 (67%), Positives = 134/161 (83%)

Query: 209 IKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGD 268
           IKQFYVNVE+EE+K E L DLY+++++TQ+VIF NTRRKV+ LT K+R+   TVSA + D
Sbjct: 1   IKQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSD 60

Query: 269 MDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGR 328
           + Q  RD IM+EFRSGSSR+LI+TDLLARGIDVQQVSLVINYDLP   ENY+HRIGR GR
Sbjct: 61  LPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGR 120

Query: 329 FGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPSNVADLL 369
           FGRKGVAINFVT +D   + +++KFY+  IEELPS++A LL
Sbjct: 121 FGRKGVAINFVTNEDVGAMRELEKFYSTQIEELPSDIATLL 161

>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 =  154 bits (391), Expect = 3e-46
 Identities = 123/199 (61%), Positives = 149/199 (74%), Gaps = 1/199 (0%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
           M L ENLLRG++ YGFE+PSAIQQR I+P  +G DV+ QAQSGTGKT TF    LQ++D 
Sbjct: 15  MELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDT 74

Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG 120
            +   QAL+LAPTRELA QI+KV+ AL  ++ +KVHAC+GGTS  ED   L+    +VVG
Sbjct: 75  SVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLR-DAQIVVG 133

Query: 121 TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMP 180
           TPGRVFD ++R+  R D IKMF+LDEADEMLS GFK+QIY IF LLP   QV + SATMP
Sbjct: 134 TPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTTQVVLLSATMP 193

Query: 181 PEALEITRKFMNKPVRILV 199
            + LE+T KFM  PVRILV
Sbjct: 194 NDVLEVTTKFMRNPVRILV 212

>d2j0sa2 c.37.1.19 (A:244-411) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]} Length = 168

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  152 bits (383), Expect = 1e-45
 Identities = 117/168 (69%), Positives = 143/168 (85%)

Query: 202 DELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHT 261
           DELTLEGIKQF+V VE+EEWK +TLCDLY+TL ITQ+VIF NT+RKVDWLT+KMR  + T
Sbjct: 1   DELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFT 60

Query: 262 VSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLH 321
           VS+ HGDM Q  R+ IM+EFRSG+SRVLI+TD+ ARG+DV QVSL+INYDLP   E Y+H
Sbjct: 61  VSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIH 120

Query: 322 RIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPSNVADLL 369
           RIGRSGR+GRKGVAINFV  DD R+L DI+++Y+  I+E+P NVADL+
Sbjct: 121 RIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVADLI 168

>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 =  146 bits (368), Expect = 7e-43
 Identities = 82/202 (40%), Positives = 114/202 (56%), Gaps = 3/202 (1%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
             L+  LLR I   GFE PS +Q   I     G+DV+ QA+SG GKTA F    LQQL+ 
Sbjct: 6   FLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEP 65

Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGG-TSVREDQRIL-QAGVHVV 118
              Q   LV+  TRELA QI K       Y+     A   G  S+++D+ +L +   H+V
Sbjct: 66  VTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIV 125

Query: 119 VGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSR-GFKDQIYDIFQLLPAKVQVGVFSA 177
           VGTPGR+  + R +SL   +IK F+LDE D+ML +   +  + +IF++ P + QV +FSA
Sbjct: 126 VGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSA 185

Query: 178 TMPPEALEITRKFMNKPVRILV 199
           T+  E   + RKFM  P+ I V
Sbjct: 186 TLSKEIRPVCRKFMQDPMEIFV 207

>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 =  144 bits (364), Expect = 6e-42
 Identities = 63/212 (29%), Positives = 99/212 (46%), Gaps = 13/212 (6%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
           + L   +   I    +++P+ IQ+  I    +  D++  AQ+G+GKTA F   I+  L  
Sbjct: 26  LKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVC 85

Query: 61  GLVQC---------QALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL 111
             +           + L+LAPTRELA QI    +       ++     GG       R +
Sbjct: 86  QDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIREV 145

Query: 112 QAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLL----P 167
           Q G H++V TPGR+ D + +  +  ++ K  VLDEAD ML  GF+ QI  I +       
Sbjct: 146 QMGCHLLVATPGRLVDFIEKNKISLEFCKYIVLDEADRMLDMGFEPQIRKIIEESNMPSG 205

Query: 168 AKVQVGVFSATMPPEALEITRKFMNKPVRILV 199
              Q  +FSAT P E  ++   F+   + + V
Sbjct: 206 INRQTLMFSATFPKEIQKLAADFLYNYIFMTV 237

>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 =  139 bits (350), Expect = 3e-40
 Identities = 75/198 (37%), Positives = 117/198 (59%), Gaps = 1/198 (0%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
             L+  LL GI+  G+EKPS IQ+  I     G D++ +A++GTGK+  +   +L++LD 
Sbjct: 8   YCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDL 67

Query: 61  GLVQCQALVLAPTRELAQQI-EKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVV 119
                QA+V+ PTRELA Q+ +  ++      G KV A  GGT++R+D   L   VHVV+
Sbjct: 68  KKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVI 127

Query: 120 GTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATM 179
            TPGR+ D++++   + D+++M VLDEAD++LS+ F   + DI   LP   Q+ ++SAT 
Sbjct: 128 ATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNRQILLYSATF 187

Query: 180 PPEALEITRKFMNKPVRI 197
           P    +     + KP  I
Sbjct: 188 PLSVQKFMNSHLEKPYEI 205

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 206

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  135 bits (340), Expect = 9e-39
 Identities = 84/197 (42%), Positives = 116/197 (58%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
             L+  LL GI+  GFEKPS IQ+  I     G D++ +A++GTGKTA F    L+++  
Sbjct: 6   FYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKP 65

Query: 61  GLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVG 120
            L + QAL++ PTRELA Q  +V+R LG + G+      GGT++R+D   L   VH++VG
Sbjct: 66  KLNKIQALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLNETVHILVG 125

Query: 121 TPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMP 180
           TPGRV D+  R+        +F++DEAD+MLSR FK  I  I   LP   Q  +FSAT P
Sbjct: 126 TPGRVLDLASRKVADLSDCSLFIMDEADKMLSRDFKTIIEQILSFLPPTHQSLLFSATFP 185

Query: 181 PEALEITRKFMNKPVRI 197
               E   K ++KP  I
Sbjct: 186 LTVKEFMVKHLHKPYEI 202

>d1s2ma2 c.37.1.19 (A:252-422) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 171

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 =  124 bits (310), Expect = 9e-35
 Identities = 69/163 (42%), Positives = 100/163 (61%), Gaps = 1/163 (0%)

Query: 203 ELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTV 262
           ELTL+GI Q+Y  VE+ + KL  L  L+  L I Q++IF N+  +V+ L  K+    ++ 
Sbjct: 1   ELTLKGITQYYAFVEERQ-KLHCLNTLFSKLQINQAIIFCNSTNRVELLAKKITDLGYSC 59

Query: 263 SATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHR 322
             +H  M Q  R+ +  EFR G  R L+ +DLL RGID+Q V++VIN+D P   E YLHR
Sbjct: 60  YYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHR 119

Query: 323 IGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPSNV 365
           IGRSGRFG  G+AIN +  +D   L+ I++     I  +P+ +
Sbjct: 120 IGRSGRFGHLGLAINLINWNDRFNLYKIEQELGTEIAAIPATI 162

>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 =  124 bits (312), Expect = 1e-33
 Identities = 50/332 (15%), Positives = 95/332 (28%), Gaps = 56/332 (16%)

Query: 32  KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYL 91
           K    I     G GKT  +   I+++        + L+LAPTR +A ++E+ +R      
Sbjct: 8   KKRLTIMDLHPGAGKTKRYLPAIVREAIKR--GLRTLILAPTRVVAAEMEEALR------ 59

Query: 92  GVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEML 151
                  +         R    G  +V       F M     +R     + ++DEA    
Sbjct: 60  ------GLPIRYQTPAIRAEHTGREIVDLMCHATFTMRLLSPIRVPNYNLIIMDEAHFTD 113

Query: 152 SRGFKDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQ 211
                 + Y   ++   +      +AT P         F      I+ +  E+       
Sbjct: 114 PASIAARGYISTRVEMGEAAGIFMTATPPG----SRDPFPQSNAPIMDEEREIPERSWNS 169

Query: 212 FYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQ 271
            +  V   +                ++V FV + +  + +   +R     V         
Sbjct: 170 GHEWVTDFKG---------------KTVWFVPSIKAGNDIAACLRKNGKKVIQLSRKTFD 214

Query: 272 NTRDIIMREFRSGSSRVLITTDLLARGIDV---------QQVSLVINYDLPTQ------- 315
           +                ++TTD+   G +          + +  VI  D   +       
Sbjct: 215 SEYIKTRTNDW----DFVVTTDISEMGANFKAERVIDPRRCMKPVILTDGEERVILAGPM 270

Query: 316 ---PENYLHRIGRSGRFGRKGVAINFVTRDDE 344
                +   R GR GR  +          +  
Sbjct: 271 PVTHSSAAQRRGRVGRNPKNENDQYIYMGEPL 302

>d1a1va2 c.37.1.14 (A:326-624) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]} Length = 299

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

 Score =  123 bits (309), Expect = 4e-33
 Identities = 25/154 (16%), Positives = 53/154 (34%), Gaps = 15/154 (9%)

Query: 209 IKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGD 268
           I++  ++   E         L E +   + +IF ++++K D L  K+ +      A +  
Sbjct: 11  IEEVALSTTGEIPFYGKAIPL-EVIKGGRHLIFCHSKKKCDELAAKLVALGINAVAYYRG 69

Query: 269 MDQNTRDI----------IMREFRSGSSRVLITTDLLARG---IDVQQVSLVINYDLPTQ 315
           +D +               +    +G    +I  +          +     +    LP  
Sbjct: 70  LDVSVIPTSGDVVVVATDALMTGFTGDFDSVIDCNTCVTQTVDFSLDPTFTIETTTLPQD 129

Query: 316 PENYLHRIGRSGRFGRKGVAINFVTRDDERMLFD 349
             +   R GR+GR G+ G+       +    +FD
Sbjct: 130 AVSRTQRRGRTGR-GKPGIYRFVAPGERPSGMFD 162

>d1hv8a2 c.37.1.19 (A:211-365) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 155

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

 Score =  117 bits (293), Expect = 2e-32
 Identities = 59/153 (38%), Positives = 92/153 (60%), Gaps = 2/153 (1%)

Query: 209 IKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGD 268
           I+Q YV V + E + E LC L +       ++F  T+R    L   +R       A HGD
Sbjct: 4   IEQSYVEVNENE-RFEALCRLLKNKEF-YGLVFCKTKRDTKELASMLRDIGFKAGAIHGD 61

Query: 269 MDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGR 328
           + Q+ R+ ++R F+    R+LI TD+++RGIDV  ++ VINY LP  PE+Y+HRIGR+GR
Sbjct: 62  LSQSQREKVIRLFKQKKIRILIATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGR 121

Query: 329 FGRKGVAINFVTRDDERMLFDIQKFYNVVIEEL 361
            G+KG AI+ + R + + L  I++   + I++L
Sbjct: 122 AGKKGKAISIINRREYKKLRYIERAMKLKIKKL 154

>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 =  112 bits (279), Expect = 6e-30
 Identities = 59/203 (29%), Positives = 101/203 (49%), Gaps = 4/203 (1%)

Query: 1   MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY 60
              Q  ++  I    F KP+ IQ+R I    +G  ++ Q+Q+GTGKT  +   I++++  
Sbjct: 6   FPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKP 65

Query: 61  GLVQCQALVLA----PTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVH 116
              + QA++ A       ++  +  K+ +       +     +GGT  ++    L    H
Sbjct: 66  ERAEVQAVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLNVQPH 125

Query: 117 VVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFS 176
           +V+GTPGR+ D +R Q+L      + V+DEAD ML  GF   +  I   +P  +Q+ VFS
Sbjct: 126 IVIGTPGRINDFIREQALDVHTAHILVVDEADLMLDMGFITDVDQIAARMPKDLQMLVFS 185

Query: 177 ATMPPEALEITRKFMNKPVRILV 199
           AT+P +     +K+M  P  + V
Sbjct: 186 ATIPEKLKPFLKKYMENPTFVHV 208

>d1wp9a2 c.37.1.19 (A:201-486) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]} Length = 286

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

 Score =  105 bits (262), Expect = 1e-26
 Identities = 38/214 (17%), Positives = 79/214 (36%), Gaps = 21/214 (9%)

Query: 143 VLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRD 202
            L  A E+L       +    + L  + + G   A+         ++  +      +K+ 
Sbjct: 81  KLHHAIELLETQGLSALRAYIKKLYEEAKAGSTKAS---------KEIFSDKR---MKKA 128

Query: 203 ELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTV 262
              L   K+  ++  K +   E + +  +    ++ ++F N R     + +++       
Sbjct: 129 ISLLVQAKEIGLDHPKMDKLKEIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKDGIKA 188

Query: 263 SATHGD--------MDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPT 314
               G         + Q  + +I+ EF  G   VL+ T +   G+DV +V LV+ Y+   
Sbjct: 189 KRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVATSVGEEGLDVPEVDLVVFYEPVP 248

Query: 315 QPENYLHRIGRSGRFGRKGVAINFVTRDDERMLF 348
                + R GR+GR    G  I  + +      +
Sbjct: 249 SAIRSIQRRGRTGR-HMPGRVIILMAKGTRDEAY 281

>d1gkub2 c.37.1.16 (B:251-498) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Length = 248

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

 Score =  103 bits (258), Expect = 2e-26
 Identities = 23/161 (14%), Positives = 57/161 (35%), Gaps = 16/161 (9%)

Query: 214 VNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNT 273
            +V   +  + TL  + E L  T  +I+  T  + + + + ++++          +   T
Sbjct: 5   EDVAVNDESISTLSSILEKLG-TGGIIYARTGEEAEEIYESLKNKFR------IGIVTAT 57

Query: 274 RDIIMREFRSGSSRVLITT----DLLARGIDVQQ-VSLVINYDLPTQPENYLHRIGRSGR 328
           +     +F  G    LI T      L RG+D+ + +   +    P    ++   I     
Sbjct: 58  KKGDYEKFVEGEIDHLIGTAHYYGTLVRGLDLPERIRFAVFVGCP----SFRVTIEDIDS 113

Query: 329 FGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPSNVADLL 369
              + V +      +   +  +       I+E+   +  ++
Sbjct: 114 LSPQMVKLLAYLYRNVDEIERLLPAVERHIDEVREILKKVM 154

>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 =  100 bits (249), Expect = 5e-26
 Identities = 58/159 (36%), Positives = 94/159 (59%), Gaps = 2/159 (1%)

Query: 208 GIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHG 267
           G++Q+YV ++  E K   L DL + L   Q VIFV + ++   L   +  ++    A H 
Sbjct: 1   GLQQYYVKLKDNE-KNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHR 59

Query: 268 DMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSG 327
            M Q  R    ++F+    R+L+ T+L  RG+D+++V++  NYD+P   + YLHR+ R+G
Sbjct: 60  GMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAG 119

Query: 328 RFGRKGVAINFVT-RDDERMLFDIQKFYNVVIEELPSNV 365
           RFG KG+AI FV+  +D ++L D+Q  + V I ELP  +
Sbjct: 120 RFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEI 158

>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 = 95.4 bits (236), Expect = 2e-23
 Identities = 34/206 (16%), Positives = 65/206 (31%), Gaps = 25/206 (12%)

Query: 8   LRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQA 67
               +     +P AIQ+       +       A +G GKT+   +  L          + 
Sbjct: 33  FVEFFRKCVGEPRAIQKMWAKRILRKESFAATAPTGVGKTSFGLAMSLFLALK---GKRC 89

Query: 68  LVLAPTRELAQQIEKVMRALGDYLGVKV------HACVGGTSVREDQRILQAGVHVVVGT 121
            V+ PT  L  Q  + +R   +  GV        +        +E+         +V+ T
Sbjct: 90  YVIFPTSLLVIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFMQNLRNFKIVITT 149

Query: 122 PGRVFDMLRRQSLRPDYIKMFVLDEADEMLSR-----------GFKDQIYDIFQLLPAKV 170
              +    R       +     +D+ D +L             GF   +     +  A+ 
Sbjct: 150 TQFLSKHYRELG----HFDFIFVDDVDAILKASKNVDKLLHLLGFHYDLKTKSWVGEARG 205

Query: 171 QVGVFSATMPPE-ALEITRKFMNKPV 195
            + V +AT       E+ R+ +N  +
Sbjct: 206 CLMVSTATAKKGKKAELFRQLLNFDI 231

>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 = 85.8 bits (211), Expect = 3e-20
 Identities = 27/189 (14%), Positives = 59/189 (31%), Gaps = 14/189 (7%)

Query: 14  YGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPT 73
           +G+++    Q+  I     G D +    +G GK+  +    L            +V++P 
Sbjct: 21  FGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLLNG------LTVVVSPL 74

Query: 74  RELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQS 133
             L +     ++A G               +          + ++   P R+      + 
Sbjct: 75  ISLMKDQVDQLQANGVAAACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDNFLEH 134

Query: 134 LRPDYIKMFVLDEADEMLSRGFKD-----QIYDIFQLLPAKVQVGVFSATMPPEALE--I 186
           L      +  +DEA  +   G         +  + Q  P  +     +AT      +  +
Sbjct: 135 LAHWNPVLLAVDEAHCISQWGHDFRPEYAALGQLRQRFP-TLPFMALTATADDTTRQDIV 193

Query: 187 TRKFMNKPV 195
               +N P+
Sbjct: 194 RLLGLNDPL 202

>d1oywa3 c.37.1.19 (A:207-406) RecQ helicase domain {Escherichia coli [TaxId: 562]} Length = 200

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

 Score = 85.1 bits (209), Expect = 5e-20
 Identities = 34/143 (23%), Positives = 67/143 (46%), Gaps = 1/143 (0%)

Query: 212 FYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQ 271
            Y+ +EK +  L+ L    +       +I+ N+R KV+    +++S+  + +A H  ++ 
Sbjct: 8   RYMLMEKFK-PLDQLMRYVQEQRGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLEN 66

Query: 272 NTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGR 331
           N R  +  +F+    ++++ T     GI+   V  V+++D+P   E+Y    GR+GR G 
Sbjct: 67  NVRADVQEKFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGL 126

Query: 332 KGVAINFVTRDDERMLFDIQKFY 354
              A+ F    D   L    +  
Sbjct: 127 PAEAMLFYDPADMAWLRRCLEEK 149

>d1jr6a_ c.37.1.14 (A:) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]} Length = 138

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

 Score = 82.8 bits (204), Expect = 7e-20
 Identities = 27/138 (19%), Positives = 52/138 (37%), Gaps = 13/138 (9%)

Query: 209 IKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGD 268
           I++  ++   E         L E +   + +IF ++++K D L  K+ +          +
Sbjct: 10  IEEVALSTTGEIPFYGKAIPL-EVIKGGRHLIFCHSKKKCDELAAKLVALGI-------N 61

Query: 269 MDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVS---LVINYDLPTQPENYLHRIGR 325
                R + +    +    V++ TD L  G      S      +   P    +   R GR
Sbjct: 62  AVAYYRGLDVSVIPTNGDVVVVATDALMTGFTGDFDSVIDCNTSDGKPQDAVSRTQRRGR 121

Query: 326 SGRFGRKGVAINFVTRDD 343
           +GR G+ G+   FV   +
Sbjct: 122 TGR-GKPGI-YRFVAPGE 137

>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 = 81.2 bits (199), Expect = 1e-18
 Identities = 25/183 (13%), Positives = 59/183 (32%), Gaps = 10/183 (5%)

Query: 2   GLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYG 61
            +    +  +   G E+    Q   +     G +++    +  GK        +  +   
Sbjct: 9   SISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGK---TLLAEMAMVREA 65

Query: 62  LVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGT 121
           +   ++L + P R LA +  +  +           +     S  E          ++V T
Sbjct: 66  IKGGKSLYVVPLRALAGEKYESFKKWEKIGLRIGISTGDYESRDEHLGD----CDIIVTT 121

Query: 122 PGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQ---IYDIFQLLPAKVQVGVFSAT 178
             +   ++R ++     +   V+DE   + S         +    + +   ++V   SAT
Sbjct: 122 SEKADSLIRNRASWIKAVSCLVVDEIHLLDSEKRGATLEILVTKMRRMNKALRVIGLSAT 181

Query: 179 MPP 181
            P 
Sbjct: 182 APN 184

>d2fwra1 c.37.1.19 (A:257-456) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]} Length = 200

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 80.3 bits (197), Expect = 2e-18
 Identities = 25/130 (19%), Positives = 50/130 (38%), Gaps = 8/130 (6%)

Query: 216 VEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRD 275
               + K+  L ++ E     + +IF      V        S+   + A      +  R+
Sbjct: 74  AFNSKNKIRKLREILERHRKDKIIIFTRHNELVYR-----ISKVFLIPAITHRTSREERE 128

Query: 276 IIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVA 335
            I+  FR+G  R ++++ +L  GIDV   ++ +          Y+ R+GR  R  +    
Sbjct: 129 EILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQRLGRILRPSKGKKE 188

Query: 336 ---INFVTRD 342
                 ++R 
Sbjct: 189 AVLYELISRG 198

>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 = 71.3 bits (173), Expect = 3e-15
 Identities = 41/198 (20%), Positives = 75/198 (37%), Gaps = 5/198 (2%)

Query: 15  GFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTR 74
              +P   Q+  I   CK  + +    +G GKT         +L       + L+LAPT+
Sbjct: 6   DLIQPRIYQEV-IYAKCKETNCLIVLPTGLGKTLIAMMIAEYRLTKY--GGKVLMLAPTK 62

Query: 75  ELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSL 134
            L  Q  +  R L +    K+ A  G  S  E++    A   V+V TP  + + L    +
Sbjct: 63  PLVLQHAESFRRLFNLPPEKIVALTGEKS-PEERSKAWARAKVIVATPQTIENDLLAGRI 121

Query: 135 RPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKP 194
             + + + V DEA   +       I   ++       V   +A+      +I     N  
Sbjct: 122 SLEDVSLIVFDEAHRAVGNYAYVFIAREYKRQAKNPLVIGLTASPGSTPEKIMEVINNLG 181

Query: 195 VRILVKRDELTLEGIKQF 212
           +  +  R E + + ++ +
Sbjct: 182 IEHIEYRSENSPD-VRPY 198

>d1t5la2 c.37.1.19 (A:415-595) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]} Length = 181

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Bacillus caldotenax [TaxId: 1395]

 Score = 69.1 bits (168), Expect = 1e-14
 Identities = 34/142 (23%), Positives = 61/142 (42%), Gaps = 13/142 (9%)

Query: 237 QSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLA 296
           ++++   T++  + LTD ++     V+  H ++    R  I+R+ R G   VL+  +LL 
Sbjct: 33  RTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLR 92

Query: 297 RGIDVQQVSLVINYDLPT-----QPENYLHRIGRSGRFGRKGVAINFVTR--------DD 343
            G+D+ +VSLV   D           + +  IGR+ R     V +   T          +
Sbjct: 93  EGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNANGHVIMYADTITKSMEIAIQE 152

Query: 344 ERMLFDIQKFYNVVIEELPSNV 365
            +    IQ+ YN     +P  V
Sbjct: 153 TKRRRAIQEEYNRKHGIVPRTV 174

>d1c4oa2 c.37.1.19 (A:410-583) Nucleotide excision repair enzyme UvrB {Thermus thermophilus [TaxId: 274]} Length = 174

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Thermus thermophilus [TaxId: 274]

 Score = 65.9 bits (160), Expect = 2e-13
 Identities = 31/121 (25%), Positives = 53/121 (43%), Gaps = 6/121 (4%)

Query: 237 QSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLA 296
           ++++ V T R  + LT  +          H ++D   R  ++R+ R G    L+  +LL 
Sbjct: 33  RTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLR 92

Query: 297 RGIDVQQVSLVINYDL-----PTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQ 351
            G+D+ +VSLV   D           + +  IGR+ R  R G    +  R  E M   I+
Sbjct: 93  EGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNAR-GEVWLYADRVSEAMQRAIE 151

Query: 352 K 352
           +
Sbjct: 152 E 152

>d2p6ra4 c.37.1.19 (A:203-403) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]} Length = 201

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 = 56.1 bits (134), Expect = 7e-10
 Identities = 32/183 (17%), Positives = 63/183 (34%), Gaps = 40/183 (21%)

Query: 207 EGIKQFYVNVEKEEWKLETLCDLYETLAITQSVI-FVNTRRKVDWLTDKMRSRD------ 259
           EG  + +        +++    + E +A    V+ F +TRR  +    K+ +        
Sbjct: 11  EGTLELFDGAFSTSRRVKFEELVEECVAENGGVLVFESTRRGAEKTAVKLSAITAKYVEN 70

Query: 260 ------------------------HTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLL 295
                                      +  H  +    R ++   FR G+ +V++ T  L
Sbjct: 71  EGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLNGQRRVVEDAFRRGNIKVVVATPTL 130

Query: 296 ARGIDVQQVSLVI-------NYDLPTQPENYLHRIGRSGRFGR--KGVAINFVTRDDERM 346
           A G+++    +++        Y    +   Y    GR+GR G   +G AI  V + D  +
Sbjct: 131 AAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIVGKRDREI 190

Query: 347 LFD 349
              
Sbjct: 191 AVK 193

>d1z3ix1 c.37.1.19 (X:390-735) Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxId: 7955]} Length = 346

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]

 Score = 45.3 bits (106), Expect = 6e-06
 Identities = 41/225 (18%), Positives = 80/225 (35%), Gaps = 29/225 (12%)

Query: 144 LDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVKRDE 203
           L    + L + F  Q   +  L   K+ V   S+          +K  N P   L+    
Sbjct: 21  LTPLQKELYKLFLKQAKPVESLQTGKISVSSLSSIT------SLKKLCNHPA--LIYEKC 72

Query: 204 LTLEGIKQFYVNVEKEEW-----------KLETLCDLYETLAITQS---VIFVNTRRKVD 249
           LT E      +++  + +           K+  L  +      T S   V+  N  + +D
Sbjct: 73  LTGEEGFDGALDLFPQNYSTKAVEPQLSGKMLVLDYILAMTRTTTSDKVVLVSNYTQTLD 132

Query: 250 WLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSS---RVLITTDLLARGIDVQQVSL 306
                 R+R +      G M    R  I+  F + SS     ++++     G+++   + 
Sbjct: 133 LFEKLCRNRRYLYVRLDGTMSIKKRAKIVERFNNPSSPEFIFMLSSKAGGCGLNLIGANR 192

Query: 307 VINYDLPTQPENYLHRIGRSGRFGRKG--VAINFVTRD--DERML 347
           ++ +D    P N    + R  R G+K        ++    +E++L
Sbjct: 193 LVMFDPDWNPANDEQAMARVWRDGQKKTCYIYRLLSTGTIEEKIL 237

>d2eyqa5 c.37.1.19 (A:779-989) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]} Length = 211

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

 Score = 41.6 bits (97), Expect = 6e-05
 Identities = 19/99 (19%), Positives = 40/99 (40%), Gaps = 4/99 (4%)

Query: 239 VIFVNTRRKVDWLTDKMRSR---DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLL 295
           V ++    +      +  +    +  ++  HG M +   + +M +F      VL+ T ++
Sbjct: 34  VYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTII 93

Query: 296 ARGIDVQQVSLVINYDLPTQPENYLHRI-GRSGRFGRKG 333
             GID+   + +I           LH++ GR GR   + 
Sbjct: 94  ETGIDIPTANTIIIERADHFGLAQLHQLRGRVGRSHHQA 132

>d1tf5a4 c.37.1.19 (A:396-570) Translocation ATPase SecA, nucleotide-binding domains {Bacillus subtilis [TaxId: 1423]} Length = 175

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]

 Score = 37.9 bits (88), Expect = 7e-04
 Identities = 20/119 (16%), Positives = 42/119 (35%), Gaps = 10/119 (8%)

Query: 236 TQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLL 295
              ++        + ++  ++++       +    +    II    + G+  V I T++ 
Sbjct: 35  QPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREAQIIEEAGQKGA--VTIATNMA 92

Query: 296 ARGIDVQQVSLVINYD--------LPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERM 346
            RG D++    V                        GRSGR G  G+   +++ +DE M
Sbjct: 93  GRGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGDPGITQFYLSMEDELM 151

>d1yksa2 c.37.1.14 (A:325-623) YFV helicase domain {Yellow fever virus [TaxId: 11089]} Length = 299

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

 Score = 36.9 bits (85), Expect = 0.002
 Identities = 16/115 (13%), Positives = 35/115 (30%), Gaps = 24/115 (20%)

Query: 237 QSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLA 296
            +  F+ + R  + +   +R    +V   +      T +      +      ++ TD+  
Sbjct: 38  PTAWFLPSIRAANVMAASLRKAGKSVVVLNRK----TFEREYPTIKQKKPDFILATDIAE 93

Query: 297 RGIDVQQVSLVINYDLPTQPENY-------------------LHRIGRSGRFGRK 332
            G ++  V  V++     +P                        R GR GR   +
Sbjct: 94  MGANL-CVERVLDCRTAFKPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNR 147

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	369
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	100.0
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	100.0
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	100.0
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	100.0
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	100.0
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	100.0
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	100.0
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	100.0
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	100.0
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	100.0
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	100.0
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	100.0
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	99.97
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	99.96
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.96
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	99.96
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.96
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.95
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	99.95
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	99.94
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	99.93
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	99.92
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	99.9
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	99.88
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	99.88
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	99.87
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.86
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	99.83
d1wp9a2	286	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.83
d2fwra1	200	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.81
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	99.8
d2p6ra4	201	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.79
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	99.75
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	99.74
d1gm5a4	206	RecG helicase domain {Thermotoga maritima [TaxId:	99.74
d1z3ix2	298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	99.72
d1gkub2	248	Helicase-like "domain" of reverse gyrase {Archaeon	99.71
d1a1va2	299	HCV helicase domain {Human hepatitis C virus (HCV)	99.68
d1z63a1	230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	99.67
d1z3ix1	346	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	99.62
d1z5za1	244	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	99.6
d1yksa2	299	YFV helicase domain {Yellow fever virus [TaxId: 11	99.39
d1tf5a4	175	Translocation ATPase SecA, nucleotide-binding doma	99.33
d1tf5a3	273	Translocation ATPase SecA, nucleotide-binding doma	99.27
d1nkta3	288	Translocation ATPase SecA, nucleotide-binding doma	99.2
d1nkta4	219	Translocation ATPase SecA, nucleotide-binding doma	98.9
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	98.63
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	98.34
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	98.15
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	98.13
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	97.63
d1ls1a2	207	GTPase domain of the signal sequence recognition p	97.6
d2qy9a2	211	GTPase domain of the signal recognition particle r	97.49
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	97.45
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	97.42
d1j8yf2	211	GTPase domain of the signal sequence recognition p	97.28
d1xbta1	133	Thymidine kinase, TK1, N-terminal domain {Human (H	97.19
d2b8ta1	139	Thymidine kinase, TK1, N-terminal domain {Ureaplas	97.18
d1vmaa2	213	GTPase domain of the signal recognition particle r	97.12
d1okkd2	207	GTPase domain of the signal recognition particle r	97.11
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	97.11
d1t5la1	413	Nucleotide excision repair enzyme UvrB {Bacillus c	97.1
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	97.01
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	96.97
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	96.88
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	96.74
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	96.73
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	96.71
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	96.7
d1xx6a1	141	Thymidine kinase, TK1, N-terminal domain {Clostrid	96.67
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	96.56
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	96.48
d1g5ta_	157	ATP:corrinoid adenosyltransferase CobA {Salmonella	96.25
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	96.1
d1c4oa1	408	Nucleotide excision repair enzyme UvrB {Thermus th	95.87
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	95.78
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	95.7
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	95.57
d1w36b1	485	Exodeoxyribonuclease V beta chain (RecB), N-termin	95.12
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	94.9
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	94.88
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	94.79
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	94.49
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	94.36
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	94.25
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	93.94
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	93.83
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	93.82
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	93.33
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	93.31
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	93.06
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	92.95
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	92.82
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	92.74
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	92.58
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	92.55
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	92.53
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	92.35
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	92.22
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	92.13
d2eyqa2	117	Transcription-repair coupling factor, TRCF {Escher	92.01
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	91.99
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	91.9
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	91.76
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	91.71
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	91.67
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	91.57
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	91.53
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	91.23
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	91.16
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	91.15
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	91.08
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	90.96
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	90.72
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	90.63
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	90.55
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	90.52
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	90.42
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	90.33
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	90.2
d1yksa2	299	YFV helicase domain {Yellow fever virus [TaxId: 11	90.19
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	90.12
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	90.11
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	90.09
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	89.93
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	89.92
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	89.6
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	89.57
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	89.45
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	89.21
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	89.2
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	89.15
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	89.08
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	89.08
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	89.07
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	88.67
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	88.56
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	88.52
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	88.47
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	88.37
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	88.23
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	88.2
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	88.11
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	87.8
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	87.74
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	87.73
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	87.5
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	87.28
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	87.22
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	87.0
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	86.94
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	86.83
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	86.37
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	86.02
d1knxa2	177	HPr kinase HprK C-terminal domain {Mycoplasma pneu	85.63
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	85.56
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	85.42
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	85.38
d1xpua3	289	Transcription termination factor Rho, ATPase domai	85.0
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	84.9
d1kkma_	176	HPr kinase HprK C-terminal domain {Lactobacillus c	84.85
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	84.81
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	84.59
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	84.38
d1ko7a2	169	HPr kinase HprK C-terminal domain {Staphylococcus	83.83
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	83.1
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	82.43
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	82.22
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	82.2
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	82.1
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	81.83
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	81.43
d1bg2a_	323	Kinesin {Human (Homo sapiens) [TaxId: 9606]}	80.98
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	80.78
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	80.64
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	80.6
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	80.54
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	80.45
d2jdid3	276	Central domain of beta subunit of F1 ATP synthase	80.19
d1fx0a3	276	Central domain of alpha subunit of F1 ATP synthase	80.16

>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=1.5e-38  Score=254.79  Aligned_cols=199  Identities=66%  Similarity=1.014  Sum_probs=187.9

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQI   80 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~   80 (369)
                      |||++.+.++|++.||.+|+++|.++++.+++|+++++.||||||||+++++++++.+......++++|++|+++|+.|.
T Consensus        22 l~L~~~l~~~L~~~g~~~pt~IQ~~aIp~il~g~dvi~~a~TGSGKTlayllPil~~l~~~~~~~~~lil~PtreLa~Qi  101 (222)
T d2j0sa1          22 MGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQI  101 (222)
T ss_dssp             GCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTTSCSCCEEEECSSHHHHHHH
T ss_pred             CCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCeEEEcCcchhhhhhhcccccccccccccCceeEEecchHHHHHHH
Confidence            68999999999999999999999999999999999999999999999999999999998877777999999999999999


Q ss_pred             HHHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHH
Q 017573           81 EKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIY  160 (369)
Q Consensus        81 ~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~  160 (369)
                      .+.+.++....++++..+.|+.........+..+++|+|+||+++.+++.......++++++|+||||.+.+.++...+.
T Consensus       102 ~~~~~~l~~~~~i~~~~~~g~~~~~~~~~~l~~~~~Ilv~TPgrl~~~~~~~~~~~~~l~~lVlDEaD~ll~~~f~~~i~  181 (222)
T d2j0sa1         102 QKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIY  181 (222)
T ss_dssp             HHHHHHHTTTTTCCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHTSTTTHHHHH
T ss_pred             HHHHHHHhCccceeEEEEeecccchhhHHHhccCCeEEeCCCCcHHhcccccccccccceeeeecchhHhhhcCcHHHHH
Confidence            99999999888999999999998888777777789999999999999999999999999999999999999999999999


Q ss_pred             HHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEe
Q 017573          161 DIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILV  199 (369)
Q Consensus       161 ~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~  199 (369)
                      .+++.+++..|++++|||.+.+..++.+.++.+|+.+.+
T Consensus       182 ~I~~~l~~~~Q~ilfSAT~~~~v~~l~~~~l~~Pv~I~V  220 (222)
T d2j0sa1         182 DVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILV  220 (222)
T ss_dssp             HHHTTSCTTCEEEEEESCCCHHHHTTGGGTCSSCEEECC
T ss_pred             HHHHhCCCCCEEEEEEEeCCHHHHHHHHHHCCCCEEEEE
Confidence            999999999999999999998888999999999987654

>d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEAD box RNA helicase rck/p54
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=3.6e-37  Score=245.25  Aligned_cols=197  Identities=38%  Similarity=0.629  Sum_probs=182.5

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQI   80 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~   80 (369)
                      |||++++.++|.++||.+|+|+|+++++.+++|++++++||||||||+++++++++++.....++.+++++|+++|+.|.
T Consensus         8 l~L~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllP~l~~~~~~~~~~~~lil~pt~el~~q~   87 (206)
T d1veca_           8 YCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRELALQV   87 (206)
T ss_dssp             SCCCHHHHHHHHTTTCCSCCHHHHHHHHHHHTTCCEEEECCSSSTTHHHHHHHHHHHCCTTSCSCCEEEECSCHHHHHHH
T ss_pred             cCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEeeccCccccccccccchhhcccccccCcceEEEeecchhhHHH
Confidence            68999999999999999999999999999999999999999999999999999999988877788999999999999999


