Citrus Sinensis ID: 015158

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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-------370-------380-------390-------400-------410--
Protein Sequence
MAGLAEGSQFDARQFDARMNDLLGSDGQDFFTSYDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVADLL
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHcccccccHHHHHHHHHHHccccEEEEcccccHHHHHHHHHHHHccccccccEEEEEEcccHHHHHHHHHHHHHHHcccccEEEEEEccccHHHHHHHHcccccEEEcccHHHHHHHcccccccccccEEEEEccccccccccHHHHHHHHHHcccccEEEEEEccccHHHHHHHHHHccccEEEEEEccccccccEEEEEEEEcccccHHHHHHHHHHHcccccEEEEEcccccHHHHHHHHHHcccEEEEEccccccHHHHHHHHHHHcccccEEEEccccccccccccccEEEEccccccccccEEccccccccccccEEEEcccHHHHHHHHHHHHHHccccccccccHHccc
Secondary Structure Prediction (SSPRO)
ccccccccccccHHcccccHHccccccccccEccccccccHHHccccHHHHHHHHHcccccccccHHHHHHHHHccccEEEEccccHHHHHHHHHHHHHHcccccccccEEEEcccHHHHHHHHHHHHHHcccccccEEEEcccccHHHHHHHHHHccEEEEEcHHHHHHHHcccccccccccEEEEccHHHHHccccHHHHHHHHHccccccEEEEEEccccHHHHHHHHHHccccEEEEcEcccccccccEEEEEEEccHHHHHHHHHHHHHcccccEEEEEEccHHHHHHHHHHHHHccccEEEEcccccHHHHHHHHHHHHccccEEEEEEHHHHccccccccEEEEEEcccccHHHHEEEEccccccccccEEEEEEcHHHHHHHHHHHHHHHHHHHHccccHHHHc
Coil and Loop (DISEMBL)
maglaegsqfdaRQFDARMNdllgsdgqdfftsyDEVYDTFDAMGLQENLLRGIYAygfekpsaiqqrgivpfckgLDVIQQaqsgtgktatfCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHAcvggtsvredqrilssgvhvvvgtpgrvFDMLRrqslrpdniriFVLDEADEMLSRGFKDQIYDIFqllppkiqvgvfsatmppEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDwltdkmrsrdhtvsathgdmdqntRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVInydlptqpenylhrigrsgrfgrkgvainfvtrdderMLFDIQKFYNVVIEELPANVADLL
Flexible Loop (DISEMBL)
maglaegsqfdaRQFDARMNDLLGSDGQDFFTSYDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTsvredqrilssgvhvvvgtpgrvfdmlrrqslrpdnirIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEitrkfmnkpVRILVKRDELTLEGIKQFhvnvekeeWKLETLCDLYETLaitqsvifvntrrkvdwltdkmrsrdhtvsathgdmdqntrDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYlhrigrsgrfgrkGVAINfvtrddermLFDIQKFYNVVIEELPANVADLL
Low Complexity Region (SEG)
MAGLAEGSQFDARQFDARMNDLLGSDGQDFFTSYDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVADLL
Disordered region (IsUnstruct)
*********************LLGSDGQDFFTSYDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDK********************DIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPA******
Disordered Region (DISOPRED)
*********************************YDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANV**LL
Disordered Region (DISEMBL)
********QFDARQFDARMNDLLGSDGQDFFTSYDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVADLL
Disordered Region (DISPRO)
*****************RMNDLLGSDGQDFFTSYDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANV****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAGLAEGSQFDARQFDARMNDLLGSDGQDFFTSYDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVADLL
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	412	2.2.26 [Sep-21-2011]
Q40465	413	Eukaryotic initiation fac	N/A	no	1.0	0.997	0.949	0.0
P41379	413	Eukaryotic initiation fac	N/A	no	1.0	0.997	0.949	0.0
Q40467	413	Eukaryotic initiation fac	N/A	no	1.0	0.997	0.944	0.0
P41382	413	Eukaryotic initiation fac	N/A	no	1.0	0.997	0.944	0.0
Q40468	413	Eukaryotic initiation fac	N/A	no	1.0	0.997	0.949	0.0
Q40470	413	Eukaryotic initiation fac	N/A	no	1.0	0.997	0.937	0.0
Q40471	413	Eukaryotic initiation fac	N/A	no	1.0	0.997	0.939	0.0
P41381	413	Eukaryotic initiation fac	N/A	no	1.0	0.997	0.932	0.0
Q6Z2Z4	414	Eukaryotic initiation fac	yes	no	1.0	0.995	0.929	0.0
P35683	414	Eukaryotic initiation fac	yes	no	1.0	0.995	0.925	0.0

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

 Score =  810 bits (2093), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 392/413 (94%), Positives = 406/413 (98%), Gaps = 1/413 (0%)

Query: 1   MAGLA-EGSQFDARQFDARMNDLLGSDGQDFFTSYDEVYDTFDAMGLQENLLRGIYAYGF 59
           MAGLA EGSQFDARQ+DA+M +LLG++ Q+FFTSYDEVY++FDAMGLQENLLRGIYAYGF
Sbjct: 1   MAGLAPEGSQFDARQYDAKMTELLGTEQQEFFTSYDEVYESFDAMGLQENLLRGIYAYGF 60

Query: 60  EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTREL 119
           EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY LVECQALVLAPTREL
Sbjct: 61  EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYSLVECQALVLAPTREL 120

Query: 120 AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRP 179
           AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL SGVHVVVGTPGRVFDMLRRQSLRP
Sbjct: 121 AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQSGVHVVVGTPGRVFDMLRRQSLRP 180

Query: 180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVR 239
           DNI++FVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVR
Sbjct: 181 DNIKMFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVR 240

Query: 240 ILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMR 299
           ILVKRDELTLEGIKQF+VNV+KEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMR
Sbjct: 241 ILVKRDELTLEGIKQFYVNVDKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMR 300

Query: 300 SRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP 359
            RDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP
Sbjct: 301 GRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP 360

Query: 360 ENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVADLL 412
           ENYLHRIG SGRFGRKGV+INFVT+DDERMLFDIQKFYNVVIEELPANVADLL
Sbjct: 361 ENYLHRIGHSGRFGRKGVSINFVTKDDERMLFDIQKFYNVVIEELPANVADLL 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|P41379|IF4A2_NICPL Eukaryotic initiation factor 4A-2 OS=Nicotiana plumbaginifolia PE=2 SV=1

 Score =  809 bits (2090), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 392/413 (94%), Positives = 406/413 (98%), Gaps = 1/413 (0%)

Query: 1   MAGLA-EGSQFDARQFDARMNDLLGSDGQDFFTSYDEVYDTFDAMGLQENLLRGIYAYGF 59
           MAG A EGSQFDARQFDA+M +LLG++ ++FFTSYDEVYD+FDAMGLQENLLRGIYAYGF
Sbjct: 1   MAGSAPEGSQFDARQFDAKMTELLGTEQEEFFTSYDEVYDSFDAMGLQENLLRGIYAYGF 60

Query: 60  EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTREL 119
           EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSG+LQQLDY LVECQALVLAPTREL
Sbjct: 61  EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGVLQQLDYSLVECQALVLAPTREL 120

Query: 120 AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRP 179
           AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL SGVHVVVGTPGRVFDMLRRQSLRP
Sbjct: 121 AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQSGVHVVVGTPGRVFDMLRRQSLRP 180

Query: 180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVR 239
           D+I++FVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVR
Sbjct: 181 DHIKMFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVR 240

Query: 240 ILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMR 299
           ILVKRDELTLEGIKQF+VNV+KEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMR
Sbjct: 241 ILVKRDELTLEGIKQFYVNVDKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMR 300

Query: 300 SRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP 359
           SRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP
Sbjct: 301 SRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP 360

Query: 360 ENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVADLL 412
           ENYLHRIGRSGRFGRKGVAIN VT+DDERMLFDIQKFYNVVIEELPANVADLL
Sbjct: 361 ENYLHRIGRSGRFGRKGVAINSVTKDDERMLFDIQKFYNVVIEELPANVADLL 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|Q40467|IF414_TOBAC Eukaryotic initiation factor 4A-14 OS=Nicotiana tabacum PE=2 SV=1

 Score =  809 bits (2090), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 390/413 (94%), Positives = 408/413 (98%), Gaps = 1/413 (0%)

Query: 1   MAGLA-EGSQFDARQFDARMNDLLGSDGQDFFTSYDEVYDTFDAMGLQENLLRGIYAYGF 59
           MAGLA EGSQFDARQ+DA+M +LLG++ ++FFTSYDEVYD+FDAMGLQENLLRGIYAYGF
Sbjct: 1   MAGLAPEGSQFDARQYDAKMTELLGTEQEEFFTSYDEVYDSFDAMGLQENLLRGIYAYGF 60

Query: 60  EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTREL 119
           EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSG+LQQLDY LVECQALVLAPTREL
Sbjct: 61  EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGVLQQLDYSLVECQALVLAPTREL 120

Query: 120 AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRP 179
           AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL SGVHVVVGTPGRVFDMLRRQSLRP
Sbjct: 121 AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQSGVHVVVGTPGRVFDMLRRQSLRP 180

Query: 180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVR 239
           D+I++FVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFM+KPVR
Sbjct: 181 DHIKMFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMSKPVR 240

Query: 240 ILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMR 299
           ILVKRD++TLEGIKQF+VNV+KEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMR
Sbjct: 241 ILVKRDDVTLEGIKQFYVNVDKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMR 300

Query: 300 SRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP 359
           SRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP
Sbjct: 301 SRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP 360

Query: 360 ENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVADLL 412
           ENYLHRIGRSGRFGRKGVAINFVT+DDERMLFDIQKFYNVVIEELPANVADLL
Sbjct: 361 ENYLHRIGRSGRFGRKGVAINFVTKDDERMLFDIQKFYNVVIEELPANVADLL 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|P41382|IF410_TOBAC Eukaryotic initiation factor 4A-10 OS=Nicotiana tabacum PE=2 SV=1

 Score =  808 bits (2087), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 390/413 (94%), Positives = 407/413 (98%), Gaps = 1/413 (0%)

Query: 1   MAGLA-EGSQFDARQFDARMNDLLGSDGQDFFTSYDEVYDTFDAMGLQENLLRGIYAYGF 59
           MAGLA EGSQFDARQ+DA+M +LLG++ ++FFTSYDEVYD+FDAMGLQENLLRGIYAYGF
Sbjct: 1   MAGLAPEGSQFDARQYDAKMTELLGTEQEEFFTSYDEVYDSFDAMGLQENLLRGIYAYGF 60

Query: 60  EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTREL 119
           EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSG+LQQLDY LVECQALVLAPTREL
Sbjct: 61  EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGVLQQLDYSLVECQALVLAPTREL 120

Query: 120 AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRP 179
           AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL SGVHVVVGTPGRVFDMLRRQSLRP
Sbjct: 121 AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQSGVHVVVGTPGRVFDMLRRQSLRP 180

Query: 180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVR 239
           D+I++FVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVR
Sbjct: 181 DHIKMFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVR 240

Query: 240 ILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMR 299
           ILVKRD++TLEGIKQF+VNV+KEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMR
Sbjct: 241 ILVKRDDVTLEGIKQFYVNVDKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMR 300

Query: 300 SRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP 359
           SRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP
Sbjct: 301 SRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP 360

Query: 360 ENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVADLL 412
           ENYLHRIGRSGRFGRKGVAINFVT+DDERML DIQKFYNVVIEELPANVADLL
Sbjct: 361 ENYLHRIGRSGRFGRKGVAINFVTKDDERMLSDIQKFYNVVIEELPANVADLL 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|Q40468|IF415_TOBAC Eukaryotic initiation factor 4A-15 OS=Nicotiana tabacum PE=2 SV=1

 Score =  806 bits (2082), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 392/413 (94%), Positives = 405/413 (98%), Gaps = 1/413 (0%)

Query: 1   MAGLA-EGSQFDARQFDARMNDLLGSDGQDFFTSYDEVYDTFDAMGLQENLLRGIYAYGF 59
           MAG A EGSQFDARQFD +MN+LL +DGQDFFTSYDEVYD+FDAMGLQENLLRGIYAYGF
Sbjct: 1   MAGAAPEGSQFDARQFDTKMNELLSADGQDFFTSYDEVYDSFDAMGLQENLLRGIYAYGF 60

Query: 60  EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTREL 119
           EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQL Y L+ECQALVLAPTREL
Sbjct: 61  EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLAYELLECQALVLAPTREL 120

Query: 120 AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRP 179
           AQQIEKVMRALGDYLGVKV ACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRP
Sbjct: 121 AQQIEKVMRALGDYLGVKVTACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRP 180

Query: 180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVR 239
           D+I++FVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVR
Sbjct: 181 DHIKMFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVR 240

Query: 240 ILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMR 299
           ILVKRDELTLEGIKQF+VNV+KEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMR
Sbjct: 241 ILVKRDELTLEGIKQFYVNVDKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMR 300

Query: 300 SRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP 359
           SRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVIN+DLPTQP
Sbjct: 301 SRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINFDLPTQP 360

Query: 360 ENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVADLL 412
           ENYLHRIGRSGRFGRKGVAINFVT+DDERML DIQ+FYNVVIEELPANVADLL
Sbjct: 361 ENYLHRIGRSGRFGRKGVAINFVTKDDERMLSDIQRFYNVVIEELPANVADLL 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|Q40470|IF4A7_TOBAC Eukaryotic initiation factor 4A-7 OS=Nicotiana tabacum PE=2 SV=1

 Score =  803 bits (2073), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 387/413 (93%), Positives = 406/413 (98%), Gaps = 1/413 (0%)

Query: 1   MAGLA-EGSQFDARQFDARMNDLLGSDGQDFFTSYDEVYDTFDAMGLQENLLRGIYAYGF 59
           MAGLA EGSQFDARQ+DA+M +LLG++ ++FFTSYDEVYD+FDAMGLQENLLRGIYAYGF
Sbjct: 1   MAGLAPEGSQFDARQYDAKMTELLGTEQEEFFTSYDEVYDSFDAMGLQENLLRGIYAYGF 60