Q ss_pred             HHHHHHhcccc-CcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHH
Q 017573           81 EKVMRALGDYL-GVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQI  159 (369)
Q Consensus        81 ~~~~~~~~~~~-~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~  159 (369)
                      .+.+..+.... +..+....++.........+...++|+|+||+++..++..+....++++++|+||||.+.+.+|...+
T Consensus        88 ~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~ivv~TPgrl~~~~~~~~~~~~~l~~lVlDEaD~ll~~~f~~~i  167 (206)
T d1veca_          88 SQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVQIM  167 (206)
T ss_dssp             HHHHHHHTTTSSSCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEEETHHHHTSTTTHHHH
T ss_pred             HHHHHHHhhcccCcccccccCCccHHHHHHHHHhccCeEEeCCccccccccchhccccccceEEEeccccccccchHHHH
Confidence            99998876544 46677777787777777777888999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEE
Q 017573          160 YDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRI  197 (369)
Q Consensus       160 ~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~  197 (369)
                      ..+++.+++..|++++|||.+.+..++.+.++.+|+.+
T Consensus       168 ~~I~~~~~~~~Q~~l~SAT~~~~v~~l~~~~l~~P~~I  205 (206)
T d1veca_         168 EDIILTLPKNRQILLYSATFPLSVQKFMNSHLEKPYEI  205 (206)
T ss_dssp             HHHHHHSCTTCEEEEEESCCCHHHHHHHHHHCSSCEEE
T ss_pred             HHHHHhCCCCCEEEEEEecCCHHHHHHHHHHCCCCEEE
Confidence            99999999999999999999999999999999998764

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=2.1e-36  Score=240.99  Aligned_cols=198  Identities=42%  Similarity=0.640  Sum_probs=178.7

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQI   80 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~   80 (369)
                      |||++++.++|.+.||.+|+|+|+++++.+++|++++++||||||||+++++++++.+.....++++++++|+++|+.|.
T Consensus         6 l~L~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvl~~A~TGsGKTla~~lp~l~~~~~~~~~~~~lil~PtreL~~qi   85 (207)
T d1t6na_           6 FLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQI   85 (207)
T ss_dssp             SCCCHHHHHHHHHTTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCTTCCCEEEECSCHHHHHHH
T ss_pred             cCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCeEEEeccccccccccccceeeeecccCCCceEEEEeccchhhHHH
Confidence            68999999999999999999999999999999999999999999999999999999988877778999999999999999


Q ss_pred             HHHHHHhccccC-cEEEEEECCcchHHHHHH-HccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhcc-CcHH
Q 017573           81 EKVMRALGDYLG-VKVHACVGGTSVREDQRI-LQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSR-GFKD  157 (369)
Q Consensus        81 ~~~~~~~~~~~~-~~v~~~~~~~~~~~~~~~-~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~-~~~~  157 (369)
                      .+.+..+....+ .......|+.....+... ....++|+|+||+++..++.+..+..+++.++|+||||.+.+. ++..
T Consensus        86 ~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~ilI~TP~rl~~~~~~~~~~l~~l~~lVlDEaD~ll~~~~~~~  165 (207)
T d1t6na_          86 SKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRR  165 (207)
T ss_dssp             HHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEESHHHHHSSHHHHH
T ss_pred             HHHHHHHHhhCCCceeEEEeccccHHHHHHHHHhcCCCEEEeCcchhhhhccCCceeccccceeehhhhhhhhhcCCcHH
Confidence            999999887654 466777777776555444 3567899999999999999998889999999999999999874 7888


Q ss_pred             HHHHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEE
Q 017573          158 QIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRIL  198 (369)
Q Consensus       158 ~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~  198 (369)
                      .+..+.+.+++..|++++|||.+.+..++.+.++.+|+.+.
T Consensus       166 ~i~~I~~~~~~~~Q~il~SAT~~~~v~~l~~~~l~~P~~I~  206 (207)
T d1t6na_         166 DVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIF  206 (207)
T ss_dssp             HHHHHHHTSCSSSEEEEEESCCCTTTHHHHHTTCSSCEEEE
T ss_pred             HHHHHHHhCCCCCEEEEEeeeCCHHHHHHHHHHCCCCEEEe
Confidence            99999999999999999999999999999999999987664

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=1.5e-36  Score=242.29  Aligned_cols=197  Identities=62%  Similarity=0.947  Sum_probs=176.1

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQI   80 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~   80 (369)
                      |||++++.++|.++||.+|+++|+++++.+++|+++++++|||||||+++++++++++.....++.+++++|+++++.|.
T Consensus        15 l~l~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKT~a~~lp~i~~l~~~~~~~~~lil~pt~el~~q~   94 (212)
T d1qdea_          15 MELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQI   94 (212)
T ss_dssp             GTCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEEECSSHHHHHHH
T ss_pred             CCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEeecccccchhhhhHhhhHhhhhccCCCcceEEEcccHHHhhhh
Confidence            68999999999999999999999999999999999999999999999999999999998888888999999999999999


Q ss_pred             HHHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHH
Q 017573           81 EKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIY  160 (369)
Q Consensus        81 ~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~  160 (369)
                      .+.+..+.......+....++.....+.... ++++|+|+||+++..++..+...+.+++++|+||||.+.+.++...+.
T Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~IvI~TP~~l~~~~~~~~~~l~~l~~lVlDEad~lld~~f~~~v~  173 (212)
T d1qdea_          95 QKVVMALAFHMDIKVHACIGGTSFVEDAEGL-RDAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIY  173 (212)
T ss_dssp             HHHHHHHTTTSCCCEEEECC----------C-TTCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHHHTTCHHHHH
T ss_pred             hhhhcccccccccceeeEeeccchhHHHHHh-cCCcEEEECCCccccccccCceecCcceEEeehhhhhhcccchHHHHH
Confidence            9999998888788888877776655554443 467999999999999999999999999999999999999999999999


Q ss_pred             HHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEE
Q 017573          161 DIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRIL  198 (369)
Q Consensus       161 ~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~  198 (369)
                      .+++.+++..|++++|||.+++..++.+.++.+|+.+.
T Consensus       174 ~I~~~~~~~~Q~vl~SAT~~~~v~~l~~~~l~~Pv~i~  211 (212)
T d1qdea_         174 QIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRIL  211 (212)
T ss_dssp             HHHHHSCTTCEEEEEESSCCHHHHHHHHHHCSSCEEEC
T ss_pred             HHHHhCCCCCeEEEEEeeCCHHHHHHHHHHCCCCEEEe
Confidence            99999999999999999999999999999999997664

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=2.4e-36  Score=241.96  Aligned_cols=200  Identities=70%  Similarity=1.072  Sum_probs=180.7

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQI   80 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~   80 (369)
                      |||++.+.++|.++||.+|+++|+++++.++.|++++++||||||||+++++++++.+.....+++++|++|+++|+.|.
T Consensus        17 l~L~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllp~l~~i~~~~~~~~alil~Pt~eL~~Q~   96 (218)
T d2g9na1          17 MNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQQI   96 (218)
T ss_dssp             SCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEEECSSHHHHHHH
T ss_pred             CCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEEcccchhhhhhhhhhhhheecccccCccEEEEcccchhhhhH
Confidence            68999999999999999999999999999999999999999999999999999999998777777999999999999999


Q ss_pred             HHHHHHhccccCcEEEEEECCcchHHHH-HHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHH
Q 017573           81 EKVMRALGDYLGVKVHACVGGTSVREDQ-RILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQI  159 (369)
Q Consensus        81 ~~~~~~~~~~~~~~v~~~~~~~~~~~~~-~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~  159 (369)
                      .+.+.++....+.......++....... ....+.++|+|+||+++..++.++....++++++|+||||.+.+.++...+
T Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IvV~TP~rl~~~l~~~~~~~~~l~~lVlDEaD~ll~~~f~~~~  176 (218)
T d2g9na1          97 QKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQI  176 (218)
T ss_dssp             HHHHHHHHTTTTCCEEEECC--CCCSTTTSSSSCCCSEEEECHHHHHHHHHTTSSCSTTCCEEEEESHHHHHHTTCHHHH
T ss_pred             HHHHhhhccccceeEEeeecccchhHHHHHHhcCCCEEEEeCChhHHHHHhcCCcccccceEEEeeecchhhcCchHHHH
Confidence            9999999988888887777765543332 223356899999999999999999899999999999999999999999999


Q ss_pred             HHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEec
Q 017573          160 YDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILVK  200 (369)
Q Consensus       160 ~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~~  200 (369)
                      ..+++.++++.|++++|||.+.+..++.+.++.+|+.+.+.
T Consensus       177 ~~Il~~~~~~~Q~il~SAT~~~~v~~~~~~~l~~pv~i~v~  217 (218)
T d2g9na1         177 YDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVK  217 (218)
T ss_dssp             HHHHHHSCTTCEEEEEESCCCHHHHHHHHHHCSSCEEEECC
T ss_pred             HHHHHhCCCCCeEEEEEecCCHHHHHHHHHHCCCCEEEEEe
Confidence            99999999999999999999999999999999999877653

>d1hv8a1 c.37.1.19 (A:3-210) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=100.00  E-value=1e-35  Score=237.54  Aligned_cols=197  Identities=35%  Similarity=0.585  Sum_probs=178.5

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCC-cEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGL-DVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQ   79 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~-~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q   79 (369)
                      ||||+.+.++|.++||.+|+|+|.++++.+++|+ ++++++|||+|||+++++++++..... .+++++|++|+++|+.|
T Consensus         9 l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~g~~d~iv~a~TGsGKT~~~~l~~~~~~~~~-~~~~~lil~pt~~l~~q   87 (208)
T d1hv8a1           9 LNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNEN-NGIEAIILTPTRELAIQ   87 (208)
T ss_dssp             SSCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCSS-SSCCEEEECSCHHHHHH
T ss_pred             cCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeeeechhcccccceeecccccccccc-cCcceEEEeeccccchh
Confidence            6899999999999999999999999999999875 999999999999999999998876544 45599999999999999


Q ss_pred             HHHHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHH
Q 017573           80 IEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQI  159 (369)
Q Consensus        80 ~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~  159 (369)
                      ..+.+.++....+.++....|+.....+.+.+ ++++|+|+||+++.+++.++....++++++|+||+|.+.+.++...+
T Consensus        88 ~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l-~~~~IlV~TP~~l~~~l~~~~~~~~~l~~lViDEad~l~~~~~~~~i  166 (208)
T d1hv8a1          88 VADEIESLKGNKNLKIAKIYGGKAIYPQIKAL-KNANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEMLNMGFIKDV  166 (208)
T ss_dssp             HHHHHHHHHCSSCCCEEEECTTSCHHHHHHHH-HTCSEEEECHHHHHHHHHTTCSCTTSCCEEEEETHHHHHTTTTHHHH
T ss_pred             hhhhhhhhcccCCeEEEEeeCCCChHHHHHhc-CCCCEEEEChHHHHHHHHcCCCCcccCcEEEEEChHHhhcCCChHHH
Confidence            99999999988889999999988776665544 46899999999999999999889999999999999999999999999


Q ss_pred             HHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEe
Q 017573          160 YDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILV  199 (369)
Q Consensus       160 ~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~  199 (369)
                      ..+++.++++.|++++|||.+.+..++.++++.++..+..
T Consensus       167 ~~I~~~~~~~~Q~i~~SAT~~~~v~~~~~~~l~~~~~I~~  206 (208)
T d1hv8a1         167 EKILNACNKDKRILLFSATMPREILNLAKKYMGDYSFIKA  206 (208)
T ss_dssp             HHHHHTSCSSCEEEEECSSCCHHHHHHHHHHCCSEEEEEC
T ss_pred             HHHHHhCCCCCeEEEEEccCCHHHHHHHHHHCCCCeEEEE
Confidence            9999999999999999999999889999999988876653

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=4.3e-35  Score=233.93  Aligned_cols=199  Identities=42%  Similarity=0.644  Sum_probs=188.2

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQI   80 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~   80 (369)
                      |||++.+.++|.+.||.+|+|+|+++++.+++|+++++.||||+|||++++++++..+.....+...++++|+..++.+.
T Consensus         6 l~L~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvi~~a~tGsGKTlay~lp~i~~~~~~~~~~~~~~~~~~~~~~~~~   85 (206)
T d1s2ma1           6 FYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVPTRELALQT   85 (206)
T ss_dssp             GCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHH
T ss_pred             cCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEecCCcchhhhhhccccccccccccccccceeeccchhhhhhh
Confidence            68999999999999999999999999999999999999999999999999999999988777777899999999999999


Q ss_pred             HHHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHH
Q 017573           81 EKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIY  160 (369)
Q Consensus        81 ~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~  160 (369)
                      ...+..+....++++....|+.........+...++|+|+||+.+..++......+.+++++|+||||.+.+.+|...+.
T Consensus        86 ~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~lV~DEaD~l~~~~f~~~v~  165 (206)
T d1s2ma1          86 SQVVRTLGKHCGISCMVTTGGTNLRDDILRLNETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSRDFKTIIE  165 (206)
T ss_dssp             HHHHHHHTTTTTCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEEESHHHHSSHHHHHHHH
T ss_pred             hhhhhhcccccCeeEEeecCccchhhHHHHhcccceEEEECCcccccccccceeecccceEEEeechhhhhhhhhHHHHH
Confidence            99999999889999999999998888888888899999999999999999999999999999999999999999999999


Q ss_pred             HHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEe
Q 017573          161 DIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILV  199 (369)
Q Consensus       161 ~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~  199 (369)
                      .+++.+++..|++++|||.+++..++..+++.+|..+..
T Consensus       166 ~I~~~l~~~~Q~il~SATl~~~v~~~~~~~l~~P~~I~~  204 (206)
T d1s2ma1         166 QILSFLPPTHQSLLFSATFPLTVKEFMVKHLHKPYEINL  204 (206)
T ss_dssp             HHHTTSCSSCEEEEEESCCCHHHHHHHHHHCSSCEEESC
T ss_pred             HHHHhCCCCCEEEEEEEeCCHHHHHHHHHHCCCCEEEEe
Confidence            999999999999999999999999999999999977654

>d1wrba1 c.37.1.19 (A:164-401) putative ATP-dependent RNA helicase VlgB {Flatworm (Dugesia japonica) [TaxId: 6161]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase VlgB
species: Flatworm (Dugesia japonica) [TaxId: 6161]

Probab=100.00  E-value=9.5e-35  Score=236.10  Aligned_cols=199  Identities=32%  Similarity=0.485  Sum_probs=181.0

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhcc---------CCCccEEEEc
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYG---------LVQCQALVLA   71 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~---------~~~~~~liv~   71 (369)
                      |||++++.++|.+.||.+|+++|.++++.+++|++++++||||+|||+++++++++.+...         ...++++|++
T Consensus        26 l~l~~~l~~~L~~~g~~~pt~iQ~~~ip~il~g~dvvi~a~TGsGKTlayllp~l~~l~~~~~~~~~~~~~~~~~alil~  105 (238)
T d1wrba1          26 LKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILA  105 (238)
T ss_dssp             GSCCCSTTTTTTTTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHTTCC------CCBCCSEEEEC
T ss_pred             CCCCHHHHHHHHHCCCCCCCHHHHHHhhhhhCCCCEEEECCCCCCcceeeHHHHHHHHHhcccccccccCCCCceEEEec
Confidence            5899999999999999999999999999999999999999999999999999999987432         2345799999


Q ss_pred             CCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhh
Q 017573           72 PTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEML  151 (369)
Q Consensus        72 P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~  151 (369)
                      |+++|+.|..+.+..+....++++....|+.....+.+....+++|+|+||+.+..++..+...+.++.++|+||+|.+.
T Consensus       106 pt~el~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~ivV~TP~~l~~~~~~~~~~l~~v~~lViDEaD~ll  185 (238)
T d1wrba1         106 PTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEKNKISLEFCKYIVLDEADRML  185 (238)
T ss_dssp             SSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCSHHHHHHHSSCCSEEEECHHHHHHHHHTTSBCCTTCCEEEEETHHHHH
T ss_pred             cchhhhcchheeeeecccCCCcEEEEEeccchhhHHHhhcccCCceeecCHHHHHhHHccCceeccccceeeeehhhhhh
Confidence            99999999999999998888999999999888777777778889999999999999999999999999999999999999


Q ss_pred             ccCcHHHHHHHHhhCC----ccCcEEEEEeeCChhHHHHHHHhcCCCEEEEe
Q 017573          152 SRGFKDQIYDIFQLLP----AKVQVGVFSATMPPEALEITRKFMNKPVRILV  199 (369)
Q Consensus       152 ~~~~~~~~~~~~~~~~----~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~  199 (369)
                      +.+|...+..+++.+.    ...|++++|||.+.+...+...++.+|+.+.+
T Consensus       186 ~~~f~~~i~~Il~~~~~~~~~~~Q~il~SAT~~~~v~~l~~~~~~~p~~i~v  237 (238)
T d1wrba1         186 DMGFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTV  237 (238)
T ss_dssp             HTTCHHHHHHHHHSSCCCCGGGCEEEEEESSCCHHHHHHHHHHCSSCEEEEE
T ss_pred             hhccHHHHHHHHHHhcCCCCCCCEEEEEeeeCCHHHHHHHHHHCCCCEEEEe
Confidence            9999999999988754    25799999999999999999999999877654

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable DEAD box RNA helicase YqfR
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=100.00  E-value=1.5e-33  Score=226.29  Aligned_cols=199  Identities=33%  Similarity=0.510  Sum_probs=174.9

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHH
Q 017573            1 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQI   80 (369)
Q Consensus         1 ~~l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~   80 (369)
                      |||++++.++|++.||.+|+++|+++++.+++|++++++||||||||+++++++++...........++++|...+..+.
T Consensus         6 l~L~~~l~~~l~~~g~~~pt~iQ~~aip~~l~G~dvii~a~TGSGKTlayllp~l~~~~~~~~~~~~~~~~~~~~~~~~~   85 (209)
T d1q0ua_           6 FPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPERAEVQAVITAPTRELATQI   85 (209)
T ss_dssp             SCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHH
T ss_pred             CCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCeEeecccccccceeeeeeeccccccccccccccccccccchhHHH
Confidence            69999999999999999999999999999999999999999999999999999999988777777899999999999988


Q ss_pred             HHHHHHhcccc----CcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcH
Q 017573           81 EKVMRALGDYL----GVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFK  156 (369)
Q Consensus        81 ~~~~~~~~~~~----~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~  156 (369)
                      .+.+.......    ...+....+.............+++|+|+||+.+..+..+......+++++|+||+|.+.+.++.
T Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~TP~~l~~~~~~~~~~~~~l~~lViDEad~ll~~~f~  165 (209)
T d1q0ua_          86 YHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLNVQPHIVIGTPGRINDFIREQALDVHTAHILVVDEADLMLDMGFI  165 (209)
T ss_dssp             HHHHHHHHTTSCGGGCCCEEEECCCSHHHHTTCCCSSCCSEEEECHHHHHHHHHTTCCCGGGCCEEEECSHHHHHHTTCH
T ss_pred             HHHHHhhhccccccccccccccccchhhHHHHHHhccCceEEEecCchhhhhhhhhccccccceEEEEeecccccccccH
Confidence            88776654333    34455555555544444445567899999999999999998888899999999999999999999


Q ss_pred             HHHHHHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCEEEEe
Q 017573          157 DQIYDIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPVRILV  199 (369)
Q Consensus       157 ~~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~~~~~  199 (369)
                      ..+..++..++++.|++++|||.+.+..++++.++.+|..+.+
T Consensus       166 ~~v~~I~~~~~~~~Q~il~SATl~~~v~~l~~~~l~~p~~i~V  208 (209)
T d1q0ua_         166 TDVDQIAARMPKDLQMLVFSATIPEKLKPFLKKYMENPTFVHV  208 (209)
T ss_dssp             HHHHHHHHTSCTTCEEEEEESCCCGGGHHHHHHHCSSCEEEEC
T ss_pred             HHHHHHHHHCCCCCEEEEEEccCCHHHHHHHHHHCCCCEEEEe
Confidence            9999999999999999999999999999999999999887654

>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=100.00  E-value=2.5e-34  Score=245.58  Aligned_cols=272  Identities=18%  Similarity=0.134  Sum_probs=180.3

Q ss_pred             cccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHH
Q 017573           30 FCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQR  109 (369)
Q Consensus        30 ~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~  109 (369)
                      +.+++++++.||||||||++++.+++......  +.+++|++|+++|+.|+.+.++++.......    .       ...
T Consensus         6 ~~~~~~~lv~~~TGsGKT~~~l~~~~~~~~~~--~~~~lvi~Ptr~La~q~~~~l~~~~~~~~~~----~-------~~~   72 (305)
T d2bmfa2           6 FRKKRLTIMDLHPGAGKTKRYLPAIVREAIKR--GLRTLILAPTRVVAAEMEEALRGLPIRYQTP----A-------IRA   72 (305)
T ss_dssp             SSTTCEEEECCCTTSSTTTTHHHHHHHHHHHH--TCCEEEEESSHHHHHHHHHHTTTSCCBCCC----------------
T ss_pred             hhcCCcEEEEECCCCCHHHHHHHHHHHHHHhc--CCEEEEEccHHHHHHHHHHHHhcCCcceeee----E-------Eee
Confidence            35789999999999999988776776554432  2389999999999999999887653221110    0       001


Q ss_pred             HHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhC--CccCcEEEEEeeCChhHHHHH
Q 017573          110 ILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLL--PAKVQVGVFSATMPPEALEIT  187 (369)
Q Consensus       110 ~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~--~~~~~~i~~saT~~~~~~~~~  187 (369)
                      .......++++|+..+..+... .....+++++|+||+|.+..+.+.  ...++...  ....+++++|||++.....  
T Consensus        73 ~~~~~~~i~~~t~~~l~~~~~~-~~~~~~~~~vViDE~H~~~~~~~~--~~~~l~~~~~~~~~~~v~~SAT~~~~~~~--  147 (305)
T d2bmfa2          73 EHTGREIVDLMCHATFTMRLLS-PIRVPNYNLIIMDEAHFTDPASIA--ARGYISTRVEMGEAAGIFMTATPPGSRDP--  147 (305)
T ss_dssp             ---CCCSEEEEEHHHHHHHHTS-SSCCCCCSEEEEESTTCCSHHHHH--HHHHHHHHHHHTSCEEEEECSSCTTCCCS--
T ss_pred             cccCccccccCCcHHHHHHHhc-CccccceeEEEeeeeeecchhhHH--HHHHHHHhhccccceEEEeecCCCcceee--
Confidence            1234568999999988766554 344567999999999988654321  11222211  2467899999998643211  


Q ss_pred             HHhcCCCEEEEecCccccccceeEEEEEccchhhhHHHHHHHHHhccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecC
Q 017573          188 RKFMNKPVRILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHG  267 (369)
Q Consensus       188 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~  267 (369)
                        .....            ..+........... +...+. . .....++++|||+++++++.+++.|++.+.++..+||
T Consensus       148 --~~~~~------------~~~~~~~~~~~~~~-~~~~~~-~-~~~~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~l~~  210 (305)
T d2bmfa2         148 --FPQSN------------APIMDEEREIPERS-WNSGHE-W-VTDFKGKTVWFVPSIKAGNDIAACLRKNGKKVIQLSR  210 (305)
T ss_dssp             --SCCCS------------SCEEEEECCCCCSC-CSSCCH-H-HHSSCSCEEEECSCHHHHHHHHHHHHHHTCCCEECCT
T ss_pred             --ecccC------------CcceEEEEeccHHH-HHHHHH-H-HHhhCCCEEEEeccHHHHHHHHHHHHhCCCCEEEeCC
Confidence              00000            00000000000000 000011 1 1224578999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEec--------------------CCCCccchhhhhcccc
Q 017573          268 DMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYD--------------------LPTQPENYLHRIGRSG  327 (369)
Q Consensus       268 ~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~--------------------~~~~~~~~~Q~~GR~~  327 (369)
                      ++....    ...|.+|..+++++|++++.|+|+ +++.|+..+                    .|.|..+|.||+||+|
T Consensus       211 ~~~~~~----~~~~~~~~~~~lvaT~~~~~G~~~-~~~~Vi~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~Qr~GR~G  285 (305)
T d2bmfa2         211 KTFDSE----YIKTRTNDWDFVVTTDISEMGANF-KAERVIDPRRCMKPVILTDGEERVILAGPMPVTHSSAAQRRGRVG  285 (305)
T ss_dssp             TCHHHH----GGGGGTSCCSEEEECGGGGTTCCC-CCSEEEECCEEEEEEEECSSSCEEEEEEEEECCHHHHHHHHTTSS
T ss_pred             cChHHH----HhhhhccchhhhhhhHHHHhcCCC-CccEEEEcCCceeeeEecCCCCceEEeccccCCHHHHhhhhcCcC
Confidence            885544    346788999999999999999999 455555322                    2456778999999999


Q ss_pred             cCCCceeEEEEecc
Q 017573          328 RFGRKGVAINFVTR  341 (369)
Q Consensus       328 R~~~~~~~~~~~~~  341 (369)
                      |.|+.+...+++..
T Consensus       286 R~~~~~~~~~~~~~  299 (305)
T d2bmfa2         286 RNPKNENDQYIYMG  299 (305)
T ss_dssp             CSSSCCCEEEEECS
T ss_pred             cCCCCceEEEEECC
Confidence            99988766655543

>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=100.00  E-value=3.6e-32  Score=206.82  Aligned_cols=161  Identities=68%  Similarity=1.042  Sum_probs=150.2

Q ss_pred             eeEEEEEccchhhhHHHHHHHHHhccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcE
Q 017573          209 IKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRV  288 (369)
Q Consensus       209 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~v  288 (369)
                      ++++++.+...+.+.+.+.++++..+.+++||||+++..++.+++.|...+..+..+||+++.++|..+++.|++|+.++
T Consensus         1 I~q~~~~v~~~e~K~~~L~~ll~~~~~~k~iIF~~s~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~l~~f~~~~~~i   80 (162)
T d1fuka_           1 IKQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRI   80 (162)
T ss_dssp             CEEEEEEEESGGGHHHHHHHHHHHTTCSCEEEEESSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSE
T ss_pred             CEEEEEEeCCcHHHHHHHHHHHHhCCCCcEEEEEEEEchHHHHHHHHhhcCceEEEeccCCchhhHHHHHHHHhhcccce
Confidence            46788888877889999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEecCCcCCCCCCCCcEEEEecCCCCccchhhhhcccccCCCceeEEEEeccccHHHHHHHHHHhccccccCCcchhhc
Q 017573          289 LITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPSNVADL  368 (369)
Q Consensus       289 li~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  368 (369)
                      ||+|+++++|+|+|++++||++++|+++..|.||+||+||.|+.|.+++++++.|...++.+++.++..++++|.++.++
T Consensus        81 Lv~Tdv~~rGiDi~~v~~VI~~d~P~~~~~yihR~GR~gR~g~~g~~i~~~~~~d~~~~~~i~~~~~~~~~~ip~~~~~l  160 (162)
T d1fuka_          81 LISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELEKFYSTQIEELPSDIATL  160 (162)
T ss_dssp             EEEEGGGTTTCCCCSCSEEEESSCCSSGGGGGGSSCSCC-----CEEEEEEETTTHHHHHHHHHHSSCCCEECCSCCTTT
T ss_pred             eeccccccccccCCCceEEEEeccchhHHHHHhhccccccCCCccEEEEEcCHHHHHHHHHHHHHHcCcCCCCChHHHHh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999887


Q ss_pred             C
Q 017573          369 L  369 (369)
Q Consensus       369 ~  369 (369)
                      |
T Consensus       161 ~  161 (162)
T d1fuka_         161 L  161 (162)
T ss_dssp             T
T ss_pred             h
Confidence            5

>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=100.00  E-value=5.2e-32  Score=207.03  Aligned_cols=167  Identities=69%  Similarity=1.147  Sum_probs=160.2

Q ss_pred             cccccceeEEEEEccchhhhHHHHHHHHHhccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHh
Q 017573          203 ELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFR  282 (369)
Q Consensus       203 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~  282 (369)
                      +.+..++.++++.++....+.+.|..++......++||||++.+.++.+++.|+..+..+..+||+++.++|.++++.|+
T Consensus         2 ~~tl~~i~q~~v~v~~~~~K~~~L~~ll~~~~~~k~iiF~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~fk   81 (168)
T d2j0sa2           2 ELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFR   81 (168)
T ss_dssp             GCSCTTEEEEEEEESSTTHHHHHHHHHHHHHTSSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHH
T ss_pred             CCCCCCcEEEEEEecChHHHHHHHHHHHHhCCCCceEEEeeeHHHHHHHHHHhhhcccchhhhhhhhhHHHHHHHHHHHh
Confidence            45668899999999988889999999999988899999999999999999999999999999999999999999999999


Q ss_pred             cCCCcEEEEecCCcCCCCCCCCcEEEEecCCCCccchhhhhcccccCCCceeEEEEeccccHHHHHHHHHHhccccccCC
Q 017573          283 SGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELP  362 (369)
Q Consensus       283 ~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  362 (369)
                      +|+.++||+|+++++|+|+|.+++||++++|++...|.||+||+||.|+.|.+++++.+.+...++.+++.++..++++|
T Consensus        82 ~g~~~iLv~Td~~~rGiDi~~v~~VIn~d~P~~~~~yihR~GR~gR~g~~G~~i~~~~~~d~~~~~~i~~~~~~~i~e~p  161 (168)
T d2j0sa2          82 SGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMP  161 (168)
T ss_dssp             HTSSCEEEECGGGSSSCCCTTEEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEEGGGHHHHHHHHHHTTCCCEECC
T ss_pred             cCCccEEeccchhcccccccCcceEEEecCCcCHHHHHhhhccccccCCCcEEEEEECHHHHHHHHHHHHHHcCcCCCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cchhhcC
Q 017573          363 SNVADLL  369 (369)
Q Consensus       363 ~~~~~~~  369 (369)
                      .++.++|
T Consensus       162 ~~~~dii  168 (168)
T d2j0sa2         162 MNVADLI  168 (168)
T ss_dssp             SCCTTTC
T ss_pred             cChHHhC
Confidence            9988875

>d1s2ma2 c.37.1.19 (A:252-422) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.97  E-value=1.3e-30  Score=200.78  Aligned_cols=164  Identities=41%  Similarity=0.732  Sum_probs=155.5

Q ss_pred             ccccceeEEEEEccchhhhHHHHHHHHHhccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhc
Q 017573          204 LTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRS  283 (369)
Q Consensus       204 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~  283 (369)
                      .+..++.+++..++. ..+...|.++++..+.+++||||++.+.++.++..|...+..+..+||+++.++|..+++.|++
T Consensus         2 ~tl~~i~q~yi~v~~-~~K~~~L~~ll~~~~~~k~iVF~~~~~~~~~l~~~L~~~g~~~~~~h~~~~~~~r~~~~~~f~~   80 (171)
T d1s2ma2           2 LTLKGITQYYAFVEE-RQKLHCLNTLFSKLQINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQ   80 (171)
T ss_dssp             CBCTTEEEEEEECCG-GGHHHHHHHHHHHSCCSEEEEECSSHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHHHHHT
T ss_pred             CCccceEEEEEEcCH-HHHHHHHHHHHHhCCCCceEEEEeeeehhhHhHHhhhcccccccccccccchhhhhhhhhhccc
Confidence            356778899998875 5799999999999988999999999999999999999999999999999999999999999999


Q ss_pred             CCCcEEEEecCCcCCCCCCCCcEEEEecCCCCccchhhhhcccccCCCceeEEEEeccccHHHHHHHHHHhccccccCCc
Q 017573          284 GSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPS  363 (369)
Q Consensus       284 ~~~~vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  363 (369)
                      |..++||+|+++++|+|+|++++||++++|+++.+|.||+||+||.|+.|.++.|+.+.+...+..+++.++.++.++|.
T Consensus        81 ~~~~ilv~Td~~~~Gid~~~v~~VI~~d~p~~~~~y~qr~GR~gR~g~~g~~i~~v~~~e~~~~~~i~~~l~~~~~~~p~  160 (171)
T d1s2ma2          81 GKVRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWNDRFNLYKIEQELGTEIAAIPA  160 (171)
T ss_dssp             TSSSEEEESSCSSSSCCCTTEEEEEESSCCSSHHHHHHHHCBSSCTTCCEEEEEEECGGGHHHHHHHHHHHTCCCEECCS
T ss_pred             CccccccchhHhhhccccceeEEEEecCCcchHHHHHHHhhhcccCCCccEEEEEeCHHHHHHHHHHHHHHCCCCCCCCc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             chhhc
Q 017573          364 NVADL  368 (369)
Q Consensus       364 ~~~~~  368 (369)
                      ++.+.
T Consensus       161 ~~d~~  165 (171)
T d1s2ma2         161 TIDKS  165 (171)
T ss_dssp             SCCGG
T ss_pred             ccchh
Confidence            88653

>d1t5ia_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.96  E-value=3.9e-29  Score=191.30  Aligned_cols=156  Identities=36%  Similarity=0.676  Sum_probs=143.8

Q ss_pred             eeEEEEEccchhhhHHHHHHHHHhccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcE
Q 017573          209 IKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRV  288 (369)
Q Consensus       209 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~v  288 (369)
                      +.++|+.+.. +.+.+.+.+++.....+++||||++++.++.+++.|.+.+.++..+||+++.++|..+++.|++|+.++
T Consensus         2 l~q~~v~~~~-~~K~~~L~~ll~~~~~~k~iIF~~~~~~~~~l~~~L~~~~~~~~~ihg~~~~~~r~~~l~~F~~g~~~i   80 (168)
T d1t5ia_           2 LQQYYVKLKD-NEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRI   80 (168)
T ss_dssp             CEEEEEECCG-GGHHHHHHHHHHHSCCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSE
T ss_pred             cEEEEEEeCh-HHHHHHHHHHHHhCCCCeEEEEEeeeecchhhhhhhccccccccccccccchhhhhhhhhhhcccccee
Confidence            5677887775 679999999999998899999999999999999999999999999999999999999999999999999


Q ss_pred             EEEecCCcCCCCCCCCcEEEEecCCCCccchhhhhcccccCCCceeEEEEeccc-cHHHHHHHHHHhccccccCCcch
Q 017573          289 LITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRD-DERMLFDIQKFYNVVIEELPSNV  365 (369)
Q Consensus       289 li~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~  365 (369)
                      ||+|+++++|+|+|.+++||++++|+++..|.||+||+||.|+.|.++.++++. +...+..+.+.++..+.++|+++
T Consensus        81 Lv~T~~~~~Gid~~~~~~vi~~~~p~~~~~yiqr~GR~gR~g~~g~~i~l~~~~~~~~~~~~i~~~~~~~~~elp~~~  158 (168)
T d1t5ia_          81 LVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEI  158 (168)
T ss_dssp             EEESSCCSTTCCGGGCSEEEESSCCSSHHHHHHHHHHHTGGGCCCEEEEEECSHHHHHHHHHHHHHHCCCEEECC---
T ss_pred             eeccccccchhhcccchhhhhhhcccchhhHhhhhhhcccCCCccEEEEEECchHHHHHHHHHHHHHcCCcccCCchh
Confidence            999999999999999999999999999999999999999999999999998775 56778889999999999998776

>d1hv8a2 c.37.1.19 (A:211-365) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=99.96  E-value=8.4e-29  Score=187.46  Aligned_cols=153  Identities=38%  Similarity=0.682  Sum_probs=143.3

Q ss_pred             cceeEEEEEccchhhhHHHHHHHHHhccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCC
Q 017573          207 EGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSS  286 (369)
Q Consensus       207 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~  286 (369)
                      .++.+.+..++. ..+.+.|..+++.. +.++||||++.+.++.+++.|+..+..+..+|++++..+|..+++.|++|+.
T Consensus         2 ~nI~~~~i~v~~-~~K~~~L~~ll~~~-~~k~IIF~~s~~~~~~l~~~L~~~g~~~~~~~~~~~~~~r~~~~~~f~~~~~   79 (155)
T d1hv8a2           2 ANIEQSYVEVNE-NERFEALCRLLKNK-EFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKI   79 (155)
T ss_dssp             SSSEEEEEECCG-GGHHHHHHHHHCST-TCCEEEECSSHHHHHHHHHHHHHTTCCEEEECSSSCHHHHHHHHHHHHTTSS
T ss_pred             CCeEEEEEEeCh-HHHHHHHHHHHccC-CCCEEEEECchHHHHHHHhhhcccccccccccccchhhhhhhhhhhhhcccc
Confidence            467888888865 57899999988754 4689999999999999999999999999999999999999999999999999


Q ss_pred             cEEEEecCCcCCCCCCCCcEEEEecCCCCccchhhhhcccccCCCceeEEEEeccccHHHHHHHHHHhccccccC
Q 017573          287 RVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEEL  361 (369)
Q Consensus       287 ~vli~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  361 (369)
                      ++||+|+++++|+|+|.+++||++++|+|+..|.||+||+||.|+.|.+++++++.|...++.+++.++.+++++
T Consensus        80 ~ilv~T~~~~~Gid~~~v~~Vi~~d~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~d~~~~~~i~~~~~~~i~~l  154 (155)
T d1hv8a2          80 RILIATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKKGKAISIINRREYKKLRYIERAMKLKIKKL  154 (155)
T ss_dssp             SEEEECTTHHHHCCCSCCSEEEESSCCSCHHHHHHHSTTTCCSSSCCEEEEEECTTSHHHHHHHHHHHTCCCCCB
T ss_pred             eeeeehhHHhhhhhhccCcEEEEecCCCCHHHHHHHHHhcCcCCCCceEEEEEchHHHHHHHHHHHHHCCCcccc
Confidence            999999999999999999999999999999999999999999999999999999999999999999999888775

>d2p6ra3 c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.96  E-value=6.1e-29  Score=197.99  Aligned_cols=184  Identities=16%  Similarity=0.212  Sum_probs=141.6

Q ss_pred             CCHHHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHH
Q 017573            3 LQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEK   82 (369)
Q Consensus         3 l~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~   82 (369)
                      +++++...|++.|+.+|+|+|+++++++.+++++++++|||+|||.+++++++..+....   ++++++|+++|+.|+.+
T Consensus        10 ~~~~~~~~l~~~g~~~l~~~Q~~ai~~l~~~~~~il~apTGsGKT~~a~l~i~~~~~~~~---~vl~l~P~~~L~~q~~~   86 (202)
T d2p6ra3          10 ISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKGG---KSLYVVPLRALAGEKYE   86 (202)
T ss_dssp             HHHHHHHHHHCC---CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHHTTC---CEEEEESSHHHHHHHHH
T ss_pred             hhHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCchhHHHHHHHHHHhhccC---cceeecccHHHHHHHHH
Confidence            578899999999999999999999999999999999999999999999888887776544   89999999999999999


Q ss_pred             HHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHH--
Q 017573           83 VMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIY--  160 (369)
Q Consensus        83 ~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~--  160 (369)
                      .++++... ...+....++.....   .....++++++|+..+...+.........++++|+||+|.+.+........  
T Consensus        87 ~~~~~~~~-~~~v~~~~~~~~~~~---~~~~~~~ii~~~~~~~~~~~~~~~~~~~~~~~ii~DE~h~~~~~~r~~~~~~~  162 (202)
T d2p6ra3          87 SFKKWEKI-GLRIGISTGDYESRD---EHLGDCDIIVTTSEKADSLIRNRASWIKAVSCLVVDEIHLLDSEKRGATLEIL  162 (202)
T ss_dssp             HHTTTTTT-TCCEEEECSSCBCCS---SCSTTCSEEEEEHHHHHHHHHTTCSGGGGCCEEEETTGGGGGCTTTHHHHHHH
T ss_pred             HHHHHhhc-cccceeeccCccccc---ccccccceeeeccHHHHHHHhccchhhhhhhhccccHHHHhcccccchHHHHH
Confidence            99887654 344555555443221   123467899999999999988888777788999999999987665443333  


Q ss_pred             -HHHhhCCccCcEEEEEeeCChhHHHHHHHhcCCCE
Q 017573          161 -DIFQLLPAKVQVGVFSATMPPEALEITRKFMNKPV  195 (369)
Q Consensus       161 -~~~~~~~~~~~~i~~saT~~~~~~~~~~~~~~~~~  195 (369)
                       ..+...+++.|+++||||.+ +..++ ..++..+.
T Consensus       163 l~~i~~~~~~~~~l~lSATl~-n~~~~-~~~l~~~~  196 (202)
T d2p6ra3         163 VTKMRRMNKALRVIGLSATAP-NVTEI-AEWLDADY  196 (202)
T ss_dssp             HHHHHHHCTTCEEEEEECCCT-THHHH-HHHTTCEE
T ss_pred             HHHHHhcCCCCcEEEEcCCCC-cHHHH-HHHcCCCe
Confidence             33444567889999999975 34444 45555443

>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=99.95  E-value=8.3e-27  Score=185.71  Aligned_cols=166  Identities=21%  Similarity=0.152  Sum_probs=131.5

Q ss_pred             CCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEE
Q 017573           17 EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVH   96 (369)
Q Consensus        17 ~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~   96 (369)
                      .+||+||+++++.+. ++++++++|||+|||+++++++...+...  +.+++|++|+++|+.|+.+.+.++....+..+.
T Consensus         8 ~~pr~~Q~~~~~~~~-~~n~lv~~pTGsGKT~i~~~~~~~~~~~~--~~~il~i~P~~~L~~q~~~~~~~~~~~~~~~v~   84 (200)
T d1wp9a1           8 IQPRIYQEVIYAKCK-ETNCLIVLPTGLGKTLIAMMIAEYRLTKY--GGKVLMLAPTKPLVLQHAESFRRLFNLPPEKIV   84 (200)
T ss_dssp             HCCCHHHHHHHHHGG-GSCEEEECCTTSCHHHHHHHHHHHHHHHS--CSCEEEECSSHHHHHHHHHHHHHHBCSCGGGEE
T ss_pred             CCCCHHHHHHHHHHh-cCCeEEEeCCCCcHHHHHHHHHHHHHHhc--CCcEEEEcCchHHHHHHHHHHHHhhccccccee
Confidence            489999999998875 56799999999999999887776665443  238999999999999999999999887788888


Q ss_pred             EEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEE
Q 017573           97 ACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFS  176 (369)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~s  176 (369)
                      ...++.......... .+.+++++|++.+...+.........++++|+||||.+....................+++++|
T Consensus        85 ~~~~~~~~~~~~~~~-~~~~i~i~t~~~~~~~~~~~~~~~~~~~~vIiDE~H~~~~~~~~~~~~~~~~~~~~~~~~l~~S  163 (200)
T d1wp9a1          85 ALTGEKSPEERSKAW-ARAKVIVATPQTIENDLLAGRISLEDVSLIVFDEAHRAVGNYAYVFIAREYKRQAKNPLVIGLT  163 (200)
T ss_dssp             EECSCSCHHHHHHHH-HHCSEEEECHHHHHHHHHTTSCCTTSCSEEEEETGGGCSTTCHHHHHHHHHHHHCSSCCEEEEE
T ss_pred             eeecccchhHHHHhh-hcccccccccchhHHHHhhhhhhccccceEEEEehhhhhcchhHHHHHHHHHhcCCCCcEEEEE
Confidence            777776655544433 3468999999999998888888888899999999999876554444444444445577899999


Q ss_pred             eeCChhHHHH
Q 017573          177 ATMPPEALEI  186 (369)
Q Consensus       177 aT~~~~~~~~  186 (369)
                      |||.......
T Consensus       164 ATp~~~~~~~  173 (200)
T d1wp9a1         164 ASPGSTPEKI  173 (200)
T ss_dssp             SCSCSSHHHH
T ss_pred             ecCCCcHHHH
Confidence            9996544433

>d1oywa3 c.37.1.19 (A:207-406) RecQ helicase domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

Probab=99.95  E-value=1.8e-26  Score=180.76  Aligned_cols=131  Identities=24%  Similarity=0.396  Sum_probs=124.3

Q ss_pred             hhhHHHHHHHHHhccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCC
Q 017573          220 EWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGI  299 (369)
Q Consensus       220 ~~~~~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~  299 (369)
                      ..+.+.+..++......++||||++.+.++.++..|...++.+..+||+++..+|.++++.|.+|+.++||+|+++++|+
T Consensus        15 ~~k~~~L~~~l~~~~~~~~IIF~~t~~~~~~l~~~l~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~ilvaTd~~~~Gi   94 (200)
T d1oywa3          15 FKPLDQLMRYVQEQRGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMGI   94 (200)
T ss_dssp             SSHHHHHHHHHHHTTTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECTTSCTTT
T ss_pred             CcHHHHHHHHHHhcCCCCEEEEEeeehhhHHhhhhhccCCceeEEecCCCcHHHHHHHHHHHhcccceEEEecchhhhcc
Confidence            44788889999888888999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCcEEEEecCCCCccchhhhhcccccCCCceeEEEEeccccHHHHHHH
Q 017573          300 DVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDI  350 (369)
Q Consensus       300 d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~  350 (369)
                      |+|++++||++++|.+..+|.|++||+||.|+.|.+++++.+.|...++.+
T Consensus        95 D~p~v~~VI~~~~P~~~~~y~qr~GR~gR~g~~g~ai~~~~~~d~~~l~~~  145 (200)
T d1oywa3          95 NKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLRRC  145 (200)
T ss_dssp             CCTTCCEEEESSCCSSHHHHHHHHTTSCTTSSCEEEEEEECHHHHHHHHHH
T ss_pred             CCCCCCEEEECCCccchHHHHHHhhhhhcCCCCceEEEecCHHHHHHHHhh
Confidence            999999999999999999999999999999999999999999887777654

>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=99.94  E-value=3.4e-28  Score=194.50  Aligned_cols=184  Identities=16%  Similarity=0.178  Sum_probs=135.6

Q ss_pred             CCCCHHHHHHHHh-CCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHH
Q 017573            1 MGLQENLLRGIYA-YGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQ   79 (369)
Q Consensus         1 ~~l~~~i~~~l~~-~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q   79 (369)
                      +||++.+...|++ |||.++||+|+++++++.+|+++++++|||+|||.++.++++..      ..++++++|+++|+.|
T Consensus         7 ~~l~~~~~~~l~~~fg~~~~rp~Q~~ai~~~l~g~~vlv~apTGsGKT~~~~~~~~~~------~~~~~~v~P~~~L~~q   80 (206)
T d1oywa2           7 LNLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLL------NGLTVVVSPLISLMKD   80 (206)
T ss_dssp             SSHHHHHHHHHHHTTCCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHS------SSEEEEECSCHHHHHH
T ss_pred             CCCCHHHHHHHHHhcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCCCcchhhhhhhhc------cCceEEeccchhhhhh
Confidence            5788888988966 59999999999999999999999999999999999998877643      2289999999999999


Q ss_pred             HHHHHHHhccccCcEEEEEECCcch----HHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCc
Q 017573           80 IEKVMRALGDYLGVKVHACVGGTSV----REDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGF  155 (369)
Q Consensus        80 ~~~~~~~~~~~~~~~v~~~~~~~~~----~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~  155 (369)
                      +.+.++.+...    ..........    ...........+++++|++.+.............++++|+||+|.+.+++.
T Consensus        81 ~~~~l~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~t~~~~~~~~~~~~~~~~~v~~lviDEaH~~~~~~~  156 (206)
T d1oywa2          81 QVDQLQANGVA----AACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDNFLEHLAHWNPVLLAVDEAHCISQWGH  156 (206)
T ss_dssp             HHHHHHHTTCC----EEEECTTSCHHHHHHHHHHHHHTCCSEEEECHHHHTSTTHHHHHTTSCEEEEEESSGGGGCTTSS
T ss_pred             HHHHHHhhccc----ccccccccccccchhHHHHHhcCCceEEEEechhhhchhhcccchhheeeeeeeeeeeeeecccc
Confidence            99999887433    2222222221    122233445789999999988654444445566689999999998876542


Q ss_pred             H-----HHHHHHHhhCCccCcEEEEEeeCChhHHH-HHHHh-cCCCE
Q 017573          156 K-----DQIYDIFQLLPAKVQVGVFSATMPPEALE-ITRKF-MNKPV  195 (369)
Q Consensus       156 ~-----~~~~~~~~~~~~~~~~i~~saT~~~~~~~-~~~~~-~~~~~  195 (369)
                      .     .....+...++ +.|++++|||+++...+ +.+.+ +.+|+
T Consensus       157 ~~~~~~~~~~~l~~~~~-~~~ii~lSATl~~~v~~di~~~L~l~~p~  202 (206)
T d1oywa2         157 DFRPEYAALGQLRQRFP-TLPFMALTATADDTTRQDIVRLLGLNDPL  202 (206)
T ss_dssp             CCCHHHHGGGGHHHHCT-TSCEEEEESCCCHHHHHHHHHHHTCCSCE
T ss_pred             chHHHHHHHHHHHHhCC-CCceEEEEeCCCHHHHHHHHHHcCCCCCc
Confidence            2     12234444444 68899999999887654 44443 56664

>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=99.93  E-value=8e-26  Score=184.48  Aligned_cols=176  Identities=19%  Similarity=0.212  Sum_probs=125.6

Q ss_pred             HHHHHHHhCCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHH
Q 017573            6 NLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMR   85 (369)
Q Consensus         6 ~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~   85 (369)
                      ++.+ +...++.+|+++|+++++.+++|+++++.||||+|||.+++++++.....+.   +++|++|+++|+.|+.++++
T Consensus        32 ~~~~-~~~~~~~~p~~~Q~~~i~~~l~g~~~~i~apTGsGKT~~~~~~~~~~~~~~~---rvliv~Pt~~La~Q~~~~l~  107 (237)
T d1gkub1          32 EFVE-FFRKCVGEPRAIQKMWAKRILRKESFAATAPTGVGKTSFGLAMSLFLALKGK---RCYVIFPTSLLVIQAAETIR  107 (237)
T ss_dssp             HHHH-HHHTTTCSCCHHHHHHHHHHHTTCCEECCCCBTSCSHHHHHHHHHHHHTTSC---CEEEEESCHHHHHHHHHHHH
T ss_pred             HHHH-HHHhccCCCCHHHHHHHHHHHCCCCEEEEecCCChHHHHHHHHHHHHHHhcC---eEEEEeccHHHHHHHHHHHH
Confidence            3444 3344778999999999999999999999999999999998888877665543   89999999999999999999


Q ss_pred             HhccccCcE----EEEEECCcchHHHHHHH--ccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHH
Q 017573           86 ALGDYLGVK----VHACVGGTSVREDQRIL--QAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQI  159 (369)
Q Consensus        86 ~~~~~~~~~----v~~~~~~~~~~~~~~~~--~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~  159 (369)
                      ++....++.    +....++..........  ..+++|+|+||+.+.+..    ....+++++|+||+|.+.+...  ..
T Consensus       108 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~Ilv~Tp~~l~~~~----~~~~~~~~vVvDE~d~~l~~~~--~~  181 (237)
T d1gkub1         108 KYAEKAGVGTENLIGYYHGRIPKREKENFMQNLRNFKIVITTTQFLSKHY----RELGHFDFIFVDDVDAILKASK--NV  181 (237)
T ss_dssp             HHHTTTCCSGGGSEEECCSSCCSHHHHHHHHSGGGCSEEEEEHHHHHHCS----TTSCCCSEEEESCHHHHHTSTH--HH
T ss_pred             HHHHHcCCceEEEEeeeecccchhhhhhhhccccccceeccChHHHHHhh----hhcCCCCEEEEEChhhhhhccc--ch
Confidence            987766543    33334444433333333  245789999998876532    3455689999999999875542  22


Q ss_pred             HHHHhh-------------CCccCcEEEEEeeCChhHH-HHHHHhc
Q 017573          160 YDIFQL-------------LPAKVQVGVFSATMPPEAL-EITRKFM  191 (369)
Q Consensus       160 ~~~~~~-------------~~~~~~~i~~saT~~~~~~-~~~~~~~  191 (369)
                      ......             .+...|++++|||++.... .+.+.++
T Consensus       182 ~~~~~~~g~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~l~r~ll  227 (237)
T d1gkub1         182 DKLLHLLGFHYDLKTKSWVGEARGCLMVSTATAKKGKKAELFRQLL  227 (237)
T ss_dssp             HHHHHHTTEEEETTTTEEEECCSSEEEECCCCSCCCTTHHHHHHHH
T ss_pred             hHHHHhcCChHHHHHHHhhCCCCCeEEEEeCCCCcccHHHHHHHHh
Confidence            222222             2346789999999875432 3334443

>d1c4oa2 c.37.1.19 (A:410-583) Nucleotide excision repair enzyme UvrB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Thermus thermophilus [TaxId: 274]

Probab=99.92  E-value=3.7e-24  Score=160.98  Aligned_cols=126  Identities=25%  Similarity=0.356  Sum_probs=107.9

Q ss_pred             HHHHHHHHh-ccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCC
Q 017573          224 ETLCDLYET-LAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQ  302 (369)
Q Consensus       224 ~~l~~~~~~-~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~  302 (369)
                      +.+..+.+. ..++++||||+++++++.+++.|.+.|+++..+||+++..+|.+++++|++|+++|||+|+++++|+|+|
T Consensus        19 dll~~i~~~~~~g~r~lvfc~t~~~~~~l~~~L~~~Gi~a~~~Hg~~~~~eR~~~l~~F~~G~~~vLVaT~v~~~GiDip   98 (174)
T d1c4oa2          19 DLMEGIRERAARGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLREGLDIP   98 (174)
T ss_dssp             HHHHHHHHHHHTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESCCCCTTCCCT
T ss_pred             HHHHHHHHHHhcCCcEEEEEcchhHHHHHHHHHHhcCCceEEEecccchHHHHHHHHHHHCCCeEEEEeeeeeeeeccCC
Confidence            344444443 2467999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCcEEEEecCCCCc-----cchhhhhcccccCCCceeEEEEeccccHHHHHHH
Q 017573          303 QVSLVINYDLPTQP-----ENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDI  350 (369)
Q Consensus       303 ~~~~vi~~~~~~~~-----~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~  350 (369)
                      ++++|+++++|.+.     ..|.|++||+||.++ |.++++....+..+.+-+
T Consensus        99 ~V~~Vi~~~~~~~~~~~~~~~~iq~~GR~gR~~~-g~~~~~~~~~~~~~~~~i  150 (174)
T d1c4oa2          99 EVSLVAILDADKEGFLRSERSLIQTIGRAARNAR-GEVWLYADRVSEAMQRAI  150 (174)
T ss_dssp             TEEEEEETTTTSCSGGGSHHHHHHHHGGGTTSTT-CEEEEECSSCCHHHHHHH
T ss_pred             CCcEEEEeccccccccchhHHHHHHhhhhhhcCC-CeeEEeecCCCHHHHHHH
Confidence            99999999987644     669999999999865 777777776655544333

>d1t5la2 c.37.1.19 (A:415-595) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Bacillus caldotenax [TaxId: 1395]

Probab=99.90  E-value=6.8e-23  Score=156.90  Aligned_cols=118  Identities=24%  Similarity=0.373  Sum_probs=101.3

Q ss_pred             HHHHHHHHhc-cCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCC
Q 017573          224 ETLCDLYETL-AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQ  302 (369)
Q Consensus       224 ~~l~~~~~~~-~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~  302 (369)
                      +.+..+.+.. .+.++||||+++++++.++..|++.|.++..+||++++++|.+++++|++|+++|||||+++++|+|+|
T Consensus        19 ~ll~~i~~~~~~~~~~iif~~~~~~~~~~~~~l~~~g~~~~~~hg~~~~~eR~~~l~~Fr~g~~~vLVaTdv~~rGiDip   98 (181)
T d1t5la2          19 DLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIP   98 (181)
T ss_dssp             HHHHHHHHHHHTTCEEEEECSSHHHHHHHHHHHHTTTCCEEEECSSCCHHHHHHHHHHHHHTSCSEEEESCCCSSSCCCT
T ss_pred             HHHHHHHHHHhcCCeEEEEeehhhhhHHHHHHHHhCCcceeEecCCccHHHHHHHHHHHHCCCCCEEEehhHHHccCCCC
Confidence            3444444433 456899999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCcEEEEecCCC-----CccchhhhhcccccCCCceeEEEEeccc
Q 017573          303 QVSLVINYDLPT-----QPENYLHRIGRSGRFGRKGVAINFVTRD  342 (369)
Q Consensus       303 ~~~~vi~~~~~~-----~~~~~~Q~~GR~~R~~~~~~~~~~~~~~  342 (369)
                      ++++||+++.|.     +...|.||+||+||.|+. .++++....
T Consensus        99 ~v~~VI~~d~p~~~~~~s~~~yi~R~GRagR~g~~-~~~~~~~~~  142 (181)
T d1t5la2          99 EVSLVAILDADKEGFLRSERSLIQTIGRAARNANG-HVIMYADTI  142 (181)
T ss_dssp             TEEEEEETTTTSCSGGGSHHHHHHHHGGGTTSTTC-EEEEECSSC
T ss_pred             CCCEEEEecCCcccccccHHHHHHHHHhhccccCc-eeEeecchh
Confidence            999999999985     567889999999998764 344444433

>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=99.88  E-value=2.7e-23  Score=172.30  Aligned_cols=154  Identities=17%  Similarity=0.107  Sum_probs=113.8

Q ss_pred             CCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEE
Q 017573           17 EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVH   96 (369)
Q Consensus        17 ~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~   96 (369)
                      ..||++|.+++..++++++.++.+|||+|||+++...+....... . .++||++|+++|+.||.+++.++.......+.
T Consensus       112 ~~~rdyQ~~av~~~l~~~~~il~~pTGsGKT~i~~~i~~~~~~~~-~-~k~Liivp~~~Lv~Q~~~~f~~~~~~~~~~~~  189 (282)
T d1rifa_         112 IEPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENY-E-GKILIIVPTTALTTQMADDFVDYRLFSHAMIK  189 (282)
T ss_dssp             CCCCHHHHHHHHHHHHHSEEEECCCTTSCHHHHHHHHHHHHHHHC-S-SEEEEECSSHHHHHHHHHHHHHHTSCCGGGEE
T ss_pred             cccchHHHHHHHHHHhcCCceeEEEcccCccHHHHHHHHHhhhcc-c-ceEEEEEcCchhHHHHHHHHHHhhccccccce
Confidence            379999999999999999999999999999998765554433332 2 28999999999999999999998655444455


Q ss_pred             EEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEE
Q 017573           97 ACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFS  176 (369)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~s  176 (369)
                      ...++......   ......++++|++++......   ..+.+++||+||||++.    ...+..++..+.+....+++|
T Consensus       190 ~~~~g~~~~~~---~~~~~~i~i~t~qs~~~~~~~---~~~~f~~VIvDEaH~~~----a~~~~~il~~~~~~~~rlGlT  259 (282)
T d1rifa_         190 KIGGGASKDDK---YKNDAPVVVGTWQTVVKQPKE---WFSQFGMMMNDECHLAT----GKSISSIISGLNNCMFKFGLS  259 (282)
T ss_dssp             ECSTTCSSTTC---CCTTCSEEEECHHHHTTSCGG---GGGGEEEEEEETGGGCC----HHHHHHHTTTCTTCCEEEEEC
T ss_pred             eecceeccccc---ccccceEEEEeeehhhhhccc---ccCCCCEEEEECCCCCC----chhHHHHHHhccCCCeEEEEE
Confidence            54444432211   223578999999887543322   23468999999999874    345566777776556679999


Q ss_pred             eeCChh
Q 017573          177 ATMPPE  182 (369)
Q Consensus       177 aT~~~~  182 (369)
                      |||+..
T Consensus       260 aT~~~~  265 (282)
T d1rifa_         260 GSLRDG  265 (282)
T ss_dssp             SSCCTT
T ss_pred             eecCCC
Confidence            998643

>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=99.88  E-value=1.6e-21  Score=154.35  Aligned_cols=171  Identities=20%  Similarity=0.235  Sum_probs=132.8

Q ss_pred             CHHHHHHH-HhCCCCCCcHhhhhhhhcccc----C--CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHH
Q 017573            4 QENLLRGI-YAYGFEKPSAIQQRGIVPFCK----G--LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTREL   76 (369)
Q Consensus         4 ~~~i~~~l-~~~~~~~~~~~Q~~~~~~~~~----~--~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l   76 (369)
                      +....+.+ ..++| .+++-|.+++..+.+    +  .+.+++|.||||||.+++.++...+..+.   ++++++|+..|
T Consensus        41 ~~~~~~~~~~~lP~-~lt~~Q~~~~~~i~~~~~~~~~~~~LL~GdvGsGKT~V~~~a~~~~~~~g~---qv~~l~Pt~~L  116 (233)
T d2eyqa3          41 DREQYQLFCDSFPF-ETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDNHK---QVAVLVPTTLL  116 (233)
T ss_dssp             CHHHHHHHHHTCCS-CCCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHTTTC---EEEEECSSHHH
T ss_pred             CHHHHHhhhhcccc-ccchhHHHHHHHHHHHHhccCccCeEEEcCCCCCcHHHHHHHHHHHHHcCC---ceEEEccHHHh
Confidence            44555555 55776 899999999988764    2  46899999999999999999998887766   99999999999


Q ss_pred             HHHHHHHHHHhccccCcEEEEEECCcchHHHH----HHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhc
Q 017573           77 AQQIEKVMRALGDYLGVKVHACVGGTSVREDQ----RILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLS  152 (369)
Q Consensus        77 ~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~----~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~  152 (369)
                      +.|+.+.+++++...+.++..+++........    ....+..+|+|+|...+.     ......++++||+||-|++.-
T Consensus       117 a~Q~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~g~~~iviGths~l~-----~~~~f~~LgLiIiDEeH~fg~  191 (233)
T d2eyqa3         117 AQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQ-----SDVKFKDLGLLIVDEEHRFGV  191 (233)
T ss_dssp             HHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHH-----SCCCCSSEEEEEEESGGGSCH
T ss_pred             HHHHHHHHHHHHhhCCCEEEeccCcccchhHHHHHHHHhCCCCCEEEeehhhhc-----cCCccccccceeeechhhhhh
Confidence            99999999999888899999999988765543    344568899999965554     345556789999999998643


Q ss_pred             cCcHHHHHHHHhhCCccCcEEEEEeeCChhHHHHHH
Q 017573          153 RGFKDQIYDIFQLLPAKVQVGVFSATMPPEALEITR  188 (369)
Q Consensus       153 ~~~~~~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~  188 (369)
                      .+    -..+ .....+..++.+||||.+....+..
T Consensus       192 kQ----~~~l-~~~~~~~~~l~~SATPiprtl~~~~  222 (233)
T d2eyqa3         192 RH----KERI-KAMRANVDILTLTATPIPRTLNMAM  222 (233)
T ss_dssp             HH----HHHH-HHHHTTSEEEEEESSCCCHHHHHHH
T ss_pred             HH----HHHH-HhhCCCCCEEEEecchhHHHHHHHH
Confidence            22    2222 2223457799999999987755543

>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=99.87  E-value=4.4e-22  Score=160.67  Aligned_cols=169  Identities=21%  Similarity=0.241  Sum_probs=131.1

Q ss_pred             HHHHHHHhCCCCCCcHhhhhhhhcccc------CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHH
Q 017573            6 NLLRGIYAYGFEKPSAIQQRGIVPFCK------GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQ   79 (369)
Q Consensus         6 ~i~~~l~~~~~~~~~~~Q~~~~~~~~~------~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q   79 (369)
                      ....-++.++| ++++-|++++..+.+      ..+.+++|.+|||||.+|+.++...+..+.   ++++++|+..|+.|
T Consensus        72 l~~~f~~~LPF-eLT~~Q~~ai~ei~~d~~~~~~m~rLL~GdvGSGKT~Va~~a~~~~~~~g~---q~~~m~Pt~~La~Q  147 (264)
T d1gm5a3          72 LAEEFIKSLPF-KLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEAGF---QTAFMVPTSILAIQ  147 (264)
T ss_dssp             HHHHHHHHSSS-CCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHHTS---CEEEECSCHHHHHH
T ss_pred             HHHHHHhhccc-cCCchHHHHHHHHHHHhhccCcceeeeeccccccccHHHHHHHHHHHhccc---ceeEEeehHhhhHH
Confidence            34445577888 899999999999864      246899999999999999999998888776   89999999999999


Q ss_pred             HHHHHHHhccccCcEEEEEECCcchHHHHH----HHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCc
Q 017573           80 IEKVMRALGDYLGVKVHACVGGTSVREDQR----ILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGF  155 (369)
Q Consensus        80 ~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~----~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~  155 (369)
                      +.+.+.++....+..+..++++....+...    +..++.+|+|+|+.-+..     .+...++++||+||-|++.-.+.
T Consensus       148 h~~~~~~~f~~~~~~v~~l~~~~~~~~r~~~~~~~~~g~~~iiIGThsl~~~-----~~~f~~LglviiDEqH~fgv~Qr  222 (264)
T d1gm5a3         148 HYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQE-----DVHFKNLGLVIIDEQHRFGVKQR  222 (264)
T ss_dssp             HHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHH-----CCCCSCCCEEEEESCCCC-----
T ss_pred             HHHHHHHhhhhccccceeeccccchHHHHHHHHHHHCCCCCEEEeehHHhcC-----CCCccccceeeeccccccchhhH
Confidence            999999999988999999999887665443    345689999999766553     23445689999999998753331


Q ss_pred             HHHHHHHHhhCCccCcEEEEEeeCChhHHHHHH
Q 017573          156 KDQIYDIFQLLPAKVQVGVFSATMPPEALEITR  188 (369)
Q Consensus       156 ~~~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~  188 (369)
                           ..+..-...+.++.|||||.+....+..
T Consensus       223 -----~~l~~~~~~~~~l~~SATPiprtl~~~~  250 (264)
T d1gm5a3         223 -----EALMNKGKMVDTLVMSATPIPRSMALAF  250 (264)
T ss_dssp             -----CCCCSSSSCCCEEEEESSCCCHHHHHHH
T ss_pred             -----HHHHHhCcCCCEEEEECCCCHHHHHHHH
Confidence                 1111222357799999999987765553

>d2fz4a1 c.37.1.19 (A:24-229) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.86  E-value=9.4e-22  Score=155.94  Aligned_cols=136  Identities=18%  Similarity=0.186  Sum_probs=101.5

Q ss_pred             CCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEE
Q 017573           18 KPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHA   97 (369)
Q Consensus        18 ~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~   97 (369)
                      +||+||+++++.+.++++.++.+|||+|||++++..+.. +     +.++||+||+++|+.||.+++.++...   .+..
T Consensus        70 ~Lr~yQ~eav~~~~~~~~~ll~~~tG~GKT~~a~~~~~~-~-----~~~~Liv~p~~~L~~q~~~~~~~~~~~---~~~~  140 (206)
T d2fz4a1          70 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINE-L-----STPTLIVVPTLALAEQWKERLGIFGEE---YVGE  140 (206)
T ss_dssp             CCCHHHHHHHHHHTTTSEEEEEESSSTTHHHHHHHHHHH-S-----CSCEEEEESSHHHHHHHHHHHGGGCGG---GEEE
T ss_pred             CcCHHHHHHHHHHHhCCCcEEEeCCCCCceehHHhHHHH-h-----cCceeEEEcccchHHHHHHHHHhhccc---chhh
Confidence            699999999999999999999999999999987655432 2     227999999999999999999887543   2333


Q ss_pred             EECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEEe
Q 017573           98 CVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSA  177 (369)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~sa  177 (369)
                      ..+..         .....++++|++.+.......   ...+++||+||||++.+..    +..+...++ ...+++|||
T Consensus       141 ~~~~~---------~~~~~i~i~t~~~~~~~~~~~---~~~~~lvIiDEaH~~~a~~----~~~i~~~~~-~~~~lgLTA  203 (206)
T d2fz4a1         141 FSGRI---------KELKPLTVSTYDSAYVNAEKL---GNRFMLLIFDEVHHLPAES----YVQIAQMSI-APFRLGLTA  203 (206)
T ss_dssp             ESSSC---------BCCCSEEEEEHHHHHHTHHHH---TTTCSEEEEECSSCCCTTT----HHHHHHTCC-CSEEEEEEE
T ss_pred             ccccc---------ccccccccceehhhhhhhHhh---CCcCCEEEEECCeeCCcHH----HHHHHhccC-CCcEEEEec
Confidence            33322         234579999999987655432   2357999999999986544    334455554 445789999


Q ss_pred             eC
Q 017573          178 TM  179 (369)
Q Consensus       178 T~  179 (369)
                      |+
T Consensus       204 Tl  205 (206)
T d2fz4a1         204 TF  205 (206)
T ss_dssp             SC
T ss_pred             CC
Confidence            97

>d1jr6a_ c.37.1.14 (A:) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=99.83  E-value=4.1e-21  Score=140.00  Aligned_cols=103  Identities=25%  Similarity=0.430  Sum_probs=91.7

Q ss_pred             HhccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEe
Q 017573          231 ETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINY  310 (369)
Q Consensus       231 ~~~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~  310 (369)
                      +....+++||||++++.++.+++.|++.+.++..+|++++.++       |++|+.++||||+++++|+| |+++.||++
T Consensus        31 ~~~~~~k~IVFc~t~~~ae~la~~L~~~G~~~~~~H~~~~~~~-------~~~~~~~vlvaTd~~~~GiD-~~v~~Vi~~  102 (138)
T d1jr6a_          31 EVIKGGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVSV-------IPTNGDVVVVATDALMTGFT-GDFDSVIDC  102 (138)
T ss_dssp             HHHTTSCEEEECSCHHHHHHHHHHHHHHTCEEEEECTTCCSCC-------CTTSSCEEEEESSSSCSSSC-CCBSEEEEC
T ss_pred             hhcCCCCEEEEeCcHHHHHHHHHHHhccccchhhhhccchhhh-------hhhhhcceeehhHHHHhccc-cccceEEEE
Confidence            4456689999999999999999999999999999999998654       67899999999999999999 999999885


Q ss_pred             c----CCCCccchhhhhcccccCCCceeEEEEecccc
Q 017573          311 D----LPTQPENYLHRIGRSGRFGRKGVAINFVTRDD  343 (369)
Q Consensus       311 ~----~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~  343 (369)
                      +    +|.+..+|.||+||+|| |++|. ++|+.+.+
T Consensus       103 ~~~~~~P~~~~~y~qr~GR~gR-g~~G~-~~~i~~~e  137 (138)
T d1jr6a_         103 NTSDGKPQDAVSRTQRRGRTGR-GKPGI-YRFVAPGE  137 (138)
T ss_dssp             SEETTEECCHHHHHHHHTTBCS-SSCEE-EEECCSSC
T ss_pred             EecCCCCCCHHHHHhHhccccC-CCCcE-EEEEcCCC
Confidence            4    68899999999999999 99995 66777654

>d1wp9a2 c.37.1.19 (A:201-486) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

Probab=99.83  E-value=1.4e-20  Score=157.43  Aligned_cols=121  Identities=21%  Similarity=0.385  Sum_probs=105.7

Q ss_pred             HHHHHHHhccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCC--------CCHHHHHHHHHHHhcCCCcEEEEecCCc
Q 017573          225 TLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGD--------MDQNTRDIIMREFRSGSSRVLITTDLLA  296 (369)
Q Consensus       225 ~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~--------~~~~~r~~~~~~f~~~~~~vli~t~~~~  296 (369)
                      .+.+++....+.++||||++...++.+++.|.+.+.++..++|.        ++..+|.++++.|++|+++|||+|++++
T Consensus       151 ~l~~~~~~~~~~k~iiF~~~~~~~~~~~~~L~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~F~~g~~~vLv~T~~~~  230 (286)
T d1wp9a2         151 IIREQLQRKQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVATSVGE  230 (286)
T ss_dssp             HHHHHHHHCTTCCEEEECSCHHHHHHHHHHHHHTTCCEEEECCSSCC-------CCHHHHHHHHHHHTSCSEEEECGGGG
T ss_pred             HHHHHHHhCCCCcEEEEeCcHHhHHHHHHHHHHcCCceEEeeccccccccchhchHHHHHHHHHHHcCCCcEEEEcccee
Confidence            33444455677899999999999999999999999998888774        5566889999999999999999999999


Q ss_pred             CCCCCCCCcEEEEecCCCCccchhhhhcccccCCCceeEEEEeccccHHH
Q 017573          297 RGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERM  346 (369)
Q Consensus       297 ~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~  346 (369)
                      +|+|+|++++||++++|+|+..|.||+||+||. +.|.++.++++++.+.
T Consensus       231 ~Gld~~~~~~Vi~~d~~~~~~~~~Qr~GR~gR~-~~~~~~~l~~~~~~ee  279 (286)
T d1wp9a2         231 EGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRH-MPGRVIILMAKGTRDE  279 (286)
T ss_dssp             GGGGSTTCCEEEESSCCHHHHHHHHHHTTSCSC-CCSEEEEEEETTSHHH
T ss_pred             ccccCCCCCEEEEeCCCCCHHHHHHHHHhCCCC-CCCEEEEEEeCCCHHH
Confidence            999999999999999999999999999999996 5788999998876553

>d2fwra1 c.37.1.19 (A:257-456) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.81  E-value=1.5e-20  Score=148.48  Aligned_cols=107  Identities=21%  Similarity=0.376  Sum_probs=99.4

Q ss_pred             hhHHHHHHHHHhccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCC
Q 017573          221 WKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID  300 (369)
Q Consensus       221 ~~~~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d  300 (369)
                      .+.+.+.+++...++.++||||++.+.++.+.+.|.     +..+||+++.++|.+++++|++|+.+||++|+++++|+|
T Consensus        79 ~K~~~l~~ll~~~~~~k~lvf~~~~~~~~~l~~~l~-----~~~i~g~~~~~~R~~~l~~F~~~~~~vLv~~~~~~~Gid  153 (200)
T d2fwra1          79 NKIRKLREILERHRKDKIIIFTRHNELVYRISKVFL-----IPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGID  153 (200)
T ss_dssp             HHHHHHHHHHHHTSSSCBCCBCSCHHHHHHHHHHTT-----CCBCCSSSCSHHHHTHHHHHHHSSCSBCBCSSCCCSSSC
T ss_pred             HHHHHHHHHHHhCCCCcEEEEeCcHHHHHHHHhhcC-----cceeeCCCCHHHHHHHHHHhhcCCeeeeeecchhhcccC
Confidence            477888899998888999999999999999998873     456799999999999999999999999999999999999


Q ss_pred             CCCCcEEEEecCCCCccchhhhhcccccCCCc
Q 017573          301 VQQVSLVINYDLPTQPENYLHRIGRSGRFGRK  332 (369)
Q Consensus       301 ~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~  332 (369)
                      +|.+++||++++++|+..+.|++||++|.|+.
T Consensus       154 l~~~~~vi~~~~~~s~~~~~Q~iGR~~R~~~~  185 (200)
T d2fwra1         154 VPDANVGVIMSGSGSAREYIQRLGRILRPSKG  185 (200)
T ss_dssp             SCCBSEEEEECCSSCCHHHHHHHHHSBCCCTT
T ss_pred             CCCCCEEEEeCCCCCHHHHHHHHHhcCCCCCC
Confidence            99999999999999999999999999999764

>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=99.80  E-value=4.2e-20  Score=137.72  Aligned_cols=136  Identities=20%  Similarity=0.199  Sum_probs=90.4

Q ss_pred             cccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHH
Q 017573           30 FCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQR  109 (369)
Q Consensus        30 ~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~  109 (369)
                      +.+|+++++.+|||+|||.+++..++.......  .++++++|++.+++|+.+.+...    +..+........      
T Consensus         4 l~~~~~~il~~~tGsGKT~~~~~~~~~~~~~~~--~~vli~~p~~~l~~q~~~~~~~~----~~~~~~~~~~~~------   71 (140)
T d1yksa1           4 LKKGMTTVLDFHPGAGKTRRFLPQILAECARRR--LRTLVLAPTRVVLSEMKEAFHGL----DVKFHTQAFSAH------   71 (140)
T ss_dssp             TSTTCEEEECCCTTSSTTTTHHHHHHHHHHHTT--CCEEEEESSHHHHHHHHHHTTTS----CEEEESSCCCCC------
T ss_pred             HHcCCcEEEEcCCCCChhHHHHHHHHHHhhhcC--ceeeeeecchhHHHHHHHHhhhh----hhhhcccccccc------
Confidence            456899999999999999888767666554432  38999999999999988776443    222222111111      