Query: 60  EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTREL 119
           EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSG+LQQLDY LVECQALVLAPTREL
Sbjct: 61  EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGVLQQLDYSLVECQALVLAPTREL 120

Query: 120 AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRP 179
           AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL SGVHVVVGTPGRVFDMLRRQSLRP
Sbjct: 121 AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQSGVHVVVGTPGRVFDMLRRQSLRP 180

Query: 180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVR 239
           D+I++FVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVR
Sbjct: 181 DHIKMFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVR 240

Query: 240 ILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMR 299
           ILVKRD++TLEGIKQF+VNV+KEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMR
Sbjct: 241 ILVKRDDVTLEGIKQFYVNVDKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMR 300

Query: 300 SRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP 359
           +RDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP
Sbjct: 301 TRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP 360

Query: 360 ENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVADLL 412
           ENYLHRIGRSGRFGRKGVAINFV +DDERML DIQ+FYNVVIEELPANVADLL
Sbjct: 361 ENYLHRIGRSGRFGRKGVAINFVIKDDERMLSDIQRFYNVVIEELPANVADLL 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|Q40471|IF4A9_TOBAC Eukaryotic initiation factor 4A-9 OS=Nicotiana tabacum PE=2 SV=1

 Score =  802 bits (2072), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 388/413 (93%), Positives = 405/413 (98%), Gaps = 1/413 (0%)

Query: 1   MAGLA-EGSQFDARQFDARMNDLLGSDGQDFFTSYDEVYDTFDAMGLQENLLRGIYAYGF 59
           MAG A EGSQFDARQ+D++M +LL ++GQDFFTSYDEVY +FDAMGL+ENLLRGIYAYGF
Sbjct: 1   MAGAAPEGSQFDARQYDSKMTELLNAEGQDFFTSYDEVYHSFDAMGLKENLLRGIYAYGF 60

Query: 60  EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTREL 119
           EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY L++CQALVLAPTREL
Sbjct: 61  EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYELLDCQALVLAPTREL 120

Query: 120 AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRP 179
           AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRP
Sbjct: 121 AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRP 180

Query: 180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVR 239
           D+I++FVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVR
Sbjct: 181 DHIKMFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVR 240

Query: 240 ILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMR 299
           ILVKRDELTLEGIKQF+VNV+KEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMR
Sbjct: 241 ILVKRDELTLEGIKQFYVNVDKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMR 300

Query: 300 SRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP 359
           SRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP
Sbjct: 301 SRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP 360

Query: 360 ENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVADLL 412
           ENYLHRIGRSGRFGRKGV+INFVT DDERML DIQ+FYNVVIEELPANVADLL
Sbjct: 361 ENYLHRIGRSGRFGRKGVSINFVTSDDERMLSDIQRFYNVVIEELPANVADLL 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|P41381|IF4A8_TOBAC Eukaryotic initiation factor 4A-8 OS=Nicotiana tabacum PE=2 SV=1

 Score =  802 bits (2071), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 385/413 (93%), Positives = 407/413 (98%), Gaps = 1/413 (0%)

Query: 1   MAGLA-EGSQFDARQFDARMNDLLGSDGQDFFTSYDEVYDTFDAMGLQENLLRGIYAYGF 59
           MA LA +G+QFDARQ+D++MNDLL +DG+DFFTSYDEVYD+FDAMGLQENLLRGIYAYGF
Sbjct: 1   MARLAPDGAQFDARQYDSKMNDLLAADGKDFFTSYDEVYDSFDAMGLQENLLRGIYAYGF 60

Query: 60  EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTREL 119
           EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLV+CQALVLAPTREL
Sbjct: 61  EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTREL 120

Query: 120 AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRP 179
           AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL++GVHV+VGTPGRVFDMLRRQSLRP
Sbjct: 121 AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILAAGVHVIVGTPGRVFDMLRRQSLRP 180

Query: 180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVR 239
           D +R+FVLDEADEMLSRGFKDQIYDIFQ+LP K+QVGVFSATMPPEAL+ITRKFMNKPVR
Sbjct: 181 DYLRMFVLDEADEMLSRGFKDQIYDIFQMLPTKVQVGVFSATMPPEALDITRKFMNKPVR 240

Query: 240 ILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMR 299
           ILVKRDELTLEGIKQF+VNV+KEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMR
Sbjct: 241 ILVKRDELTLEGIKQFYVNVDKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMR 300

Query: 300 SRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP 359
           +RDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP
Sbjct: 301 TRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP 360

Query: 360 ENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVADLL 412
           ENYLHRIGRSGRFGRKGVAINFVT DDERMLFDIQKFYNV+IEELP+NVADLL
Sbjct: 361 ENYLHRIGRSGRFGRKGVAINFVTTDDERMLFDIQKFYNVIIEELPSNVADLL 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|Q6Z2Z4|IF4A3_ORYSJ Eukaryotic initiation factor 4A-3 OS=Oryza sativa subsp. japonica GN=Os02g0146600 PE=2 SV=1

 Score =  795 bits (2054), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 385/414 (92%), Positives = 405/414 (97%), Gaps = 2/414 (0%)

Query: 1   MAGLA-EGSQFDARQFDARMNDLLG-SDGQDFFTSYDEVYDTFDAMGLQENLLRGIYAYG 58
           MAG+A EGSQFDA+ +D++M +LL   D ++FFTSYDEV+++FD MGLQENLLRGIYAYG
Sbjct: 1   MAGMAPEGSQFDAKHYDSKMQELLHQGDNEEFFTSYDEVFESFDDMGLQENLLRGIYAYG 60

Query: 59  FEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRE 118
           FEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQ+LVLAPTRE
Sbjct: 61  FEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQSLVLAPTRE 120

Query: 119 LAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLR 178
           LAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL+SGVHVVVGTPGRVFDMLRRQSLR
Sbjct: 121 LAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILASGVHVVVGTPGRVFDMLRRQSLR 180

Query: 179 PDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPV 238
           PD+I++FVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPV
Sbjct: 181 PDHIKMFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPV 240

Query: 239 RILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKM 298
           RILVKRDELTLEGIKQF+VNVEKE+WKL+TLCDLYETLAITQSVIFVNTRRKVDWLTDKM
Sbjct: 241 RILVKRDELTLEGIKQFYVNVEKEDWKLDTLCDLYETLAITQSVIFVNTRRKVDWLTDKM 300

Query: 299 RSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQ 358
           RSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQ
Sbjct: 301 RSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQ 360

Query: 359 PENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVADLL 412
           PENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQ+FYNV IEELPANVADLL
Sbjct: 361 PENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQRFYNVTIEELPANVADLL 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|P35683|IF4A1_ORYSJ Eukaryotic initiation factor 4A-1 OS=Oryza sativa subsp. japonica GN=Os06g0701100 PE=2 SV=2

 Score =  789 bits (2037), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 383/414 (92%), Positives = 402/414 (97%), Gaps = 2/414 (0%)

Query: 1   MAGLA-EGSQFDARQFDARMNDLLG-SDGQDFFTSYDEVYDTFDAMGLQENLLRGIYAYG 58
           MAG+A EGSQFDA+ +D++M +LL   + ++FFTSYDEV+++FD MGLQENLLRGIYAYG
Sbjct: 1   MAGMAPEGSQFDAKHYDSKMQELLNQGETEEFFTSYDEVHESFDDMGLQENLLRGIYAYG 60

Query: 59  FEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRE 118
           FEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY +VECQALVLAPTRE
Sbjct: 61  FEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYAVVECQALVLAPTRE 120

Query: 119 LAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLR 178
           LAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL+SGVHVVVGTPGRVFDMLRRQSLR
Sbjct: 121 LAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILASGVHVVVGTPGRVFDMLRRQSLR 180

Query: 179 PDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPV 238
           PD I++FVLDEADEMLSRGFKDQIYDIFQLLP KIQVGVFSATMPPEALEITRKFMNKPV
Sbjct: 181 PDYIKMFVLDEADEMLSRGFKDQIYDIFQLLPSKIQVGVFSATMPPEALEITRKFMNKPV 240

Query: 239 RILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKM 298
           RILVKRDELTLEGIKQF+VNVEKEEWKL+TLCDLYETLAITQSVIFVNTRRKVDWLTDKM
Sbjct: 241 RILVKRDELTLEGIKQFYVNVEKEEWKLDTLCDLYETLAITQSVIFVNTRRKVDWLTDKM 300

Query: 299 RSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQ 358
           R RDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQ
Sbjct: 301 RGRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQ 360

Query: 359 PENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVADLL 412
           PENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQ+FYNVVIEELPANVADLL
Sbjct: 361 PENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQRFYNVVIEELPANVADLL 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

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	412
224073500	413	predicted protein [Populus trichocarpa]	1.0	0.997	0.953	0.0
147779855	413	hypothetical protein VITISV_040122 [Viti	1.0	0.997	0.956	0.0
363807008	413	uncharacterized protein LOC100786735 [Gl	1.0	0.997	0.951	0.0
225429488	413	PREDICTED: eukaryotic initiation factor	1.0	0.997	0.953	0.0
356530401	413	PREDICTED: eukaryotic initiation factor	1.0	0.997	0.951	0.0
356507010	413	PREDICTED: eukaryotic initiation factor	1.0	0.997	0.956	0.0
449458151	413	PREDICTED: eukaryotic initiation factor	1.0	0.997	0.951	0.0
2500518	413	RecName: Full=Eukaryotic initiation fact	1.0	0.997	0.949	0.0
224142804	413	predicted protein [Populus trichocarpa]	1.0	0.997	0.949	0.0
359484301	803	PREDICTED: eukaryotic initiation factor	1.0	0.513	0.946	0.0

>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 =  816 bits (2108), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 394/413 (95%), Positives = 408/413 (98%), Gaps = 1/413 (0%)

Query: 1   MAGLA-EGSQFDARQFDARMNDLLGSDGQDFFTSYDEVYDTFDAMGLQENLLRGIYAYGF 59
           MAGLA EGSQFD++Q+DA+MNDLL +DGQDFFTSYDEVYDTFD+MGLQENLLRGIYAYGF
Sbjct: 1   MAGLAPEGSQFDSKQYDAKMNDLLANDGQDFFTSYDEVYDTFDSMGLQENLLRGIYAYGF 60

Query: 60  EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTREL 119
           EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLV+CQALVLAPTREL
Sbjct: 61  EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTREL 120

Query: 120 AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRP 179
           AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL +GVHVVVGTPGRVFDMLRRQSLRP
Sbjct: 121 AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRP 180

Query: 180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVR 239
           D I++FVLDEADEMLSRGFKDQIYDIFQLLP K+QVGVFSATMPPEALEITRKFMNKPVR
Sbjct: 181 DYIKMFVLDEADEMLSRGFKDQIYDIFQLLPSKVQVGVFSATMPPEALEITRKFMNKPVR 240

Query: 240 ILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMR 299
           ILVKRDELTLEGIKQFHVNV+KEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMR
Sbjct: 241 ILVKRDELTLEGIKQFHVNVDKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMR 300

Query: 300 SRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP 359
           SRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP
Sbjct: 301 SRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP 360

Query: 360 ENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVADLL 412
           ENYLHRIGRSGRFGRKGVAINFVTRDD+RMLFDIQKFYNVVIEELP+NVADLL
Sbjct: 361 ENYLHRIGRSGRFGRKGVAINFVTRDDDRMLFDIQKFYNVVIEELPSNVADLL 413

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147779855|emb|CAN61608.1| hypothetical protein VITISV_040122 [Vitis vinifera]

 Score =  814 bits (2103), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 395/413 (95%), Positives = 409/413 (99%), Gaps = 1/413 (0%)

Query: 1   MAGLA-EGSQFDARQFDARMNDLLGSDGQDFFTSYDEVYDTFDAMGLQENLLRGIYAYGF 59
           MAGLA EGSQFDARQ+D++MN+LLG+DGQDFFTSYDEVYD+FDAMGLQENLLRGIYAYGF
Sbjct: 1   MAGLAPEGSQFDARQYDSKMNELLGTDGQDFFTSYDEVYDSFDAMGLQENLLRGIYAYGF 60

Query: 60  EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTREL 119
           EKPSAIQQRGIVPF KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTREL
Sbjct: 61  EKPSAIQQRGIVPFIKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTREL 120

Query: 120 AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRP 179
           AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRP
Sbjct: 121 AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRP 180

Query: 180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVR 239
           D I++FVLDEADEMLSRGFKDQIYDIFQLLP KIQVGVFSATMPPEALEITRKFMNKPVR
Sbjct: 181 DYIKMFVLDEADEMLSRGFKDQIYDIFQLLPSKIQVGVFSATMPPEALEITRKFMNKPVR 240

Query: 240 ILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMR 299
           ILVKRDELTLEGIKQF+VNV+KEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMR
Sbjct: 241 ILVKRDELTLEGIKQFYVNVDKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMR 300

Query: 300 SRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP 359
           SRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP
Sbjct: 301 SRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP 360

Query: 360 ENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVADLL 412
           ENYLHRIGRSGRFGRKGVAINFVT+DDERMLFDIQ+FYNVV+EELP+NVADLL
Sbjct: 361 ENYLHRIGRSGRFGRKGVAINFVTKDDERMLFDIQRFYNVVVEELPSNVADLL 413

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|363807008|ref|NP_001242064.1| uncharacterized protein LOC100786735 [Glycine max] gi|255635856|gb|ACU18275.1| unknown [Glycine max]

 Score =  814 bits (2102), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 393/413 (95%), Positives = 406/413 (98%), Gaps = 1/413 (0%)

Query: 1   MAGLA-EGSQFDARQFDARMNDLLGSDGQDFFTSYDEVYDTFDAMGLQENLLRGIYAYGF 59
           MAGLA EGSQFDARQ+D +MN+LL SDGQDFFTSYDEVYD+FDAMGLQ+NLLRGIYAYGF
Sbjct: 1   MAGLAPEGSQFDARQYDTKMNELLTSDGQDFFTSYDEVYDSFDAMGLQDNLLRGIYAYGF 60