Q ss_pred             HHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcH-HHHHHHHhhCCccCcEEEEEeeCC
Q 017573          110 ILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFK-DQIYDIFQLLPAKVQVGVFSATMP  180 (369)
Q Consensus       110 ~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~-~~~~~~~~~~~~~~~~i~~saT~~  180 (369)
                       ...+..+.+.+...+...... .....++++||+||||++....+. +.+...... .++.++++||||||
T Consensus        72 -~~~~~~~~~~~~~~l~~~~~~-~~~~~~~~lvIiDEaH~~~~~~~~~~~~~~~~~~-~~~~~~l~lTATPp  140 (140)
T d1yksa1          72 -GSGREVIDAMCHATLTYRMLE-PTRVVNWEVIIMDEAHFLDPASIAARGWAAHRAR-ANESATILMTATPP  140 (140)
T ss_dssp             -CCSSCCEEEEEHHHHHHHHTS-SSCCCCCSEEEETTTTCCSHHHHHHHHHHHHHHH-TTSCEEEEECSSCT
T ss_pred             -cccccchhhhhHHHHHHHHhc-cccccceeEEEEccccccChhhHHHHHHHHHHhh-CCCCCEEEEEcCCC
Confidence             112356777777777654433 455677999999999987433322 122222333 35788999999996

>d2p6ra4 c.37.1.19 (A:203-403) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.79  E-value=2.2e-19  Score=140.66  Aligned_cols=121  Identities=23%  Similarity=0.382  Sum_probs=100.5

Q ss_pred             HHHHHHHHHhccCCCeEEEeCCHhhHHHHHHHHhhC------------------------------CCeeEEecCCCCHH
Q 017573          223 LETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSR------------------------------DHTVSATHGDMDQN  272 (369)
Q Consensus       223 ~~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~------------------------------~~~~~~~~~~~~~~  272 (369)
                      .+.+.+.+..  ++++||||++++.++.++..|...                              ...++.+|++++++
T Consensus        30 ~~l~~~~i~~--~~~~LVF~~sRk~~~~~A~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~GIa~hh~~l~~~  107 (201)
T d2p6ra4          30 EELVEECVAE--NGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLNG  107 (201)
T ss_dssp             HHHHHHHHHT--TCCEEEECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECTTSCHH
T ss_pred             HHHHHHHHHc--CCcEEEEeCCHHHHHHHHHHHHHHHHhhhchhHHHHHHHHhhhhhhhHHHHHHHhccHHHHHHHhhhh
Confidence            3444454443  568999999999998888777542                              12388999999999


Q ss_pred             HHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEE-------ecCCCCccchhhhhcccccCCC--ceeEEEEecccc
Q 017573          273 TRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVIN-------YDLPTQPENYLHRIGRSGRFGR--KGVAINFVTRDD  343 (369)
Q Consensus       273 ~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~-------~~~~~~~~~~~Q~~GR~~R~~~--~~~~~~~~~~~~  343 (369)
                      +|..+.+.|++|.++|||||+.++.|+|+|..++||.       .+.+.+..+|.|++||+||.|.  .|.++++..+.+
T Consensus       108 ~r~~ie~~f~~g~i~vlvaT~~l~~Gin~p~~~vvi~~~~~~d~~~~~~~~~~~~q~~GRAGR~g~~~~G~~~l~~~~~~  187 (201)
T d2p6ra4         108 QRRVVEDAFRRGNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIVGKRD  187 (201)
T ss_dssp             HHHHHHHHHHTTSCCEEEECSTTTSSSCCCBSEEEECCSEEESSSEEECCHHHHHHHHTTBSCTTTCSCEEEEEECCGGG
T ss_pred             hHHHHHHHHhCCCceEEEechHHHhhcCCCCceEEEecceeccCCcCCCCHHHHHHHhcccCCCCCCCeeEEEEEeCCCC
Confidence            9999999999999999999999999999998888875       4556789999999999999884  688998888876


Q ss_pred             HH
Q 017573          344 ER  345 (369)
Q Consensus       344 ~~  345 (369)
                      .+
T Consensus       188 ~~  189 (201)
T d2p6ra4         188 RE  189 (201)
T ss_dssp             HH
T ss_pred             hH
Confidence            65

>d1a1va1 c.37.1.14 (A:190-325) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=99.75  E-value=2.8e-18  Score=126.62  Aligned_cols=127  Identities=15%  Similarity=0.083  Sum_probs=85.4

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHc
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQ  112 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~  112 (369)
                      .+..++.+|||+|||.++...+.   ..   +.+++|++|++.|++||.+.+.+.....   .....++..       ..
T Consensus         8 ~~~~ll~apTGsGKT~~~~~~~~---~~---~~~vli~~P~~~l~~q~~~~~~~~~~~~---~~~~~~~~~-------~~   71 (136)
T d1a1va1           8 FQVAHLHAPTGSGKSTKVPAAYA---AQ---GYKVLVLNPSVAATLGFGAYMSKAHGVD---PNIRTGVRT-------IT   71 (136)
T ss_dssp             CEEEEEECCTTSCTTTHHHHHHH---TT---TCCEEEEESCHHHHHHHHHHHHHHHSCC---CEEECSSCE-------EC
T ss_pred             CCEEEEEeCCCCCHHHHHHHHHH---Hc---CCcEEEEcChHHHHHHHHHHHHHHhhcc---ccccccccc-------cc
Confidence            46789999999999987543332   22   2389999999999999999998875432   222222222       12


Q ss_pred             cCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCC--ccCcEEEEEeeC
Q 017573          113 AGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLP--AKVQVGVFSATM  179 (369)
Q Consensus       113 ~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~--~~~~~i~~saT~  179 (369)
                      ....+.++|++.......   ....+++++|+||+|++.... ...+..++..+.  +..+++++||||
T Consensus        72 ~~~~~~~~~~~~~~~~~~---~~~~~~~~vIiDE~H~~~~~~-~~~~~~~l~~~~~~~~~~~l~~TATP  136 (136)
T d1a1va1          72 TGSPITYSTYGKFLADGG---CSGGAYDIIICDECHSTDATS-ILGIGTVLDQAETAGARLVVLATATP  136 (136)
T ss_dssp             CCCSEEEEEHHHHHHTTG---GGGCCCSEEEEETTTCCSHHH-HHHHHHHHHHTTTTTCSEEEEEESSC
T ss_pred             cccceEEEeeeeeccccc---hhhhcCCEEEEecccccCHHH-HHHHHHHHHHHHHCCCCcEEEEeCCC
Confidence            235688888877654432   244568999999999874332 233445555443  356789999997

>d2eyqa5 c.37.1.19 (A:779-989) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=99.74  E-value=2.9e-17  Score=125.81  Aligned_cols=109  Identities=17%  Similarity=0.253  Sum_probs=99.9

Q ss_pred             cCCCeEEEeCCHhhHHHHHHHHhhC--CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEec
Q 017573          234 AITQSVIFVNTRRKVDWLTDKMRSR--DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYD  311 (369)
Q Consensus       234 ~~~k~lv~~~~~~~~~~~~~~l~~~--~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~  311 (369)
                      .++++.+.||.++..+.+.+.+++.  +.++..+||.|+++++++++..|.+|+++|||||.+++.|+|+|+++.+|+.+
T Consensus        30 rGgQvy~V~p~I~~~e~~~~~l~~~~p~~~i~~lHGkm~~~eke~im~~F~~g~~~ILv~TtvIEvGiDvpnA~~iiI~~  109 (211)
T d2eyqa5          30 RGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIER  109 (211)
T ss_dssp             TTCEEEEECCCSSCHHHHHHHHHHHCTTSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESSTTGGGSCCTTEEEEEETT
T ss_pred             cCCeEEEEEcCccchhhHHHHHHHhCCceEEEEEEeccCHHHHHHHHHHHHcCCcceEEEehhhhhccCCCCCcEEEEec
Confidence            4678999999999999998888775  56899999999999999999999999999999999999999999999999888


Q ss_pred             CC-CCccchhhhhcccccCCCceeEEEEeccc
Q 017573          312 LP-TQPENYLHRIGRSGRFGRKGVAINFVTRD  342 (369)
Q Consensus       312 ~~-~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~  342 (369)
                      .. +..+++-|.-||+||.++.+.|++++++.
T Consensus       110 a~rfGLaQLhQLRGRVGR~~~~s~c~l~~~~~  141 (211)
T d2eyqa5         110 ADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHP  141 (211)
T ss_dssp             TTSSCHHHHHHHHTTCCBTTBCEEEEEEECCG
T ss_pred             chhccccccccccceeeecCccceEEEEecCC
Confidence            75 47889999999999999999999998753

>d1gm5a4 c.37.1.19 (A:550-755) RecG helicase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=99.74  E-value=8.1e-19  Score=136.15  Aligned_cols=120  Identities=21%  Similarity=0.311  Sum_probs=96.7

Q ss_pred             cCCCeEEEeCCHhhHH--------HHHHHHhhC---CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCC
Q 017573          234 AITQSVIFVNTRRKVD--------WLTDKMRSR---DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQ  302 (369)
Q Consensus       234 ~~~k~lv~~~~~~~~~--------~~~~~l~~~---~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~  302 (369)
                      .++++.+.||.+++.+        ...+.|.+.   +.++..+||+|++++|++++++|.+|+++|||||.++++|+|+|
T Consensus        28 ~g~QvyvVcP~Ieese~~~~~~~~e~~~~l~~~~~p~~~v~~lHG~m~~~eke~~m~~F~~g~~~iLVaTtViE~GIDip  107 (206)
T d1gm5a4          28 RGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDILVSTTVIEVGIDVP  107 (206)
T ss_dssp             TSCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHHHHHTTTSSSBCCCSSCCCSCSCCT
T ss_pred             cCCCEEEEEeeecccccccchhhHHHHHHHHHhcCCCCeEEEEeecccHHHHHHHHHHHHCCCEEEEEEehhhhcccccc
Confidence            4457778888765544        334444333   45788999999999999999999999999999999999999999


Q ss_pred             CCcEEEEecCCC-CccchhhhhcccccCCCceeEEEEeccccHHHHHHHHHH
Q 017573          303 QVSLVINYDLPT-QPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKF  353 (369)
Q Consensus       303 ~~~~vi~~~~~~-~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~  353 (369)
                      ++++||+++.+. ..+.+-|..||+||.++.|.|++++++.+....+.+..+
T Consensus       108 ~a~~iii~~a~~fglsqlhQlrGRvGR~~~~~~~~l~~~~~~~~~~~rl~~~  159 (206)
T d1gm5a4         108 RANVMVIENPERFGLAQLHQLRGRVGRGGQEAYCFLVVGDVGEEAMERLRFF  159 (206)
T ss_dssp             TCCEEEBCSCSSSCTTHHHHHHHTSCCSSTTCEEECCCCSCCHHHHHHHHHH
T ss_pred             CCcEEEEEccCCccHHHHHhhhhheeeccccceeEeeeccccccchhhhhhc
Confidence            999999998876 688888999999999999999999988777666665443

>d1z3ix2 c.37.1.19 (X:92-389) Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxId: 7955]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Rad54-like, Rad54L
species: Zebra fish (Danio rerio) [TaxId: 7955]

Probab=99.72  E-value=4.4e-17  Score=136.68  Aligned_cols=158  Identities=15%  Similarity=0.130  Sum_probs=106.4

Q ss_pred             CCcHhhhhhhhccc---------cCCcEEEEcCCCChhhHHHHHHHHHhhhccC----CCccEEEEcCCHHHHHHHHHHH
Q 017573           18 KPSAIQQRGIVPFC---------KGLDVIQQAQSGTGKTATFCSGILQQLDYGL----VQCQALVLAPTRELAQQIEKVM   84 (369)
Q Consensus        18 ~~~~~Q~~~~~~~~---------~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~----~~~~~liv~P~~~l~~q~~~~~   84 (369)
                      .++|||.+++..+.         .+.++++..++|.|||+.++..+...+....    ...++|||||. ++..||.+++
T Consensus        55 ~Lr~hQ~~gv~~l~~~~~~~~~~~~~g~iLaDemGlGKT~qaia~l~~l~~~~~~~~~~~~~~LIV~P~-sl~~qW~~Ei  133 (298)
T d1z3ix2          55 VLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLIWTLLKQSPDCKPEIDKVIVVSPS-SLVRNWYNEV  133 (298)
T ss_dssp             TCCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHHHHHHHHHHHCCTTSSCSCSCEEEEECH-HHHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHHHhhhhccCCceEEEeCCCCCHHHHHHHHHHHHHHhcccccCCCCcEEEEccc-hhhHHHHHHH
Confidence            68999999997653         3567999999999999887665555444332    12369999997 5889999999


Q ss_pred             HHhccccCcEEEEEECCcchHHHHHH---Hc-----cCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcH
Q 017573           85 RALGDYLGVKVHACVGGTSVREDQRI---LQ-----AGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFK  156 (369)
Q Consensus        85 ~~~~~~~~~~v~~~~~~~~~~~~~~~---~~-----~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~  156 (369)
                      .+++... ..+...+++.........   ..     ...+++++|++.+......  +....++++|+||+|++.+..  
T Consensus       134 ~k~~~~~-~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~i~sy~~~~~~~~~--l~~~~~~~vI~DEaH~ikn~~--  208 (298)
T d1z3ix2         134 GKWLGGR-VQPVAIDGGSKDEIDSKLVNFISQQGMRIPTPILIISYETFRLHAEV--LHKGKVGLVICDEGHRLKNSD--  208 (298)
T ss_dssp             HHHHGGG-CCEEEECSSCHHHHHHHHHHHHCCCSSCCSCCEEEEEHHHHHHHTTT--TTTSCCCEEEETTGGGCCTTC--
T ss_pred             HhhcCCc-eeEEEEeCchHHHHHHHHHHhhhccCccccceEEEEeecccccchhc--ccccceeeeeccccccccccc--
Confidence            9987653 344445554443322211   11     2457999999988654332  334458999999999986554  


Q ss_pred             HHHHHHHhhCCccCcEEEEEeeCChh
Q 017573          157 DQIYDIFQLLPAKVQVGVFSATMPPE  182 (369)
Q Consensus       157 ~~~~~~~~~~~~~~~~i~~saT~~~~  182 (369)
                      .........+. ....+++||||..+
T Consensus       209 s~~~~a~~~l~-~~~rllLTGTPi~N  233 (298)
T d1z3ix2         209 NQTYLALNSMN-AQRRVLISGTPIQN  233 (298)
T ss_dssp             HHHHHHHHHHC-CSEEEEECSSCSGG
T ss_pred             chhhhhhhccc-cceeeeecchHHhh
Confidence            22333333443 34578899999754

>d1gkub2 c.37.1.16 (B:251-498) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.71  E-value=9e-20  Score=148.85  Aligned_cols=124  Identities=16%  Similarity=0.232  Sum_probs=103.3

Q ss_pred             hhhHHHHHHHHHhccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEe----cCC
Q 017573          220 EWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITT----DLL  295 (369)
Q Consensus       220 ~~~~~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t----~~~  295 (369)
                      +.+...+..++.... +++||||++.+.++.+++.|+..      +||+++.++|.+++++|.+|+++|||||    +.+
T Consensus        11 ~~~~~~l~~~l~~~~-~~~iif~~~~~~~~~l~~~l~~~------~hg~~~~~~R~~~~~~f~~g~~~vLVaT~a~~~v~   83 (248)
T d1gkub2          11 DESISTLSSILEKLG-TGGIIYARTGEEAEEIYESLKNK------FRIGIVTATKKGDYEKFVEGEIDHLIGTAHYYGTL   83 (248)
T ss_dssp             CCCTTTTHHHHTTSC-SCEEEEESSHHHHHHHHHTTTTS------SCEEECTTSSSHHHHHHHHTSCSEEEEECC-----
T ss_pred             chHHHHHHHHHHHhC-CCEEEEECCHHHHHHHHHHHHHh------ccCCCCHHHHHHHHHHHHhCCCeEEEEeccccchh
Confidence            446677788887654 68999999999999999999763      7999999999999999999999999999    678


Q ss_pred             cCCCCCCC-CcEEEEecCCCCccchhhhhcccccCCCceeEEEEeccccHHHHHHHHHHh
Q 017573          296 ARGIDVQQ-VSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFY  354 (369)
Q Consensus       296 ~~G~d~~~-~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~~~~~~~~~~~~  354 (369)
                      ++|+|+|+ +++||++++|+    |.|++||+||.|+.|.+++++...+......+.+..
T Consensus        84 ~rGlDip~~v~~VI~~d~P~----~~~r~gR~~R~g~~~~~~~~~~~~~~~~~~~l~~~~  139 (248)
T d1gkub2          84 VRGLDLPERIRFAVFVGCPS----FRVTIEDIDSLSPQMVKLLAYLYRNVDEIERLLPAV  139 (248)
T ss_dssp             -CCSCCTTTCCEEEEESCCE----EEEECSCGGGSCHHHHHHHHTTTSCHHHHHTTCTTT
T ss_pred             hhccCccccccEEEEeCCCc----chhhhhhhhccCcceEeeeeccHhhHHHHHHHHHHH
Confidence            99999996 99999999984    889999999999999988888887776655444333

>d1a1va2 c.37.1.14 (A:326-624) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=99.68  E-value=7.3e-18  Score=135.16  Aligned_cols=107  Identities=18%  Similarity=0.216  Sum_probs=93.5

Q ss_pred             cCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHH----------HHHHHHHhcCCCcEEEEecCCcC---CCC
Q 017573          234 AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTR----------DIIMREFRSGSSRVLITTDLLAR---GID  300 (369)
Q Consensus       234 ~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r----------~~~~~~f~~~~~~vli~t~~~~~---G~d  300 (369)
                      ..+++||||++++.++.+++.|++.++++..+|++++.+.|          .++++.|.+|+.+++|+|+...+   |+|
T Consensus        35 kggk~LVFcnSR~~aE~La~~L~~~Gi~a~~~Hgglsq~~R~~~gd~~i~~~~aLe~f~~G~~dvVVaT~~~a~g~~giD  114 (299)
T d1a1va2          35 KGGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVSVIPTSGDVVVVATDALMTGFTGDFDSVIDCNTCVTQTVDFS  114 (299)
T ss_dssp             HSSEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCGGGSCSSSSEEEEECTTC---CCCCBSEEEECCEEEEEEEECC
T ss_pred             cCCCEEEECCcHHHHHHHHHHHHHCCCCEEEEeCCchHHHHHhccchHHHHHHHHHHHhcCCCcEEEEEeehhccCCCCC
Confidence            46799999999999999999999999999999999998876          46788899999999999998887   678


Q ss_pred             CCCCcEEEEecCCCCccchhhhhcccccCCCceeEEEEecc
Q 017573          301 VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTR  341 (369)
Q Consensus       301 ~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~  341 (369)
                      ++.+.+|+.++.|.|..+|+||+||+|| |++|....+...
T Consensus       115 id~V~~VI~~d~P~SvesyIQRiGRTGR-Gr~G~~~~l~~~  154 (299)
T d1a1va2         115 LDPTFTIETTTLPQDAVSRTQRRGRTGR-GKPGIYRFVAPG  154 (299)
T ss_dssp             CSSSCEEEEEEEECBHHHHHHHHTTBCS-SSCEEEEESCSC
T ss_pred             CCcceEEEeCCCCCCHHHHHhhccccCC-CCCceEEEEecC
Confidence            8888899999999999999999999999 899977655554

>d1z63a1 c.37.1.19 (A:432-661) Helicase of the SNF2/Rad54 hamily {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Helicase of the SNF2/Rad54 hamily
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.67  E-value=9.3e-17  Score=129.47  Aligned_cols=153  Identities=16%  Similarity=0.153  Sum_probs=103.1

Q ss_pred             CCcHhhhhhhhccc----cCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCc
Q 017573           18 KPSAIQQRGIVPFC----KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGV   93 (369)
Q Consensus        18 ~~~~~Q~~~~~~~~----~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~   93 (369)
                      +|+|||.+++..+.    .+.++++..++|.|||..++..+......... .++|||||. .+..||.+++.++....  
T Consensus        12 ~L~~yQ~~~v~~~~~~~~~~~g~iLaDe~GlGKT~~~i~~~~~~~~~~~~-~~~LIv~p~-~l~~~W~~e~~~~~~~~--   87 (230)
T d1z63a1          12 NLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAVFSDAKKENEL-TPSLVICPL-SVLKNWEEELSKFAPHL--   87 (230)
T ss_dssp             CCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHHHHHHHHHHTTCC-SSEEEEECS-TTHHHHHHHHHHHCTTS--
T ss_pred             chhHHHHHHHHHHHHhhhcCCCEEEEeCCCCChHHHHHHhhhhhhhcccc-cccceecch-hhhhHHHHHHHhhcccc--
Confidence            68999999997654    35779999999999999986665555444433 389999995 77888999999886543  


Q ss_pred             EEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCccCcEE
Q 017573           94 KVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVG  173 (369)
Q Consensus        94 ~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i  173 (369)
                      .+......... .    ...+.++++++++.+.....   +....++++|+||+|.+.+...  ........+. ....+
T Consensus        88 ~~~~~~~~~~~-~----~~~~~~vvi~~~~~~~~~~~---l~~~~~~~vI~DEah~~k~~~s--~~~~~~~~l~-a~~r~  156 (230)
T d1z63a1          88 RFAVFHEDRSK-I----KLEDYDIILTTYAVLLRDTR---LKEVEWKYIVIDEAQNIKNPQT--KIFKAVKELK-SKYRI  156 (230)
T ss_dssp             CEEECSSSTTS-C----CGGGSSEEEEEHHHHTTCHH---HHTCCEEEEEEETGGGGSCTTS--HHHHHHHTSC-EEEEE
T ss_pred             cceeeccccch-h----hccCcCEEEeeHHHHHhHHH---HhcccceEEEEEhhhcccccch--hhhhhhhhhc-cceEE
Confidence            23222221111 1    12347899999988854322   1223479999999999975542  2334444554 34578


Q ss_pred             EEEeeCChhHHH
Q 017573          174 VFSATMPPEALE  185 (369)
Q Consensus       174 ~~saT~~~~~~~  185 (369)
                      ++||||..+...
T Consensus       157 ~LTgTPi~n~~~  168 (230)
T d1z63a1         157 ALTGTPIENKVD  168 (230)
T ss_dssp             EECSSCSTTCHH
T ss_pred             EEecchHHhHHH
Confidence            899999765433

>d1z3ix1 c.37.1.19 (X:390-735) Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxId: 7955]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Rad54-like, Rad54L
species: Zebra fish (Danio rerio) [TaxId: 7955]

Probab=99.62  E-value=1.8e-15  Score=127.95  Aligned_cols=123  Identities=18%  Similarity=0.227  Sum_probs=105.3

Q ss_pred             hhhHHHHHHHHHh---ccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCc---EEEEec
Q 017573          220 EWKLETLCDLYET---LAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSR---VLITTD  293 (369)
Q Consensus       220 ~~~~~~l~~~~~~---~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~---vli~t~  293 (369)
                      ..|+..+..++..   .++.|+|||++.......+.+.|...++.+..++|.++..+|.++++.|++++..   +|++|.
T Consensus       100 S~Kl~~L~~ll~~~~~~~g~KvlIFs~~~~~ld~l~~~l~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~~vlLls~~  179 (346)
T d1z3ix1         100 SGKMLVLDYILAMTRTTTSDKVVLVSNYTQTLDLFEKLCRNRRYLYVRLDGTMSIKKRAKIVERFNNPSSPEFIFMLSSK  179 (346)
T ss_dssp             SHHHHHHHHHHHHHHHHCCCEEEEEESCHHHHHHHHHHHHHHTCCEEEECSSCCHHHHHHHHHHHHSTTCCCCEEEEEGG
T ss_pred             CHHHHHHHHHHHHHHHhcCCceeEEeehhhhhHHHHHHHhhhhccccccccchhHHHHHHHHHhhhcccccceeeeecch
Confidence            3466666666643   4567999999999999999999999999999999999999999999999987543   566778


Q ss_pred             CCcCCCCCCCCcEEEEecCCCCccchhhhhcccccCCCceeEEE--Eeccc
Q 017573          294 LLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAIN--FVTRD  342 (369)
Q Consensus       294 ~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~--~~~~~  342 (369)
                      +.++|+|++.+++||+++++||+....|++||+.|.|+...|.+  ++..+
T Consensus       180 agg~GlnL~~a~~vi~~d~~wnp~~~~Qa~~R~~R~GQ~~~V~v~rli~~~  230 (346)
T d1z3ix1         180 AGGCGLNLIGANRLVMFDPDWNPANDEQAMARVWRDGQKKTCYIYRLLSTG  230 (346)
T ss_dssp             GSCTTCCCTTEEEEEECSCCSSHHHHHHHHTTSSSTTCCSCEEEEEEEETT
T ss_pred             hhhhccccccceEEEEecCCCccchHhHhhhcccccCCCCceEEEEEEeCC
Confidence            99999999999999999999999999999999999998865544  44444

>d1z5za1 c.37.1.19 (A:663-906) Helicase of the SNF2/Rad54 hamily {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Helicase of the SNF2/Rad54 hamily
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.60  E-value=5.6e-15  Score=119.83  Aligned_cols=123  Identities=15%  Similarity=0.217  Sum_probs=90.2

Q ss_pred             hhhHHHHHHHHHhc--cCCCeEEEeCCHhhHHHHHHHHhhC-CCeeEEecCCCCHHHHHHHHHHHhcCC-CcEEEEe-cC
Q 017573          220 EWKLETLCDLYETL--AITQSVIFVNTRRKVDWLTDKMRSR-DHTVSATHGDMDQNTRDIIMREFRSGS-SRVLITT-DL  294 (369)
Q Consensus       220 ~~~~~~l~~~~~~~--~~~k~lv~~~~~~~~~~~~~~l~~~-~~~~~~~~~~~~~~~r~~~~~~f~~~~-~~vli~t-~~  294 (369)
                      ..|+..+.+++...  .++|+||||........+...+... +..+..++|+++..+|.++++.|.+++ ..+++++ .+
T Consensus        68 S~K~~~l~~~l~~~~~~g~kviIFs~~~~~~~~l~~~l~~~~~~~~~~i~G~~~~~~R~~~i~~F~~~~~~~vll~~~~~  147 (244)
T d1z5za1          68 SGKMIRTMEIIEEALDEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVKA  147 (244)
T ss_dssp             CHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHHHCSCCCEECTTSCHHHHHHHHHHHHHCTTCCEEEEECCT
T ss_pred             hhHHHHHHHHHHhhcccccceEEEeeceehHHHHHHHHHhhccceEEEEecccchhccchhhhhhhccccchhccccccc
Confidence            34777777777543  5679999999999999998888654 788889999999999999999998764 6677655 68


Q ss_pred             CcCCCCCCCCcEEEEecCCCCccchhhhhcccccCCCcee--EEEEeccc
Q 017573          295 LARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGV--AINFVTRD  342 (369)
Q Consensus       295 ~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~--~~~~~~~~  342 (369)
                      .++|+|++.+++||+++++||+..+.|++||+.|.|+...  ++.++..+
T Consensus       148 ~g~Glnl~~a~~vi~~~~~wn~~~~~Qa~~R~~R~Gq~~~v~i~~l~~~~  197 (244)
T d1z5za1         148 GGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVG  197 (244)
T ss_dssp             TCCCCCCTTCSEEEECSCCSCTTTC--------------CCEEEEEEETT
T ss_pred             cccccccchhhhhhhcCchhhhHHHhhhcceeeecCCCCceEEEEEeeCC
Confidence            9999999999999999999999999999999999997654  44444554

>d1yksa2 c.37.1.14 (A:325-623) YFV helicase domain {Yellow fever virus [TaxId: 11089]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

Probab=99.39  E-value=4e-13  Score=110.04  Aligned_cols=101  Identities=14%  Similarity=0.223  Sum_probs=78.8

Q ss_pred             CCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCCCCcEEEEecCC-
Q 017573          235 ITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLP-  313 (369)
Q Consensus       235 ~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~~~~~vi~~~~~-  313 (369)
                      .+++++||++.++++.+++.|++.+.++..+||.+..+++.+    |.+++.+++|+|+++++|+|+ ++..||..+.. 
T Consensus        36 ~g~~~~F~~s~~~~~~~a~~L~~~g~~V~~l~~~~~~~e~~~----~~~~~~~~~~~t~~~~~~~~~-~~~~vid~g~~~  110 (299)
T d1yksa2          36 KRPTAWFLPSIRAANVMAASLRKAGKSVVVLNRKTFEREYPT----IKQKKPDFILATDIAEMGANL-CVERVLDCRTAF  110 (299)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHTTCCEEECCSSSCC------------CCCSEEEESSSTTCCTTC-CCSEEEECCEEE
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHhcCCeEEEEcCcCcHhHHhh----hhcCCcCEEEEechhhhceec-CceEEEecCcee
Confidence            579999999999999999999999999999999998777554    578999999999999999999 59999865532 


Q ss_pred             ------------------CCccchhhhhcccccCCCceeEEEEec
Q 017573          314 ------------------TQPENYLHRIGRSGRFGRKGVAINFVT  340 (369)
Q Consensus       314 ------------------~~~~~~~Q~~GR~~R~~~~~~~~~~~~  340 (369)
                                        .|..+..||.||+||.+....++.++.
T Consensus       111 ~~~~~~~~~~~~~~~~~~~~~~~~~qr~gr~gr~~~~~~~~~~y~  155 (299)
T d1yksa2         111 KPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNRDGDSYYYS  155 (299)
T ss_dssp             EEEEETTTTEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEEC
T ss_pred             ceeeecCCCCeeEEeeeecCHHHHHHhcccccccCCCceEEEEeC
Confidence                              345566899999999865444444444

>d1tf5a4 c.37.1.19 (A:396-570) Translocation ATPase SecA, nucleotide-binding domains {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Translocation ATPase SecA, nucleotide-binding domains
species: Bacillus subtilis [TaxId: 1423]

Probab=99.33  E-value=8.9e-12  Score=91.89  Aligned_cols=122  Identities=16%  Similarity=0.238  Sum_probs=94.9

Q ss_pred             hhhhHHHHHHHHHh-c-cCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCC-CcEEEEecCC
Q 017573          219 EEWKLETLCDLYET-L-AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGS-SRVLITTDLL  295 (369)
Q Consensus       219 ~~~~~~~l~~~~~~-~-~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~-~~vli~t~~~  295 (369)
                      ...|...+.+.+.. + .+.++||++.|++.++.+++.|++.+.+..++++.....+.. ++.  ..|. -.|.|+|+++
T Consensus        16 ~~eK~~AIi~eV~~~~~~grPVLIgT~SIe~SE~ls~~L~~~gi~h~vLnAk~~~~Ea~-II~--~Ag~~g~VtIATNmA   92 (175)
T d1tf5a4          16 MEGKFKAVAEDVAQRYMTGQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREAQ-IIE--EAGQKGAVTIATNMA   92 (175)
T ss_dssp             HHHHHHHHHHHHHHHHHHTCCEEEEESCHHHHHHHHHHHHTTTCCCEEECSSCHHHHHH-HHT--TTTSTTCEEEEETTS
T ss_pred             HHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHcCCCceeehhhhHHHHHH-HHH--hccCCCceeehhhHH
Confidence            34455555444432 2 457999999999999999999999999999999986544433 333  2333 3599999999


Q ss_pred             cCCCCCC--------CCcEEEEecCCCCccchhhhhcccccCCCceeEEEEecccc
Q 017573          296 ARGIDVQ--------QVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDD  343 (369)
Q Consensus       296 ~~G~d~~--------~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~~~~~~  343 (369)
                      ++|.|+.        +--+||....+.|...-.|..||+||.|.+|...+|++-.|
T Consensus        93 GRGtDikl~~~v~~~GGLhVI~t~~~~s~Rid~Ql~GR~gRQGdpGs~~~~~sleD  148 (175)
T d1tf5a4          93 GRGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGDPGITQFYLSMED  148 (175)
T ss_dssp             STTCCCCCCTTSGGGTSEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEETTS
T ss_pred             HcCCCccchHHHHhCCCcEEEEeccCcchhHHHHHhcchhhhCCCcccEEEEEcCH
Confidence            9999974        23457888889999999999999999999999999987654

>d1tf5a3 c.37.1.19 (A:1-226,A:349-395) Translocation ATPase SecA, nucleotide-binding domains {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Translocation ATPase SecA, nucleotide-binding domains
species: Bacillus subtilis [TaxId: 1423]

Probab=99.27  E-value=3.2e-11  Score=94.78  Aligned_cols=162  Identities=21%  Similarity=0.254  Sum_probs=115.2

Q ss_pred             CCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEE
Q 017573           18 KPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHA   97 (369)
Q Consensus        18 ~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~   97 (369)
                      ++++.|--.--.+  .+.-+.+..||-|||+++.+++.-....++   .+-+|+.+.-|++.=++++..++..+|+.+..
T Consensus        80 RhyDVQLiGgi~L--~~G~iaem~TGEGKTL~a~l~a~l~al~g~---~vhvvTvNdyLA~RDae~m~~iy~~lGlsvg~  154 (273)
T d1tf5a3          80 FPFKVQLMGGVAL--HDGNIAEMKTGEGKTLTSTLPVYLNALTGK---GVHVVTVNEYLASRDAEQMGKIFEFLGLTVGL  154 (273)
T ss_dssp             CCCHHHHHHHHHH--HTTSEEECCTTSCHHHHHHHHHHHHHTTSS---CEEEEESSHHHHHHHHHHHHHHHHHTTCCEEE
T ss_pred             EEehhHHHHHHHH--HhhhheeecCCCcchhHHHHHHHHHHhcCC---CceEEecCccccchhhhHHhHHHHHcCCCccc
Confidence            4555555444444  445699999999999998877765555544   79999999999999999999999999999998


Q ss_pred             EECCcchHHHHHHHccCCcEEEeccHHH-HHHHHcCCC------CCCCccEEEEechhHhh-ccC-------------cH
Q 017573           98 CVGGTSVREDQRILQAGVHVVVGTPGRV-FDMLRRQSL------RPDYIKMFVLDEADEML-SRG-------------FK  156 (369)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~iiv~t~~~l-~~~~~~~~~------~~~~~~~viiDE~H~~~-~~~-------------~~  156 (369)
                      ...+......+...  .+||+++|...| +..++....      ....+.+.|+||++.+. +..             ..
T Consensus       155 ~~~~~~~~~r~~~Y--~~di~Ygt~~e~~fDyLrd~~~~~~~~~~~r~~~~aIvDEvDsiliDeartpliisg~~~~~a~  232 (273)
T d1tf5a3         155 NLNSMSKDEKREAY--AADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSILIDEARTPLIISGQSMTLAT  232 (273)
T ss_dssp             CCTTSCHHHHHHHH--HSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEEETHHHHHTTTTTCEEEEEEEEEEEEE
T ss_pred             cccccCHHHHHHHh--hCCceecchhhhhhhhcchhhhcChhhhccCCCCEEEEEcchhhhhhccCCceEeccCccchhh
Confidence            88777766555444  478999999888 455554322      13447899999999876 211             01


Q ss_pred             HHHHHHHhhCCccCcEEEEEeeCChhHHHHHHH
Q 017573          157 DQIYDIFQLLPAKVQVGVFSATMPPEALEITRK  189 (369)
Q Consensus       157 ~~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~  189 (369)
                      -.+.++++..+   ++.+||+|......++..-
T Consensus       233 it~q~~f~~y~---~l~gmtgta~~~~~e~~~i  262 (273)
T d1tf5a3         233 ITFQNYFRMYE---KLAGMTGTAKTEEEEFRNI  262 (273)
T ss_dssp             EEHHHHHTTSS---EEEEEESCCGGGHHHHHHH
T ss_pred             hhHHHHHHHHH---HHhCCccccHHHHHHHHhc
Confidence            12345555554   5889999997665544443

>d1nkta4 c.37.1.19 (A:397-615) Translocation ATPase SecA, nucleotide-binding domains {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Translocation ATPase SecA, nucleotide-binding domains
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=98.90  E-value=2.2e-08  Score=74.96  Aligned_cols=123  Identities=20%  Similarity=0.240  Sum_probs=93.1

Q ss_pred             hhhHHHHHHHH-Hhc-cCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCC-CcEEEEecCCc
Q 017573          220 EWKLETLCDLY-ETL-AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGS-SRVLITTDLLA  296 (369)
Q Consensus       220 ~~~~~~l~~~~-~~~-~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~-~~vli~t~~~~  296 (369)
                      ..+...+.+-+ ..+ .+.++||-+.|++..+.+.+.|.+.+++..++++.....+-. |+.  ..|. -.|-|+|++++
T Consensus        17 ~~K~~Avv~ei~~~h~~GqPVLVGT~SVe~SE~lS~lL~~~gi~h~vLNAK~herEAe-IIA--qAG~~GaVTIATNMAG   93 (219)
T d1nkta4          17 EAKYIAVVDDVAERYAKGQPVLIGTTSVERSEYLSRQFTKRRIPHNVLNAKYHEQEAT-IIA--VAGRRGGVTVATNMAG   93 (219)
T ss_dssp             HHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHTTCCCEEECSSCHHHHHH-HHH--TTTSTTCEEEEETTCS
T ss_pred             HHHHHHHHHHHHHHHhcCCCEEEeeCcHHHHHHHHHHHHHhccchhccchhhHHHHHH-HHH--hcccCCcEEeeccccC
Confidence            34555444433 333 456999999999999999999999999999999985544333 333  3343 34999999999


Q ss_pred             CCCCCC----------------------------------------------------CCcEEEEecCCCCccchhhhhc
Q 017573          297 RGIDVQ----------------------------------------------------QVSLVINYDLPTQPENYLHRIG  324 (369)
Q Consensus       297 ~G~d~~----------------------------------------------------~~~~vi~~~~~~~~~~~~Q~~G  324 (369)
                      +|.||.                                                    +-=+||-.....|...=.|.-|
T Consensus        94 RGTDI~LGgn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGL~VIGTErHeSrRIDnQLRG  173 (219)
T d1nkta4          94 RGTDIVLGGNVDFLTDQRLRERGLDPVETPEEYEAAWHSELPIVKEEASKEAKEVIEAGGLYVLGTERHESRRIDNQLRG  173 (219)
T ss_dssp             TTCCCCTTCCHHHHHHHHHHHTTCCTTTSHHHHHHHHHHHHHHHHHHTTHHHHHHHHTTSEEEEECSCCSSHHHHHHHHH
T ss_pred             CCCceeecCchhhhhHHHhhhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcEEEeccccccccccccccc
Confidence            999983                                                    1124666666777777899999


Q ss_pred             ccccCCCceeEEEEeccccHH
Q 017573          325 RSGRFGRKGVAINFVTRDDER  345 (369)
Q Consensus       325 R~~R~~~~~~~~~~~~~~~~~  345 (369)
                      |+||.|.+|.+.+|++-.|.-
T Consensus       174 RsGRQGDPGsSrFflSLeDdL  194 (219)
T d1nkta4         174 RSGRQGDPGESRFYLSLGDEL  194 (219)
T ss_dssp             TSSGGGCCEEEEEEEETTSHH
T ss_pred             cccccCCCccceeEEeccHHH
Confidence            999999999999999876653

>d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Exodeoxyribonuclease V alpha chain (RecD)
species: Escherichia coli [TaxId: 562]

Probab=98.63  E-value=7.1e-08  Score=81.27  Aligned_cols=147  Identities=17%  Similarity=0.172  Sum_probs=86.7

Q ss_pred             CCCCCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhc-cCCCccEEEEcCCHHHHHHHHHHHHHhccccC
Q 017573           14 YGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY-GLVQCQALVLAPTRELAQQIEKVMRALGDYLG   92 (369)
Q Consensus        14 ~~~~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~-~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~   92 (369)
                      ++-....+.|++|+..+..++-++|.||+|+|||.+....+...... ...+.++++.+||..-+..+.+.........+
T Consensus       144 ~~~~~~~~~Q~~A~~~al~~~~~vI~G~pGTGKTt~i~~~l~~l~~~~~~~~~~I~l~ApTgkAA~~L~e~~~~~~~~~~  223 (359)
T d1w36d1         144 FPVSDEINWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQMADGERCRIRLAAPTGKAAARLTESLGKALRQLP  223 (359)
T ss_dssp             CCCTTSCCHHHHHHHHHHTBSEEEEECCTTSTHHHHHHHHHHHHHHTCSSCCCCEEEEBSSHHHHHHHHHHHTHHHHHSS
T ss_pred             ccCcccccHHHHHHHHHHcCCeEEEEcCCCCCceehHHHHHHHHHHHHhccCCeEEEecCcHHHHHHHHHHHHHHHhhcC
Confidence            45556788999999999999999999999999998754322222211 22334899999998888777766644322211


Q ss_pred             cEEEEEECCcchHHHHHHHccCCcEEEeccHHHH------HHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhC
Q 017573           93 VKVHACVGGTSVREDQRILQAGVHVVVGTPGRVF------DMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLL  166 (369)
Q Consensus        93 ~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~------~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~  166 (369)
                      ........              ...-..|.+.+.      ..+.........++++|+||+-++.    ...+..++..+
T Consensus       224 ~~~~~~~~--------------~~~~~~t~~~ll~~~~~~~~~~~~~~~~l~~d~lIIDEaSmv~----~~l~~~ll~~~  285 (359)
T d1w36d1         224 LTDEQKKR--------------IPEDASTLHRLLGAQPGSQRLRHHAGNPLHLDVLVVDEASMID----LPMMSRLIDAL  285 (359)
T ss_dssp             CCSCCCCS--------------CSCCCBTTTSCC-----------CTTSCCSCSEEEECSGGGCB----HHHHHHHHHTC
T ss_pred             chhhhhhh--------------hhhhhhHHHHHHhhhhcchHHHHhhhcccccceeeehhhhccC----HHHHHHHHHHh
Confidence            10000000              000011111110      1122233344457999999999863    34566777888


Q ss_pred             CccCcEEEEEee
Q 017573          167 PAKVQVGVFSAT  178 (369)
Q Consensus       167 ~~~~~~i~~saT  178 (369)
                      ++..++|++.-.
T Consensus       286 ~~~~~lILvGD~  297 (359)
T d1w36d1         286 PDHARVIFLGDR  297 (359)
T ss_dssp             CTTCEEEEEECT
T ss_pred             cCCCEEEEECCh
Confidence            888887765544

>d1uaaa1 c.37.1.19 (A:2-307) DEXX box DNA helicase {Escherichia coli, RepD [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Escherichia coli, RepD [TaxId: 562]

Probab=98.34  E-value=5.4e-07  Score=74.71  Aligned_cols=69  Identities=16%  Similarity=0.117  Sum_probs=54.0

Q ss_pred             CCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhc-cCCCccEEEEcCCHHHHHHHHHHHHHhc
Q 017573           18 KPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY-GLVQCQALVLAPTRELAQQIEKVMRALG   88 (369)
Q Consensus        18 ~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~-~~~~~~~liv~P~~~l~~q~~~~~~~~~   88 (369)
                      +|+|-|++++..  ....++|.|++|||||.+++..+...+.. +.+..++++++++++++....+.+.+..
T Consensus         1 ~L~~eQ~~av~~--~~~~~lI~g~aGTGKTt~l~~rv~~ll~~~~~~~~~ILvlt~tn~a~~~i~~~~~~~~   70 (306)
T d1uaaa1           1 RLNPGQQQAVEF--VTGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVGQTL   70 (306)
T ss_dssp             CCCHHHHHHHHC--CSSEEEECCCTTSCHHHHHHHHHHHHHHHHCCCGGGEEEEESSHHHHHHHHHHHHHHS
T ss_pred             CcCHHHHHHHhC--CCCCEEEEeeCCccHHHHHHHHHHHHHHhcCCChhHEEEEeCcHHHHHHHHHHHHHhc
Confidence            478999999976  35679999999999998877665555443 2233489999999999998888877654

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=98.15  E-value=1.7e-06  Score=66.94  Aligned_cols=41  Identities=17%  Similarity=0.105  Sum_probs=30.5

Q ss_pred             CCcHhhhhhhhcccc----C---CcEEEEcCCCChhhHHHHHHHHHhh
Q 017573           18 KPSAIQQRGIVPFCK----G---LDVIQQAQSGTGKTATFCSGILQQL   58 (369)
Q Consensus        18 ~~~~~Q~~~~~~~~~----~---~~~li~~~tG~GKT~~~~~~~~~~~   58 (369)
                      .++|+|+++++.+.+    +   ..+++.||+|+|||..+...+...+
T Consensus         2 ~~yPw~~~~~~~l~~~~~~~~l~h~lLl~Gp~G~GKtt~a~~~a~~l~   49 (207)
T d1a5ta2           2 RWYPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALSRYLL   49 (207)
T ss_dssp             CCCGGGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHHHHHHHHT
T ss_pred             CCCcccHHHHHHHHHHHHcCCcCeEEEEECCCCCcHHHHHHHHHHhcc
Confidence            357999998887753    2   3489999999999988765555443

>d1pjra1 c.37.1.19 (A:1-318) DEXX box DNA helicase {Bacillus stearothermophilus, PcrA [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Bacillus stearothermophilus, PcrA [TaxId: 1422]

Probab=98.13  E-value=3.3e-06  Score=70.21  Aligned_cols=69  Identities=17%  Similarity=0.182  Sum_probs=54.9

Q ss_pred             CCCcHhhhhhhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhccC-CCccEEEEcCCHHHHHHHHHHHHHh
Q 017573           17 EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGL-VQCQALVLAPTRELAQQIEKVMRAL   87 (369)
Q Consensus        17 ~~~~~~Q~~~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~-~~~~~liv~P~~~l~~q~~~~~~~~   87 (369)
                      ..|++-|++++++.  +..++|.|++|||||.+++-.+...+..+. ...+++++++++..+......+.+.
T Consensus        10 ~~L~~eQ~~~v~~~--~g~~lV~g~aGSGKTt~l~~ri~~ll~~~~~~p~~il~lt~t~~aa~~~~~~~~~~   79 (318)
T d1pjra1          10 AHLNKEQQEAVRTT--EGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTNKAAREMRERVQSL   79 (318)
T ss_dssp             TTSCHHHHHHHHCC--SSCEEEEECTTSCHHHHHHHHHHHHHHTTCCCGGGEEEEESSHHHHHHHHHHHHHH
T ss_pred             HhCCHHHHHHHhCC--CCCEEEEecCCccHHHHHHHHHHHHHHcCCCCHHHeEeEeccHHHHHHHHHHHHhh
Confidence            35889999999863  567999999999999988776666555432 2238999999999999988887764

>d1ls1a2 c.37.1.10 (A:89-295) GTPase domain of the signal sequence recognition protein Ffh {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Thermus aquaticus [TaxId: 271]

Probab=97.60  E-value=0.0002  Score=54.57  Aligned_cols=130  Identities=25%  Similarity=0.320  Sum_probs=68.3

Q ss_pred             EEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCC--HHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHcc
Q 017573           36 VIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPT--RELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQA  113 (369)
Q Consensus        36 ~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~--~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~  113 (369)
                      +++.+|||+|||.+..-.+.....++   .++.+++.-  +.=+.   ++++.+....++.+...........-..    
T Consensus        13 i~lvGp~GvGKTTTiaKLA~~~~~~g---~kV~lit~Dt~R~gA~---eQL~~~a~~l~v~~~~~~~~~~~~~~~~----   82 (207)
T d1ls1a2          13 WFLVGLQGSGKTTTAAKLALYYKGKG---RRPLLVAADTQRPAAR---EQLRLLGEKVGVPVLEVMDGESPESIRR----   82 (207)
T ss_dssp             EEEECCTTTTHHHHHHHHHHHHHHTT---CCEEEEECCSSCHHHH---HHHHHHHHHHTCCEEECCTTCCHHHHHH----
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCC---CcEEEEecccccchHH---HHHHHHHHhcCCccccccccchhhHHHH----
Confidence            57799999999988766655444333   267766653  23222   3344444444555544333222111100    


Q ss_pred             CCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhc-cCcHHHHHHHHhhCCccCcEEEEEeeCChhHHHHHHHh
Q 017573          114 GVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLS-RGFKDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKF  190 (369)
Q Consensus       114 ~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~-~~~~~~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~  190 (369)
                                .......     ....+++++|=+-+... ......+..+.+..++...++.++|+...+..+....+
T Consensus        83 ----------~~~~~~~-----~~~~d~vlIDTaGr~~~d~~~~~el~~~~~~~~~~~~llv~~a~~~~~~~~~~~~f  145 (207)
T d1ls1a2          83 ----------RVEEKAR-----LEARDLILVDTAGRLQIDEPLMGELARLKEVLGPDEVLLVLDAMTGQEALSVARAF  145 (207)
T ss_dssp             ----------HHHHHHH-----HHTCCEEEEECCCCSSCCHHHHHHHHHHHHHHCCSEEEEEEEGGGTHHHHHHHHHH
T ss_pred             ----------HHHHHHh-----hccCcceeecccccchhhhhhHHHHHHHHhhcCCceEEEEeccccchhHHHHHHHH
Confidence                      0000111     11247788887665432 22345555666666666666778888776665555544

>d2qy9a2 c.37.1.10 (A:285-495) GTPase domain of the signal recognition particle receptor FtsY {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Escherichia coli [TaxId: 562]

Probab=97.49  E-value=0.00012  Score=55.68  Aligned_cols=132  Identities=16%  Similarity=0.222  Sum_probs=65.4

Q ss_pred             EEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHccCC
Q 017573           36 VIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGV  115 (369)
Q Consensus        36 ~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~  115 (369)
                      +++.+|||+|||.+..-.+.. +...  +.++.+++.-.--+. -.++++.+....++.+............        
T Consensus        12 i~lvGptGvGKTTTiAKLA~~-~~~~--g~kV~lit~Dt~R~g-A~eQL~~~a~~l~v~~~~~~~~~d~~~~--------   79 (211)
T d2qy9a2          12 ILMVGVNGVGKTTTIGKLARQ-FEQQ--GKSVMLAAGDTFRAA-AVEQLQVWGQRNNIPVIAQHTGADSASV--------   79 (211)
T ss_dssp             EEEECCTTSCHHHHHHHHHHH-HHTT--TCCEEEECCCTTCHH-HHHHHHHHHHHTTCCEECCSTTCCHHHH--------
T ss_pred             EEEECCCCCCHHHHHHHHHHH-HHHC--CCcEEEEeccccccc-chhhhhhhhhhcCCcccccccCCCHHHH--------
Confidence            567999999999887666543 3322  226766665332221 2344555555556665433332221110        


Q ss_pred             cEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhc-cCcHHHHHHHHhhCC------ccCcEEEEEeeCChhHHHHHH
Q 017573          116 HVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLS-RGFKDQIYDIFQLLP------AKVQVGVFSATMPPEALEITR  188 (369)
Q Consensus       116 ~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~-~~~~~~~~~~~~~~~------~~~~~i~~saT~~~~~~~~~~  188 (369)
                               +.+....  .....++++++|=+-+... ....+++..+.+...      +...++.++|+...+......
T Consensus        80 ---------l~~~~~~--a~~~~~d~ilIDTaGr~~~d~~~~~el~~l~~~~~~~~~~~p~~~~LVl~a~~~~~~~~~~~  148 (211)
T d2qy9a2          80 ---------IFDAIQA--AKARNIDVLIADTAGRLQNKSHLMEELKKIVRVMKKLDVEAPHEVMLTIDASTGQNAVSQAK  148 (211)
T ss_dssp             ---------HHHHHHH--HHHTTCSEEEECCCCCGGGHHHHHHHHHHHHHHHTTTCTTCCSEEEEEEEGGGTHHHHHHHH
T ss_pred             ---------HHHHHHH--HHHcCCCEEEeccCCCccccHHHHHHHHHHHHHHhhhcccCcceeeeehhcccCcchHHHHh
Confidence                     1111110  0012258888887754321 222334444433332      234466688888766555444


Q ss_pred             Hh
Q 017573          189 KF  190 (369)
Q Consensus       189 ~~  190 (369)
                      .+
T Consensus       149 ~~  150 (211)
T d2qy9a2         149 LF  150 (211)
T ss_dssp             HH
T ss_pred             hh
Confidence            43

>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=97.45  E-value=0.00016  Score=54.84  Aligned_cols=116  Identities=9%  Similarity=0.070  Sum_probs=63.6

Q ss_pred             hhhhhhcccc---CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEE
Q 017573           23 QQRGIVPFCK---GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACV   99 (369)
Q Consensus        23 Q~~~~~~~~~---~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~   99 (369)
                      |.+.+..+.+   +.++++.||.|+|||..+...+-........-+-++++.|...                        
T Consensus         2 ~~~~l~~~i~~~~~~~~l~~G~~g~gk~~~a~~l~~~i~~~~~~h~D~~~i~~~~~------------------------   57 (198)
T d2gnoa2           2 QLETLKRIIEKSEGISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPEGE------------------------   57 (198)
T ss_dssp             HHHHHHHHHHTCSSEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTEEEECCSSS------------------------
T ss_pred             HHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHhccccCCCCEEEEeCCcC------------------------
Confidence            4555555554   3578999999999998875444322111111123555555310                        


Q ss_pred             CCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEEeeC
Q 017573          100 GGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATM  179 (369)
Q Consensus       100 ~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~saT~  179 (369)
                                      .|=|-....+.+.+..... ....+++|+||+|.+... ....+.+++..-|+...++++|..+
T Consensus        58 ----------------~I~Id~IR~i~~~~~~~~~-~~~~KviIId~ad~l~~~-aqNaLLK~LEEPp~~t~fiLit~~~  119 (198)
T d2gnoa2          58 ----------------NIGIDDIRTIKDFLNYSPE-LYTRKYVIVHDCERMTQQ-AANAFLKALEEPPEYAVIVLNTRRW  119 (198)
T ss_dssp             ----------------CBCHHHHHHHHHHHTSCCS-SSSSEEEEETTGGGBCHH-HHHHTHHHHHSCCTTEEEEEEESCG
T ss_pred             ----------------CCCHHHHHHHHHHHhhCcc-cCCCEEEEEeCccccchh-hhhHHHHHHhCCCCCceeeeccCCh
Confidence                            0000011112222222222 233689999999998543 3556667777767777677665554


Q ss_pred             C
Q 017573          180 P  180 (369)
Q Consensus       180 ~  180 (369)
                      .
T Consensus       120 ~  120 (198)
T d2gnoa2         120 H  120 (198)
T ss_dssp             G
T ss_pred             h
Confidence            3

>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=97.42  E-value=0.0006  Score=52.30  Aligned_cols=103  Identities=16%  Similarity=0.243  Sum_probs=56.8

Q ss_pred             cEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHccC
Q 017573           35 DVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAG  114 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~  114 (369)
                      .++++||+|+|||-.+.....+....+.   .++++ +......+....+..-                           
T Consensus        38 ~l~l~G~~G~GKTHLl~A~~~~~~~~~~---~~~~~-~~~~~~~~~~~~~~~~---------------------------   86 (213)
T d1l8qa2          38 PIFIYGSVGTGKTHLLQAAGNEAKKRGY---RVIYS-SADDFAQAMVEHLKKG---------------------------   86 (213)
T ss_dssp             SEEEECSSSSSHHHHHHHHHHHHHHTTC---CEEEE-EHHHHHHHHHHHHHHT---------------------------
T ss_pred             cEEEECCCCCcHHHHHHHHHHHhccCcc---ceEEe-chHHHHHHHHHHHHcc---------------------------
Confidence            3899999999999765433333333222   45554 4334443333332210                           


Q ss_pred             CcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhcc-CcHHHHHHHHhhCCccCcEEEEEeeCCh
Q 017573          115 VHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSR-GFKDQIYDIFQLLPAKVQVGVFSATMPP  181 (369)
Q Consensus       115 ~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~-~~~~~~~~~~~~~~~~~~~i~~saT~~~  181 (369)
                            ..+.+...+..       .+++++|++|.+... .+...+..+++.+......+.+|++.++
T Consensus        87 ------~~~~~~~~~~~-------~dll~iDDi~~i~~~~~~~~~lf~lin~~~~~~~~iiits~~~p  141 (213)
T d1l8qa2          87 ------TINEFRNMYKS-------VDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHP  141 (213)
T ss_dssp             ------CHHHHHHHHHT-------CSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESSCG
T ss_pred             ------chhhHHHHHhh-------ccchhhhhhhhhcCchHHHHHHHHHHHHHhhccceEEEecCCcc
Confidence                  12222233332       699999999998643 3455667777665543334445555443

>d1j8yf2 c.37.1.10 (F:87-297) GTPase domain of the signal sequence recognition protein Ffh {Archaeon Acidianus ambivalens [TaxId: 2283]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Archaeon Acidianus ambivalens [TaxId: 2283]

Probab=97.28  E-value=0.00018  Score=54.87  Aligned_cols=130  Identities=18%  Similarity=0.250  Sum_probs=60.1

Q ss_pred             EEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCC--HHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHcc
Q 017573           36 VIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPT--RELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQA  113 (369)
Q Consensus        36 ~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~--~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~  113 (369)
                      +++.+|||+|||.+..-.+......+   .++.+++--  |.=+   .++++.+....++.+.............     
T Consensus        15 i~lvGptGvGKTTTiAKLA~~~~~~g---~kV~lit~Dt~R~ga---~eQL~~~a~~l~v~~~~~~~~~~~~~~~-----   83 (211)
T d1j8yf2          15 IMLVGVQGTGKATTAGKLAYFYKKKG---FKVGLVGADVYRPAA---LEQLQQLGQQIGVPVYGEPGEKDVVGIA-----   83 (211)
T ss_dssp             EEEECSCCC----HHHHHHHHHHHTT---CCEEEEECCCSSHHH---HHHHHHHHHHHTCCEECCTTCCCHHHHH-----
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCC---CceEEEEeeccccch---hHHHHHhccccCcceeecccchhhhHHH-----
Confidence            56789999999988765554333222   266666652  2222   2334444444455553322222111000     


Q ss_pred             CCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhcc---CcHHHHHHHHhhCCccCcEEEEEeeCChhHHHHHHHh
Q 017573          114 GVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSR---GFKDQIYDIFQLLPAKVQVGVFSATMPPEALEITRKF  190 (369)
Q Consensus       114 ~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~---~~~~~~~~~~~~~~~~~~~i~~saT~~~~~~~~~~~~  190 (369)
                               .........     ...+++++|=+-+....   .....+..+....++....+.++|+...+..+....+
T Consensus        84 ---------~~a~~~~~~-----~~~d~IlIDTaGr~~~~~~~~~~~el~~~~~~~~~~~~~LVl~a~~~~~~~~~~~~~  149 (211)
T d1j8yf2          84 ---------KRGVEKFLS-----EKMEIIIVDTAGRHGYGEEAALLEEMKNIYEAIKPDEVTLVIDASIGQKAYDLASKF  149 (211)
T ss_dssp             ---------HHHHHHHHH-----TTCSEEEEECCCSCCTTCHHHHHHHHHHHHHHHCCSEEEEEEEGGGGGGHHHHHHHH
T ss_pred             ---------HHHHHHhhc-----cCCceEEEecCCcCccchhhHHHHHHHHHHhhcCCceEEEEEecccCcchHHHHhhh
Confidence                     000011111     12578888866432111   1124455556666555556778888776555444433

>d1xbta1 c.37.1.24 (A:18-150) Thymidine kinase, TK1, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.19  E-value=0.00071  Score=47.35  Aligned_cols=37  Identities=11%  Similarity=0.096  Sum_probs=25.3

Q ss_pred             EEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHH
Q 017573           36 VIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRE   75 (369)
Q Consensus        36 ~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~   75 (369)
                      -++.||+.||||.-.+..+......+   .+++++-|...
T Consensus         5 ~li~GpMfsGKTt~Li~~~~~~~~~g---~~v~~ikp~~D   41 (133)
T d1xbta1           5 QVILGPMFSGKSTELMRRVRRFQIAQ---YKCLVIKYAKD   41 (133)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHHTTT---CCEEEEEETTC
T ss_pred             EEEEecccCHHHHHHHHHHHHHHHcC---CcEEEEecccc
Confidence            47899999999976544444333333   27999998743

>d2b8ta1 c.37.1.24 (A:11-149) Thymidine kinase, TK1, N-terminal domain {Ureaplasma urealyticum [TaxId: 2130]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Ureaplasma urealyticum [TaxId: 2130]

Probab=97.18  E-value=0.00095  Score=47.08  Aligned_cols=88  Identities=19%  Similarity=0.160  Sum_probs=51.7

Q ss_pred             EEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHccCC
Q 017573           36 VIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGV  115 (369)
Q Consensus        36 ~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~  115 (369)
                      -++.||+.||||.-.+..+......+.   +++++-|...--         .    +-.+....| ..          ..
T Consensus         5 ~~i~GpMfsGKTteLi~~~~~~~~~~~---kv~~ikp~~D~R---------~----~~~i~s~~g-~~----------~~   57 (139)
T d2b8ta1           5 EFITGPMFAGKTAELIRRLHRLEYADV---KYLVFKPKIDTR---------S----IRNIQSRTG-TS----------LP   57 (139)
T ss_dssp             EEEECSTTSCHHHHHHHHHHHHHHTTC---CEEEEEECCCGG---------G----CSSCCCCCC-CS----------SC
T ss_pred             EEEEccccCHHHHHHHHHHHHHHHCCC---cEEEEEEccccc---------c----cceEEcccC-ce----------ee
Confidence            478999999999775544443333333   899999974310         1    111111111 11          12


Q ss_pred             cEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhh
Q 017573          116 HVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEML  151 (369)
Q Consensus       116 ~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~  151 (369)
                      .+.+.+...+...+..... ....++|.+||+|.+.
T Consensus        58 ~~~~~~~~~~~~~~~~~~~-~~~~dvI~IDE~QFf~   92 (139)
T d2b8ta1          58 SVEVESAPEILNYIMSNSF-NDETKVIGIDEVQFFD   92 (139)
T ss_dssp             CEEESSTHHHHHHHHSTTS-CTTCCEEEECSGGGSC
T ss_pred             eEEeccchhhHHHHHhhcc-ccCcCEEEechhhhcc
Confidence            4566666666666655433 3457999999999863

>d1vmaa2 c.37.1.10 (A:82-294) GTPase domain of the signal recognition particle receptor FtsY {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermotoga maritima [TaxId: 2336]

Probab=97.12  E-value=0.001  Score=50.55  Aligned_cols=57  Identities=23%  Similarity=0.285  Sum_probs=32.7

Q ss_pred             cEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCC--HHHHHHHHHHHHHhccccCcEEEE
Q 017573           35 DVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPT--RELAQQIEKVMRALGDYLGVKVHA   97 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~--~~l~~q~~~~~~~~~~~~~~~v~~   97 (369)
                      -+++.+|||+|||.+..-.+.....++.   ++.+++--  |.=+   .++++.+....+..+..
T Consensus        13 vi~lvGptGvGKTTTiAKLAa~~~~~~~---kV~lit~Dt~R~gA---~eQL~~~a~~l~i~~~~   71 (213)
T d1vmaa2          13 VIMVVGVNGTGKTTSCGKLAKMFVDEGK---SVVLAAADTFRAAA---IEQLKIWGERVGATVIS   71 (213)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHHTTC---CEEEEEECTTCHHH---HHHHHHHHHHHTCEEEC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCC---ceEEEeecccccch---hHHHHHHhhhcCccccc
Confidence            3678999999999887655554433332   56555532  2222   23444444444666544

>d1okkd2 c.37.1.10 (D:97-303) GTPase domain of the signal recognition particle receptor FtsY {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermus aquaticus [TaxId: 271]

Probab=97.11  E-value=0.00096  Score=50.54  Aligned_cols=37  Identities=24%  Similarity=0.199  Sum_probs=24.9

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcC
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAP   72 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P   72 (369)
                      ++-+++.+|||+|||.+..-.+......+   .++.+++.
T Consensus         6 ~~vi~lvGptGvGKTTTiaKLA~~~~~~g---~kV~lit~   42 (207)
T d1okkd2           6 GRVVLVVGVNGVGKTTTIAKLGRYYQNLG---KKVMFCAG   42 (207)
T ss_dssp             SSEEEEECSTTSSHHHHHHHHHHHHHTTT---CCEEEECC
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHCC---CcEEEEEe
Confidence            35568899999999988766554333232   26766664

>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=97.11  E-value=0.001  Score=52.07  Aligned_cols=37  Identities=14%  Similarity=0.275  Sum_probs=23.0

Q ss_pred             CccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEE
Q 017573          138 YIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVF  175 (369)
Q Consensus       138 ~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~  175 (369)
                      ...++|+||+|.+.... ...+..++...+....+++.
T Consensus       115 ~~kviiIde~d~l~~~~-q~~Llk~lE~~~~~~~~il~  151 (239)
T d1njfa_         115 RFKVYLIDEVHMLSRHS-FNALLKTLEEPPEHVKFLLA  151 (239)
T ss_dssp             SSEEEEEETGGGSCHHH-HHHHHHHHHSCCTTEEEEEE
T ss_pred             CCEEEEEECcccCCHHH-HHHHHHHHhcCCCCeEEEEE
Confidence            35799999999975332 34555666655555544443

>d1t5la1 c.37.1.19 (A:2-414) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Bacillus caldotenax [TaxId: 1395]

Probab=97.10  E-value=0.00037  Score=58.93  Aligned_cols=67  Identities=25%  Similarity=0.346  Sum_probs=51.7

Q ss_pred             CCcHhhhhhhhcccc----C-CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccc
Q 017573           18 KPSAIQQRGIVPFCK----G-LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDY   90 (369)
Q Consensus        18 ~~~~~Q~~~~~~~~~----~-~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~   90 (369)
                      .|.--|-+|++.+.+    | +..++.|-||||||+++. .++...  +   ..+|||+|+..++.|+++++..+...
T Consensus        11 ~p~gDQP~aI~~l~~~l~~g~~~q~l~GltGS~ka~~iA-~l~~~~--~---rp~LVVt~n~~~A~qL~~dL~~~l~~   82 (413)
T d1t5la1          11 EPQGDQPQAIAKLVDGLRRGVKHQTLLGATGTGKTFTIS-NVIAQV--N---KPTLVIAHNKTLAGQLYSELKEFFPH   82 (413)
T ss_dssp             CCCTTHHHHHHHHHHHHHHTCSEEEEEECTTSCHHHHHH-HHHHHH--T---CCEEEECSSHHHHHHHHHHHHHHCTT
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCcEEEeCCCCcHHHHHHH-HHHHHh--C---CCEEEEeCCHHHHHHHHHHHHHHcCC
Confidence            577778888877765    3 568899999999997753 333322  1   17999999999999999999998644

>d1gm5a3 c.37.1.19 (A:286-549) RecG helicase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=97.01  E-value=0.0028  Score=49.81  Aligned_cols=90  Identities=18%  Similarity=0.150  Sum_probs=67.7

Q ss_pred             ccCCCeEEEeCCHhhHHH----HHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecC-CcCCCCCCCCcEE
Q 017573          233 LAITQSVIFVNTRRKVDW----LTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDL-LARGIDVQQVSLV  307 (369)
Q Consensus       233 ~~~~k~lv~~~~~~~~~~----~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~-~~~G~d~~~~~~v  307 (369)
                      ..+.++++.+|+.--+..    +.+.|...+..+..++|.++..+|.+++....+|+++|+|+|.+ +...+.+.++..|
T Consensus       130 ~~g~q~~~m~Pt~~La~Qh~~~~~~~f~~~~~~v~~l~~~~~~~~r~~~~~~~~~g~~~iiIGThsl~~~~~~f~~Lglv  209 (264)
T d1gm5a3         130 EAGFQTAFMVPTSILAIQHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQEDVHFKNLGLV  209 (264)
T ss_dssp             HHTSCEEEECSCHHHHHHHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHHCCCCSCCCEE
T ss_pred             hcccceeEEeehHhhhHHHHHHHHHhhhhccccceeeccccchHHHHHHHHHHHCCCCCEEEeehHHhcCCCCcccccee
Confidence            345799999999876655    45555556789999999999999999999999999999999984 4456788888888


Q ss_pred             EEecCCCCccchhhhhc
Q 017573          308 INYDLPTQPENYLHRIG  324 (369)
Q Consensus       308 i~~~~~~~~~~~~Q~~G  324 (369)
                      |+-....  -.+.|+.+
T Consensus       210 iiDEqH~--fgv~Qr~~  224 (264)
T d1gm5a3         210 IIDEQHR--FGVKQREA  224 (264)
T ss_dssp             EEESCCC--C-----CC
T ss_pred             eeccccc--cchhhHHH
Confidence            8776542  34566553

>d1sxjb2 c.37.1.20 (B:7-230) Replication factor C4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.97  E-value=0.00058  Score=52.98  Aligned_cols=41  Identities=20%  Similarity=0.293  Sum_probs=25.7

Q ss_pred             CccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEEeeC
Q 017573          138 YIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATM  179 (369)
Q Consensus       138 ~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~saT~  179 (369)
                      ...++|+||+|.+.... ...+...+...+....+++.+...
T Consensus       101 ~~kviiiDe~d~~~~~~-~~~ll~~~e~~~~~~~~i~~~~~~  141 (224)
T d1sxjb2         101 KHKIVILDEADSMTAGA-QQALRRTMELYSNSTRFAFACNQS  141 (224)
T ss_dssp             CCEEEEEESGGGSCHHH-HHTTHHHHHHTTTTEEEEEEESCG
T ss_pred             ceEEEEEecccccchhH-HHHHhhhccccccceeeeeccCch
Confidence            35799999999886443 344445555555566555555444

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.88  E-value=0.00033  Score=55.49  Aligned_cols=38  Identities=8%  Similarity=0.197  Sum_probs=25.2

Q ss_pred             CccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEE
Q 017573          138 YIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFS  176 (369)
Q Consensus       138 ~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~s  176 (369)
                      .+.++|+||+|.+... ....+..++...+....+++.|
T Consensus       131 ~~~iiiide~d~l~~~-~~~~l~~~~e~~~~~~~~Il~t  168 (252)
T d1sxje2         131 RYKCVIINEANSLTKD-AQAALRRTMEKYSKNIRLIMVC  168 (252)
T ss_dssp             CCEEEEEECTTSSCHH-HHHHHHHHHHHSTTTEEEEEEE
T ss_pred             CceEEEeccccccccc-cchhhhcccccccccccceeee
Confidence            3579999999987544 3445666667666666555543

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Thermus thermophilus [TaxId: 274]

Probab=96.74  E-value=0.0055  Score=47.92  Aligned_cols=18  Identities=28%  Similarity=0.274  Sum_probs=15.8

Q ss_pred             CCcEEEEcCCCChhhHHH
Q 017573           33 GLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~   50 (369)
                      .+.+++.||+|+|||..+
T Consensus        42 ~~giLl~GppGtGKT~la   59 (247)
T d1ixza_          42 PKGVLLVGPPGVGKTHLA   59 (247)
T ss_dssp             CSEEEEECCTTSSHHHHH
T ss_pred             CceEEEecCCCCChhHHH
Confidence            367999999999999875

>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=96.73  E-value=0.0097  Score=45.69  Aligned_cols=88  Identities=17%  Similarity=0.161  Sum_probs=71.1

Q ss_pred             cCCCeEEEeCCHhhHHHHHHHHhh----CCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecC-CcCCCCCCCCcEEE
Q 017573          234 AITQSVIFVNTRRKVDWLTDKMRS----RDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDL-LARGIDVQQVSLVI  308 (369)
Q Consensus       234 ~~~k~lv~~~~~~~~~~~~~~l~~----~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~-~~~G~d~~~~~~vi  308 (369)
                      .+.++++.+|+.-.+....+.+++    .+.++..+|+..+..+|.+++..+.+|+.+|+|+|.+ +...+.++++..||
T Consensus       103 ~g~qv~~l~Pt~~La~Q~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~g~~~iviGths~l~~~~~f~~LgLiI  182 (233)
T d2eyqa3         103 NHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQSDVKFKDLGLLI  182 (233)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHHSCCCCSSEEEEE
T ss_pred             cCCceEEEccHHHhHHHHHHHHHHHHhhCCCEEEeccCcccchhHHHHHHHHhCCCCCEEEeehhhhccCCcccccccee
Confidence            567899999999888877777764    5778999999999999999999999999999999984 44468888888888


Q ss_pred             EecCCCCccchhhhh
Q 017573          309 NYDLPTQPENYLHRI  323 (369)
Q Consensus       309 ~~~~~~~~~~~~Q~~  323 (369)
                      +-+...  ..+.|+.
T Consensus       183 iDEeH~--fg~kQ~~  195 (233)
T d2eyqa3         183 VDEEHR--FGVRHKE  195 (233)
T ss_dssp             EESGGG--SCHHHHH
T ss_pred             eechhh--hhhHHHH
Confidence            766542  2345554

>d1iqpa2 c.37.1.20 (A:2-232) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=96.71  E-value=0.0027  Score=49.27  Aligned_cols=18  Identities=22%  Similarity=0.314  Sum_probs=15.7

Q ss_pred             CcEEEEcCCCChhhHHHH
Q 017573           34 LDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~   51 (369)
                      .++++.||+|+|||..+-
T Consensus        46 ~~lll~Gp~G~GKTtla~   63 (231)
T d1iqpa2          46 PHLLFAGPPGVGKTTAAL   63 (231)
T ss_dssp             CEEEEESCTTSSHHHHHH
T ss_pred             CeEEEECCCCCcHHHHHH
Confidence            579999999999997764

>d1sxjc2 c.37.1.20 (C:12-238) Replication factor C3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.70  E-value=0.0014  Score=50.83  Aligned_cols=38  Identities=21%  Similarity=0.374  Sum_probs=23.7

Q ss_pred             CCCccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEE
Q 017573          136 PDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGV  174 (369)
Q Consensus       136 ~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~  174 (369)
                      .....++|+||+|.+.... ...+..++...++...+++
T Consensus        97 ~~~~kiiiiDe~d~~~~~~-~~~Ll~~le~~~~~~~~~~  134 (227)
T d1sxjc2          97 SKGFKLIILDEADAMTNAA-QNALRRVIERYTKNTRFCV  134 (227)
T ss_dssp             SCSCEEEEETTGGGSCHHH-HHHHHHHHHHTTTTEEEEE
T ss_pred             CCCeEEEEEeccccchhhH-HHHHHHHhhhcccceeecc
Confidence            3445799999999875443 4455555666555554444

>d1xx6a1 c.37.1.24 (A:2-142) Thymidine kinase, TK1, N-terminal domain {Clostridium acetobutylicum [TaxId: 1488]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Clostridium acetobutylicum [TaxId: 1488]

Probab=96.67  E-value=0.0025  Score=44.87  Aligned_cols=38  Identities=13%  Similarity=0.059  Sum_probs=25.4

Q ss_pred             cEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHH
Q 017573           35 DVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRE   75 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~   75 (369)
                      =-++.||+.||||.-.+..+......+.   +++++.|...
T Consensus         9 l~lI~GpMfSGKTteLi~~~~~~~~~g~---~vl~i~~~~D   46 (141)
T d1xx6a1           9 VEVIVGPMYSGKSEELIRRIRRAKIAKQ---KIQVFKPEID   46 (141)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHTTC---CEEEEEEC--
T ss_pred             EEEEEeccccHHHHHHHHHHHHhhhcCC---cEEEEEeccc
Confidence            3588999999999775544433333333   8999999753

>d1sxjd2 c.37.1.20 (D:26-262) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.56  E-value=0.0057  Score=47.46  Aligned_cols=40  Identities=18%  Similarity=0.318  Sum_probs=23.6

Q ss_pred             ccEEEEechhHhhccCcHHHHHHHHhhCCccCcEEEEEeeC
Q 017573          139 IKMFVLDEADEMLSRGFKDQIYDIFQLLPAKVQVGVFSATM  179 (369)
Q Consensus       139 ~~~viiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~~saT~  179 (369)
                      ..++|+||+|.+.... ...+..+....+....++..+...
T Consensus       109 ~~viiiDe~d~l~~~~-~~~l~~~~~~~~~~~~~i~~~~~~  148 (237)
T d1sxjd2         109 YKIIILDEADSMTADA-QSALRRTMETYSGVTRFCLICNYV  148 (237)
T ss_dssp             CEEEEETTGGGSCHHH-HHHHHHHHHHTTTTEEEEEEESCG
T ss_pred             ceEEEEecccccCHHH-HHHHhhcccccccccccccccccc
Confidence            5689999999886543 334444455555455444443333