Query: 60  EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTREL 119
           EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY + ECQALVLAPTREL
Sbjct: 61  EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYSVTECQALVLAPTREL 120

Query: 120 AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRP 179
           AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRP
Sbjct: 121 AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRP 180

Query: 180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVR 239
           D I++FVLDEADEMLSRGFKDQIYDIFQLLP KIQVGVFSATMPPEALEITRKFMNKPVR
Sbjct: 181 DYIKMFVLDEADEMLSRGFKDQIYDIFQLLPSKIQVGVFSATMPPEALEITRKFMNKPVR 240

Query: 240 ILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMR 299
           ILVKRDELTLEGIKQFHVNVEKEEWKL+TLCDLYETLAITQSVIFVNTRRKVDWLTDKMR
Sbjct: 241 ILVKRDELTLEGIKQFHVNVEKEEWKLDTLCDLYETLAITQSVIFVNTRRKVDWLTDKMR 300

Query: 300 SRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP 359
           SRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP
Sbjct: 301 SRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP 360

Query: 360 ENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVADLL 412
           ENYLHRIGRSGRFGRKGVAINFVTRDDE+MLFDIQKFYNV+IEELP+NVA+LL
Sbjct: 361 ENYLHRIGRSGRFGRKGVAINFVTRDDEKMLFDIQKFYNVIIEELPSNVAELL 413

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225429488|ref|XP_002278119.1| PREDICTED: eukaryotic initiation factor 4A-11 [Vitis vinifera] gi|296081635|emb|CBI20640.3| unnamed protein product [Vitis vinifera]

 Score =  813 bits (2101), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 394/413 (95%), Positives = 409/413 (99%), Gaps = 1/413 (0%)

Query: 1   MAGLA-EGSQFDARQFDARMNDLLGSDGQDFFTSYDEVYDTFDAMGLQENLLRGIYAYGF 59
           MAGLA EGSQFDARQ+D++MN+LLG+DGQDFFTSYDEVY++FDAMGLQENLLRGIYAYGF
Sbjct: 1   MAGLAPEGSQFDARQYDSKMNELLGTDGQDFFTSYDEVYESFDAMGLQENLLRGIYAYGF 60

Query: 60  EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTREL 119
           EKPSAIQQRGIVPF KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTREL
Sbjct: 61  EKPSAIQQRGIVPFIKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTREL 120

Query: 120 AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRP 179
           AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRP
Sbjct: 121 AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRP 180

Query: 180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVR 239
           D I++FVLDEADEMLSRGFKDQIYDIFQLLP KIQVGVFSATMPPEALEITRKFMNKPVR
Sbjct: 181 DYIKMFVLDEADEMLSRGFKDQIYDIFQLLPSKIQVGVFSATMPPEALEITRKFMNKPVR 240

Query: 240 ILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMR 299
           ILVKRDELTLEGIKQF+VNV+KEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMR
Sbjct: 241 ILVKRDELTLEGIKQFYVNVDKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMR 300

Query: 300 SRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP 359
           SRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP
Sbjct: 301 SRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP 360

Query: 360 ENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVADLL 412
           ENYLHRIGRSGRFGRKGVAINFVT+DDERMLFDIQ+FYNVV+EELP+NVADLL
Sbjct: 361 ENYLHRIGRSGRFGRKGVAINFVTKDDERMLFDIQRFYNVVVEELPSNVADLL 413

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356530401|ref|XP_003533770.1| PREDICTED: eukaryotic initiation factor 4A-15-like isoform 1 [Glycine max] gi|356530403|ref|XP_003533771.1| PREDICTED: eukaryotic initiation factor 4A-15-like isoform 2 [Glycine max]

 Score =  813 bits (2100), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 393/413 (95%), Positives = 406/413 (98%), Gaps = 1/413 (0%)

Query: 1   MAGLA-EGSQFDARQFDARMNDLLGSDGQDFFTSYDEVYDTFDAMGLQENLLRGIYAYGF 59
           MAG+A EGSQFDARQ+D +MN+LL SDGQDFFTSYDEVYD+FDAMGLQENLLRGIYAYGF
Sbjct: 1   MAGIAPEGSQFDARQYDTKMNELLTSDGQDFFTSYDEVYDSFDAMGLQENLLRGIYAYGF 60

Query: 60  EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTREL 119
           EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY + ECQALVLAPTREL
Sbjct: 61  EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYSVTECQALVLAPTREL 120

Query: 120 AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRP 179
           AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRP
Sbjct: 121 AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRP 180

Query: 180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVR 239
           D I++FVLDEADEMLSRGFKDQIYDIFQLLP KIQVGVFSATMPPEALEITRKFMNKPVR
Sbjct: 181 DYIKMFVLDEADEMLSRGFKDQIYDIFQLLPSKIQVGVFSATMPPEALEITRKFMNKPVR 240

Query: 240 ILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMR 299
           ILVKRDELTLEGIKQFHVNVEKEEWKL+TLCDLYETLAITQSVIFVNTRRKVDWLTDKMR
Sbjct: 241 ILVKRDELTLEGIKQFHVNVEKEEWKLDTLCDLYETLAITQSVIFVNTRRKVDWLTDKMR 300

Query: 300 SRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP 359
           SRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP
Sbjct: 301 SRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP 360

Query: 360 ENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVADLL 412
           ENYLHRIGRSGRFGRKGVAINFVT+DDE+MLFDIQKFYNVVIEELP+NVA+LL
Sbjct: 361 ENYLHRIGRSGRFGRKGVAINFVTKDDEKMLFDIQKFYNVVIEELPSNVAELL 413

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356507010|ref|XP_003522265.1| PREDICTED: eukaryotic initiation factor 4A-11-like [Glycine max]

 Score =  811 bits (2094), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 395/413 (95%), Positives = 406/413 (98%), Gaps = 1/413 (0%)

Query: 1   MAGLA-EGSQFDARQFDARMNDLLGSDGQDFFTSYDEVYDTFDAMGLQENLLRGIYAYGF 59
           MAGLA EGSQFDARQ+DA+MN+LLG+DGQDFFTSYDEV ++FDAMGLQENLLRGIYAYGF
Sbjct: 1   MAGLAPEGSQFDARQYDAKMNELLGTDGQDFFTSYDEVCESFDAMGLQENLLRGIYAYGF 60

Query: 60  EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTREL 119
           EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSG+LQQLDY LVECQALVLAPTREL
Sbjct: 61  EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGVLQQLDYSLVECQALVLAPTREL 120

Query: 120 AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRP 179
           AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLR 
Sbjct: 121 AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRS 180

Query: 180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVR 239
           DNIR+FVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVR
Sbjct: 181 DNIRMFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVR 240

Query: 240 ILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMR 299
           ILVKRDELTLEGIKQF VNV+KE+WKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMR
Sbjct: 241 ILVKRDELTLEGIKQFFVNVDKEDWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMR 300

Query: 300 SRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP 359
           SRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP
Sbjct: 301 SRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP 360

Query: 360 ENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVADLL 412
           ENYLHRIGRSGRFGRKGVAINFVT DDERMLFDIQKFYNV IEELPANVADL+
Sbjct: 361 ENYLHRIGRSGRFGRKGVAINFVTGDDERMLFDIQKFYNVQIEELPANVADLI 413

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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 =  811 bits (2094), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 393/413 (95%), Positives = 407/413 (98%), Gaps = 1/413 (0%)

Query: 1   MAGLA-EGSQFDARQFDARMNDLLGSDGQDFFTSYDEVYDTFDAMGLQENLLRGIYAYGF 59
           MAGLA EGSQFDARQ+D++MN+LL +DGQDFFTSYDEVYD+FD+MGLQENLLRGIYAYGF
Sbjct: 1   MAGLAPEGSQFDARQYDSKMNELLSADGQDFFTSYDEVYDSFDSMGLQENLLRGIYAYGF 60

Query: 60  EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTREL 119
           EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLV+CQALVLAPTREL
Sbjct: 61  EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVQCQALVLAPTREL 120

Query: 120 AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRP 179
           AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL +GVHVVVGTPGRVFDMLRRQSLRP
Sbjct: 121 AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLRP 180

Query: 180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVR 239
           D IR+FVLDEADEMLSRGFKDQIYDIFQLLP KIQVGVFSATMPPEALEITRKFMNKPVR
Sbjct: 181 DYIRMFVLDEADEMLSRGFKDQIYDIFQLLPSKIQVGVFSATMPPEALEITRKFMNKPVR 240

Query: 240 ILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMR 299
           ILVKRDELTLEGIKQF+VNV+KE+WKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMR
Sbjct: 241 ILVKRDELTLEGIKQFYVNVDKEDWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMR 300

Query: 300 SRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP 359
           SRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP
Sbjct: 301 SRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP 360

Query: 360 ENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVADLL 412
           ENYLHRIGRSGRFGRKGVAINFVT +DERMLFDIQKFYNVVIEELPANVADLL
Sbjct: 361 ENYLHRIGRSGRFGRKGVAINFVTTEDERMLFDIQKFYNVVIEELPANVADLL 413

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|2500518|sp|Q40465.1|IF411_TOBAC RecName: Full=Eukaryotic initiation factor 4A-11; Short=eIF-4A-11; AltName: Full=ATP-dependent RNA helicase eIF4A-11 gi|485987|emb|CAA55737.1| unnamed protein product [Nicotiana tabacum]

 Score =  810 bits (2093), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 392/413 (94%), Positives = 406/413 (98%), Gaps = 1/413 (0%)

Query: 1   MAGLA-EGSQFDARQFDARMNDLLGSDGQDFFTSYDEVYDTFDAMGLQENLLRGIYAYGF 59
           MAGLA EGSQFDARQ+DA+M +LLG++ Q+FFTSYDEVY++FDAMGLQENLLRGIYAYGF
Sbjct: 1   MAGLAPEGSQFDARQYDAKMTELLGTEQQEFFTSYDEVYESFDAMGLQENLLRGIYAYGF 60

Query: 60  EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTREL 119
           EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY LVECQALVLAPTREL
Sbjct: 61  EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYSLVECQALVLAPTREL 120

Query: 120 AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRP 179
           AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL SGVHVVVGTPGRVFDMLRRQSLRP
Sbjct: 121 AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQSGVHVVVGTPGRVFDMLRRQSLRP 180

Query: 180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVR 239
           DNI++FVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVR
Sbjct: 181 DNIKMFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVR 240

Query: 240 ILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMR 299
           ILVKRDELTLEGIKQF+VNV+KEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMR
Sbjct: 241 ILVKRDELTLEGIKQFYVNVDKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMR 300

Query: 300 SRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP 359
            RDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP
Sbjct: 301 GRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP 360

Query: 360 ENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVADLL 412
           ENYLHRIG SGRFGRKGV+INFVT+DDERMLFDIQKFYNVVIEELPANVADLL
Sbjct: 361 ENYLHRIGHSGRFGRKGVSINFVTKDDERMLFDIQKFYNVVIEELPANVADLL 413

Source: Nicotiana tabacum

Species: Nicotiana tabacum

Genus: Nicotiana

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224142804|ref|XP_002324737.1| predicted protein [Populus trichocarpa] gi|118481206|gb|ABK92554.1| unknown [Populus trichocarpa] gi|222866171|gb|EEF03302.1| predicted protein [Populus trichocarpa]

 Score =  810 bits (2093), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 392/413 (94%), Positives = 407/413 (98%), Gaps = 1/413 (0%)

Query: 1   MAGLA-EGSQFDARQFDARMNDLLGSDGQDFFTSYDEVYDTFDAMGLQENLLRGIYAYGF 59
           MAGLA EGSQFDARQFD++MN+LL +DGQDFFTSYDEVYDTFDAMGL+ENLLRGIYAYGF
Sbjct: 1   MAGLAPEGSQFDARQFDSKMNELLTTDGQDFFTSYDEVYDTFDAMGLKENLLRGIYAYGF 60

Query: 60  EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTREL 119
           EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY +VECQALVLAPTREL
Sbjct: 61  EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYDVVECQALVLAPTREL 120

Query: 120 AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRP 179
           AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILS+GVHVVVGTPGRVFDMLRRQSLRP
Sbjct: 121 AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSAGVHVVVGTPGRVFDMLRRQSLRP 180

Query: 180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVR 239
           D I++FVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVR
Sbjct: 181 DYIKMFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVR 240

Query: 240 ILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMR 299
           ILVKRDELTLEGIKQF+VNV+KEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMR
Sbjct: 241 ILVKRDELTLEGIKQFYVNVDKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMR 300

Query: 300 SRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP 359
           SRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP
Sbjct: 301 SRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP 360

Query: 360 ENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVADLL 412
           ENYLHRIGRSGRFGRKGVAINFVT+DDERML DIQ+FYNV +EELP+NVADLL
Sbjct: 361 ENYLHRIGRSGRFGRKGVAINFVTKDDERMLSDIQRFYNVTVEELPSNVADLL 413

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  810 bits (2091), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 391/413 (94%), Positives = 406/413 (98%), Gaps = 1/413 (0%)

Query: 1   MAGLA-EGSQFDARQFDARMNDLLGSDGQDFFTSYDEVYDTFDAMGLQENLLRGIYAYGF 59
           MAG+A EGSQFD R +DA+M +LL +DGQDFFTSYDEVYD+FD+MGLQENLLRGIYAYGF
Sbjct: 391 MAGVAPEGSQFDTRNYDAKMTELLSTDGQDFFTSYDEVYDSFDSMGLQENLLRGIYAYGF 450

Query: 60  EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTREL 119
           EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTREL
Sbjct: 451 EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTREL 510

Query: 120 AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRP 179
           AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRP
Sbjct: 511 AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRP 570

Query: 180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVR 239
           D I++FVLDEADEMLSRGFKDQIYDIFQLLP K+QVGVFSATMPPEALEITRKFMNKPVR
Sbjct: 571 DYIKMFVLDEADEMLSRGFKDQIYDIFQLLPSKVQVGVFSATMPPEALEITRKFMNKPVR 630

Query: 240 ILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMR 299
           ILVKRDELTLEGIKQF+VNV+KEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMR
Sbjct: 631 ILVKRDELTLEGIKQFYVNVDKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMR 690