>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Escherichia coli [TaxId: 562]

Probab=96.48  E-value=0.007  Score=47.53  Aligned_cols=18  Identities=33%  Similarity=0.324  Sum_probs=16.0

Q ss_pred             CCcEEEEcCCCChhhHHH
Q 017573           33 GLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~   50 (369)
                      .+.+++.||+|+|||..+
T Consensus        45 ~~~iLL~GppGtGKT~la   62 (256)
T d1lv7a_          45 PKGVLMVGPPGTGKTLLA   62 (256)
T ss_dssp             CCEEEEECCTTSCHHHHH
T ss_pred             CCeEEeeCCCCCCccHHH
Confidence            477999999999999875

>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=96.25  E-value=0.024  Score=40.33  Aligned_cols=137  Identities=18%  Similarity=0.141  Sum_probs=72.2

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcch-HHHHHHHc
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSV-REDQRILQ  112 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~-~~~~~~~~  112 (369)
                      .-+.|.-..|-|||.+++-.++.++-.+.   +++++-=.+.-...  .+.. .....+........+... ........
T Consensus         3 G~i~vytG~GKGKTTAAlG~alRA~G~G~---rV~ivQFlKg~~~~--ge~~-~~~~~~~~~~~~~~~~~~~~~~~e~~~   76 (157)
T d1g5ta_           3 GIIIVFTGNGKGKTTAAFGTAARAVGHGK---NVGVVQFIKGTWPN--GERN-LLEPHGVEFQVMATGFTWETQNREADT   76 (157)
T ss_dssp             CCEEEEESSSSCHHHHHHHHHHHHHHTTC---CEEEEESSCCSSCC--HHHH-HHGGGTCEEEECCTTCCCCGGGHHHHH
T ss_pred             cEEEEEeCCCCCcHHHHHHHHHHHhcCCC---EEEEEEEecCCccc--chhh-hhcccCcEEEEecCCCcccCCChHHHH
Confidence            34678888999999999999998888776   78887633321000  0011 111223333221111110 00000000


Q ss_pred             cCCcEEEeccHHHHHHHHcCCCCCCCccEEEEechhHhhccC--cHHHHHHHHhhCCccCcEEEEEeeCChhHH
Q 017573          113 AGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADEMLSRG--FKDQIYDIFQLLPAKVQVGVFSATMPPEAL  184 (369)
Q Consensus       113 ~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~~~~~~--~~~~~~~~~~~~~~~~~~i~~saT~~~~~~  184 (369)
                      .       ..+........ ......+++||+||+-...+.+  ..+.+..+++..|....+|+....+++.+.
T Consensus        77 ~-------~a~~~~~~a~~-~~~~~~~dllILDEi~~Ai~~gli~~~~v~~ll~~rp~~~evVlTGr~~p~~L~  142 (157)
T d1g5ta_          77 A-------ACMAVWQHGKR-MLADPLLDMVVLDELTYMVAYDYLPLEEVISALNARPGHQTVIITGRGCHRDIL  142 (157)
T ss_dssp             H-------HHHHHHHHHHH-HTTCTTCSEEEEETHHHHHHTTSSCHHHHHHHHHTSCTTCEEEEECSSCCHHHH
T ss_pred             H-------HHHHHHHHHHH-HhhcCccCEEeHHHHHHHHHcCCCCHHHHHHHHHhCCCCCEEEEECCCCCHHHH
Confidence            0       00111121111 1333447999999999887655  346777778877777776654333554443

>d1tf7a2 c.37.1.11 (A:256-497) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=96.10  E-value=0.018  Score=44.61  Aligned_cols=39  Identities=21%  Similarity=0.190  Sum_probs=30.3

Q ss_pred             cCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCC
Q 017573           32 KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPT   73 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~   73 (369)
                      .+.-+++.+++|+|||..++-.+.+....+.   ++++++..
T Consensus        25 ~gsl~li~G~pGsGKT~l~~qia~~~~~~~~---~~~~is~e   63 (242)
T d1tf7a2          25 KDSIILATGATGTGKTLLVSRFVENACANKE---RAILFAYE   63 (242)
T ss_dssp             SSCEEEEEECTTSSHHHHHHHHHHHHHTTTC---CEEEEESS
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHHhcc---ccceeecc
Confidence            3567899999999999988877777665544   78887754

>d1c4oa1 c.37.1.19 (A:2-409) Nucleotide excision repair enzyme UvrB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Thermus thermophilus [TaxId: 274]

Probab=95.87  E-value=0.0066  Score=51.15  Aligned_cols=67  Identities=34%  Similarity=0.447  Sum_probs=49.1

Q ss_pred             CCcHhhhhhhhccc----cCCc-EEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccc
Q 017573           18 KPSAIQQRGIVPFC----KGLD-VIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDY   90 (369)
Q Consensus        18 ~~~~~Q~~~~~~~~----~~~~-~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~   90 (369)
                      +|+.-|-+++..+.    +|++ ..+.+.+||+||+++. .+.....  .   .+|||||+...+.++++++..+...
T Consensus         8 ~p~~dqp~aI~~l~~~L~~g~~~~~L~GlsgS~ka~~~A-~l~~~~~--r---p~LvVt~~~~~A~~l~~dL~~~l~~   79 (408)
T d1c4oa1           8 SPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVTMA-KVIEALG--R---PALVLAPNKILAAQLAAEFRELFPE   79 (408)
T ss_dssp             CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHH-HHHHHHT--C---CEEEEESSHHHHHHHHHHHHHHCTT
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCcEEEecCCCCHHHHHHH-HHHHHhC--C---CEEEEeCCHHHHHHHHHHHHHhcCc
Confidence            56666767776654    4544 6889999999997643 2332221  1   7999999999999999999988643

>d1ofha_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=95.78  E-value=0.0035  Score=50.97  Aligned_cols=48  Identities=10%  Similarity=0.099  Sum_probs=30.1

Q ss_pred             CCHHHHHHHHhCCCCCCcHhhhhh-----------hhccc----cCCcEEEEcCCCChhhHHH
Q 017573            3 LQENLLRGIYAYGFEKPSAIQQRG-----------IVPFC----KGLDVIQQAQSGTGKTATF   50 (369)
Q Consensus         3 l~~~i~~~l~~~~~~~~~~~Q~~~-----------~~~~~----~~~~~li~~~tG~GKT~~~   50 (369)
                      -|.+|...|.+.=+.+....+.-+           +....    ..+++++.||||+|||..+
T Consensus         4 ~p~~i~~~L~~~ViGQd~A~~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GPpG~GKT~lA   66 (309)
T d1ofha_           4 TPREIVSELDQHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIA   66 (309)
T ss_dssp             CHHHHHHHHHTTCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHH
T ss_pred             CHHHHHHHhcCcccChHHHHHHHHHHHHHHHHHhccCCCCccCCCCceEEEECCCCCCHHHHH
Confidence            467888888775454443221111           11111    3588999999999999876

>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=95.70  E-value=0.013  Score=43.82  Aligned_cols=99  Identities=18%  Similarity=0.198  Sum_probs=71.0

Q ss_pred             HHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHH----HccCCcEEEeccHHHHHH
Q 017573           53 GILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRI----LQAGVHVVVGTPGRVFDM  128 (369)
Q Consensus        53 ~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~----~~~~~~iiv~t~~~l~~~  128 (369)
                      ++...+..+.   ++.||||...-.+...+.+.+...  +.++..+||..+..+....    ..++.+|+|+|     ..
T Consensus        23 ~I~~El~rGg---Qvy~V~p~I~~~e~~~~~l~~~~p--~~~i~~lHGkm~~~eke~im~~F~~g~~~ILv~T-----tv   92 (211)
T d2eyqa5          23 AILREILRGG---QVYYLYNDVENIQKAAERLAELVP--EARIAIGHGQMRERELERVMNDFHHQRFNVLVCT-----TI   92 (211)
T ss_dssp             HHHHHHTTTC---EEEEECCCSSCHHHHHHHHHHHCT--TSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEES-----ST
T ss_pred             HHHHHHHcCC---eEEEEEcCccchhhHHHHHHHhCC--ceEEEEEEeccCHHHHHHHHHHHHcCCcceEEEe-----hh
Confidence            4555555444   999999999888888888888765  5688889998877665443    34689999999     33


Q ss_pred             HHcCCCCCCCccEEEEechhHhhccCcHHHHHHHHhhC
Q 017573          129 LRRQSLRPDYIKMFVLDEADEMLSRGFKDQIYDIFQLL  166 (369)
Q Consensus       129 ~~~~~~~~~~~~~viiDE~H~~~~~~~~~~~~~~~~~~  166 (369)
                      ++. +++..+..++|+.+++++.    ..++..+.-+.
T Consensus        93 IEv-GiDvpnA~~iiI~~a~rfG----LaQLhQLRGRV  125 (211)
T d2eyqa5          93 IET-GIDIPTANTIIIERADHFG----LAQLHQLRGRV  125 (211)
T ss_dssp             TGG-GSCCTTEEEEEETTTTSSC----HHHHHHHHTTC
T ss_pred             hhh-ccCCCCCcEEEEecchhcc----cccccccccee
Confidence            333 4677778899999999863    33344444443

>d1g6oa_ c.37.1.11 (A:) Hexameric traffic ATPase, HP0525 {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric traffic ATPase, HP0525
species: Helicobacter pylori [TaxId: 210]

Probab=95.57  E-value=0.0082  Score=48.87  Aligned_cols=52  Identities=21%  Similarity=0.239  Sum_probs=34.0

Q ss_pred             Hhhhhhhhcc-ccCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHH
Q 017573           21 AIQQRGIVPF-CKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTREL   76 (369)
Q Consensus        21 ~~Q~~~~~~~-~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l   76 (369)
                      +-+...+..+ ..+++++|.||||||||.. +.+++..+....   +++.+-...++
T Consensus       153 ~~~~~~l~~~v~~~~nili~G~tgSGKTT~-l~al~~~i~~~~---rivtiEd~~El  205 (323)
T d1g6oa_         153 EQAISAIKDGIAIGKNVIVCGGTGSGKTTY-IKSIMEFIPKEE---RIISIEDTEEI  205 (323)
T ss_dssp             HHHHHHHHHHHHHTCCEEEEESTTSSHHHH-HHHHGGGSCTTC---CEEEEESSCCC
T ss_pred             HHHHHHHHHHHHhCCCEEEEeeccccchHH-HHHHhhhccccc---ceeeccchhhh
Confidence            3344444443 3578999999999999976 455555554333   77777666554

>d1w36b1 c.37.1.19 (B:1-485) Exodeoxyribonuclease V beta chain (RecB), N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Exodeoxyribonuclease V beta chain (RecB), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=95.12  E-value=0.024  Score=48.95  Aligned_cols=55  Identities=24%  Similarity=0.141  Sum_probs=41.8

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhccC---------CCccEEEEcCCHHHHHHHHHHHHHh
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDYGL---------VQCQALVLAPTRELAQQIEKVMRAL   87 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~~~---------~~~~~liv~P~~~l~~q~~~~~~~~   87 (369)
                      .+..+|.|+.|||||.+...-++..+..+.         ....+|+|+=|+.-+.++.+++.+.
T Consensus        16 ~g~~lv~A~AGsGKT~~l~~r~~~ll~~~~~~~~~~~~~~~~~IL~lTFT~kAA~Emk~RI~~~   79 (485)
T d1w36b1          16 QGERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLVVTFTEAATAELRGRIRSN   79 (485)
T ss_dssp             SSCEEEECCTTSCHHHHHHHHHHHHHTTCSSSSSCSSCCCGGGEEEEESCHHHHHHHHHHHHHH
T ss_pred             CCCeEEEEcCchHHHHHHHHHHHHHHhhCcccccccCCCCcccEeEeccHHHHHHHHHHHHHHH
Confidence            477999999999999988777776664321         1126999999998888887776554

>d2i3ba1 c.37.1.11 (A:1-189) Cancer-related NTPase, C1orf57 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Cancer-related NTPase, C1orf57
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.90  E-value=0.016  Score=42.60  Aligned_cols=37  Identities=19%  Similarity=0.107  Sum_probs=23.7

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcC
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAP   72 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P   72 (369)
                      +++++.||+|+|||..+. .++..+...... ..++.++
T Consensus         2 k~v~ItG~~GtGKTtl~~-~i~~~l~~~~~~-v~~~~~~   38 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTLIH-KASEVLKSSGVP-VDGFYTE   38 (189)
T ss_dssp             CCEEEESCCSSCHHHHHH-HHHHHHHHTTCC-CEEEECC
T ss_pred             cEEEEECCCCCcHHHHHH-HHHHHHHHCCCE-EEEEEec
Confidence            689999999999998644 444455443322 3444444

>d1um8a_ c.37.1.20 (A:) ClpX {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpX
species: Helicobacter pylori [TaxId: 210]

Probab=94.88  E-value=0.0092  Score=49.47  Aligned_cols=18  Identities=22%  Similarity=0.362  Sum_probs=16.0

Q ss_pred             CCcEEEEcCCCChhhHHH
Q 017573           33 GLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~   50 (369)
                      -.++++.||||.|||..+
T Consensus        68 ~~niLfiGPTGvGKTElA   85 (364)
T d1um8a_          68 KSNILLIGPTGSGKTLMA   85 (364)
T ss_dssp             CCCEEEECCTTSSHHHHH
T ss_pred             CcceeeeCCCCccHHHHH
Confidence            377999999999999876

>d1jbka_ c.37.1.20 (A:) ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=94.79  E-value=0.11  Score=38.24  Aligned_cols=114  Identities=12%  Similarity=0.072  Sum_probs=63.5

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhccC-----CCccEEEEcCCHHHH------HHHHHHHHHhcccc---CcE-EEE
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDYGL-----VQCQALVLAPTRELA------QQIEKVMRALGDYL---GVK-VHA   97 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~~~-----~~~~~liv~P~~~l~------~q~~~~~~~~~~~~---~~~-v~~   97 (369)
                      ..+.++.+|+|.|||.++-..+. .+..+.     .+ +-++-....+|+      .+|.+.+.......   .-+ +..
T Consensus        43 k~n~lLvG~pGVGKTalv~~LA~-ri~~~~vp~~L~~-~~i~~ld~~~LiAg~~~rG~~E~rl~~il~e~~~~~~~iILf  120 (195)
T d1jbka_          43 KNNPVLIGEPGVGKTAIVEGLAQ-RIINGEVPEGLKG-RRVLALDMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVILF  120 (195)
T ss_dssp             SCEEEEECCTTSCHHHHHHHHHH-HHHHTCSCGGGTT-CEEEEECHHHHHTTTCSHHHHHHHHHHHHHHHHHSTTTEEEE
T ss_pred             CCCeEEEecCCcccHHHHHHHHH-HHHhCCCCHHHcC-ceEEEeeHHHHhccCCccHHHHHHHHHHHHHHhcCCCcEEEE
Confidence            46899999999999977644443 333221     12 445555555554      36666665443221   112 222


Q ss_pred             EEC------------Ccc-hHHHHHHHc-cCCc-EEEeccHHHHHHHHcCCCCCCCccEEEEechh
Q 017573           98 CVG------------GTS-VREDQRILQ-AGVH-VVVGTPGRVFDMLRRQSLRPDYIKMFVLDEAD  148 (369)
Q Consensus        98 ~~~------------~~~-~~~~~~~~~-~~~~-iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H  148 (369)
                      +..            +.. ....+..+. ++.. |.-|||+.+...+.........|..|-++|..
T Consensus       121 IDeih~l~~~g~~~g~~d~~~~Lkp~L~rg~l~~IgatT~eey~~~~e~d~aL~rrF~~I~V~Ep~  186 (195)
T d1jbka_         121 IDELHTMVGAGKADGAMDAGNMLKPALARGELHCVGATTLDEYRQYIEKDAALERRFQKVFVAEPS  186 (195)
T ss_dssp             EETGGGGTT------CCCCHHHHHHHHHTTSCCEEEEECHHHHHHHTTTCHHHHTTEEEEECCCCC
T ss_pred             cchHHHHhcCCCCCCcccHHHHHHHHHhCCCceEEecCCHHHHHHHHHcCHHHHhcCCEeecCCCC
Confidence            221            111 111222222 3334 34568888888877776667778999999875

>d1kaga_ c.37.1.2 (A:) Shikimate kinase (AroK) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Escherichia coli [TaxId: 562]

Probab=94.49  E-value=0.012  Score=42.43  Aligned_cols=19  Identities=16%  Similarity=0.176  Sum_probs=16.5

Q ss_pred             CCcEEEEcCCCChhhHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~   51 (369)
                      .+++++.||+|+|||+++-
T Consensus         2 ~k~I~l~G~~GsGKSTvak   20 (169)
T d1kaga_           2 KRNIFLVGPMGAGKSTIGR   20 (169)
T ss_dssp             CCCEEEECCTTSCHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHH
Confidence            5789999999999998764

>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=94.36  E-value=0.18  Score=36.34  Aligned_cols=74  Identities=18%  Similarity=0.234  Sum_probs=57.7

Q ss_pred             cEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHH----HccCCcEEEeccHHHHHHHHcCCCCCCCccE
Q 017573           66 QALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRI----LQAGVHVVVGTPGRVFDMLRRQSLRPDYIKM  141 (369)
Q Consensus        66 ~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~----~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~  141 (369)
                      ++||.|+++.-++.+.+.+.+.    |+++..++|+.+..+....    ..++.+|+|+|.      +...+++...+++
T Consensus        33 r~lvfc~t~~~~~~l~~~L~~~----Gi~a~~~Hg~~~~~eR~~~l~~F~~G~~~vLVaT~------v~~~GiDip~V~~  102 (174)
T d1c4oa2          33 RTLVTVLTVRMAEELTSFLVEH----GIRARYLHHELDAFKRQALIRDLRLGHYDCLVGIN------LLREGLDIPEVSL  102 (174)
T ss_dssp             EEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESC------CCCTTCCCTTEEE
T ss_pred             cEEEEEcchhHHHHHHHHHHhc----CCceEEEecccchHHHHHHHHHHHCCCeEEEEeee------eeeeeccCCCCcE
Confidence            8999999999998888888775    8899999999886665544    346899999993      3344577777888


Q ss_pred             EEEechhH
Q 017573          142 FVLDEADE  149 (369)
Q Consensus       142 viiDE~H~  149 (369)
                      ||+=.++.
T Consensus       103 Vi~~~~~~  110 (174)
T d1c4oa2         103 VAILDADK  110 (174)
T ss_dssp             EEETTTTS
T ss_pred             EEEecccc
Confidence            88766554

>d1p9ra_ c.37.1.11 (A:) Extracellular secretion NTPase EpsE {Vibrio cholerae [TaxId: 666]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Extracellular secretion NTPase EpsE
species: Vibrio cholerae [TaxId: 666]

Probab=94.25  E-value=0.026  Score=47.43  Aligned_cols=41  Identities=22%  Similarity=0.260  Sum_probs=29.4

Q ss_pred             CcHhhhhhhhccccC--CcEEEEcCCCChhhHHHHHHHHHhhhc
Q 017573           19 PSAIQQRGIVPFCKG--LDVIQQAQSGTGKTATFCSGILQQLDY   60 (369)
Q Consensus        19 ~~~~Q~~~~~~~~~~--~~~li~~~tG~GKT~~~~~~~~~~~~~   60 (369)
                      +.+.|.+.+..+...  .-+++.||||||||.++ ..+++.+..
T Consensus       142 ~~~~~~~~l~~l~~~~~GliLvtGpTGSGKSTTl-~~~l~~~~~  184 (401)
T d1p9ra_         142 MTAHNHDNFRRLIKRPHGIILVTGPTGSGKSTTL-YAGLQELNS  184 (401)
T ss_dssp             CCHHHHHHHHHHHTSSSEEEEEECSTTSCHHHHH-HHHHHHHCC
T ss_pred             ccHHHHHHHHHHHhhhhceEEEEcCCCCCccHHH-HHHhhhhcC
Confidence            457777788777654  55899999999999775 445555543

>d1g41a_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=93.94  E-value=0.012  Score=50.03  Aligned_cols=18  Identities=22%  Similarity=0.359  Sum_probs=16.3

Q ss_pred             CCcEEEEcCCCChhhHHH
Q 017573           33 GLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~   50 (369)
                      .+|+|+.||||+|||+.+
T Consensus        49 ksNILliGPTGvGKTlLA   66 (443)
T d1g41a_          49 PKNILMIGPTGVGKTEIA   66 (443)
T ss_dssp             CCCEEEECCTTSSHHHHH
T ss_pred             cccEEEECCCCCCHHHHH
Confidence            579999999999999876

>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6, N-domain
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=93.83  E-value=0.036  Score=43.61  Aligned_cols=26  Identities=23%  Similarity=0.267  Sum_probs=19.6

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHhhhc
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQLDY   60 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~~~~   60 (369)
                      .++++.||+|+|||.++ -.++..+..
T Consensus        44 ~~lll~GppGtGKT~l~-~~l~~~l~~   69 (276)
T d1fnna2          44 PRATLLGRPGTGKTVTL-RKLWELYKD   69 (276)
T ss_dssp             CEEEEECCTTSSHHHHH-HHHHHHHTT
T ss_pred             CceEEECCCCCCHHHHH-HHHHHHHhc
Confidence            67999999999999765 445555543

>d1in4a2 c.37.1.20 (A:17-254) Holliday junction helicase RuvB {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermotoga maritima [TaxId: 2336]

Probab=93.82  E-value=0.02  Score=44.33  Aligned_cols=17  Identities=29%  Similarity=0.317  Sum_probs=15.4

Q ss_pred             CcEEEEcCCCChhhHHH
Q 017573           34 LDVIQQAQSGTGKTATF   50 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~   50 (369)
                      .++++.||+|+|||..+
T Consensus        36 ~~~L~~GPpGtGKT~lA   52 (238)
T d1in4a2          36 DHVLLAGPPGLGKTTLA   52 (238)
T ss_dssp             CCEEEESSTTSSHHHHH
T ss_pred             CeEEEECCCCCcHHHHH
Confidence            57999999999999876

>d1ixsb2 c.37.1.20 (B:4-242) Holliday junction helicase RuvB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermus thermophilus [TaxId: 274]

Probab=93.33  E-value=0.023  Score=43.99  Aligned_cols=17  Identities=24%  Similarity=0.263  Sum_probs=15.4

Q ss_pred             CcEEEEcCCCChhhHHH
Q 017573           34 LDVIQQAQSGTGKTATF   50 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~   50 (369)
                      .++++.||+|+|||..+
T Consensus        36 ~~~Ll~GPpG~GKTtla   52 (239)
T d1ixsb2          36 EHLLLFGPPGLGKTTLA   52 (239)
T ss_dssp             CCEEEECCTTSCHHHHH
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            68999999999999776

>d1e9ra_ c.37.1.11 (A:) Bacterial conjugative coupling protein TrwB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Bacterial conjugative coupling protein TrwB
species: Escherichia coli [TaxId: 562]

Probab=93.31  E-value=0.044  Score=46.60  Aligned_cols=43  Identities=16%  Similarity=0.279  Sum_probs=30.1

Q ss_pred             cCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHH
Q 017573           32 KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELA   77 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~   77 (369)
                      ..++++|.|+||+|||..+...+.+.+..+.   .++|+=|..++.
T Consensus        49 ~~~H~~I~G~tGsGKT~~l~~li~~~~~~g~---~~iiiD~kge~~   91 (433)
T d1e9ra_          49 EPRHLLVNGATGTGKSVLLRELAYTGLLRGD---RMVIVDPNGDML   91 (433)
T ss_dssp             GGGCEEEEECTTSSHHHHHHHHHHHHHHTTC---EEEEEEETTHHH
T ss_pred             ccceEEEEeCCCCcHHHHHHHHHHHHHhCCC---CEEEEeCChhHH
Confidence            4588999999999999775444444444433   677777876543

>d1tf7a1 c.37.1.11 (A:14-255) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=93.06  E-value=0.042  Score=42.14  Aligned_cols=40  Identities=18%  Similarity=0.040  Sum_probs=28.0

Q ss_pred             cCCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCC
Q 017573           32 KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPT   73 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~   73 (369)
                      .|.-+++.|++|+|||..++-.+.+.+..+..  +++++..-
T Consensus        25 ~G~~~~I~G~~G~GKT~la~~~~~~~~~~~~~--~~~~~s~e   64 (242)
T d1tf7a1          25 IGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDE--PGVFVTFE   64 (242)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHHHCC--CEEEEESS
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHHhcCC--Cccccccc
Confidence            45778999999999998776555554443322  67777654

>d1rkba_ c.37.1.1 (A:) Adenylate kinase {Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]

Probab=92.95  E-value=0.028  Score=40.68  Aligned_cols=18  Identities=22%  Similarity=0.285  Sum_probs=15.3

Q ss_pred             CcEEEEcCCCChhhHHHH
Q 017573           34 LDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~   51 (369)
                      -.+++.||+|||||+++-
T Consensus         5 ~~I~i~G~pGsGKTTia~   22 (173)
T d1rkba_           5 PNILLTGTPGVGKTTLGK   22 (173)
T ss_dssp             CCEEEECSTTSSHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHH
Confidence            468999999999998763

>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=92.82  E-value=0.46  Score=33.75  Aligned_cols=72  Identities=14%  Similarity=0.261  Sum_probs=54.1

Q ss_pred             ccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHH----ccCCcEEEeccHHHHHHHHcCCCCCCCcc
Q 017573           65 CQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL----QAGVHVVVGTPGRVFDMLRRQSLRPDYIK  140 (369)
Q Consensus        65 ~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~----~~~~~iiv~t~~~l~~~~~~~~~~~~~~~  140 (369)
                      .++||.|.++..++++++.+...    +..+..++++.........+    .+...|+|+|.     . ...+++...++
T Consensus        28 ~k~iIF~~s~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~l~~f~~~~~~iLv~Td-----v-~~rGiDi~~v~   97 (162)
T d1fuka_          28 TQAVIFCNTRRKVEELTTKLRND----KFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTD-----L-LARGIDVQQVS   97 (162)
T ss_dssp             SCEEEEESSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEG-----G-GTTTCCCCSCS
T ss_pred             CcEEEEEEEEchHHHHHHHHhhc----CceEEEeccCCchhhHHHHHHHHhhcccceeeccc-----c-ccccccCCCce
Confidence            38999999999999988887765    77888999988766654433    35788999994     2 34457777788


Q ss_pred             EEEEec
Q 017573          141 MFVLDE  146 (369)
Q Consensus       141 ~viiDE  146 (369)
                      .||.=+
T Consensus        98 ~VI~~d  103 (162)
T d1fuka_          98 LVINYD  103 (162)
T ss_dssp             EEEESS
T ss_pred             EEEEec
Confidence            777644

>d1cr2a_ c.37.1.11 (A:) Gene 4 protein (g4p, DNA primase), helicase domain {Bacteriophage T7 [TaxId: 10760]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Gene 4 protein (g4p, DNA primase), helicase domain
species: Bacteriophage T7 [TaxId: 10760]

Probab=92.74  E-value=0.12  Score=40.65  Aligned_cols=45  Identities=18%  Similarity=0.082  Sum_probs=31.2

Q ss_pred             hhhccccCCcEEEEcCCCChhhHHHHHHHHHhhh-ccCCCccEEEEcCC
Q 017573           26 GIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLD-YGLVQCQALVLAPT   73 (369)
Q Consensus        26 ~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~-~~~~~~~~liv~P~   73 (369)
                      ++.=+..|.-+++.|+||+|||..++-.+.+... .+.   ++++++.-
T Consensus        28 ~~~G~~~G~l~vi~G~~G~GKT~~~~~la~~~a~~~g~---~v~~~s~E   73 (277)
T d1cr2a_          28 KTLGARGGEVIMVTSGSGMGKSTFVRQQALQWGTAMGK---KVGLAMLE   73 (277)
T ss_dssp             HHCSBCTTCEEEEECSTTSSHHHHHHHHHHHHHHTSCC---CEEEEESS
T ss_pred             HhcCCCCCeEEEEEeCCCCCHHHHHHHHHHhhhhhccc---ceeEeeec
Confidence            3333556778999999999999776666555432 333   78888754

>d1ly1a_ c.37.1.1 (A:) Polynucleotide kinase, kinase domain {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Polynucleotide kinase, kinase domain
species: Bacteriophage T4 [TaxId: 10665]

Probab=92.58  E-value=0.025  Score=40.07  Aligned_cols=16  Identities=19%  Similarity=0.271  Sum_probs=13.7

Q ss_pred             cEEEEcCCCChhhHHH
Q 017573           35 DVIQQAQSGTGKTATF   50 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~   50 (369)
                      -+++.|++|||||..+
T Consensus         4 lIii~G~pGsGKTTla   19 (152)
T d1ly1a_           4 IILTIGCPGSGKSTWA   19 (152)
T ss_dssp             EEEEECCTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            3688999999999865

>d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=92.55  E-value=0.014  Score=45.59  Aligned_cols=18  Identities=22%  Similarity=0.250  Sum_probs=15.6

Q ss_pred             CcEEEEcCCCChhhHHHH
Q 017573           34 LDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~   51 (369)
                      ..+++.||+|+|||.++-
T Consensus        53 ~~lll~GPpG~GKTt~a~   70 (253)
T d1sxja2          53 RAAMLYGPPGIGKTTAAH   70 (253)
T ss_dssp             SEEEEECSTTSSHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHH
Confidence            579999999999997753

>d1szpa2 c.37.1.11 (A:145-395) DNA repair protein Rad51, catalytic domain {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: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=92.53  E-value=0.042  Score=42.47  Aligned_cols=42  Identities=14%  Similarity=-0.031  Sum_probs=27.6

Q ss_pred             cCCcEEEEcCCCChhhHHHHHHHHHhhhc---cCCCccEEEEcCC
Q 017573           32 KGLDVIQQAQSGTGKTATFCSGILQQLDY---GLVQCQALVLAPT   73 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~~~~~~~~~~---~~~~~~~liv~P~   73 (369)
                      .|+-+++.||+|+|||..++-.+.+....   ...+.+++++.-.
T Consensus        33 ~G~~~li~G~pGsGKT~l~lq~~~~~~~~~~~~~~~~~~~~i~~~   77 (251)
T d1szpa2          33 TGSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTE   77 (251)
T ss_dssp             SSSEEEEEESTTSSHHHHHHHHTTTTTSCTTTTCCSCEEEEEESS
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHhhhhhhhccCCceEEEEeec
Confidence            35678999999999998876665544322   2223367776543

>d1lw7a2 c.37.1.1 (A:220-411) Transcriptional regulator NadR, ribosylnicotinamide kinase domain {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Transcriptional regulator NadR, ribosylnicotinamide kinase domain
species: Haemophilus influenzae [TaxId: 727]

Probab=92.35  E-value=0.023  Score=41.83  Aligned_cols=18  Identities=17%  Similarity=0.174  Sum_probs=15.7

Q ss_pred             CCcEEEEcCCCChhhHHH
Q 017573           33 GLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~   50 (369)
                      .+.+++.||+|+|||+.+
T Consensus         7 ~K~I~i~G~~GsGKTTla   24 (192)
T d1lw7a2           7 AKTVAILGGESSGKSVLV   24 (192)
T ss_dssp             CEEEEEECCTTSHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHH
Confidence            467999999999999765

>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=92.22  E-value=0.72  Score=33.36  Aligned_cols=93  Identities=22%  Similarity=0.259  Sum_probs=64.7

Q ss_pred             cEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHH----ccCCcEEEeccHHHHHHHHcCCCCCCCccE
Q 017573           66 QALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL----QAGVHVVVGTPGRVFDMLRRQSLRPDYIKM  141 (369)
Q Consensus        66 ~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~----~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~  141 (369)
                      +++|.|+++.-++.....+.+.    ++.+..++|+.+..+....+    .+..+|+|+|     . +...+++...+++
T Consensus        33 ~~iif~~~~~~~~~~~~~l~~~----g~~~~~~hg~~~~~eR~~~l~~Fr~g~~~vLVaT-----d-v~~rGiDip~v~~  102 (181)
T d1t5la2          33 RTLVTTLTKKMAEDLTDYLKEA----GIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGI-----N-LLREGLDIPEVSL  102 (181)
T ss_dssp             EEEEECSSHHHHHHHHHHHHTT----TCCEEEECSSCCHHHHHHHHHHHHHTSCSEEEES-----C-CCSSSCCCTTEEE
T ss_pred             eEEEEeehhhhhHHHHHHHHhC----CcceeEecCCccHHHHHHHHHHHHCCCCCEEEeh-----h-HHHccCCCCCCCE
Confidence            8999999999888877777654    88999999998876655433    4689999999     3 3344577788899


Q ss_pred             EEEechhHhh-ccCcHHHHHHHHhhCCc
Q 017573          142 FVLDEADEML-SRGFKDQIYDIFQLLPA  168 (369)
Q Consensus       142 viiDE~H~~~-~~~~~~~~~~~~~~~~~  168 (369)
                      ||.-++.... ..++...+.++-+....
T Consensus       103 VI~~d~p~~~~~~s~~~yi~R~GRagR~  130 (181)
T d1t5la2         103 VAILDADKEGFLRSERSLIQTIGRAARN  130 (181)
T ss_dssp             EEETTTTSCSGGGSHHHHHHHHGGGTTS
T ss_pred             EEEecCCcccccccHHHHHHHHHhhccc
Confidence            9887776421 12233334444444433

>d1y63a_ c.37.1.1 (A:) Probable kinase LmjF30.1890 {Leishmania major [TaxId: 5664]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Probable kinase LmjF30.1890
species: Leishmania major [TaxId: 5664]

Probab=92.13  E-value=0.044  Score=39.70  Aligned_cols=18  Identities=33%  Similarity=0.669  Sum_probs=15.6

Q ss_pred             CCcEEEEcCCCChhhHHH
Q 017573           33 GLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~   50 (369)
                      +-++++.||+|+|||+++
T Consensus         5 ~~~I~i~G~~GsGKTT~~   22 (174)
T d1y63a_           5 GINILITGTPGTGKTSMA   22 (174)
T ss_dssp             SCEEEEECSTTSSHHHHH
T ss_pred             CCEEEEEeCCCCCHHHHH
Confidence            456999999999999876

>d2eyqa2 c.37.1.19 (A:349-465) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=92.01  E-value=0.15  Score=34.16  Aligned_cols=76  Identities=13%  Similarity=0.060  Sum_probs=57.3

Q ss_pred             HHHHHHHHHhccCCCeEEEeCCHhhHHHHHHHHhhCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecCCcCCCCCC
Q 017573          223 LETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQ  302 (369)
Q Consensus       223 ~~~l~~~~~~~~~~k~lv~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~G~d~~  302 (369)
                      ...+..+++.. ..++|+.+.+...++.+.+.|...+..+..+.+..          .+.++  .+.|+...+..|+-+|
T Consensus        23 ~~~L~~~i~~~-~~~Vli~a~s~g~~erl~e~L~~~~i~~~~~~~~~----------~~~~~--~~~i~~~~l~~GF~~~   89 (117)
T d2eyqa2          23 LDALRKFLETF-DGPVVFSVESEGRREALGELLARIKIAPQRIMRLD----------EASDR--GRYLMIGAAEHGFVDT   89 (117)
T ss_dssp             THHHHHHHTTC-CSCCCEEESSHHHHHHHHHHHGGGTCCCEECSSGG----------GCCTT--CCEEEECCCCSCEEET
T ss_pred             HHHHHHHHHhC-CCeEEEEECCccHHHHHHHHHHHcCCCceEecChh----------hhcCc--eEEEEEecCccccccC
Confidence            45667776553 45899999999999999999999998876665431          12333  3667778889999999


Q ss_pred             CCcEEEEec
Q 017573          303 QVSLVINYD  311 (369)
Q Consensus       303 ~~~~vi~~~  311 (369)
                      ....+++.+
T Consensus        90 ~~~l~vItE   98 (117)
T d2eyqa2          90 VRNLALICE   98 (117)
T ss_dssp             TTTEEEEEH
T ss_pred             CCCEEEEEc
Confidence            999888765

>d2bdta1 c.37.1.25 (A:1-176) Hypothetical protein BH3686 {Bacillus halodurans [TaxId: 86665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein BH3686
species: Bacillus halodurans [TaxId: 86665]

Probab=91.99  E-value=0.042  Score=39.68  Aligned_cols=16  Identities=31%  Similarity=0.389  Sum_probs=14.1

Q ss_pred             cEEEEcCCCChhhHHH
Q 017573           35 DVIQQAQSGTGKTATF   50 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~   50 (369)
                      -+++.||+|+|||+++
T Consensus         4 lI~i~G~~GsGKTTva   19 (176)
T d2bdta1           4 LYIITGPAGVGKSTTC   19 (176)
T ss_dssp             EEEEECSTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            4789999999999875

>d1gvnb_ c.37.1.21 (B:) Plasmid maintenance system epsilon/zeta, toxin zeta subunit {Streptococcus pyogenes [TaxId: 1314]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
domain: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
species: Streptococcus pyogenes [TaxId: 1314]

Probab=91.90  E-value=0.035  Score=43.69  Aligned_cols=17  Identities=29%  Similarity=0.380  Sum_probs=15.0

Q ss_pred             CcEEEEcCCCChhhHHH
Q 017573           34 LDVIQQAQSGTGKTATF   50 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~   50 (369)
                      +.+++.||+|+|||..+
T Consensus        33 ~~ilL~GpPGtGKT~la   49 (273)
T d1gvnb_          33 TAFLLGGQPGSGKTSLR   49 (273)
T ss_dssp             EEEEEECCTTSCTHHHH
T ss_pred             EEEEEECCCCCCHHHHH
Confidence            46899999999999875

>d1zp6a1 c.37.1.25 (A:6-181) Hypothetical protein Atu3015 {Agrobacterium tumefaciens [TaxId: 358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein Atu3015
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=91.76  E-value=0.039  Score=40.03  Aligned_cols=19  Identities=21%  Similarity=0.372  Sum_probs=15.8

Q ss_pred             cCCcEEEEcCCCChhhHHH
Q 017573           32 KGLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~   50 (369)
                      .|+-+++.||+|||||+++
T Consensus         3 ~g~iI~l~G~~GsGKSTia   21 (176)
T d1zp6a1           3 GGNILLLSGHPGSGKSTIA   21 (176)
T ss_dssp             TTEEEEEEECTTSCHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHH
Confidence            3556789999999999875

>d1viaa_ c.37.1.2 (A:) Shikimate kinase (AroK) {Campylobacter jejuni [TaxId: 197]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Campylobacter jejuni [TaxId: 197]

Probab=91.71  E-value=0.054  Score=38.85  Aligned_cols=18  Identities=17%  Similarity=0.233  Sum_probs=15.5

Q ss_pred             CcEEEEcCCCChhhHHHH
Q 017573           34 LDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~   51 (369)
                      +++++.|++|+|||.++-
T Consensus         1 k~I~liG~~GsGKsTi~k   18 (161)
T d1viaa_           1 KNIVFIGFMGSGKSTLAR   18 (161)
T ss_dssp             CCEEEECCTTSCHHHHHH
T ss_pred             CcEEEECCCCCCHHHHHH
Confidence            578999999999998763

>d1hv8a1 c.37.1.19 (A:3-210) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=91.67  E-value=0.6  Score=34.69  Aligned_cols=74  Identities=12%  Similarity=0.175  Sum_probs=53.8

Q ss_pred             cCCCeEEEeCCHhhHHHHHHHHhhC----CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecC-----C-cCCCCCCC
Q 017573          234 AITQSVIFVNTRRKVDWLTDKMRSR----DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDL-----L-ARGIDVQQ  303 (369)
Q Consensus       234 ~~~k~lv~~~~~~~~~~~~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~-----~-~~G~d~~~  303 (369)
                      .+.+++|.+++.+.+..+.+.++..    +..+...+|+.+..+..+.++     ..+|+|+|+.     + ...+++.+
T Consensus        71 ~~~~~lil~pt~~l~~q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~-----~~~IlV~TP~~l~~~l~~~~~~~~~  145 (208)
T d1hv8a1          71 NGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALK-----NANIVVGTPGRILDHINRGTLNLKN  145 (208)
T ss_dssp             SSCCEEEECSCHHHHHHHHHHHHHHHCSSCCCEEEECTTSCHHHHHHHHH-----TCSEEEECHHHHHHHHHTTCSCTTS
T ss_pred             cCcceEEEeeccccchhhhhhhhhhcccCCeEEEEeeCCCChHHHHHhcC-----CCCEEEEChHHHHHHHHcCCCCccc
Confidence            4458999999999998887777543    567888888887766554432     3679999952     2 33468888


Q ss_pred             CcEEEEecC
Q 017573          304 VSLVINYDL  312 (369)
Q Consensus       304 ~~~vi~~~~  312 (369)
                      ++++|+-+.
T Consensus       146 l~~lViDEa  154 (208)
T d1hv8a1         146 VKYFILDEA  154 (208)
T ss_dssp             CCEEEEETH
T ss_pred             CcEEEEECh
Confidence            999987654

>d1n0wa_ c.37.1.11 (A:) DNA repair protein Rad51, catalytic domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.57  E-value=0.059  Score=40.80  Aligned_cols=29  Identities=17%  Similarity=-0.091  Sum_probs=22.5

Q ss_pred             cCCcEEEEcCCCChhhHHHHHHHHHhhhc
Q 017573           32 KGLDVIQQAQSGTGKTATFCSGILQQLDY   60 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~~~~~~~~~~   60 (369)
                      .|+-+++.||+|+|||..++-.+.+....
T Consensus        22 ~G~v~~i~G~~GsGKT~l~l~la~~~~~~   50 (242)
T d1n0wa_          22 TGSITEMFGEFRTGKTQICHTLAVTCQLP   50 (242)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHTTSC
T ss_pred             CCEEEEEEeCCCCCHHHHHHHHHHHHHHh
Confidence            35678999999999998877766665543

>d1d2na_ c.37.1.20 (A:) Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=91.53  E-value=0.041  Score=42.71  Aligned_cols=17  Identities=29%  Similarity=0.403  Sum_probs=15.1

Q ss_pred             CcEEEEcCCCChhhHHH
Q 017573           34 LDVIQQAQSGTGKTATF   50 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~   50 (369)
                      +.+++.||+|+|||..+
T Consensus        41 ~~vLL~GppGtGKT~la   57 (246)
T d1d2na_          41 VSVLLEGPPHSGKTALA   57 (246)
T ss_dssp             EEEEEECSTTSSHHHHH
T ss_pred             eEEEEECcCCCCHHHHH
Confidence            46999999999999775

>d1byia_ c.37.1.10 (A:) Dethiobiotin synthetase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Dethiobiotin synthetase
species: Escherichia coli [TaxId: 562]

Probab=91.23  E-value=0.084  Score=39.87  Aligned_cols=34  Identities=15%  Similarity=0.159  Sum_probs=23.7

Q ss_pred             CcEEEEcC-CCChhhHHHHHHHHHhhhccCCCccEEEE
Q 017573           34 LDVIQQAQ-SGTGKTATFCSGILQQLDYGLVQCQALVL   70 (369)
Q Consensus        34 ~~~li~~~-tG~GKT~~~~~~~~~~~~~~~~~~~~liv   70 (369)
                      |.++|++- ||.|||.+++..+......+.   +++++
T Consensus         2 ~~~~i~gt~~GVGKTtvs~~La~aLa~~G~---rVl~i   36 (224)
T d1byia_           2 KRYFVTGTDTEVGKTVASCALLQAAKAAGY---RTAGY   36 (224)
T ss_dssp             EEEEEEESSTTSCHHHHHHHHHHHHHHTTC---CEEEE
T ss_pred             ceEEEEECCCCccHHHHHHHHHHHHHHCCC---eEEEE
Confidence            45677777 699999887666555545544   77776

>d1v5wa_ c.37.1.11 (A:) Meiotic recombination protein DMC1/LIM15 homolog {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Meiotic recombination protein DMC1/LIM15 homolog
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.16  E-value=0.11  Score=40.14  Aligned_cols=52  Identities=10%  Similarity=-0.080  Sum_probs=32.5

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhccCC---CccEEEEcCCHHHHHHHHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDYGLV---QCQALVLAPTRELAQQIEKVM   84 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~---~~~~liv~P~~~l~~q~~~~~   84 (369)
                      |.-++|.+|+|+|||..++..+.+....+..   ...++++.........+...+
T Consensus        37 G~~~~i~G~~GsGKT~lalq~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   91 (258)
T d1v5wa_          37 MAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPDRLRDI   91 (258)
T ss_dssp             SEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHhhhhcccccceEEEechHHHHHHHHHHHH
Confidence            4568999999999998887777655443221   224566655544444444433

>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

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: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=91.15  E-value=0.044  Score=42.91  Aligned_cols=18  Identities=28%  Similarity=0.314  Sum_probs=15.8

Q ss_pred             CCcEEEEcCCCChhhHHH
Q 017573           33 GLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~   50 (369)
                      .+.+++.||+|+|||..+
T Consensus        38 ~~giLL~GppGtGKT~l~   55 (258)
T d1e32a2          38 PRGILLYGPPGTGKTLIA   55 (258)
T ss_dssp             CCEEEEECCTTSSHHHHH
T ss_pred             CceeEEecCCCCCchHHH
Confidence            478999999999999764

>d1u94a1 c.37.1.11 (A:6-268) RecA protein, ATPase-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: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Escherichia coli [TaxId: 562]

Probab=91.08  E-value=0.12  Score=40.25  Aligned_cols=43  Identities=16%  Similarity=0.040  Sum_probs=30.9

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHH
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQ   79 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q   79 (369)
                      +-+.+.+|+|+|||..++..+.+....+.   .++|+---.+...+
T Consensus        55 ~itei~G~~gsGKTtl~l~~~~~~q~~g~---~~vyidtE~~~~~~   97 (263)
T d1u94a1          55 RIVEIYGPESSGKTTLTLQVIAAAQREGK---TCAFIDAEHALDPI   97 (263)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHHHHTTC---CEEEEESSCCCCHH
T ss_pred             eEEEEecCCCcHHHHHHHHHHHHHHcCCC---EEEEEccccccCHH
Confidence            45799999999999988777777665543   67777654444443

>d1m8pa3 c.37.1.15 (A:391-573) ATP sulfurylase C-terminal domain {Fungus (Penicillium chrysogenum) [TaxId: 5076]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ATP sulfurylase C-terminal domain
domain: ATP sulfurylase C-terminal domain
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=90.96  E-value=0.058  Score=39.19  Aligned_cols=20  Identities=20%  Similarity=0.318  Sum_probs=16.2

Q ss_pred             cCCcEEEEcCCCChhhHHHH
Q 017573           32 KGLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~   51 (369)
                      +|.-+++.|++|||||+++-
T Consensus         5 ~g~~I~l~G~~GsGKTTia~   24 (183)
T d1m8pa3           5 QGFTIFLTGYMNSGKDAIAR   24 (183)
T ss_dssp             CCEEEEEECSTTSSHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHH
Confidence            45567899999999998863

>d1zina1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {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: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=90.72  E-value=0.065  Score=39.15  Aligned_cols=17  Identities=18%  Similarity=0.296  Sum_probs=14.7

Q ss_pred             cEEEEcCCCChhhHHHH
Q 017573           35 DVIQQAQSGTGKTATFC   51 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~   51 (369)
                      ++++.||+|||||+.+-
T Consensus         2 ~I~i~G~pGSGKsT~a~   18 (182)
T d1zina1           2 NLVLMGLPGAGKGTQAE   18 (182)
T ss_dssp             EEEEECSTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            47899999999998764

>d1e6ca_ c.37.1.2 (A:) Shikimate kinase (AroK) {Erwinia chrysanthemi [TaxId: 556]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Erwinia chrysanthemi [TaxId: 556]

Probab=90.63  E-value=0.084  Score=38.14  Aligned_cols=19  Identities=16%  Similarity=0.097  Sum_probs=15.9

Q ss_pred             CcEEEEcCCCChhhHHHHH
Q 017573           34 LDVIQQAQSGTGKTATFCS   52 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~   52 (369)
                      +.+++.|++|+|||+++-.
T Consensus         3 ~~Iil~G~~GsGKSTia~~   21 (170)
T d1e6ca_           3 EPIFMVGARGCGMTTVGRE   21 (170)
T ss_dssp             CCEEEESCTTSSHHHHHHH
T ss_pred             CCEEEECCCCCCHHHHHHH
Confidence            5688999999999987643

>d1ak2a1 c.37.1.1 (A:14-146,A:177-233) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]

Probab=90.55  E-value=0.079  Score=39.07  Aligned_cols=20  Identities=20%  Similarity=0.335  Sum_probs=16.5

Q ss_pred             CCcEEEEcCCCChhhHHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFCS   52 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~   52 (369)
                      |-++++.||+|||||+.+-.
T Consensus         3 ~~riil~G~pGSGKsT~a~~   22 (190)
T d1ak2a1           3 GVRAVLLGPPGAGKGTQAPK   22 (190)
T ss_dssp             CCEEEEECCTTSSHHHHHHH
T ss_pred             ccEEEEECCCCCCHHHHHHH
Confidence            45788999999999988743

>d1qhxa_ c.37.1.3 (A:) Chloramphenicol phosphotransferase {Streptomyces venezuelae [TaxId: 54571]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Chloramphenicol phosphotransferase
domain: Chloramphenicol phosphotransferase
species: Streptomyces venezuelae [TaxId: 54571]

Probab=90.52  E-value=0.061  Score=38.91  Aligned_cols=18  Identities=22%  Similarity=0.259  Sum_probs=15.2

Q ss_pred             CCcEEEEcCCCChhhHHH
Q 017573           33 GLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~   50 (369)
                      .+-+++.|++|||||.++
T Consensus         3 ~kiI~l~G~~GsGKsTva   20 (178)
T d1qhxa_           3 TRMIILNGGSSAGKSGIV   20 (178)
T ss_dssp             CCEEEEECCTTSSHHHHH
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            456788999999999776

>d1knqa_ c.37.1.17 (A:) Gluconate kinase {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: Gluconate kinase
domain: Gluconate kinase
species: Escherichia coli [TaxId: 562]

Probab=90.42  E-value=0.057  Score=38.92  Aligned_cols=18  Identities=28%  Similarity=0.270  Sum_probs=14.8

Q ss_pred             CcEEEEcCCCChhhHHHH
Q 017573           34 LDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~   51 (369)
                      +=+++.|++|||||..+-
T Consensus         7 ~iivl~G~~GsGKsT~a~   24 (171)
T d1knqa_           7 HIYVLMGVSGSGKSAVAS   24 (171)
T ss_dssp             EEEEEECSTTSCHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHH
Confidence            347889999999998763

>d1pzna2 c.37.1.11 (A:96-349) DNA repair protein Rad51, catalytic domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=90.33  E-value=0.073  Score=41.22  Aligned_cols=27  Identities=15%  Similarity=-0.097  Sum_probs=21.8

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhh
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLD   59 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~   59 (369)
                      |+-++|.+|+|+|||..++-.+.+...
T Consensus        36 G~~~li~G~pGsGKT~~~lq~~~~~~~   62 (254)
T d1pzna2          36 QAITEVFGEFGSGKTQLAHTLAVMVQL   62 (254)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHHHTTS
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHHHhhc
Confidence            466899999999999888777666553

>d1r6bx2 c.37.1.20 (X:169-436) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=90.20  E-value=0.2  Score=38.99  Aligned_cols=116  Identities=16%  Similarity=0.162  Sum_probs=60.1

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhccC-----CCccEEEEcCCHHHH-----HHHHHHHHHhcccc--CcEEEEEEC
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDYGL-----VQCQALVLAPTRELA-----QQIEKVMRALGDYL--GVKVHACVG  100 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~~~-----~~~~~liv~P~~~l~-----~q~~~~~~~~~~~~--~~~v~~~~~  100 (369)
                      ..+.++.||+|.|||..+-..+. .+..+.     .+..++.+-+.+-++     .+|.+.+.......  .-++..+..
T Consensus        39 k~n~lLVG~~GvGKTalv~~la~-ri~~~~vp~~l~~~~i~~l~~~~liag~~~~g~~e~r~~~i~~~~~~~~~iIlfiD  117 (268)
T d1r6bx2          39 KNNPLLVGESGVGKTAIAEGLAW-RIVQGDVPEVMADCTIYSLDIGSLLAGTKYRGDFEKRFKALLKQLEQDTNSILFID  117 (268)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHH-HHHHTCSCGGGTTCEEEECCCC---CCCCCSSCHHHHHHHHHHHHSSSSCEEEEET
T ss_pred             cCCcEEECCCCCcHHHHHHHHHH-HHHhCCcccccccceeEEeeechHhccCccchhHHHHHHHHHHHhhccCCceEEec
Confidence            36899999999999977544433 333321     121344433332221     23444443332211  122222221


Q ss_pred             ---------Ccc--hHHHHHHHc-----cCCc-EEEeccHHHHHHHHcCCCCCCCccEEEEechhH
Q 017573          101 ---------GTS--VREDQRILQ-----AGVH-VVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADE  149 (369)
Q Consensus       101 ---------~~~--~~~~~~~~~-----~~~~-iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~  149 (369)
                               +..  .....+.+.     ++.. |.-||++.+.............|..|-++|...
T Consensus       118 eih~l~~~g~~~g~~~d~a~~Lkp~L~rg~i~vIgatT~eey~~~~e~d~al~rrF~~I~V~Eps~  183 (268)
T d1r6bx2         118 EIHTIIGAGAASGGQVDAANLIKPLLSSGKIRVIGSTTYQEFSNIFEKDRALARRFQKIDITEPSI  183 (268)
T ss_dssp             TTTTTTTSCCSSSCHHHHHHHHSSCSSSCCCEEEEEECHHHHHCCCCCTTSSGGGEEEEECCCCCH
T ss_pred             chHHHhcCCCCCCccccHHHHhhHHHhCCCCeEEEeCCHHHHHHHHhhcHHHHhhhcccccCCCCH
Confidence                     111  112223332     2333 445688888877777776777799999999985

>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=90.19  E-value=0.21  Score=39.56  Aligned_cols=52  Identities=21%  Similarity=0.164  Sum_probs=39.2

Q ss_pred             cEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEec
Q 017573           66 QALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGT  121 (369)
Q Consensus        66 ~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t  121 (369)
                      +++|+||+..-+++.++.+++.    +.+|..+++.....+......+..+++|+|
T Consensus        38 ~~~~F~~s~~~~~~~a~~L~~~----g~~V~~l~~~~~~~e~~~~~~~~~~~~~~t   89 (299)
T d1yksa2          38 PTAWFLPSIRAANVMAASLRKA----GKSVVVLNRKTFEREYPTIKQKKPDFILAT   89 (299)
T ss_dssp             CEEEECSCHHHHHHHHHHHHHT----TCCEEECCSSSCC--------CCCSEEEES
T ss_pred             CEEEEeCCHHHHHHHHHHHHhc----CCeEEEEcCcCcHhHHhhhhcCCcCEEEEe
Confidence            8999999999999999988875    667889999888777777777788999999

>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=90.12  E-value=1.1  Score=31.37  Aligned_cols=69  Identities=17%  Similarity=0.369  Sum_probs=49.5

Q ss_pred             cEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHH----HccCCcEEEeccHHHHHHHHcCCCCCCCccE
Q 017573           66 QALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRI----LQAGVHVVVGTPGRVFDMLRRQSLRPDYIKM  141 (369)
Q Consensus        66 ~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~----~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~  141 (369)
                      ++||.|+++.-++++.+.+++.    +..+..++++.........    ..++..++|+|.     .+.+ +++...+++
T Consensus        30 k~IIF~~s~~~~~~l~~~L~~~----g~~~~~~~~~~~~~~r~~~~~~f~~~~~~ilv~T~-----~~~~-Gid~~~v~~   99 (155)
T d1hv8a2          30 YGLVFCKTKRDTKELASMLRDI----GFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATD-----VMSR-GIDVNDLNC   99 (155)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHT----TCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECT-----THHH-HCCCSCCSE
T ss_pred             CEEEEECchHHHHHHHhhhccc----ccccccccccchhhhhhhhhhhhhcccceeeeehh-----HHhh-hhhhccCcE
Confidence            8999999999998888888765    7788888888765554433    245778999983     2222 355566777


Q ss_pred             EEE
Q 017573          142 FVL  144 (369)
Q Consensus       142 vii  144 (369)
                      ||.
T Consensus       100 Vi~  102 (155)
T d1hv8a2         100 VIN  102 (155)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            764

>d2cdna1 c.37.1.1 (A:1-181) Adenylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=90.11  E-value=0.092  Score=38.34  Aligned_cols=18  Identities=22%  Similarity=0.329  Sum_probs=15.1

Q ss_pred             cEEEEcCCCChhhHHHHH
Q 017573           35 DVIQQAQSGTGKTATFCS   52 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~~   52 (369)
                      ++++.||+|||||+.+-.
T Consensus         2 ~I~i~G~pGsGKsT~a~~   19 (181)
T d2cdna1           2 RVLLLGPPGAGKGTQAVK   19 (181)
T ss_dssp             EEEEECCTTSSHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            578999999999987644

>d1s3ga1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus globisporus [TaxId: 1459]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus globisporus [TaxId: 1459]

Probab=90.09  E-value=0.093  Score=38.36  Aligned_cols=19  Identities=16%  Similarity=0.202  Sum_probs=15.3

Q ss_pred             cEEEEcCCCChhhHHHHHH
Q 017573           35 DVIQQAQSGTGKTATFCSG   53 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~~~   53 (369)
                      .+++.||+|||||+.+-..
T Consensus         2 ~I~i~G~pGSGKsT~a~~L   20 (182)
T d1s3ga1           2 NIVLMGLPGAGKGTQADRI   20 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            3789999999999876433

>d2i1qa2 c.37.1.11 (A:65-322) DNA repair protein Rad51, catalytic domain {Archaeon Methanococcus voltae [TaxId: 2188]}

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: DNA repair protein Rad51, catalytic domain
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=89.93  E-value=0.082  Score=40.79  Aligned_cols=29  Identities=14%  Similarity=0.032  Sum_probs=23.6

Q ss_pred             cCCcEEEEcCCCChhhHHHHHHHHHhhhc
Q 017573           32 KGLDVIQQAQSGTGKTATFCSGILQQLDY   60 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~~~~~~~~~~   60 (369)
                      .|+-++|.|++|+|||..++..+.+.+..
T Consensus        33 ~G~l~~i~G~~G~GKT~~~l~~a~~~~~~   61 (258)
T d2i1qa2          33 SQSVTEFAGVFGSGKTQIMHQSCVNLQNP   61 (258)
T ss_dssp             TTEEEEEEESTTSSHHHHHHHHHHHTTCG
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHhc
Confidence            35678999999999999888887776543

>d1zaka1 c.37.1.1 (A:3-127,A:159-222) Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Maize (Zea mays) [TaxId: 4577]

Probab=89.92  E-value=0.1  Score=38.44  Aligned_cols=17  Identities=18%  Similarity=0.255  Sum_probs=14.9

Q ss_pred             cEEEEcCCCChhhHHHH
Q 017573           35 DVIQQAQSGTGKTATFC   51 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~   51 (369)
                      .+++.||+|||||+.+-
T Consensus         5 ~I~i~GppGsGKsT~a~   21 (189)
T d1zaka1           5 KVMISGAPASGKGTQCE   21 (189)
T ss_dssp             CEEEEESTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            58999999999998764

>d1e4va1 c.37.1.1 (A:1-121,A:157-214) Adenylate kinase {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: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Escherichia coli [TaxId: 562]

Probab=89.60  E-value=0.087  Score=38.38  Aligned_cols=17  Identities=18%  Similarity=0.124  Sum_probs=14.5

Q ss_pred             cEEEEcCCCChhhHHHH
Q 017573           35 DVIQQAQSGTGKTATFC   51 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~   51 (369)
                      ++++.||+|||||+.+-
T Consensus         2 ~I~i~G~pGSGKsT~~~   18 (179)
T d1e4va1           2 RIILLGAPVAGKGTQAQ   18 (179)
T ss_dssp             EEEEEESTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            47889999999998863

>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=89.57  E-value=1.4  Score=32.28  Aligned_cols=69  Identities=12%  Similarity=0.212  Sum_probs=50.5

Q ss_pred             ccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHH----HccCCcEEEeccHHHHHHHHcCCCCCCCcc
Q 017573           65 CQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRI----LQAGVHVVVGTPGRVFDMLRRQSLRPDYIK  140 (369)
Q Consensus        65 ~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~----~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~  140 (369)
                      .++||.|+++..++.+...+...    ++.+...+++.........    ..+..+|+|+|.     . ...+++...++
T Consensus        31 ~~~IIF~~t~~~~~~l~~~l~~~----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~ilvaTd-----~-~~~GiD~p~v~  100 (200)
T d1oywa3          31 KSGIIYCNSRAKVEDTAARLQSK----GISAAAYHAGLENNVRADVQEKFQRDDLQIVVATV-----A-FGMGINKPNVR  100 (200)
T ss_dssp             CCEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECT-----T-SCTTTCCTTCC
T ss_pred             CCEEEEEeeehhhHHhhhhhccC----CceeEEecCCCcHHHHHHHHHHHhcccceEEEecc-----h-hhhccCCCCCC
Confidence            38999999999999888877765    7788889988876554433    345788999993     2 23346666677


Q ss_pred             EEE
Q 017573          141 MFV  143 (369)
Q Consensus       141 ~vi  143 (369)
                      +||
T Consensus       101 ~VI  103 (200)
T d1oywa3         101 FVV  103 (200)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            665

>d3adka_ c.37.1.1 (A:) Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Pig (Sus scrofa) [TaxId: 9823]

Probab=89.45  E-value=0.092  Score=38.87  Aligned_cols=22  Identities=18%  Similarity=0.176  Sum_probs=17.7

Q ss_pred             cccCCcEEEEcCCCChhhHHHH
Q 017573           30 FCKGLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        30 ~~~~~~~li~~~tG~GKT~~~~   51 (369)
                      +.+.+-+++.||+|||||+.+-
T Consensus         5 ~~~~~iI~l~G~pGSGKsT~a~   26 (194)
T d3adka_           5 LKKSKIIFVVGGPGSGKGTQCE   26 (194)
T ss_dssp             HHTSCEEEEEECTTSSHHHHHH
T ss_pred             ccCCcEEEEECCCCCCHHHHHH
Confidence            3456778999999999998764

>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=89.21  E-value=1  Score=32.05  Aligned_cols=72  Identities=8%  Similarity=0.122  Sum_probs=51.0

Q ss_pred             cEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHH----ccCCcEEEeccHHHHHHHHcCCCCCCCccE
Q 017573           66 QALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL----QAGVHVVVGTPGRVFDMLRRQSLRPDYIKM  141 (369)
Q Consensus        66 ~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~----~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~  141 (369)
                      ++||.|+++.-++.+.+.+.+.    +..+..++|+.+..+....+    .+...++|+|.     .+ ..+++...++.
T Consensus        29 k~iIF~~~~~~~~~l~~~L~~~----~~~~~~ihg~~~~~~r~~~l~~F~~g~~~iLv~T~-----~~-~~Gid~~~~~~   98 (168)
T d1t5ia_          29 QVVIFVKSVQRCIALAQLLVEQ----NFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATN-----LF-GRGMDIERVNI   98 (168)
T ss_dssp             SEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEESS-----CC-STTCCGGGCSE
T ss_pred             eEEEEEeeeecchhhhhhhccc----cccccccccccchhhhhhhhhhhccccceeeeccc-----cc-cchhhcccchh
Confidence            8999999999888888877764    67888999988766554433    35788999993     22 33455555676


Q ss_pred             EEEech
Q 017573          142 FVLDEA  147 (369)
Q Consensus       142 viiDE~  147 (369)
                      +|.=+.
T Consensus        99 vi~~~~  104 (168)
T d1t5ia_          99 AFNYDM  104 (168)
T ss_dssp             EEESSC
T ss_pred             hhhhhc
Confidence            655444

>d1np6a_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Escherichia coli [TaxId: 562]

Probab=89.20  E-value=0.21  Score=35.54  Aligned_cols=23  Identities=35%  Similarity=0.404  Sum_probs=16.1

Q ss_pred             EEEEcCCCChhhHHHHHHHHHhhh
Q 017573           36 VIQQAQSGTGKTATFCSGILQQLD   59 (369)
Q Consensus        36 ~li~~~tG~GKT~~~~~~~~~~~~   59 (369)
                      +.|.|+.|||||+.+ -.++..+.
T Consensus         5 i~itG~~GSGKTTL~-~~L~~~l~   27 (170)
T d1np6a_           5 LAFAAWSGTGKTTLL-KKLIPALC   27 (170)
T ss_dssp             EEEECCTTSCHHHHH-HHHHHHHH
T ss_pred             EEEEcCCCCCHHHHH-HHHHHHHH
Confidence            678999999999764 33444443

>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=89.15  E-value=1.4  Score=31.41  Aligned_cols=73  Identities=14%  Similarity=0.194  Sum_probs=54.1

Q ss_pred             cEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHH----HccCCcEEEeccHHHHHHHHcCCCCCCCccE
Q 017573           66 QALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRI----LQAGVHVVVGTPGRVFDMLRRQSLRPDYIKM  141 (369)
Q Consensus        66 ~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~----~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~  141 (369)
                      ++||.|+++.-++.++..+...    +..+..++++....+....    ..+..+++|+|.      ....+++...+++
T Consensus        34 k~iVF~~~~~~~~~l~~~L~~~----g~~~~~~h~~~~~~~r~~~~~~f~~~~~~ilv~Td------~~~~Gid~~~v~~  103 (171)
T d1s2ma2          34 QAIIFCNSTNRVELLAKKITDL----GYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSD------LLTRGIDIQAVNV  103 (171)
T ss_dssp             EEEEECSSHHHHHHHHHHHHHH----TCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESS------CSSSSCCCTTEEE
T ss_pred             ceEEEEeeeehhhHhHHhhhcc----cccccccccccchhhhhhhhhhcccCccccccchh------HhhhccccceeEE
Confidence            8999999999888888877765    7888888988876554433    345788999994      2344577777888


Q ss_pred             EEEechh
Q 017573          142 FVLDEAD  148 (369)
Q Consensus       142 viiDE~H  148 (369)
                      ||.-++-
T Consensus       104 VI~~d~p  110 (171)
T d1s2ma2         104 VINFDFP  110 (171)
T ss_dssp             EEESSCC
T ss_pred             EEecCCc
Confidence            8765554

>d2ak3a1 c.37.1.1 (A:0-124,A:162-225) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]

Probab=89.08  E-value=0.1  Score=38.41  Aligned_cols=19  Identities=21%  Similarity=0.270  Sum_probs=15.6

Q ss_pred             CcEEEEcCCCChhhHHHHH
Q 017573           34 LDVIQQAQSGTGKTATFCS   52 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~   52 (369)
                      -++++.||+|||||+.+-.
T Consensus         7 mrIiliG~PGSGKtT~a~~   25 (189)
T d2ak3a1           7 LRAAIMGAPGSGKGTVSSR   25 (189)
T ss_dssp             CEEEEECCTTSSHHHHHHH
T ss_pred             eeEEEECCCCCCHHHHHHH
Confidence            3678999999999987643

>d1khta_ c.37.1.1 (A:) Adenylate kinase {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=89.08  E-value=0.19  Score=36.45  Aligned_cols=25  Identities=20%  Similarity=0.202  Sum_probs=17.6

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHhhh
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQLD   59 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~~~   59 (369)
                      +-+++.|++|+|||+.+- .+...+.
T Consensus         2 kiI~i~G~~GsGKsT~~~-~L~~~l~   26 (190)
T d1khta_           2 KVVVVTGVPGVGSTTSSQ-LAMDNLR   26 (190)
T ss_dssp             CEEEEECCTTSCHHHHHH-HHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHH-HHHHHHH
Confidence            457899999999997653 3333443

>d1qf9a_ c.37.1.1 (A:) UMP/CMP kinase {Dictyostelium discoideum [TaxId: 44689]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Dictyostelium discoideum [TaxId: 44689]

Probab=89.07  E-value=0.12  Score=38.12  Aligned_cols=17  Identities=24%  Similarity=0.304  Sum_probs=14.5

Q ss_pred             cEEEEcCCCChhhHHHH
Q 017573           35 DVIQQAQSGTGKTATFC   51 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~   51 (369)
                      -+++.||+|||||+.+-
T Consensus         8 iI~i~G~pGSGKsT~a~   24 (194)
T d1qf9a_           8 VVFVLGGPGSGKGTQCA   24 (194)
T ss_dssp             EEEEEESTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            47899999999998763

>d1yj5a2 c.37.1.1 (A:351-522) 5' polynucleotide kinase-3' phosphatase, C-terminal domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: 5' polynucleotide kinase-3' phosphatase, C-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=88.67  E-value=0.094  Score=38.00  Aligned_cols=17  Identities=24%  Similarity=0.302  Sum_probs=14.5

Q ss_pred             CcEEEEcCCCChhhHHH
Q 017573           34 LDVIQQAQSGTGKTATF   50 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~   50 (369)
                      .-++++|++|||||..+
T Consensus        15 ~liil~G~pGsGKST~a   31 (172)
T d1yj5a2          15 EVVVAVGFPGAGKSTFI   31 (172)
T ss_dssp             CEEEEECCTTSSHHHHH
T ss_pred             EEEEEECCCCCCHHHHH
Confidence            45899999999999754

>d1ukza_ c.37.1.1 (A:) Uridylate kinase {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: Nucleotide and nucleoside kinases
domain: Uridylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=88.56  E-value=0.12  Score=38.14  Aligned_cols=17  Identities=18%  Similarity=0.212  Sum_probs=14.5

Q ss_pred             cEEEEcCCCChhhHHHH
Q 017573           35 DVIQQAQSGTGKTATFC   51 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~   51 (369)
                      -+++.||+|||||..+-
T Consensus        10 iI~i~GppGSGKsT~a~   26 (196)
T d1ukza_          10 VIFVLGGPGAGKGTQCE   26 (196)
T ss_dssp             EEEEECSTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            47889999999998764

>d1ny5a2 c.37.1.20 (A:138-384) Transcriptional activator sigm54 (NtrC1), C-terminal domain {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: Transcriptional activator sigm54 (NtrC1), C-terminal domain
species: Aquifex aeolicus [TaxId: 63363]

Probab=88.52  E-value=0.39  Score=36.93  Aligned_cols=22  Identities=27%  Similarity=0.388  Sum_probs=17.8

Q ss_pred             ccccCCcEEEEcCCCChhhHHH
Q 017573           29 PFCKGLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        29 ~~~~~~~~li~~~tG~GKT~~~   50 (369)
                      ....+..+++.|++|+|||.+|
T Consensus        19 ~a~~~~pvlI~Ge~GtGK~~~A   40 (247)
T d1ny5a2          19 ISCAECPVLITGESGVGKEVVA   40 (247)
T ss_dssp             HTTCCSCEEEECSTTSSHHHHH
T ss_pred             HhCCCCCEEEECCCCcCHHHHH
Confidence            3345678999999999999765

>d1nlfa_ c.37.1.11 (A:) Hexameric replicative helicase repA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric replicative helicase repA
species: Escherichia coli [TaxId: 562]

Probab=88.47  E-value=0.25  Score=38.64  Aligned_cols=62  Identities=18%  Similarity=0.117  Sum_probs=37.0

Q ss_pred             hhhccccCCcEEEEcCCCChhhHHHHHHHHHhhhcc-------CCCccEEEEcCCHHHHHHHHHHHHHhc
Q 017573           26 GIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYG-------LVQCQALVLAPTRELAQQIEKVMRALG   88 (369)
Q Consensus        26 ~~~~~~~~~~~li~~~tG~GKT~~~~~~~~~~~~~~-------~~~~~~liv~P~~~l~~q~~~~~~~~~   88 (369)
                      +++-+..+.-.++.|++|+|||..++..+++.....       ..+.+++|+.-- .-..++.+++....
T Consensus        22 li~G~~pg~~~~i~G~~G~GKS~l~l~la~~ia~g~~~~~~~~~~~~~vl~~~~E-~~~~~~~~Rl~~~~   90 (274)
T d1nlfa_          22 VLPNMVAGTVGALVSPGGAGKSMLALQLAAQIAGGPDLLEVGELPTGPVIYLPAE-DPPTAIHHRLHALG   90 (274)
T ss_dssp             EETTEETTSEEEEEESTTSSHHHHHHHHHHHHHTCCCTTCCCCCCCCCEEEEESS-SCHHHHHHHHHHHH
T ss_pred             HhCCccCCcEEEEEeCCCCCHHHHHHHHHHHHHcCCCcccccccCCCceEEEecc-chHHHHHHHHHHHh
Confidence            455566678889999999999987766555432111       112257776542 23344555555543

>d1akya1 c.37.1.1 (A:3-130,A:169-220) Adenylate kinase {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: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=88.37  E-value=0.15  Score=37.17  Aligned_cols=18  Identities=17%  Similarity=0.289  Sum_probs=15.1

Q ss_pred             CcEEEEcCCCChhhHHHH
Q 017573           34 LDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~   51 (369)
                      -.+++.||+|||||+.+-
T Consensus         3 mrIvl~G~pGSGKtT~a~   20 (180)
T d1akya1           3 IRMVLIGPPGAGKGTQAP   20 (180)
T ss_dssp             CEEEEECCTTSSHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHH
Confidence            357899999999998764

>d1g8pa_ c.37.1.20 (A:) ATPase subunit of magnesium chelatase, BchI {Rhodobacter capsulatus [TaxId: 1061]}

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: ATPase subunit of magnesium chelatase, BchI
species: Rhodobacter capsulatus [TaxId: 1061]

Probab=88.23  E-value=0.061  Score=43.84  Aligned_cols=19  Identities=26%  Similarity=0.267  Sum_probs=16.3

Q ss_pred             cCCcEEEEcCCCChhhHHH
Q 017573           32 KGLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~   50 (369)
                      .+.++++.||+|+|||..+
T Consensus        27 ~~h~vLl~G~pG~GKT~la   45 (333)
T d1g8pa_          27 GIGGVLVFGDRGTGKSTAV   45 (333)
T ss_dssp             GGCCEEEECCGGGCTTHHH
T ss_pred             CCCeEEEECCCCccHHHHH
Confidence            4578999999999999764

>d1teva_ c.37.1.1 (A:) UMP/CMP kinase {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: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.20  E-value=0.16  Score=37.45  Aligned_cols=16  Identities=25%  Similarity=0.364  Sum_probs=14.1

Q ss_pred             EEEEcCCCChhhHHHH
Q 017573           36 VIQQAQSGTGKTATFC   51 (369)
Q Consensus        36 ~li~~~tG~GKT~~~~   51 (369)
                      +++.||+|||||+.+-
T Consensus         4 I~i~GppGSGKsT~a~   19 (194)
T d1teva_           4 VFVLGGPGAGKGTQCA   19 (194)
T ss_dssp             EEEECCTTSSHHHHHH
T ss_pred             EEEECCCCCCHHHHHH
Confidence            6899999999998864

>d2iyva1 c.37.1.2 (A:2-166) Shikimate kinase (AroK) {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=88.11  E-value=0.15  Score=36.48  Aligned_cols=18  Identities=17%  Similarity=0.219  Sum_probs=14.9

Q ss_pred             cEEEEcCCCChhhHHHHH
Q 017573           35 DVIQQAQSGTGKTATFCS   52 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~~   52 (369)
                      ++++.|++|+|||.++-.
T Consensus         3 ~IvliG~~G~GKSTig~~   20 (165)
T d2iyva1           3 KAVLVGLPGSGKSTIGRR   20 (165)
T ss_dssp             SEEEECSTTSSHHHHHHH
T ss_pred             cEEEECCCCCCHHHHHHH
Confidence            578889999999987643