Query: 300 SRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP 359
           SRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVIN+DLPTQP
Sbjct: 691 SRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINFDLPTQP 750

Query: 360 ENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVADLL 412
           ENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQ+FYNVVIEELP+NVADLL
Sbjct: 751 ENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQRFYNVVIEELPSNVADLL 803

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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	412
TAIR|locus:2020078	412	EIF4A-2 "eif4a-2" [Arabidopsis	0.995	0.995	0.922	3.9e-202
TAIR|locus:2030285	414	AT1G72730 [Arabidopsis thalian	1.0	0.995	0.881	2.4e-195
TAIR|locus:2088237	415	EIF4A1 "eukaryotic translation	0.941	0.934	0.923	7.5e-192
UNIPROTKB|Q8JFP1	407	EIF4A2 "Eukaryotic initiation	0.924	0.936	0.730	6.2e-149
UNIPROTKB|Q3SZ65	407	EIF4A2 "Eukaryotic initiation	0.944	0.955	0.713	2.7e-148
UNIPROTKB|E2R3J1	407	EIF4A2 "Uncharacterized protei	0.944	0.955	0.713	2.7e-148
UNIPROTKB|Q14240	407	EIF4A2 "Eukaryotic initiation	0.944	0.955	0.713	2.7e-148
UNIPROTKB|A6M930	407	EIF4A2 "Eukaryotic translation	0.944	0.955	0.713	2.7e-148
MGI|MGI:106906	407	Eif4a2 "eukaryotic translation	0.944	0.955	0.713	2.7e-148
RGD|1309225	407	Eif4a2 "eukaryotic translation	0.944	0.955	0.713	2.7e-148

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

 Score = 1956 (693.6 bits), Expect = 3.9e-202, P = 3.9e-202
 Identities = 382/414 (92%), Positives = 402/414 (97%)

Query:     1 MAGLA-EGSQFDARQFDARMNDLLGSDGQD-FFTSYDEVYDTFDAMGLQENLLRGIYAYG 58
             MAG A EG+QFD RQFD R+N++L  DGQD FFTSYDEV+++FDAMGLQENLLRGIYAYG
Sbjct:     1 MAGSAPEGTQFDTRQFDQRLNEVL--DGQDEFFTSYDEVHESFDAMGLQENLLRGIYAYG 58

Query:    59 FEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRE 118
             FEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSG+LQQLDY L++CQALVLAPTRE
Sbjct:    59 FEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGVLQQLDYALLQCQALVLAPTRE 118

Query:   119 LAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLR 178
             LAQQIEKVMRALGDY GVKVHACVGGTSVREDQRIL +GVHVVVGTPGRVFDMLRRQSLR
Sbjct:   119 LAQQIEKVMRALGDYQGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLRRQSLR 178

Query:   179 PDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPV 238
             PD I++FVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFM+KPV
Sbjct:   179 PDCIKMFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMSKPV 238

Query:   239 RILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKM 298
             RILVKRDELTLEGIKQF+VNVEKE+WKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKM
Sbjct:   239 RILVKRDELTLEGIKQFYVNVEKEDWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKM 298

Query:   299 RSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQ 358
             RSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVIN+DLPTQ
Sbjct:   299 RSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINFDLPTQ 358

Query:   359 PENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVADLL 412
             PENYLHRIGRSGRFGRKGVAINFVT DD+RMLFDIQKFYNVV+EELP+NVADLL
Sbjct:   359 PENYLHRIGRSGRFGRKGVAINFVTLDDQRMLFDIQKFYNVVVEELPSNVADLL 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 = 1892 (671.1 bits), Expect = 2.4e-195, P = 2.4e-195
 Identities = 365/414 (88%), Positives = 395/414 (95%)

Query:     1 MAGLA-EGSQFDARQFDARMNDLLGSDGQD-FFTSYDEVYDTFDAMGLQENLLRGIYAYG 58
             MAG+A +G+Q+D RQFD +MN +LG +G++ F+T+YDEV D+FDAM LQ +LLRGIYAYG
Sbjct:     1 MAGMASDGTQYDPRQFDTKMNAILGEEGEETFYTNYDEVCDSFDAMELQPDLLRGIYAYG 60

Query:    59 FEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRE 118
             FEKPSAIQQRGI+PFCKGLDVIQQAQSGTGKTATFCSG+LQQLD  LV+CQALVLAPTRE
Sbjct:    61 FEKPSAIQQRGIIPFCKGLDVIQQAQSGTGKTATFCSGVLQQLDISLVQCQALVLAPTRE 120

Query:   119 LAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLR 178
             LAQQIEKVMRALGDYLGVK  ACVGGTSVREDQR+L SGVHVVVGTPGRVFD+LRRQSLR
Sbjct:   121 LAQQIEKVMRALGDYLGVKAQACVGGTSVREDQRVLQSGVHVVVGTPGRVFDLLRRQSLR 180

Query:   179 PDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPV 238
              D I++FVLDEADEMLSRGFKDQIYDIFQLLP K+QVGVFSATMPPEALEITRKFMNKPV
Sbjct:   181 ADAIKMFVLDEADEMLSRGFKDQIYDIFQLLPSKVQVGVFSATMPPEALEITRKFMNKPV 240

Query:   239 RILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKM 298
             RILVKRDELTLEGIKQF+VNV+KEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKM
Sbjct:   241 RILVKRDELTLEGIKQFYVNVDKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKM 300

Query:   299 RSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQ 358
             RSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVIN+DLPTQ
Sbjct:   301 RSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINFDLPTQ 360

Query:   359 PENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVADLL 412
             PENYLHRIGRSGRFGRKGVAINF+T +DERM+ DIQ+FYNVV+EELP+NVADLL
Sbjct:   361 PENYLHRIGRSGRFGRKGVAINFMTSEDERMMADIQRFYNVVVEELPSNVADLL 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 = 1859 (659.5 bits), Expect = 7.5e-192, P = 7.5e-192
 Identities = 362/392 (92%), Positives = 383/392 (97%)

Query:     1 MAGLA-EGSQFDARQFDARMNDLLGSDGQD-FFTSYDEVYDTFDAMGLQENLLRGIYAYG 58
             MAG A EG+QFDARQFD ++N++L  +GQD FFTSYD+V+++FDAMGLQENLLRGIYAYG
Sbjct:     1 MAGSAPEGTQFDARQFDQKLNEVL--EGQDEFFTSYDDVHESFDAMGLQENLLRGIYAYG 58

Query:    59 FEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRE 118
             FEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSG+LQQLD+ L++CQALVLAPTRE
Sbjct:    59 FEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGVLQQLDFSLIQCQALVLAPTRE 118

Query:   119 LAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLR 178
             LAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL +GVHVVVGTPGRVFDML+RQSLR
Sbjct:   119 LAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILQAGVHVVVGTPGRVFDMLKRQSLR 178

Query:   179 PDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPV 238
              DNI++FVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFM+KPV
Sbjct:   179 ADNIKMFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMSKPV 238

Query:   239 RILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKM 298
             RILVKRDELTLEGIKQF+VNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKM
Sbjct:   239 RILVKRDELTLEGIKQFYVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKM 298

Query:   299 RSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQ 358
             RSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVIN+DLPTQ
Sbjct:   299 RSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINFDLPTQ 358

Query:   359 PENYLHRIGRSGRFGRKGVAINFVTRDDERML 390
             PENYLHRIGRSGRFGRKGVAINFVTRDDERML
Sbjct:   359 PENYLHRIGRSGRFGRKGVAINFVTRDDERML 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 = 1454 (516.9 bits), Expect = 6.2e-149, P = 6.2e-149
 Identities = 279/382 (73%), Positives = 327/382 (85%)

Query:    32 TSYDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTA 91
             ++++E+ D FD M L+E+LLRGIYAYGFEKPSAIQQR I+P  KG DVI QAQSGTGKTA
Sbjct:    26 SNWNEIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTA 85

Query:    92 TFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVRED- 150
             TF   ILQQL+  L E QALVLAPTRELAQQI+KV+ ALGDY+G   HAC+GGT+VR + 
Sbjct:    86 TFAISILQQLEIDLKETQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRNEM 145

Query:   151 QRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLP 210
             Q++ +   H+VVGTPGRVFDML R+ L P  I++FVLDEADEMLSRGFKDQIY+IFQ L 
Sbjct:   146 QKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSRGFKDQIYEIFQKLS 205

Query:   211 PKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLC 270
               IQV + SATMP + LE+T+KFM +P+RILVK++ELTLEGIKQF++NVE+EEWKL+TLC
Sbjct:   206 TNIQVVLLSATMPMDVLEVTKKFMREPIRILVKKEELTLEGIKQFYINVEREEWKLDTLC 265

Query:   271 DLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSR 330
             DLYETL ITQ+VIF+NTRRKVDWLT+KM +RD TVSA HGDMDQ  RD+IMREFRSGSSR
Sbjct:   266 DLYETLTITQAVIFLNTRRKVDWLTEKMHARDFTVSALHGDMDQKERDVIMREFRSGSSR 325

Query:   331 VLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERML 390
             VLITTDLLARGIDVQQVSLVINYDLPT  ENY+HRIGR GRFGRKGVAINFVT +D+R+L
Sbjct:   326 VLITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINFVTEEDKRIL 385

Query:   391 FDIQKFYNVVIEELPANVADLL 412
              DI+ FYN  +EE+P NVADL+
Sbjct:   386 RDIETFYNTTVEEMPMNVADLI 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 = 1448 (514.8 bits), Expect = 2.7e-148, P = 2.7e-148
 Identities = 281/394 (71%), Positives = 329/394 (83%)

Query:    24 GSDGQD----FFTSYDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDV 79
             G +G D      ++++E+ D FD M L+E+LLRGIYAYGFEKPSAIQQR I+P  KG DV
Sbjct:    14 GPEGMDPDGVIESNWNEIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDV 73

Query:    80 IQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVH 139
             I QAQSGTGKTATF   ILQQL+    E QALVLAPTRELAQQI+KV+ ALGDY+G   H
Sbjct:    74 IAQAQSGTGKTATFAISILQQLEIEFKETQALVLAPTRELAQQIQKVILALGDYMGATCH 133

Query:   140 ACVGGTSVRED-QRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGF 198
             AC+GGT+VR + Q++ +   H+VVGTPGRVFDML R+ L P  I++FVLDEADEMLSRGF
Sbjct:   134 ACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSRGF 193

Query:   199 KDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVN 258
             KDQIY+IFQ L   IQV + SATMP + LE+T+KFM  P+RILVK++ELTLEGIKQF++N
Sbjct:   194 KDQIYEIFQKLNTSIQVVLLSATMPTDVLEVTKKFMRDPIRILVKKEELTLEGIKQFYIN 253

Query:   259 VEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRD 318
             VE+EEWKL+TLCDLYETL ITQ+VIF+NTRRKVDWLT+KM +RD TVSA HGDMDQ  RD
Sbjct:   254 VEREEWKLDTLCDLYETLTITQAVIFLNTRRKVDWLTEKMHARDFTVSALHGDMDQKERD 313

Query:   319 IIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVA 378
             +IMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPT  ENY+HRIGR GRFGRKGVA
Sbjct:   314 VIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVA 373

Query:   379 INFVTRDDERMLFDIQKFYNVVIEELPANVADLL 412
             INFVT +D+R+L DI+ FYN  +EE+P NVADL+
Sbjct:   374 INFVTEEDKRILRDIETFYNTTVEEMPMNVADLI 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 = 1448 (514.8 bits), Expect = 2.7e-148, P = 2.7e-148
 Identities = 281/394 (71%), Positives = 329/394 (83%)

Query:    24 GSDGQD----FFTSYDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDV 79
             G +G D      ++++E+ D FD M L+E+LLRGIYAYGFEKPSAIQQR I+P  KG DV
Sbjct:    14 GPEGMDPDGVIESNWNEIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDV 73

Query:    80 IQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVH 139
             I QAQSGTGKTATF   ILQQL+    E QALVLAPTRELAQQI+KV+ ALGDY+G   H
Sbjct:    74 IAQAQSGTGKTATFAISILQQLEIEFKETQALVLAPTRELAQQIQKVILALGDYMGATCH 133

Query:   140 ACVGGTSVRED-QRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGF 198
             AC+GGT+VR + Q++ +   H+VVGTPGRVFDML R+ L P  I++FVLDEADEMLSRGF
Sbjct:   134 ACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSRGF 193

Query:   199 KDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVN 258
             KDQIY+IFQ L   IQV + SATMP + LE+T+KFM  P+RILVK++ELTLEGIKQF++N
Sbjct:   194 KDQIYEIFQKLNTSIQVVLLSATMPTDVLEVTKKFMRDPIRILVKKEELTLEGIKQFYIN 253

Query:   259 VEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRD 318
             VE+EEWKL+TLCDLYETL ITQ+VIF+NTRRKVDWLT+KM +RD TVSA HGDMDQ  RD
Sbjct:   254 VEREEWKLDTLCDLYETLTITQAVIFLNTRRKVDWLTEKMHARDFTVSALHGDMDQKERD 313

Query:   319 IIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVA 378
             +IMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPT  ENY+HRIGR GRFGRKGVA
Sbjct:   314 VIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVA 373

Query:   379 INFVTRDDERMLFDIQKFYNVVIEELPANVADLL 412
             INFVT +D+R+L DI+ FYN  +EE+P NVADL+
Sbjct:   374 INFVTEEDKRILRDIETFYNTTVEEMPMNVADLI 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 = 1448 (514.8 bits), Expect = 2.7e-148, P = 2.7e-148
 Identities = 281/394 (71%), Positives = 329/394 (83%)

Query:    24 GSDGQD----FFTSYDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDV 79
             G +G D      ++++E+ D FD M L+E+LLRGIYAYGFEKPSAIQQR I+P  KG DV
Sbjct:    14 GPEGMDPDGVIESNWNEIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDV 73

Query:    80 IQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVH 139
             I QAQSGTGKTATF   ILQQL+    E QALVLAPTRELAQQI+KV+ ALGDY+G   H
Sbjct:    74 IAQAQSGTGKTATFAISILQQLEIEFKETQALVLAPTRELAQQIQKVILALGDYMGATCH 133