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=87.80  E-value=0.085  Score=41.57  Aligned_cols=15  Identities=27%  Similarity=0.202  Sum_probs=12.6

Q ss_pred             EEEEcCCCChhhHHH
Q 017573           36 VIQQAQSGTGKTATF   50 (369)
Q Consensus        36 ~li~~~tG~GKT~~~   50 (369)
                      +++.||+|+|||.++
T Consensus        49 l~l~GppGtGKT~l~   63 (287)
T d1w5sa2          49 YGSIGRVGIGKTTLA   63 (287)
T ss_dssp             EECTTCCSSSHHHHH
T ss_pred             EEeECCCCCCHHHHH
Confidence            466799999999775

>d1x6va3 c.37.1.4 (A:34-228) Adenosine-5'phosphosulfate kinase (APS kinase) {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: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.74  E-value=0.084  Score=38.93  Aligned_cols=18  Identities=33%  Similarity=0.298  Sum_probs=14.6

Q ss_pred             CcEEEEcCCCChhhHHHH
Q 017573           34 LDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~   51 (369)
                      .-+++.|++|||||.++-
T Consensus        20 ~vI~L~G~pGSGKTTiAk   37 (195)
T d1x6va3          20 CTVWLTGLSGAGKTTVSM   37 (195)
T ss_dssp             EEEEEESSCHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHH
Confidence            446688999999998763

>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=87.73  E-value=1.4  Score=31.20  Aligned_cols=98  Identities=15%  Similarity=0.232  Sum_probs=64.8

Q ss_pred             cEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHH---
Q 017573           35 DVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL---  111 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~---  111 (369)
                      ...+..+....|... +..++...    ...++++.|+++.-++...+.+...    +..+..++++.........+   
T Consensus        10 q~~v~v~~~~~K~~~-L~~ll~~~----~~~k~iiF~~~~~~~~~~~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f   80 (168)
T d2j0sa2          10 QFFVAVEREEWKFDT-LCDLYDTL----TITQAVIFCNTKRKVDWLTEKMREA----NFTVSSMHGDMPQKERESIMKEF   80 (168)
T ss_dssp             EEEEEESSTTHHHHH-HHHHHHHH----TSSEEEEECSSHHHHHHHHHHHHHT----TCCCEEECTTSCHHHHHHHHHHH
T ss_pred             EEEEEecChHHHHHH-HHHHHHhC----CCCceEEEeeeHHHHHHHHHHhhhc----ccchhhhhhhhhHHHHHHHHHHH
Confidence            344445555567543 33344332    2238999999999998888877765    67788888888766654433   


Q ss_pred             -ccCCcEEEeccHHHHHHHHcCCCCCCCccEEEEech
Q 017573          112 -QAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFVLDEA  147 (369)
Q Consensus       112 -~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~  147 (369)
                       .+..+++|+|-     .+ ..+++...+++||.=++
T Consensus        81 k~g~~~iLv~Td-----~~-~rGiDi~~v~~VIn~d~  111 (168)
T d2j0sa2          81 RSGASRVLISTD-----VW-ARGLDVPQVSLIINYDL  111 (168)
T ss_dssp             HHTSSCEEEECG-----GG-SSSCCCTTEEEEEESSC
T ss_pred             hcCCccEEeccc-----hh-cccccccCcceEEEecC
Confidence             45789999994     33 44677777887765443

>d1mo6a1 c.37.1.11 (A:1-269) RecA protein, ATPase-domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=87.50  E-value=0.29  Score=38.11  Aligned_cols=48  Identities=17%  Similarity=0.133  Sum_probs=32.4

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHHHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQIEKV   83 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q~~~~   83 (369)
                      ++-..+.+|.|+|||..++..+......+.   .++|+-.-.++..++.+.
T Consensus        60 g~i~e~~G~~~~GKT~l~l~~~~~~q~~g~---~~vyIDtE~~~~~e~a~~  107 (269)
T d1mo6a1          60 GRVIEIYGPESSGKTTVALHAVANAQAAGG---VAAFIDAEHALDPDYAKK  107 (269)
T ss_dssp             SSEEEEECSSSSSHHHHHHHHHHHHHHTTC---EEEEEESSCCCCHHHHHH
T ss_pred             ceeEEEecCCCcHHHHHHHHHHHHHhcCCC---EEEEEECCccCCHHHHHH
Confidence            355799999999999888776665554443   677766554554444333

>d1svma_ c.37.1.20 (A:) Papillomavirus large T antigen helicase domain {Simian virus 40 [TaxId: 10633]}

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: Papillomavirus large T antigen helicase domain
species: Simian virus 40 [TaxId: 10633]

Probab=87.28  E-value=0.19  Score=41.19  Aligned_cols=19  Identities=16%  Similarity=0.053  Sum_probs=16.1

Q ss_pred             CCcEEEEcCCCChhhHHHH
Q 017573           33 GLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~   51 (369)
                      ++.+++.||+|+|||..+.
T Consensus       154 ~~~~~~~g~~~~gk~~~~~  172 (362)
T d1svma_         154 KRYWLFKGPIDSGKTTLAA  172 (362)
T ss_dssp             CCEEEEECSTTSSHHHHHH
T ss_pred             cCeEEEECCCCCCHHHHHH
Confidence            4679999999999997753

>d1ye8a1 c.37.1.11 (A:1-178) Hypothetical kinase-like protein Aq_1292 {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: RecA protein-like (ATPase-domain)
domain: Hypothetical kinase-like protein Aq 1292
species: Aquifex aeolicus [TaxId: 63363]

Probab=87.22  E-value=0.16  Score=36.66  Aligned_cols=24  Identities=29%  Similarity=0.537  Sum_probs=17.3

Q ss_pred             cEEEEcCCCChhhHHHHHHHHHhhh
Q 017573           35 DVIQQAQSGTGKTATFCSGILQQLD   59 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~~~~~~~~~   59 (369)
                      .+++.||+|+|||.. +..++..+.
T Consensus         2 ki~I~G~~G~GKSTL-l~~i~~~l~   25 (178)
T d1ye8a1           2 KIIITGEPGVGKTTL-VKKIVERLG   25 (178)
T ss_dssp             EEEEECCTTSSHHHH-HHHHHHHHG
T ss_pred             EEEEECCCCcHHHHH-HHHHHhcCC
Confidence            378999999999975 344554443

>d1xp8a1 c.37.1.11 (A:15-282) RecA protein, ATPase-domain {Deinococcus radiodurans [TaxId: 1299]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Deinococcus radiodurans [TaxId: 1299]

Probab=87.00  E-value=0.34  Score=37.68  Aligned_cols=43  Identities=14%  Similarity=0.002  Sum_probs=30.2

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEcCCHHHHHH
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTRELAQQ   79 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~P~~~l~~q   79 (369)
                      +-+.+.+|.|+|||..++..+.+....+.   +++|+-.-.++..+
T Consensus        58 ~itei~G~~~sGKT~l~l~~~~~aqk~g~---~v~yiDtE~~~~~~  100 (268)
T d1xp8a1          58 RITEIYGPESGGKTTLALAIVAQAQKAGG---TCAFIDAEHALDPV  100 (268)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHHHHTTC---CEEEEESSCCCCHH
T ss_pred             eEEEEecCCccchHHHHHHHHHHHHhCCC---EEEEEECCccCCHH
Confidence            45799999999999888776666554432   78887655444443

>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=86.94  E-value=1  Score=33.82  Aligned_cols=104  Identities=12%  Similarity=0.115  Sum_probs=64.2

Q ss_pred             CCCeEEEeCCHhhHHHHHHHHhhC----CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecC------CcCCCCCCCC
Q 017573          235 ITQSVIFVNTRRKVDWLTDKMRSR----DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDL------LARGIDVQQV  304 (369)
Q Consensus       235 ~~k~lv~~~~~~~~~~~~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~------~~~G~d~~~~  304 (369)
                      ..+++|++++++.+..+++.+.+.    +..+..+.|+.+..+....++   . ..+|+|+|+.      -...+++..+
T Consensus        85 ~~~~lil~PtreLa~Qi~~~~~~l~~~~~i~~~~~~g~~~~~~~~~~l~---~-~~~Ilv~TPgrl~~~~~~~~~~~~~l  160 (222)
T d2j0sa1          85 ETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLD---Y-GQHVVAGTPGRVFDMIRRRSLRTRAI  160 (222)
T ss_dssp             SCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECTTSCHHHHHHHHH---H-CCSEEEECHHHHHHHHHTTSSCCTTC
T ss_pred             CceeEEecchHHHHHHHHHHHHHHhCccceeEEEEeecccchhhHHHhc---c-CCeEEeCCCCcHHhcccccccccccc
Confidence            347899999999999888777543    557888888877666554443   2 3579999962      2455777889


Q ss_pred             cEEEEecCCCC-ccchhhhhcccccCCCceeEEEEeccc
Q 017573          305 SLVINYDLPTQ-PENYLHRIGRSGRFGRKGVAINFVTRD  342 (369)
Q Consensus       305 ~~vi~~~~~~~-~~~~~Q~~GR~~R~~~~~~~~~~~~~~  342 (369)
                      +++|+-+...- ...|...+.+..+.-....-.++++..
T Consensus       161 ~~lVlDEaD~ll~~~f~~~i~~I~~~l~~~~Q~ilfSAT  199 (222)
T d2j0sa1         161 KMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISAT  199 (222)
T ss_dssp             CEEEEETHHHHTSTTTHHHHHHHHTTSCTTCEEEEEESC
T ss_pred             eeeeecchhHhhhcCcHHHHHHHHHhCCCCCEEEEEEEe
Confidence            99886543210 112333344444432333444555544

>d1r7ra3 c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

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: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=86.83  E-value=0.19  Score=39.20  Aligned_cols=18  Identities=28%  Similarity=0.272  Sum_probs=15.9

Q ss_pred             CCcEEEEcCCCChhhHHH
Q 017573           33 GLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~   50 (369)
                      .+.+++.||+|+|||..+
T Consensus        41 ~~giLL~Gp~GtGKT~l~   58 (265)
T d1r7ra3          41 SKGVLFYGPPGCGKTLLA   58 (265)
T ss_dssp             CCEEEEBCCTTSSHHHHH
T ss_pred             CCeEEEECCCCCcchhHH
Confidence            478999999999999765

>d1qvra2 c.37.1.20 (A:149-535) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=86.37  E-value=2.3  Score=34.79  Aligned_cols=114  Identities=15%  Similarity=0.112  Sum_probs=56.5

Q ss_pred             CCcEEEEcCCCChhhHHHHHHHHHhhhccC-----CCccEEEEcCCHHHH------HHHHHHHHHhcccc---CcEEEEE
Q 017573           33 GLDVIQQAQSGTGKTATFCSGILQQLDYGL-----VQCQALVLAPTRELA------QQIEKVMRALGDYL---GVKVHAC   98 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~~~~~~~~~~~~~-----~~~~~liv~P~~~l~------~q~~~~~~~~~~~~---~~~v~~~   98 (369)
                      ..|.++.||+|.|||.++-..+ .++..+.     .+.+++-+-+ ..|.      .+|.+.+.......   .-++..+
T Consensus        43 k~n~llvG~~GvGKtaiv~~la-~~i~~~~vp~~l~~~~i~~ld~-~~l~ag~~~~g~~e~r~~~i~~~~~~~~~~~ilf  120 (387)
T d1qvra2          43 KNNPVLIGEPGVGKTAIVEGLA-QRIVKGDVPEGLKGKRIVSLQM-GSLLAGAKYRGEFEERLKAVIQEVVQSQGEVILF  120 (387)
T ss_dssp             CCCCEEEECTTSCHHHHHHHHH-HHHHHTCSCTTSTTCEEEEECC------------CHHHHHHHHHHHHHTTCSSEEEE
T ss_pred             CCCCeEECCCCCCHHHHHHHHH-HHHHhCCCCHHHcCceEEEeeH-hhhhcccCcchhHHHHHHHHHHHhccCCCceEEE
Confidence            3679999999999997754333 3333332     1223444444 3433      24555554432111   1122111


Q ss_pred             E---------CCcc-h----HHHHHHHc-cCCc-EEEeccHHHHHHHHcCCCCCCCccEEEEechhH
Q 017573           99 V---------GGTS-V----REDQRILQ-AGVH-VVVGTPGRVFDMLRRQSLRPDYIKMFVLDEADE  149 (369)
Q Consensus        99 ~---------~~~~-~----~~~~~~~~-~~~~-iiv~t~~~l~~~~~~~~~~~~~~~~viiDE~H~  149 (369)
                      .         |+.. .    ...+..+. +... |.-||++.+.. +........+|..|-++|-+.
T Consensus       121 ide~h~l~~~g~~~g~~d~a~~Lkp~L~rg~~~~I~~tT~~ey~~-~e~d~al~rrF~~v~v~ep~~  186 (387)
T d1qvra2         121 IDELHTVVGAGKAEGAVDAGNMLKPALARGELRLIGATTLDEYRE-IEKDPALERRFQPVYVDEPTV  186 (387)
T ss_dssp             ECCC-------------------HHHHHTTCCCEEEEECHHHHHH-HTTCTTTCSCCCCEEECCCCH
T ss_pred             eccHHHHhcCCCCCCcccHHHHHHHHHhCCCcceeeecCHHHHHH-hcccHHHHHhcccccCCCCcH
Confidence            1         1110 0    11112222 3344 44667787855 566666677899999999985

>d1rz3a_ c.37.1.6 (A:) Hypothetical protein rbstp0775 {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: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein rbstp0775
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=86.02  E-value=0.2  Score=36.73  Aligned_cols=14  Identities=29%  Similarity=0.131  Sum_probs=12.3

Q ss_pred             EEEcCCCChhhHHH
Q 017573           37 IQQAQSGTGKTATF   50 (369)
Q Consensus        37 li~~~tG~GKT~~~   50 (369)
                      -|.||+|||||+.+
T Consensus        26 gI~G~~GSGKSTla   39 (198)
T d1rz3a_          26 GIDGLSRSGKTTLA   39 (198)
T ss_dssp             EEEECTTSSHHHHH
T ss_pred             EEECCCCCCHHHHH
Confidence            48999999999765

>d1knxa2 c.91.1.2 (A:133-309) HPr kinase HprK C-terminal domain {Mycoplasma pneumoniae [TaxId: 2104]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Mycoplasma pneumoniae [TaxId: 2104]

Probab=85.63  E-value=0.2  Score=36.15  Aligned_cols=21  Identities=29%  Similarity=0.438  Sum_probs=18.0

Q ss_pred             cCCcEEEEcCCCChhhHHHHH
Q 017573           32 KGLDVIQQAQSGTGKTATFCS   52 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~~   52 (369)
                      .++.+++.++.|+|||..++.
T Consensus        14 ~g~gvli~G~sG~GKS~lal~   34 (177)
T d1knxa2          14 FGVGVLLTGRSGIGKSECALD   34 (177)
T ss_dssp             TTEEEEEEESSSSSHHHHHHH
T ss_pred             CCEEEEEEcCCCCCHHHHHHH
Confidence            578899999999999977643

>d1nksa_ c.37.1.1 (A:) Adenylate kinase {Archaeon Sulfolobus acidocaldarius [TaxId: 2285]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Sulfolobus acidocaldarius [TaxId: 2285]

Probab=85.56  E-value=0.37  Score=34.97  Aligned_cols=23  Identities=26%  Similarity=0.401  Sum_probs=16.0

Q ss_pred             EEEEcCCCChhhHHHHHHHHHhhh
Q 017573           36 VIQQAQSGTGKTATFCSGILQQLD   59 (369)
Q Consensus        36 ~li~~~tG~GKT~~~~~~~~~~~~   59 (369)
                      +++.|++|+|||+.+- .+...+.
T Consensus         4 ivi~G~~GsGKTT~~~-~La~~L~   26 (194)
T d1nksa_           4 GIVTGIPGVGKSTVLA-KVKEILD   26 (194)
T ss_dssp             EEEEECTTSCHHHHHH-HHHHHHH
T ss_pred             EEEECCCCCCHHHHHH-HHHHHHH
Confidence            4679999999997753 3334443

>d1gkya_ c.37.1.1 (A:) Guanylate kinase {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: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=85.42  E-value=0.2  Score=36.65  Aligned_cols=17  Identities=29%  Similarity=0.507  Sum_probs=14.5

Q ss_pred             CcEEEEcCCCChhhHHH
Q 017573           34 LDVIQQAQSGTGKTATF   50 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~   50 (369)
                      +-+++.||+|+|||..+
T Consensus         2 rpIvl~GpsG~GK~tl~   18 (186)
T d1gkya_           2 RPIVISGPSGTGKSTLL   18 (186)
T ss_dssp             CCEEEECCTTSSHHHHH
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            45899999999999754

>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=85.38  E-value=0.83  Score=31.30  Aligned_cols=64  Identities=22%  Similarity=0.288  Sum_probs=47.0

Q ss_pred             cEEEEcCCHHHHHHHHHHHHHhccccCcEEEEEECCcchHHHHHHHccCCcEEEeccHHHHHHHHcCCCCCCCccEEE
Q 017573           66 QALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRPDYIKMFV  143 (369)
Q Consensus        66 ~~liv~P~~~l~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~t~~~l~~~~~~~~~~~~~~~~vi  143 (369)
                      ++||.|+++.-++++++.+++.    ++++..++++......   ..+..+++|+|     ..+.++ ++ ..++.||
T Consensus        37 k~IVFc~t~~~ae~la~~L~~~----G~~~~~~H~~~~~~~~---~~~~~~vlvaT-----d~~~~G-iD-~~v~~Vi  100 (138)
T d1jr6a_          37 RHLIFCHSKKKCDELAAKLVAL----GINAVAYYRGLDVSVI---PTNGDVVVVAT-----DALMTG-FT-GDFDSVI  100 (138)
T ss_dssp             CEEEECSCHHHHHHHHHHHHHH----TCEEEEECTTCCSCCC---TTSSCEEEEES-----SSSCSS-SC-CCBSEEE
T ss_pred             CEEEEeCcHHHHHHHHHHHhcc----ccchhhhhccchhhhh---hhhhcceeehh-----HHHHhc-cc-cccceEE
Confidence            8999999999999999888775    7888888988764443   24567899999     333333 44 3466654

>d1xpua3 c.37.1.11 (A:129-417) Transcription termination factor Rho, ATPase 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: RecA protein-like (ATPase-domain)
domain: Transcription termination factor Rho, ATPase domain
species: Escherichia coli [TaxId: 562]

Probab=85.00  E-value=0.41  Score=37.54  Aligned_cols=28  Identities=18%  Similarity=0.083  Sum_probs=21.7

Q ss_pred             cccCCcEEEEcCCCChhhHHHHHHHHHh
Q 017573           30 FCKGLDVIQQAQSGTGKTATFCSGILQQ   57 (369)
Q Consensus        30 ~~~~~~~li~~~tG~GKT~~~~~~~~~~   57 (369)
                      +-+|+...|.++.|+|||..+...+.+.
T Consensus        40 igrGQr~~I~g~~g~GKT~l~~~i~~~~   67 (289)
T d1xpua3          40 IGRGQRGLIVAPPKAGKTMLLQNIAQSI   67 (289)
T ss_dssp             CBTTCEEEEEECSSSSHHHHHHHHHHHH
T ss_pred             ccCCCeeeEeCCCCCCHHHHHHHHHHHH
Confidence            4479999999999999997765444433

>d1znwa1 c.37.1.1 (A:20-201) Guanylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=84.90  E-value=0.28  Score=35.60  Aligned_cols=18  Identities=28%  Similarity=0.401  Sum_probs=15.3

Q ss_pred             CCcEEEEcCCCChhhHHH
Q 017573           33 GLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        33 ~~~~li~~~tG~GKT~~~   50 (369)
                      |+-+++.||.|+|||..+
T Consensus         2 G~iivl~GpsG~GK~tl~   19 (182)
T d1znwa1           2 GRVVVLSGPSAVGKSTVV   19 (182)
T ss_dssp             CCEEEEECSTTSSHHHHH
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            566899999999999764

>d1kkma_ c.91.1.2 (A:) HPr kinase HprK C-terminal domain {Lactobacillus casei [TaxId: 1582]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Lactobacillus casei [TaxId: 1582]

Probab=84.85  E-value=0.25  Score=35.66  Aligned_cols=21  Identities=38%  Similarity=0.509  Sum_probs=17.8

Q ss_pred             ccCCcEEEEcCCCChhhHHHH
Q 017573           31 CKGLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        31 ~~~~~~li~~~tG~GKT~~~~   51 (369)
                      ..++.+++.++.|+|||..++
T Consensus        12 ~~g~gvl~~G~sG~GKStlal   32 (176)
T d1kkma_          12 IYGLGVLITGDSGVGKSETAL   32 (176)
T ss_dssp             ETTEEEEEECCTTSCHHHHHH
T ss_pred             ECCEEEEEEeCCCCCHHHHHH
Confidence            357889999999999998764

>d1s96a_ c.37.1.1 (A:) Guanylate kinase {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: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Escherichia coli [TaxId: 562]

Probab=84.59  E-value=0.23  Score=37.02  Aligned_cols=19  Identities=37%  Similarity=0.494  Sum_probs=16.0

Q ss_pred             cCCcEEEEcCCCChhhHHH
Q 017573           32 KGLDVIQQAQSGTGKTATF   50 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~   50 (369)
                      +|+-+++.||.|+|||...
T Consensus         1 ~G~livi~GPSG~GK~tl~   19 (205)
T d1s96a_           1 QGTLYIVSAPSGAGKSSLI   19 (205)
T ss_dssp             CCCEEEEECCTTSCHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHH
Confidence            4667899999999999764

>d1yrba1 c.37.1.10 (A:1-244) ATP(GTP)-binding protein PAB0955 {Pyrococcus abyssi [TaxId: 29292]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: ATP(GTP)-binding protein PAB0955
species: Pyrococcus abyssi [TaxId: 29292]

Probab=84.38  E-value=0.5  Score=35.87  Aligned_cols=31  Identities=19%  Similarity=0.266  Sum_probs=19.6

Q ss_pred             EEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEE
Q 017573           36 VIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVL   70 (369)
Q Consensus        36 ~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv   70 (369)
                      ++|.|+.|+|||.. +-.+++....++   ++.+|
T Consensus         3 i~v~G~~GsGKTTL-l~~ll~~~~~~~---~~~iv   33 (244)
T d1yrba1           3 VVFVGTAGSGKTTL-TGEFGRYLEDNY---KVAYV   33 (244)
T ss_dssp             EEEECSTTSSHHHH-HHHHHHHHTTTS---CEEEE
T ss_pred             EEEEcCCCCcHHHH-HHHHHHHHhhCC---eEEEE
Confidence            57899999999964 444454443322   45555

>d1ko7a2 c.91.1.2 (A:130-298) HPr kinase HprK C-terminal domain {Staphylococcus xylosus [TaxId: 1288]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Staphylococcus xylosus [TaxId: 1288]

Probab=83.83  E-value=0.29  Score=35.05  Aligned_cols=21  Identities=33%  Similarity=0.482  Sum_probs=17.8

Q ss_pred             ccCCcEEEEcCCCChhhHHHH
Q 017573           31 CKGLDVIQQAQSGTGKTATFC   51 (369)
Q Consensus        31 ~~~~~~li~~~tG~GKT~~~~   51 (369)
                      ..++.+++.++.|+|||..++
T Consensus        13 ~~g~gvli~G~sg~GKS~la~   33 (169)
T d1ko7a2          13 VYGVGVLITGDSGIGKSETAL   33 (169)
T ss_dssp             ETTEEEEEEESTTSSHHHHHH
T ss_pred             ECCEEEEEEeCCCCCHHHHHH
Confidence            357889999999999997654

>d1ckea_ c.37.1.1 (A:) CMP kinase {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: Nucleotide and nucleoside kinases
domain: CMP kinase
species: Escherichia coli [TaxId: 562]

Probab=83.10  E-value=0.38  Score=36.00  Aligned_cols=17  Identities=24%  Similarity=0.329  Sum_probs=13.6

Q ss_pred             EEEEcCCCChhhHHHHH
Q 017573           36 VIQQAQSGTGKTATFCS   52 (369)
Q Consensus        36 ~li~~~tG~GKT~~~~~   52 (369)
                      +.|.||+||||++.+-.
T Consensus         6 I~I~GppGSGKgT~ak~   22 (225)
T d1ckea_           6 ITIDGPSGAGKGTLCKA   22 (225)
T ss_dssp             EEEECCTTSSHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            46679999999988643

>d1xjca_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {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: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=82.43  E-value=0.79  Score=32.40  Aligned_cols=23  Identities=13%  Similarity=-0.007  Sum_probs=15.9

Q ss_pred             EEEEcCCCChhhHHHHHHHHHhhh
Q 017573           36 VIQQAQSGTGKTATFCSGILQQLD   59 (369)
Q Consensus        36 ~li~~~tG~GKT~~~~~~~~~~~~   59 (369)
                      +-|.|+.|||||+.. ..++..+.
T Consensus         4 i~I~G~~gSGKTTli-~~l~~~L~   26 (165)
T d1xjca_           4 WQVVGYKHSGKTTLM-EKWVAAAV   26 (165)
T ss_dssp             EEEECCTTSSHHHHH-HHHHHHHH
T ss_pred             EEEEeCCCCCHHHHH-HHHHHHHH
Confidence            358999999999764 34444444

>d1lvga_ c.37.1.1 (A:) Guanylate kinase {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=82.22  E-value=0.43  Score=34.90  Aligned_cols=16  Identities=31%  Similarity=0.557  Sum_probs=13.9

Q ss_pred             cEEEEcCCCChhhHHH
Q 017573           35 DVIQQAQSGTGKTATF   50 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~   50 (369)
                      -+++.||+|+|||..+
T Consensus         2 pIvl~GPsGsGK~tl~   17 (190)
T d1lvga_           2 PVVLSGPSGAGKSTLL   17 (190)
T ss_dssp             CEEEECCTTSSHHHHH
T ss_pred             eEEEECCCCCCHHHHH
Confidence            4789999999999764

>d1r6bx3 c.37.1.20 (X:437-751) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=82.20  E-value=0.35  Score=38.75  Aligned_cols=17  Identities=24%  Similarity=0.376  Sum_probs=14.7

Q ss_pred             cEEEEcCCCChhhHHHH
Q 017573           35 DVIQQAQSGTGKTATFC   51 (369)
Q Consensus        35 ~~li~~~tG~GKT~~~~   51 (369)
                      .+++.||||+|||..+-
T Consensus        54 ~~lf~Gp~GvGKT~lak   70 (315)
T d1r6bx3          54 SFLFAGPTGVGKTEVTV   70 (315)
T ss_dssp             EEEEECSTTSSHHHHHH
T ss_pred             EEEEECCCcchhHHHHH
Confidence            58999999999997763

>d1q3ta_ c.37.1.1 (A:) CMP kinase {Streptococcus pneumoniae [TaxId: 1313]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: CMP kinase
species: Streptococcus pneumoniae [TaxId: 1313]

Probab=82.10  E-value=0.45  Score=35.67  Aligned_cols=18  Identities=11%  Similarity=0.097  Sum_probs=13.9

Q ss_pred             EEEEcCCCChhhHHHHHH
Q 017573           36 VIQQAQSGTGKTATFCSG   53 (369)
Q Consensus        36 ~li~~~tG~GKT~~~~~~   53 (369)
                      +.|-||+|||||+++-..
T Consensus         6 IaIdGp~GsGKgT~ak~L   23 (223)
T d1q3ta_           6 IAIDGPASSGKSTVAKII   23 (223)
T ss_dssp             EEEECSSCSSHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHH
Confidence            456799999999887433

>d1odfa_ c.37.1.6 (A:) Hypothetical protein Ygr205W {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: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein Ygr205W
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=81.83  E-value=0.58  Score=36.65  Aligned_cols=14  Identities=29%  Similarity=0.380  Sum_probs=11.6

Q ss_pred             EEEcCCCChhhHHH
Q 017573           37 IQQAQSGTGKTATF   50 (369)
Q Consensus        37 li~~~tG~GKT~~~   50 (369)
                      -|.|++|||||+.+
T Consensus        31 Gi~G~qGSGKSTl~   44 (286)
T d1odfa_          31 FFSGPQGSGKSFTS   44 (286)
T ss_dssp             EEECCTTSSHHHHH
T ss_pred             EeECCCCCCHHHHH
Confidence            46899999999654

>d1ihua1 c.37.1.10 (A:1-296) Arsenite-translocating ATPase ArsA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Arsenite-translocating ATPase ArsA
species: Escherichia coli [TaxId: 562]

Probab=81.43  E-value=0.77  Score=36.04  Aligned_cols=35  Identities=20%  Similarity=0.402  Sum_probs=26.8

Q ss_pred             CcEEEEcCCCChhhHHHHHHHHHhhhccCCCccEEEEc
Q 017573           34 LDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLA   71 (369)
Q Consensus        34 ~~~li~~~tG~GKT~~~~~~~~~~~~~~~~~~~~liv~   71 (369)
                      +-+++.+-=|.|||+++...+......+.   ++++|-
T Consensus         9 ~~i~~sGKGGVGKTTvaa~lA~~lA~~G~---rVLlvD   43 (296)
T d1ihua1           9 PYLFFTGKGGVGKTSISCATAIRLAEQGK---RVLLVS   43 (296)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHHHHTTC---CEEEEE
T ss_pred             eEEEEECCCcChHHHHHHHHHHHHHHCCC---CEEEEe
Confidence            55788899999999998777666655544   788776

>d1bg2a_ c.37.1.9 (A:) Kinesin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.98  E-value=0.39  Score=38.65  Aligned_cols=23  Identities=26%  Similarity=0.445  Sum_probs=17.7

Q ss_pred             hccccCCc--EEEEcCCCChhhHHH
Q 017573           28 VPFCKGLD--VIQQAQSGTGKTATF   50 (369)
Q Consensus        28 ~~~~~~~~--~li~~~tG~GKT~~~   50 (369)
                      +.+.+|.+  ++..|+||||||.+.
T Consensus        69 ~~~l~G~n~~i~aYGqtgSGKTyT~   93 (323)
T d1bg2a_          69 KDVLEGYNGTIFAYGQTSSGKTHTM   93 (323)
T ss_dssp             HHHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHHcCCCcceeeecccCCCCceec
Confidence            34456655  689999999999875

>d1uj2a_ c.37.1.6 (A:) Uridine-cytidine kinase 2 {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: Phosphoribulokinase/pantothenate kinase
domain: Uridine-cytidine kinase 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.78  E-value=0.35  Score=36.06  Aligned_cols=15  Identities=13%  Similarity=0.266  Sum_probs=12.6

Q ss_pred             EEEEcCCCChhhHHH
Q 017573           36 VIQQAQSGTGKTATF   50 (369)
Q Consensus        36 ~li~~~tG~GKT~~~   50 (369)
                      +-|.|++|||||+.+
T Consensus         5 IgI~G~~gSGKSTla   19 (213)
T d1uj2a_           5 IGVSGGTASGKSSVC   19 (213)
T ss_dssp             EEEECSTTSSHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            357899999999775

>d1bifa1 c.37.1.7 (A:37-249) 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
domain: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=80.64  E-value=0.91  Score=33.40  Aligned_cols=16  Identities=19%  Similarity=0.152  Sum_probs=13.8

Q ss_pred             EEEEcCCCChhhHHHH
Q 017573           36 VIQQAQSGTGKTATFC   51 (369)
Q Consensus        36 ~li~~~tG~GKT~~~~   51 (369)
                      ++++|.+|+|||+.+-
T Consensus         5 i~l~GlpgsGKSTla~   20 (213)
T d1bifa1           5 IVMVGLPARGKTYISK   20 (213)
T ss_dssp             EEEECCTTSSHHHHHH
T ss_pred             EEEECCCCCCHHHHHH
Confidence            6889999999998763

>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=80.60  E-value=2.1  Score=31.45  Aligned_cols=104  Identities=7%  Similarity=0.124  Sum_probs=62.2

Q ss_pred             CCeEEEeCCHhhHHHHHHHHhhCC-----CeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEecC-----C-cCCCCCCCC
Q 017573          236 TQSVIFVNTRRKVDWLTDKMRSRD-----HTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDL-----L-ARGIDVQQV  304 (369)
Q Consensus       236 ~k~lv~~~~~~~~~~~~~~l~~~~-----~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~-----~-~~G~d~~~~  304 (369)
                      .++++.+++++.+..+.+.++...     .......|+.+.......   ......+++|+|+.     + ...+++.++
T Consensus        70 ~~~lil~PtreL~~qi~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~---l~~~~~~ilI~TP~rl~~~~~~~~~~l~~l  146 (207)
T d1t6na_          70 VSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEV---LKKNCPHIVVGTPGRILALARNKSLNLKHI  146 (207)
T ss_dssp             CCEEEECSCHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHH---HHHSCCSEEEECHHHHHHHHHTTSSCCTTC
T ss_pred             ceEEEEeccchhhHHHHHHHHHHHhhCCCceeEEEeccccHHHHHHH---HHhcCCCEEEeCcchhhhhccCCceecccc
Confidence            478999999999988887776442     346677777766554333   23456789999962     2 234678889


Q ss_pred             cEEEEecCCCCc--cchhhhhcccccCCCceeEEEEeccc
Q 017573          305 SLVINYDLPTQP--ENYLHRIGRSGRFGRKGVAINFVTRD  342 (369)
Q Consensus       305 ~~vi~~~~~~~~--~~~~Q~~GR~~R~~~~~~~~~~~~~~  342 (369)
                      ..+++-+...-.  ..+.+.+-+..+.-....-+++++..
T Consensus       147 ~~lVlDEaD~ll~~~~~~~~i~~I~~~~~~~~Q~il~SAT  186 (207)
T d1t6na_         147 KHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSAT  186 (207)
T ss_dssp             CEEEEESHHHHHSSHHHHHHHHHHHHTSCSSSEEEEEESC
T ss_pred             ceeehhhhhhhhhcCCcHHHHHHHHHhCCCCCEEEEEeee
Confidence            988876542111  12333344444432233344555543

>d2pmka1 c.37.1.12 (A:467-707) Haemolysin B ATP-binding protein {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: ABC transporter ATPase domain-like
domain: Haemolysin B ATP-binding protein
species: Escherichia coli [TaxId: 562]

Probab=80.54  E-value=0.43  Score=36.43  Aligned_cols=20  Identities=25%  Similarity=0.313  Sum_probs=17.2

Q ss_pred             cccCCcEEEEcCCCChhhHH
Q 017573           30 FCKGLDVIQQAQSGTGKTAT   49 (369)
Q Consensus        30 ~~~~~~~li~~~tG~GKT~~   49 (369)
                      +..|+.+.|.+|+|||||+.
T Consensus        26 i~~Ge~vaIvG~sGsGKSTL   45 (241)
T d2pmka1          26 IKQGEVIGIVGRSGSGKSTL   45 (241)
T ss_dssp             EETTCEEEEECSTTSSHHHH
T ss_pred             EcCCCEEEEECCCCCCHHHH
Confidence            44688999999999999964

>d1w44a_ c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}

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: NTPase P4
species: Bacteriophage phi-12 [TaxId: 161736]

Probab=80.45  E-value=0.44  Score=38.04  Aligned_cols=18  Identities=28%  Similarity=0.340  Sum_probs=13.9

Q ss_pred             Cc-EEEEcCCCChhhHHHH
Q 017573           34 LD-VIQQAQSGTGKTATFC   51 (369)
Q Consensus        34 ~~-~li~~~tG~GKT~~~~   51 (369)
                      ++ +++.+|+|+|||+.+-
T Consensus       123 ~g~~l~~G~pG~GKT~la~  141 (321)
T d1w44a_         123 SGMVIVTGKGNSGKTPLVH  141 (321)
T ss_dssp             SEEEEEECSSSSCHHHHHH
T ss_pred             CceEEEECCCCccHHHHHH
Confidence            44 4558999999998763

>d2jdid3 c.37.1.11 (D:82-357) Central domain of beta subunit of F1 ATP synthase {Rat (Rattus norvegicus) [TaxId: 10116]}

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: Central domain of beta subunit of F1 ATP synthase
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=80.19  E-value=2.8  Score=32.37  Aligned_cols=25  Identities=28%  Similarity=0.218  Sum_probs=20.0

Q ss_pred             cCCcEEEEcCCCChhhHHHHHHHHH
Q 017573           32 KGLDVIQQAQSGTGKTATFCSGILQ   56 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~~~~~~   56 (369)
                      +|+...+.++.|+|||..+...+.+
T Consensus        67 kGQr~~If~~~g~GKt~l~~~i~~~   91 (276)
T d2jdid3          67 KGGKIGLFGGAGVGKTVLIMELINN   91 (276)
T ss_dssp             TTCEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CCCEEEeeCCCCCCHHHHHHHHHHH
Confidence            4799999999999999776554443

>d1fx0a3 c.37.1.11 (A:97-372) Central domain of alpha subunit of F1 ATP synthase {Spinach (Spinacia oleracea), chloroplast [TaxId: 3562]}

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: Central domain of alpha subunit of F1 ATP synthase
species: Spinach (Spinacia oleracea), chloroplast [TaxId: 3562]

Probab=80.16  E-value=2.4  Score=32.84  Aligned_cols=26  Identities=35%  Similarity=0.385  Sum_probs=20.6

Q ss_pred             cCCcEEEEcCCCChhhHHHHHHHHHh
Q 017573           32 KGLDVIQQAQSGTGKTATFCSGILQQ   57 (369)
Q Consensus        32 ~~~~~li~~~tG~GKT~~~~~~~~~~   57 (369)
                      +|+...+.++.|+|||..+...+...
T Consensus        66 ~GQr~~Ifg~~g~GKt~l~~~~~~~~   91 (276)
T d1fx0a3          66 RGQRELIIGDRQTGKTAVATDTILNQ   91 (276)
T ss_dssp             TTCBCBEEESSSSSHHHHHHHHHHTC
T ss_pred             CCceEeeccCCCCChHHHHHHHHhhh
Confidence            68999999999999997765544443