Query:   140 ACVGGTSVRED-QRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGF 198
             AC+GGT+VR + Q++ +   H+VVGTPGRVFDML R+ L P  I++FVLDEADEMLSRGF
Sbjct:   134 ACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSRGF 193

Query:   199 KDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVN 258
             KDQIY+IFQ L   IQV + SATMP + LE+T+KFM  P+RILVK++ELTLEGIKQF++N
Sbjct:   194 KDQIYEIFQKLNTSIQVVLLSATMPTDVLEVTKKFMRDPIRILVKKEELTLEGIKQFYIN 253

Query:   259 VEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRD 318
             VE+EEWKL+TLCDLYETL ITQ+VIF+NTRRKVDWLT+KM +RD TVSA HGDMDQ  RD
Sbjct:   254 VEREEWKLDTLCDLYETLTITQAVIFLNTRRKVDWLTEKMHARDFTVSALHGDMDQKERD 313

Query:   319 IIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVA 378
             +IMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPT  ENY+HRIGR GRFGRKGVA
Sbjct:   314 VIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVA 373

Query:   379 INFVTRDDERMLFDIQKFYNVVIEELPANVADLL 412
             INFVT +D+R+L DI+ FYN  +EE+P NVADL+
Sbjct:   374 INFVTEEDKRILRDIETFYNTTVEEMPMNVADLI 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 = 1448 (514.8 bits), Expect = 2.7e-148, P = 2.7e-148
 Identities = 281/394 (71%), Positives = 329/394 (83%)

Query:    24 GSDGQD----FFTSYDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDV 79
             G +G D      ++++E+ D FD M L+E+LLRGIYAYGFEKPSAIQQR I+P  KG DV
Sbjct:    14 GPEGMDPDGVIESNWNEIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDV 73

Query:    80 IQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVH 139
             I QAQSGTGKTATF   ILQQL+    E QALVLAPTRELAQQI+KV+ ALGDY+G   H
Sbjct:    74 IAQAQSGTGKTATFAISILQQLEIEFKETQALVLAPTRELAQQIQKVILALGDYMGATCH 133

Query:   140 ACVGGTSVRED-QRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGF 198
             AC+GGT+VR + Q++ +   H+VVGTPGRVFDML R+ L P  I++FVLDEADEMLSRGF
Sbjct:   134 ACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSRGF 193

Query:   199 KDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVN 258
             KDQIY+IFQ L   IQV + SATMP + LE+T+KFM  P+RILVK++ELTLEGIKQF++N
Sbjct:   194 KDQIYEIFQKLNTSIQVVLLSATMPTDVLEVTKKFMRDPIRILVKKEELTLEGIKQFYIN 253

Query:   259 VEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRD 318
             VE+EEWKL+TLCDLYETL ITQ+VIF+NTRRKVDWLT+KM +RD TVSA HGDMDQ  RD
Sbjct:   254 VEREEWKLDTLCDLYETLTITQAVIFLNTRRKVDWLTEKMHARDFTVSALHGDMDQKERD 313

Query:   319 IIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVA 378
             +IMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPT  ENY+HRIGR GRFGRKGVA
Sbjct:   314 VIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVA 373

Query:   379 INFVTRDDERMLFDIQKFYNVVIEELPANVADLL 412
             INFVT +D+R+L DI+ FYN  +EE+P NVADL+
Sbjct:   374 INFVTEEDKRILRDIETFYNTTVEEMPMNVADLI 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 = 1448 (514.8 bits), Expect = 2.7e-148, P = 2.7e-148
 Identities = 281/394 (71%), Positives = 329/394 (83%)

Query:    24 GSDGQD----FFTSYDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDV 79
             G +G D      ++++E+ D FD M L+E+LLRGIYAYGFEKPSAIQQR I+P  KG DV
Sbjct:    14 GPEGMDPDGVIESNWNEIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDV 73

Query:    80 IQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVH 139
             I QAQSGTGKTATF   ILQQL+    E QALVLAPTRELAQQI+KV+ ALGDY+G   H
Sbjct:    74 IAQAQSGTGKTATFAISILQQLEIEFKETQALVLAPTRELAQQIQKVILALGDYMGATCH 133

Query:   140 ACVGGTSVRED-QRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGF 198
             AC+GGT+VR + Q++ +   H+VVGTPGRVFDML R+ L P  I++FVLDEADEMLSRGF
Sbjct:   134 ACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSRGF 193

Query:   199 KDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVN 258
             KDQIY+IFQ L   IQV + SATMP + LE+T+KFM  P+RILVK++ELTLEGIKQF++N
Sbjct:   194 KDQIYEIFQKLNTSIQVVLLSATMPTDVLEVTKKFMRDPIRILVKKEELTLEGIKQFYIN 253

Query:   259 VEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRD 318
             VE+EEWKL+TLCDLYETL ITQ+VIF+NTRRKVDWLT+KM +RD TVSA HGDMDQ  RD
Sbjct:   254 VEREEWKLDTLCDLYETLTITQAVIFLNTRRKVDWLTEKMHARDFTVSALHGDMDQKERD 313

Query:   319 IIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVA 378
             +IMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPT  ENY+HRIGR GRFGRKGVA
Sbjct:   314 VIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVA 373

Query:   379 INFVTRDDERMLFDIQKFYNVVIEELPANVADLL 412
             INFVT +D+R+L DI+ FYN  +EE+P NVADL+
Sbjct:   374 INFVTEEDKRILRDIETFYNTTVEEMPMNVADLI 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 = 1448 (514.8 bits), Expect = 2.7e-148, P = 2.7e-148
 Identities = 281/394 (71%), Positives = 329/394 (83%)

Query:    24 GSDGQD----FFTSYDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDV 79
             G +G D      ++++E+ D FD M L+E+LLRGIYAYGFEKPSAIQQR I+P  KG DV
Sbjct:    14 GPEGMDPDGVIESNWNEIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDV 73

Query:    80 IQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVH 139
             I QAQSGTGKTATF   ILQQL+    E QALVLAPTRELAQQI+KV+ ALGDY+G   H
Sbjct:    74 IAQAQSGTGKTATFAISILQQLEIEFKETQALVLAPTRELAQQIQKVILALGDYMGATCH 133

Query:   140 ACVGGTSVRED-QRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGF 198
             AC+GGT+VR + Q++ +   H+VVGTPGRVFDML R+ L P  I++FVLDEADEMLSRGF
Sbjct:   134 ACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSRGF 193

Query:   199 KDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVN 258
             KDQIY+IFQ L   IQV + SATMP + LE+T+KFM  P+RILVK++ELTLEGIKQF++N
Sbjct:   194 KDQIYEIFQKLNTSIQVVLLSATMPTDVLEVTKKFMRDPIRILVKKEELTLEGIKQFYIN 253

Query:   259 VEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRD 318
             VE+EEWKL+TLCDLYETL ITQ+VIF+NTRRKVDWLT+KM +RD TVSA HGDMDQ  RD
Sbjct:   254 VEREEWKLDTLCDLYETLTITQAVIFLNTRRKVDWLTEKMHARDFTVSALHGDMDQKERD 313

Query:   319 IIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVA 378
             +IMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPT  ENY+HRIGR GRFGRKGVA
Sbjct:   314 VIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVA 373

Query:   379 INFVTRDDERMLFDIQKFYNVVIEELPANVADLL 412
             INFVT +D+R+L DI+ FYN  +EE+P NVADL+
Sbjct:   374 INFVTEEDKRILRDIETFYNTTVEEMPMNVADLI 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	0.7060	0.9247	0.9621	N/A	no
Q40470	IF4A7_TOBAC	3, ., 6, ., 4, ., 1, 3	0.9370	1.0	0.9975	N/A	no
Q40471	IF4A9_TOBAC	3, ., 6, ., 4, ., 1, 3	0.9394	1.0	0.9975	N/A	no
P0CQ73	FAL1_CRYNB	3, ., 6, ., 4, ., 1, 3	0.6933	0.9101	0.9469	N/A	no
A7EGL7	IF4A_SCLS1	3, ., 6, ., 4, ., 1, 3	0.7007	0.9247	0.9572	N/A	no
P10630	IF4A2_MOUSE	3, ., 6, ., 4, ., 1, 3	0.7157	0.9441	0.9557	yes	no
P35683	IF4A1_ORYSJ	3, ., 6, ., 4, ., 1, 3	0.9251	1.0	0.9951	yes	no
Q4R4Y9	IF4A2_MACFA	3, ., 6, ., 4, ., 1, 3	0.7131	0.9441	0.9534	N/A	no
A1D7N3	IF4A_NEOFI	3, ., 6, ., 4, ., 1, 3	0.7060	0.9247	0.9572	N/A	no
Q41741	IF4A_MAIZE	3, ., 6, ., 4, ., 1, 3	0.9176	0.9927	0.9975	N/A	no
O42226	I4A3B_XENLA	3, ., 6, ., 4, ., 1, 3	0.6701	0.9320	0.9275	N/A	no
A4QVP2	IF4A_MAGO7	3, ., 6, ., 4, ., 1, 3	0.7060	0.9247	0.9621	N/A	no
Q6Z2Z4	IF4A3_ORYSJ	3, ., 6, ., 4, ., 1, 3	0.9299	1.0	0.9951	yes	no
Q4P331	IF4A_USTMA	3, ., 6, ., 4, ., 1, 3	0.6921	0.9514	0.9537	N/A	no
Q3SZ54	IF4A1_BOVIN	3, ., 6, ., 4, ., 1, 3	0.7014	0.9611	0.9753	no	no
P41382	IF410_TOBAC	3, ., 6, ., 4, ., 1, 3	0.9443	1.0	0.9975	N/A	no
Q7RV88	IF4A_NEUCR	3, ., 6, ., 4, ., 1, 3	0.7086	0.9247	0.9596	N/A	no
P41381	IF4A8_TOBAC	3, ., 6, ., 4, ., 1, 3	0.9322	1.0	0.9975	N/A	no
P47943	IF4A_SCHPO	3, ., 6, ., 4, ., 1, 3	0.7086	0.9247	0.9719	yes	no
P0CQ72	FAL1_CRYNJ	3, ., 6, ., 4, ., 1, 3	0.6933	0.9101	0.9469	yes	no
Q2UPY3	IF4A_ASPOR	3, ., 6, ., 4, ., 1, 3	0.6893	0.9587	0.9382	yes	no
Q5R4X1	IF4A2_PONAB	3, ., 6, ., 4, ., 1, 3	0.7157	0.9441	0.9557	yes	no
Q14240	IF4A2_HUMAN	3, ., 6, ., 4, ., 1, 3	0.7157	0.9441	0.9557	yes	no
P41377	IF4A2_ARATH	3, ., 6, ., 4, ., 1, 3	0.9227	0.9951	0.9951	yes	no
P41376	IF4A1_ARATH	3, ., 6, ., 4, ., 1, 3	0.9227	0.9951	0.9951	yes	no
Q40467	IF414_TOBAC	3, ., 6, ., 4, ., 1, 3	0.9443	1.0	0.9975	N/A	no
Q40466	IF413_TOBAC	3, ., 6, ., 4, ., 1, 3	0.9380	0.8592	0.9971	N/A	no
Q40465	IF411_TOBAC	3, ., 6, ., 4, ., 1, 3	0.9491	1.0	0.9975	N/A	no
O02494	IF4A_CRYPV	3, ., 6, ., 4, ., 1, 3	0.6771	0.9247	0.9407	yes	no
Q40468	IF415_TOBAC	3, ., 6, ., 4, ., 1, 3	0.9491	1.0	0.9975	N/A	no
Q02748	IF4A_DROME	3, ., 6, ., 4, ., 1, 3	0.7060	0.9247	0.9454	yes	no
P41379	IF4A2_NICPL	3, ., 6, ., 4, ., 1, 3	0.9491	1.0	0.9975	N/A	no
Q5RKI1	IF4A2_RAT	3, ., 6, ., 4, ., 1, 3	0.7157	0.9441	0.9557	yes	no
Q9CAI7	IF4A3_ARATH	3, ., 6, ., 4, ., 1, 3	0.8816	1.0	0.9951	no	no
Q5R5F5	IF4A1_PONAB	3, ., 6, ., 4, ., 1, 3	0.6965	0.9611	0.9753	yes	no
Q1DQ20	IF4A_COCIM	3, ., 6, ., 4, ., 1, 3	0.7007	0.9247	0.9572	N/A	no
Q4R8K5	IF4A1_MACFA	3, ., 6, ., 4, ., 1, 3	0.6990	0.9611	0.9753	N/A	no
Q2HFP1	IF4A_CHAGB	3, ., 6, ., 4, ., 1, 3	0.7007	0.9247	0.9596	N/A	no
P41378	IF4A_WHEAT	3, ., 6, ., 4, ., 1, 3	0.9251	1.0	0.9951	N/A	no
P27639	IF4A_CAEEL	3, ., 6, ., 4, ., 1, 3	0.6498	0.9611	0.9850	yes	no
A1CJT5	IF4A_ASPCL	3, ., 6, ., 4, ., 1, 3	0.7034	0.9247	0.9572	N/A	no
Q3SZ65	IF4A2_BOVIN	3, ., 6, ., 4, ., 1, 3	0.7157	0.9441	0.9557	yes	no
P29562	IF4A1_RABIT	3, ., 6, ., 4, ., 1, 3	0.7081	0.9441	0.9773	no	no
Q8JFP1	IF4A2_CHICK	3, ., 6, ., 4, ., 1, 3	0.7329	0.9247	0.9361	yes	no
A6RJ45	IF4A_BOTFB	3, ., 6, ., 4, ., 1, 3	0.7034	0.9247	0.9572	N/A	no
P60842	IF4A1_HUMAN	3, ., 6, ., 4, ., 1, 3	0.7014	0.9611	0.9753	no	no
P60843	IF4A1_MOUSE	3, ., 6, ., 4, ., 1, 3	0.7014	0.9611	0.9753	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	0.993
3rd Layer	3.6.4	0.998

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	grail3.0110000802	SubName- Full=Putative uncharacterized protein; (413 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	grail3.0040005401	SubName- Full=Putative uncharacterized protein; (1166 aa)						•			0.800
	eugene3.00061309	hypothetical protein (798 aa)						•			0.800
	estExt_fgenesh4_pm.C_LG_XVIII0340	hypothetical protein (793 aa)						•			0.800

---

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	412
PTZ00424	401	PTZ00424, PTZ00424, helicase 45; Provisional	0.0
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	1e-139
cd00268	203	cd00268, DEADc, DEAD-box helicases	1e-103
PRK11776	460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	3e-94
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	3e-78
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	2e-74
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	6e-72
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	2e-65
PRK01297	475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	4e-65
PLN00206	518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	1e-59
PRK04837	423	PRK04837, PRK04837, ATP-dependent RNA helicase Rhl	4e-57
PRK04537	572	PRK04537, PRK04537, ATP-dependent RNA helicase Rhl	4e-56
pfam00270	169	pfam00270, DEAD, DEAD/DEAH box helicase	2e-55
smart00487	201	smart00487, DEXDc, DEAD-like helicases superfamily	5e-52
cd00079	131	cd00079, HELICc, Helicase superfamily c-terminal d	9e-42
cd00046	144	cd00046, DEXDc, DEAD-like helicases superfamily	3e-41
pfam00271	78	pfam00271, Helicase_C, Helicase conserved C-termin	2e-27
smart00490	82	smart00490, HELICc, helicase superfamily c-termina	1e-26
COG1201	814	COG1201, Lhr, Lhr-like helicases [General function	4e-19
COG1205	851	COG1205, COG1205, Distinct helicase family with a	9e-15
COG0514	590	COG0514, RecQ, Superfamily II DNA helicase [DNA re	2e-14
COG1202	830	COG1202, COG1202, Superfamily II helicase, archaea	2e-12
TIGR00614	470	TIGR00614, recQ_fam, ATP-dependent DNA helicase, R	7e-10
TIGR01389	591	TIGR01389, recQ, ATP-dependent DNA helicase RecQ	3e-09
COG1204	766	COG1204, COG1204, Superfamily II helicase [General	2e-08
PRK11057	607	PRK11057, PRK11057, ATP-dependent DNA helicase Rec	2e-08
COG1061	442	COG1061, SSL2, DNA or RNA helicases of superfamily	3e-07
TIGR04121	803	TIGR04121, DEXH_lig_assoc, DEXH box helicase, DNA	3e-07
TIGR00643	630	TIGR00643, recG, ATP-dependent DNA helicase RecG	8e-07
COG1111	542	COG1111, MPH1, ERCC4-like helicases [DNA replicati	1e-05
PLN03137	1195	PLN03137, PLN03137, ATP-dependent DNA helicase; Q4	5e-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 =  633 bits (1635), Expect = 0.0
 Identities = 273/381 (71%), Positives = 317/381 (83%)

Query: 32  TSYDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTA 91
           ++YDE+ D+FDA+ L E+LLRGIY+YGFEKPSAIQQRGI P   G D I QAQSGTGKTA
Sbjct: 21  SNYDEIVDSFDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTA 80

Query: 92  TFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQ 151
           TF    LQ +DY L  CQAL+LAPTRELAQQI+KV+ ALGDYL V+ HACVGGT VR+D 
Sbjct: 81  TFVIAALQLIDYDLNACQALILAPTRELAQQIQKVVLALGDYLKVRCHACVGGTVVRDDI 140

Query: 152 RILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPP 211
             L +GVH+VVGTPGRV+DM+ ++ LR D++++F+LDEADEMLSRGFK QIYD+F+ LPP
Sbjct: 141 NKLKAGVHMVVGTPGRVYDMIDKRHLRVDDLKLFILDEADEMLSRGFKGQIYDVFKKLPP 200

Query: 212 KIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCD 271
            +QV +FSATMP E LE+T KFM  P RILVK+DELTLEGI+QF+V VEKEEWK +TLCD
Sbjct: 201 DVQVALFSATMPNEILELTTKFMRDPKRILVKKDELTLEGIRQFYVAVEKEEWKFDTLCD 260

Query: 272 LYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRV 331
           LYETL ITQ++I+ NTRRKVD+LT KM  RD TVS  HGDMDQ  RD+IMREFRSGS+RV
Sbjct: 261 LYETLTITQAIIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRV 320

Query: 332 LITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLF 391
           LITTDLLARGIDVQQVSLVINYDLP  PENY+HRIGRSGRFGRKGVAINFVT DD   L 
Sbjct: 321 LITTDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSGRFGRKGVAINFVTPDDIEQLK 380

Query: 392 DIQKFYNVVIEELPANVADLL 412
           +I++ YN  IEE+P  VAD L
Sbjct: 381 EIERHYNTQIEEMPMEVADYL 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 =  406 bits (1045), Expect = e-139
 Identities = 168/392 (42%), Positives = 233/392 (59%), Gaps = 6/392 (1%)

Query: 18  RMNDLLGSDGQDFFTSYDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGL 77
           R   L  +         ++    F ++GL   LL+ +   GFE+P+ IQ   I     G 
Sbjct: 8   RFVKLKSAHNVALSRGEEKTPPEFASLGLSPELLQALKDLGFEEPTPIQLAAIPLILAGR 67

Query: 78  DVIQQAQSGTGKTATFCSGILQQLD--YGLVECQALVLAPTRELAQQIEKVMRALGDYL- 134
           DV+ QAQ+GTGKTA F   +LQ++          AL+LAPTRELA QI + +R LG  L 
Sbjct: 68  DVLGQAQTGTGKTAAFLLPLLQKILKSVERKYVSALILAPTRELAVQIAEELRKLGKNLG 127

Query: 135 GVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEML 194
           G++V    GG S+R+    L  GV +VV TPGR+ D+++R  L    +   VLDEAD ML
Sbjct: 128 GLRVAVVYGGVSIRKQIEALKRGVDIVVATPGRLLDLIKRGKLDLSGVETLVLDEADRML 187

Query: 195 SRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDEL--TLEGI 252
             GF D I  I + LPP  Q  +FSATMP +  E+ R+++N PV I V  ++L  TL+ I
Sbjct: 188 DMGFIDDIEKILKALPPDRQTLLFSATMPDDIRELARRYLNDPVEIEVSVEKLERTLKKI 247

Query: 253 KQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDM 312
           KQF++ VE EE KLE L  L +     + ++FV T+R V+ L + +R R   V+A HGD+
Sbjct: 248 KQFYLEVESEEEKLELLLKLLKDEDEGRVIVFVRTKRLVEELAESLRKRGFKVAALHGDL 307

Query: 313 DQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRF 372
            Q  RD  + +F+ G  RVL+ TD+ ARG+D+  VS VINYDLP  PE+Y+HRIGR+GR 
Sbjct: 308 PQEERDRALEKFKDGELRVLVATDVAARGLDIPDVSHVINYDLPLDPEDYVHRIGRTGRA 367

Query: 373 GRKGVAINFVT-RDDERMLFDIQKFYNVVIEE 403
           GRKGVAI+FVT  ++ + L  I+K     +  
Sbjct: 368 GRKGVAISFVTEEEEVKKLKRIEKRLERKLPS 399

Length = 513

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

 Score =  302 bits (777), Expect = e-103
 Identities = 107/203 (52%), Positives = 132/203 (65%), Gaps = 2/203 (0%)

Query: 41  FDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQ 100
           F+ +GL   LLRGIYA GFEKP+ IQ R I P   G DVI QAQ+G+GKTA F   IL++
Sbjct: 1   FEELGLSPELLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEK 60

Query: 101 LDY--GLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGV 158
           LD        QAL+LAPTRELA QI +V R LG +  +KV    GGTS+ +  R L  G 
Sbjct: 61  LDPSPKKDGPQALILAPTRELALQIAEVARKLGKHTNLKVVVIYGGTSIDKQIRKLKRGP 120

Query: 159 HVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVF 218
           H+VV TPGR+ D+L R  L    ++  VLDEAD ML  GF+DQI +I +LLP   Q  +F
Sbjct: 121 HIVVATPGRLLDLLERGKLDLSKVKYLVLDEADRMLDMGFEDQIREILKLLPKDRQTLLF 180

Query: 219 SATMPPEALEITRKFMNKPVRIL 241
           SATMP E  ++ RKF+  PVRIL
Sbjct: 181 SATMPKEVRDLARKFLRNPVRIL 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 (744), Expect = 3e-94
 Identities = 134/375 (35%), Positives = 202/375 (53%), Gaps = 7/375 (1%)

Query: 41  FDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQ 100
           F  + L   LL  +   G+ + + IQ + +     G DVI QA++G+GKTA F  G+LQ+
Sbjct: 6   FSTLPLPPALLANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQK 65

Query: 101 LDYGLVECQALVLAPTRELAQQIEKVMRALGDYL-GVKVHACVGGTSVREDQRILSSGVH 159
           LD      QALVL PTRELA Q+ K +R L  ++  +KV    GG  +      L  G H
Sbjct: 66  LDVKRFRVQALVLCPTRELADQVAKEIRRLARFIPNIKVLTLCGGVPMGPQIDSLEHGAH 125

Query: 160 VVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFS 219
           ++VGTPGR+ D LR+ +L  D +   VLDEAD ML  GF+D I  I +  P + Q  +FS
Sbjct: 126 IIVGTPGRILDHLRKGTLDLDALNTLVLDEADRMLDMGFQDAIDAIIRQAPARRQTLLFS 185

Query: 220 ATMPPEALEITRKFMNKPVRILV--KRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLA 277
           AT P     I+++F   PV + V    D      I+Q    V  +E +L  L  L     
Sbjct: 186 ATYPEGIAAISQRFQRDPVEVKVESTHDLPA---IEQRFYEVSPDE-RLPALQRLLLHHQ 241

Query: 278 ITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDL 337
               V+F NT+++   + D + ++  +  A HGD++Q  RD ++  F + S  VL+ TD+
Sbjct: 242 PESCVVFCNTKKECQEVADALNAQGFSALALHGDLEQRDRDQVLVRFANRSCSVLVATDV 301

Query: 338 LARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFY 397
            ARG+D++ +  VINY+L   PE ++HRIGR+GR G KG+A++ V  ++ +    I+ + 
Sbjct: 302 AARGLDIKALEAVINYELARDPEVHVHRIGRTGRAGSKGLALSLVAPEEMQRANAIEDYL 361

Query: 398 NVVIEELPANVADLL 412
              +   P      L
Sbjct: 362 GRKLNWEPLPSLSPL 376

Length = 460

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

 Score =  253 bits (648), Expect = 3e-78
 Identities = 146/378 (38%), Positives = 207/378 (54%), Gaps = 2/378 (0%)

Query: 36  EVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCS 95
           E   TF  +GL+  +L  +   G+EKPS IQ   I     G DV+  AQ+G+GKTA F  
Sbjct: 3   EFETTFADLGLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSL 62

Query: 96  GILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYL-GVKVHACVGGTSVREDQRIL 154
            +L  LD  L   Q LVLAPTRELA Q+ + M     ++ GV V A  GG       R L
Sbjct: 63  PLLHNLDPELKAPQILVLAPTRELAVQVAEAMTDFSKHMRGVNVVALYGGQRYDVQLRAL 122

Query: 155 SSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQ 214
             G  +VVGTPGR+ D L+R +L    +   VLDEADEML  GF + +  I   +P   Q
Sbjct: 123 RQGPQIVVGTPGRLLDHLKRGTLDLSKLSGLVLDEADEMLRMGFIEDVETIMAQIPEGHQ 182

Query: 215 VGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYE 274
             +FSATMP     ITR+FM +P  + ++    T   I Q +  V     K E L    E
Sbjct: 183 TALFSATMPEAIRRITRRFMKEPQEVRIQSSVTTRPDISQSYWTVWGMR-KNEALVRFLE 241

Query: 275 TLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLIT 334
                 ++IFV T+     + + +    +  +A +GDM+Q  R+  +   + G   +LI 
Sbjct: 242 AEDFDAAIIFVRTKNATLEVAEALERNGYNSAALNGDMNQALREQTLERLKDGRLDILIA 301

Query: 335 TDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQ 394
           TD+ ARG+DV+++SLV+NYD+P   E+Y+HRIGR+GR GR G A+ FV   + R+L +I+
Sbjct: 302 TDVAARGLDVERISLVVNYDIPMDSESYVHRIGRTGRAGRAGRALLFVENRERRLLRNIE 361

Query: 395 KFYNVVIEELPANVADLL 412
           +   + I E+    A+LL
Sbjct: 362 RTMKLTIPEVELPNAELL 379

Length = 629

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

 Score =  238 bits (610), Expect = 2e-74
 Identities = 131/362 (36%), Positives = 203/362 (56%), Gaps = 7/362 (1%)

Query: 40  TFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQ 99
           +FD++GL  ++LR +   G+ +P+ IQQ+ I    +G D++  AQ+GTGKTA F   +LQ
Sbjct: 2   SFDSLGLSPDILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQ 61

Query: 100 QLDY------GLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRI 153
            L        G    +AL+L PTRELA QI + +R    YL ++     GG S+      
Sbjct: 62  HLITRQPHAKGRRPVRALILTPTRELAAQIGENVRDYSKYLNIRSLVVFGGVSINPQMMK 121

Query: 154 LSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKI 213
           L  GV V+V TPGR+ D+  + +++ D + I VLDEAD ML  GF   I  +   LP K 
Sbjct: 122 LRGGVDVLVATPGRLLDLEHQNAVKLDQVEILVLDEADRMLDMGFIHDIRRVLAKLPAKR 181

Query: 214 QVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLY 273
           Q  +FSAT   +   +  K ++ P+ I V R     E + Q HV+   ++ K E L  + 
Sbjct: 182 QNLLFSATFSDDIKALAEKLLHNPLEIEVARRNTASEQVTQ-HVHFVDKKRKRELLSQMI 240

Query: 274 ETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLI 333
                 Q ++F  T+   + L +++       +A HG+  Q  R   + +F+SG  RVL+
Sbjct: 241 GKGNWQQVLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALADFKSGDIRVLV 300

Query: 334 TTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDI 393
            TD+ ARG+D++++  V+NY+LP  PE+Y+HRIGR+GR    G A++ V  D+ ++L DI
Sbjct: 301 ATDIAARGLDIEELPHVVNYELPNVPEDYVHRIGRTGRAAATGEALSLVCVDEHKLLRDI 360

Query: 394 QK 395
           +K
Sbjct: 361 EK 362

Length = 456

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

 Score =  231 bits (592), Expect = 6e-72
 Identities = 129/379 (34%), Positives = 191/379 (50%), Gaps = 18/379 (4%)

Query: 40  TFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQ 99
           TF  + L E+LL  +   G+ +P+AIQ   I P   G DV+  A +GTGKTA F    LQ
Sbjct: 2   TFSELELDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQ 61

Query: 100 QL-DY-----GLVECQA--LVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQ 151
            L D+     G        L+L PTRELA Q+    R L  +  + +    GG +     
Sbjct: 62  HLLDFPRRKSG----PPRILILTPTRELAMQVADQARELAKHTHLDIATITGGVAYMNHA 117

Query: 152 RILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPP 211
            + S    +VV TPGR+   ++ ++     +   +LDEAD ML  GF   I  I      
Sbjct: 118 EVFSENQDIVVATPGRLLQYIKEENFDCRAVETLILDEADRMLDMGFAQDIETIAAETRW 177

Query: 212 KIQVGVFSATMPPEALE-ITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLC 270
           + Q  +FSAT+  +A++    + +N PV +  +      + I Q++   +  E K   LC
Sbjct: 178 RKQTLLFSATLEGDAVQDFAERLLNDPVEVEAEPSRRERKKIHQWYYRADDLEHKTALLC 237

Query: 271 DLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSR 330
            L +   +T+S++FV TR +V  L   +R          G+M Q  R+  ++    G   
Sbjct: 238 HLLKQPEVTRSIVFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRVN 297

Query: 331 VLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERML 390
           VL+ TD+ ARGID+  VS VIN+D+P   + YLHRIGR+GR GRKG AI+ V   D  +L
Sbjct: 298 VLVATDVAARGIDIDDVSHVINFDMPRSADTYLHRIGRTGRAGRKGTAISLVEAHDHLLL 357

Query: 391 FDIQKFYNV-----VIEEL 404
             I+++        VI+EL
Sbjct: 358 GKIERYIEEPLKARVIDEL 376

Length = 434

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

 Score =  217 bits (555), Expect = 2e-65
 Identities = 131/369 (35%), Positives = 189/369 (51%), Gaps = 18/369 (4%)

Query: 40  TFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFC----S 95
           +F+     + +L+ +   GF +P+ IQ +G      G D+I  A++G+GKT  F      
Sbjct: 131 SFEYTSFPDYILKSLKNAGFTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLPAIV 190

Query: 96  GILQQ--LDYG---LVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVRED 150
            I  Q  L YG   +V    LVLAPTRELA+QI +     G    ++     GG   R  
Sbjct: 191 HINAQPLLRYGDGPIV----LVLAPTRELAEQIREQCNKFGASSKIRNTVAYGGVPKRGQ 246

Query: 151 QRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLP 210
              L  GV +++  PGR+ D L         +   VLDEAD ML  GF+ QI  I   + 
Sbjct: 247 IYALRRGVEILIACPGRLIDFLESNVTNLRRVTYLVLDEADRMLDMGFEPQIRKIVSQIR 306

Query: 211 PKIQVGVFSATMPPEALEITRKFM-NKPVRILVKRDELTL-EGIKQFHVNVEKEEWKLET 268
           P  Q  ++SAT P E   + R     +PV + V   +LT    IKQ  V V +E  K   
Sbjct: 307 PDRQTLMWSATWPKEVQSLARDLCKEEPVHVNVGSLDLTACHNIKQ-EVFVVEEHEKRGK 365

Query: 269 LCDLYETLAITQS--VIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRS 326
           L  L + +       +IFV T++  D+LT ++R         HGD  Q  R  ++ EF++
Sbjct: 366 LKMLLQRIMRDGDKILIFVETKKGADFLTKELRLDGWPALCIHGDKKQEERTWVLNEFKT 425

Query: 327 GSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDD 386
           G S ++I TD+ +RG+DV+ V  VIN+D P Q E+Y+HRIGR+GR G KG +  F+T D 
Sbjct: 426 GKSPIMIATDVASRGLDVKDVKYVINFDFPNQIEDYVHRIGRTGRAGAKGASYTFLTPDK 485

Query: 387 ERMLFDIQK 395
            R+  D+ K
Sbjct: 486 YRLARDLVK 494

Length = 545

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

 Score =  215 bits (549), Expect = 4e-65
 Identities = 123/378 (32%), Positives = 194/378 (51%), Gaps = 11/378 (2%)

Query: 28  QDFFTSYDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGT 87
           +DF     E    F    L   L+  I+  GF   + IQ + +     G D I +AQ+GT
Sbjct: 76  EDFVVEPQEGKTRFHDFNLAPELMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGT 135

Query: 88  GKTATFCSGILQQL-------DYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHA 140
           GKTA F   I+ QL       +  + E +AL++APTREL  QI K   AL  Y G+ V  
Sbjct: 136 GKTAAFLISIINQLLQTPPPKERYMGEPRALIIAPTRELVVQIAKDAAALTKYTGLNVMT 195

Query: 141 CVGGTSVREDQRILSSG-VHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFK 199
            VGG    +  + L +    ++V TPGR+ D  +R  +  D + + VLDEAD ML  GF 
Sbjct: 196 FVGGMDFDKQLKQLEARFCDILVATPGRLLDFNQRGEVHLDMVEVMVLDEADRMLDMGFI 255

Query: 200 DQIYDIFQLLPPKI--QVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHV 257
            Q+  I +  P K   Q  +FSAT   + + + +++   P  + ++ + +  + ++Q HV
Sbjct: 256 PQVRQIIRQTPRKEERQTLLFSATFTDDVMNLAKQWTTDPAIVEIEPENVASDTVEQ-HV 314

Query: 258 NVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTR 317
                  K + L +L       + ++F N + +V  + +++       +   GD+ Q+ R
Sbjct: 315 YAVAGSDKYKLLYNLVTQNPWERVMVFANRKDEVRRIEERLVKDGINAAQLSGDVPQHKR 374

Query: 318 DIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGV 377
              +  FR G  RVL+ TD+  RGI +  +S VIN+ LP  P++Y+HRIGR+GR G  GV
Sbjct: 375 IKTLEGFREGKIRVLVATDVAGRGIHIDGISHVINFTLPEDPDDYVHRIGRTGRAGASGV 434

Query: 378 AINFVTRDDERMLFDIQK 395
           +I+F   DD   L +I++
Sbjct: 435 SISFAGEDDAFQLPEIEE 452

Length = 475

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

 Score =  201 bits (514), Expect = 1e-59
 Identities = 123/368 (33%), Positives = 192/368 (52%), Gaps = 25/368 (6%)

Query: 40  TFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATF------ 93
           +F + GL   LL  +   G+E P+ IQ + I     G  ++  A +G+GKTA+F      
Sbjct: 122 SFSSCGLPPKLLLNLETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPIIS 181

Query: 94  -CSGILQQLDYGLVECQ---ALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVRE 149
            C  I         E +   A+VL PTREL  Q+E   + LG  L  K    VGG ++ +
Sbjct: 182 RCCTIRSG---HPSEQRNPLAMVLTPTRELCVQVEDQAKVLGKGLPFKTALVVGGDAMPQ 238

Query: 150 DQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLL 209
               +  GV ++VGTPGR+ D+L +  +  DN+ + VLDE D ML RGF+DQ+  IFQ L
Sbjct: 239 QLYRIQQGVELIVGTPGRLIDLLSKHDIELDNVSVLVLDEVDCMLERGFRDQVMQIFQAL 298

Query: 210 PPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETL 269
             + QV +FSAT+ PE  +         + I +       + +KQ  + VE ++ K +  
Sbjct: 299 -SQPQVLLFSATVSPEVEKFASSLAKDIILISIGNPNRPNKAVKQLAIWVETKQKKQK-- 355

Query: 270 CDLYETLAITQ-----SVIFVNTRRKVDWLTDKMRSRDHTVSAT-HGDMDQNTRDIIMRE 323
             L++ L   Q     +V+FV++R   D L + +       + + HG+     R  +M+ 
Sbjct: 356 --LFDILKSKQHFKPPAVVFVSSRLGADLLANAITVVTGLKALSIHGEKSMKERREVMKS 413

Query: 324 FRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVT 383
           F  G   V++ T +L RG+D+ +V  VI +D+P   + Y+H+IGR+ R G KG AI FV 
Sbjct: 414 FLVGEVPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQIGRASRMGEKGTAIVFVN 473

Query: 384 RDDERMLF 391
            +++R LF
Sbjct: 474 -EEDRNLF 480

Length = 518

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

 Score =  192 bits (491), Expect = 4e-57
 Identities = 117/352 (33%), Positives = 181/352 (51%), Gaps = 14/352 (3%)

Query: 41  FDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQ 100
           F    L   ++  +   GF   + IQ   +     G DV  QAQ+GTGKT  F +     
Sbjct: 10  FSDFALHPQVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHY 69

Query: 101 L-------DYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRI 153
           L       D  + + +AL++APTRELA QI      L    G+K+    GG    +  ++
Sbjct: 70  LLSHPAPEDRKVNQPRALIMAPTRELAVQIHADAEPLAQATGLKLGLAYGGDGYDKQLKV 129

Query: 154 LSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKI 213
           L SGV +++GT GR+ D  ++  +    I++ VLDEAD M   GF   I  +F+ +PP  
Sbjct: 130 LESGVDILIGTTGRLIDYAKQNHINLGAIQVVVLDEADRMFDLGFIKDIRWLFRRMPPAN 189

Query: 214 Q--VGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQ--FHVNVEKEEWKLETL 269
           Q    +FSAT+     E+  + MN P  + V+ ++ T   IK+  F+ + E+   K+  L
Sbjct: 190 QRLNMLFSATLSYRVRELAFEHMNNPEYVEVEPEQKTGHRIKEELFYPSNEE---KMRLL 246

Query: 270 CDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSS 329
             L E     +++IF NT+ + + +   + +  H V    GD+ Q  R  I+ EF  G  
Sbjct: 247 QTLIEEEWPDRAIIFANTKHRCEEIWGHLAADGHRVGLLTGDVAQKKRLRILEEFTRGDL 306

Query: 330 RVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINF 381
            +L+ TD+ ARG+ +  V+ V NYDLP   E+Y+HRIGR+GR G  G +I+ 
Sbjct: 307 DILVATDVAARGLHIPAVTHVFNYDLPDDCEDYVHRIGRTGRAGASGHSISL 358

Length = 423

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

 Score =  193 bits (492), Expect = 4e-56
 Identities = 123/369 (33%), Positives = 192/369 (52%), Gaps = 15/369 (4%)

Query: 40  TFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQ 99
           TF +  L   LL G+ + GF + + IQ   +     G DV  QAQ+GTGKT  F   ++ 
Sbjct: 10  TFSSFDLHPALLAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMN 69

Query: 100 QL-------DYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQR 152
           +L       D    + +AL+LAPTRELA QI K     G  LG++     GG    + + 
Sbjct: 70  RLLSRPALADRKPEDPRALILAPTRELAIQIHKDAVKFGADLGLRFALVYGGVDYDKQRE 129

Query: 153 ILSSGVHVVVGTPGRVFDMLRRQ---SLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLL 209
           +L  GV V++ TPGR+ D +++    SL      I VLDEAD M   GF   I  + + +
Sbjct: 130 LLQQGVDVIIATPGRLIDYVKQHKVVSLHA--CEICVLDEADRMFDLGFIKDIRFLLRRM 187

Query: 210 PPKI--QVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLE 267
           P +   Q  +FSAT+    LE+  + MN+P +++V+ + +T   ++Q  +    +E K  
Sbjct: 188 PERGTRQTLLFSATLSHRVLELAYEHMNEPEKLVVETETITAARVRQ-RIYFPADEEKQT 246

Query: 268 TLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSG 327
            L  L       ++++FVNT+  V+ +   +    + V    GD+ Q  R+ ++  F+ G
Sbjct: 247 LLLGLLSRSEGARTMVFVNTKAFVERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQKG 306

Query: 328 SSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDE 387
              +L+ TD+ ARG+ +  V  V NYDLP   E+Y+HRIGR+ R G +G AI+F      
Sbjct: 307 QLEILVATDVAARGLHIDGVKYVYNYDLPFDAEDYVHRIGRTARLGEEGDAISFACERYA 366

Query: 388 RMLFDIQKF 396
             L DI+ +
Sbjct: 367 MSLPDIEAY 375

Length = 572

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

 Score =  180 bits (458), Expect = 2e-55
 Identities = 73/169 (43%), Positives = 102/169 (60%), Gaps = 2/169 (1%)

Query: 63  SAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQ 122
           + IQ + I     G DV+ QA +G+GKT  F   ILQ L       QALVLAPTRELA+Q
Sbjct: 1   TPIQAQAIPAILSGKDVLVQAPTGSGKTLAFLLPILQALLPKKGGPQALVLAPTRELAEQ 60

Query: 123 IEKVMRALGDYLGVKVHACVGGTSVREDQRILSSG-VHVVVGTPGRVFDMLRRQSLRP-D 180
           I + ++ L   LG++V    GGTS++E  R L  G   ++VGTPGR+ D+LRR  L+   
Sbjct: 61  IYEELKKLFKILGLRVALLTGGTSLKEQARKLKKGKADILVGTPGRLLDLLRRGKLKLLK 120

Query: 181 NIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEI 229
           N+++ VLDEA  +L  GF D + +I   LPP  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 =  172 bits (438), Expect = 5e-52
 Identities = 82/204 (40%), Positives = 110/204 (53%), Gaps = 5/204 (2%)

Query: 54  IYAYGFEKPSAIQQRGIVPFCKGL-DVIQQAQSGTGKTATFCSGILQQLDYGLVECQALV 112
           I  +GFE     Q+  I     GL DVI  A +G+GKT       L+ L  G    + LV
Sbjct: 1   IEKFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGK-GGRVLV 59

Query: 113 LAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGV-HVVVGTPGRVFDM 171
           L PTRELA+Q  + ++ LG  LG+KV    GG S RE  R L SG   ++V TPGR+ D+
Sbjct: 60  LVPTRELAEQWAEELKKLGPSLGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDL 119

Query: 172 LRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITR 231
           L    L   N+ + +LDEA  +L  GF DQ+  + +LLP  +Q+ + SAT P E   +  
Sbjct: 120 LENDKLSLSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNVQLLLLSATPPEEIENLLE 179

Query: 232 KFMNKPVRILVKRDELTLEGIKQF 255
            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 =  143 bits (363), Expect = 9e-42
 Identities = 57/132 (43%), Positives = 84/132 (63%), Gaps = 4/132 (3%)

Query: 252 IKQFHVNVEKEEWKLETLCDLYETLAIT--QSVIFVNTRRKVDWLTDKMRSRDHTVSATH 309
           IKQ+ + VE  + KLE L +L +       + +IF  +++ +D L + +R     V+A H
Sbjct: 2   IKQYVLPVE--DEKLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAALH 59

Query: 310 GDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRS 369
           GD  Q  R+ ++++FR G   VL+ TD++ARGID+  VS+VINYDLP  P +YL RIGR+
Sbjct: 60  GDGSQEEREEVLKDFREGEIVVLVATDVIARGIDLPNVSVVINYDLPWSPSSYLQRIGRA 119

Query: 370 GRFGRKGVAINF 381
           GR G+KG AI  
Sbjct: 120 GRAGQKGTAILL 131

Length = 131

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

 Score =  142 bits (360), Expect = 3e-41
 Identities = 60/145 (41%), Positives = 85/145 (58%), Gaps = 2/145 (1%)

Query: 78  DVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVK 137
           DV+  A +G+GKT      IL+ LD  L   Q LVLAPTRELA Q+ + ++ L    G+K
Sbjct: 2   DVLLAAPTGSGKTLAALLPILELLDS-LKGGQVLVLAPTRELANQVAERLKELFGE-GIK 59

Query: 138 VHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRG 197
           V   +GGTS+++ +++LS    +VVGTPGR+ D L R  L    + + +LDEA  +L++G
Sbjct: 60  VGYLIGGTSIKQQEKLLSGKTDIVVGTPGRLLDELERLKLSLKKLDLLILDEAHRLLNQG 119

Query: 198 FKDQIYDIFQLLPPKIQVGVFSATM 222
           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 = 2e-27
 Identities = 37/78 (47%), Positives = 52/78 (66%)

Query: 296 DKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDL 355
             +R     V+  HG + Q  R+ I+ +FR+G S+VL+ TD+  RGID+  V+LVINYDL
Sbjct: 1   KLLRKPGIKVARLHGGLSQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNLVINYDL 60

Query: 356 PTQPENYLHRIGRSGRFG 373
           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 = 1e-26
 Identities = 33/82 (40%), Positives = 51/82 (62%)

Query: 292 DWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVI 351
           + L + ++     V+  HG + Q  R+ I+ +F +G  +VL+ TD+  RG+D+  V LVI
Sbjct: 1   EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVI 60

Query: 352 NYDLPTQPENYLHRIGRSGRFG 373
            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 = 89.6 bits (223), Expect = 4e-19
 Identities = 88/357 (24%), Positives = 147/357 (41%), Gaps = 40/357 (11%)

Query: 59  FEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVEC--------QA 110
           F   +  Q+  I     G +V+  A +G+GKT       L  ++  L            A
Sbjct: 20  FTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEA---AFLPVINELLSLGKGKLEDGIYA 76

Query: 111 LVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFD 170
           L ++P + L   I + +      LG++V    G T   E Q++L +  H+++ TP  +  
Sbjct: 77  LYISPLKALNNDIRRRLEEPLRELGIEVAVRHGDTPQSEKQKMLKNPPHILITTPESLAI 136

Query: 171 MLR----RQSLRPDNIRIFVLDEADEMLS--RGFKDQI---YDIFQLLPPKIQ-VGVFSA 220
           +L     R+ LR  ++R  ++DE   +    RG   Q+    +  + L    Q +G+ SA
Sbjct: 137 LLNSPKFRELLR--DVRYVIVDEIHALAESKRG--VQLALSLERLRELAGDFQRIGL-SA 191

Query: 221 TMPPEALEITRKFM---NKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLA 277
           T+ P   E   KF+     P  I+       LE IK      +   +  E    LYE +A
Sbjct: 192 TVGP--PEEVAKFLVGFGDPCEIVDVSAAKKLE-IKVISPVEDLI-YDEELWAALYERIA 247

Query: 278 --ITQSV---IFVNTRRKVDWLTDKMRSR-DHTVSATHGDMDQNTRDIIMREFRSGSSRV 331
             + +     IF NTR   + L  +++      +   HG + +  R  +    + G  + 
Sbjct: 248 ELVKKHRTTLIFTNTRSGAERLAFRLKKLGPDIIEVHHGSLSRELRLEVEERLKEGELKA 307

Query: 332 LITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSG-RFGRKGVAINFVTRDDE 387
           ++ T  L  GID+  + LVI    P     +L RIGR+G R G     I      D+
Sbjct: 308 VVATSSLELGIDIGDIDLVIQLGSPKSVNRFLQRIGRAGHRLGEVSKGIIIAEDRDD 364

Length = 814

>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 = 75.9 bits (187), Expect = 9e-15
 Identities = 78/352 (22%), Positives = 129/352 (36%), Gaps = 52/352 (14%)

Query: 75  KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYL 134
           +G +V+    +G+GKT +F   IL  L       +AL+L PT  LA    + +R L   L
Sbjct: 84  EGRNVVVTTGTGSGKTESFLLPILDHLLRDP-SARALLLYPTNALANDQAERLRELISDL 142

Query: 135 GVKVHACV--GGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRP--------DNIRI 184
             KV      G T   E + I+ +   +++  P    DML    LR          N++ 
Sbjct: 143 PGKVTFGRYTGDTPPEERRAIIRNPPDILLTNP----DMLHYLLLRNHDAWLWLLRNLKY 198

Query: 185 FVLDEAD----------EMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFM 234
            V+DE             +L R          +     +Q+   SAT+     E   +  
Sbjct: 199 LVVDELHTYRGVQGSEVALLLRRLLR----RLRRYGSPLQIICTSATLA-NPGEFAEELF 253

Query: 235 NKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLA---ITQSV-------IF 284
            +   + V  D     G++ F           E++               V       +F
Sbjct: 254 GRDFEVPVDEDGSP-RGLRYFVRREPPIRELAESIRRSALAELATLAALLVRNGIQTLVF 312

Query: 285 VNTRRKV--DWLTDKMRSRD------HTVSATHGDMDQNTRDIIMREFRSGSSRVLITTD 336
             +R++V   +L+ + R           VS     + +  R  I  EF+ G    +I T+
Sbjct: 313 FRSRKQVELLYLSPRRRLVREGGKLLDAVSTYRAGLHREERRRIEAEFKEGELLGVIATN 372

Query: 337 LLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKG-VAINFVTRDDE 387
            L  GID+  +  VI Y  P        +  R+GR GR+G  ++  V    +
Sbjct: 373 ALELGIDIGSLDAVIAYGYPGVSVLSFRQ--RAGRAGRRGQESLVLVVLRSD 422

Length = 851

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

 Score = 75.0 bits (185), Expect = 2e-14
 Identities = 54/235 (22%), Positives = 98/235 (41%), Gaps = 23/235 (9%)

Query: 166 GRVFDMLRRQSLRPDNIRIFVLDEADEMLSR---GFK---DQIYDIFQLLPPKIQVGVFS 219
            R  ++L+R       I +  +DEA   +S+    F+    ++  +   LP    V   +
Sbjct: 121 PRFLELLKRLP-----ISLVAIDEA-HCISQWGHDFRPDYRRLGRLRAGLP-NPPVLALT 173

Query: 220 ATMPPEALE--ITRKFMNKPVRIL--VKRDELTLEGIKQFHVNVEKEEWKLETLCDLYET 275
           AT  P   +    +  +           R  L L+ + +     ++  +    L  L ++
Sbjct: 174 ATATPRVRDDIREQLGLQDANIFRGSFDRPNLALK-VVEKGEPSDQLAFLATVLPQLSKS 232

Query: 276 LAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITT 335
                 +I+  TR+KV+ L + +R    +  A H  +    R+ + + F +   +V++ T
Sbjct: 233 -----GIIYCLTRKKVEELAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKVMVAT 287

Query: 336 DLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERML 390
           +    GID   V  VI+YDLP   E+Y    GR+GR G    AI   + +D R  
Sbjct: 288 NAFGMGIDKPDVRFVIHYDLPGSIESYYQETGRAGRDGLPAEAILLYSPEDIRWQ 342

Length = 590

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

 Score = 68.7 bits (168), Expect = 2e-12
 Identities = 97/392 (24%), Positives = 160/392 (40%), Gaps = 51/392 (13%)

Query: 13  RQFDARMNDLLGSDGQDFFTSYDEVYDT--------FDAMGLQENLLRGIYAYGFEKPSA 64
              D R + L   +     T YDEV            D + + E   R +   G E+   
Sbjct: 164 EMLDPRFDPLEDPE----LTRYDEVTAETDEVERVPVDELDIPEKFKRMLKREGIEELLP 219

Query: 65  IQ----QRGIVPFCKGLDVIQQAQSGTGKTATF-CSGILQQLDYGLVECQALVLAPTREL 119
           +Q    + G++   +G +++  + + +GKT     +GI + L  G    + L L P   L
Sbjct: 220 VQVLAVEAGLL---EGENLLVVSATASGKTLIGELAGIPRLLSGGK---KMLFLVPLVAL 273

Query: 120 AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL----SSGVHVVVGT-PGRVFDMLRR 174
           A Q  +  +     LG+KV   VG + ++  +  +    S    ++VGT  G   D L R
Sbjct: 274 ANQKYEDFKERYSKLGLKVAIRVGMSRIKTREEPVVVDTSPDADIIVGTYEG--IDYLLR 331

Query: 175 QSLRPDNIRIFVLDEAD--EMLSRGFK-DQIYDIFQLLPPKIQVGVFSATMP-PEALEIT 230
                 +I   V+DE    E   RG + D +    + L P  Q    SAT+  PE  E+ 
Sbjct: 332 TGKDLGDIGTVVIDEIHTLEDEERGPRLDGLIGRLRYLFPGAQFIYLSATVGNPE--ELA 389

Query: 231 RKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLE-TLCDL-YETLAIT----QSVIF 284
           +K   K V  L     + LE    F  N E E+W +   L    + T +      Q+++F
Sbjct: 390 KKLGAKLV--LYDERPVPLERHLVFARN-ESEKWDIIARLVKREFSTESSKGYRGQTIVF 446

Query: 285 VNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGID- 343
             +RR+   L D +  +    +  H  +    R  + R F +     ++TT  LA G+D 
Sbjct: 447 TYSRRRCHELADALTGKGLKAAPYHAGLPYKERKSVERAFAAQELAAVVTTAALAAGVDF 506

Query: 344 -VQQV---SLVINYDLPTQPENYLHRIGRSGR 371
              QV   SL +  +  +    +   +GR+GR
Sbjct: 507 PASQVIFESLAMGIEWLS-VREFQQMLGRAGR 537

Length = 830

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

 Score = 60.2 bits (146), Expect = 7e-10
 Identities = 28/105 (26%), Positives = 50/105 (47%)

Query: 282 VIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARG 341
           +I+  +R+K + +T  +++      A H  ++ + RD +  +F+    +V++ T     G
Sbjct: 230 IIYCPSRKKSEQVTASLQNLGIAAGAYHAGLEISARDDVHHKFQRDEIQVVVATVAFGMG 289

Query: 342 IDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDD 386
           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 = 3e-09
 Identities = 30/98 (30%), Positives = 51/98 (52%)

Query: 282 VIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARG 341
           +I+ ++R+KV+ L +++ S+  +  A H  +    R     +F     +V++ T+    G
Sbjct: 228 IIYASSRKKVEELAERLESQGISALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMG 287

Query: 342 IDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAI 379
           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|224125 COG1204, COG1204, Superfamily II helicase [General function prediction only]

 Score = 56.2 bits (136), Expect = 2e-08
 Identities = 67/319 (21%), Positives = 127/319 (39%), Gaps = 61/319 (19%)

Query: 75  KGLDVIQQAQSGTGKTATFCSGILQQL-DYGLVECQALVLAPTRELAQQIEKVMRALGDY 133
              +V+  A +G+GKT      IL  L + G    + + + P + LA++  +    L + 
Sbjct: 46  SDENVLISAPTGSGKTLIALLAILSTLLEGGG---KVVYIVPLKALAEEKYEEFSRLEEL 102

Query: 134 LGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEM 193
            G++V     G    +D+R+  +   V+V TP ++  + R++    + + + V+DE   +
Sbjct: 103 -GIRV-GISTGDYDLDDERL--ARYDVIVTTPEKLDSLTRKRPSWIEEVDLVVIDEI-HL 157

Query: 194 LS---RG-FKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMN-KPVRILVKRDEL- 247
           L    RG   + I    + L   I++   SAT+ P A E+   ++N K V    +   L 
Sbjct: 158 LGDRTRGPVLESIVARMRRLNELIRIVGLSATL-PNAEEVA-DWLNAKLVESDWRPVPLR 215

Query: 248 --TLEGIKQFHVNVEKEEWKLE----TLCDLYETLA-ITQSVIFVNTRR----------- 289
                       + +K+ W L      L  + E+LA   Q ++FV++R+           
Sbjct: 216 RGVPYVGAFLGADGKKKTWPLLIDNLALELVLESLAEGGQVLVFVHSRKEAEKTAKKLRI 275

Query: 290 ------------KVDWLTDKMRSRDHTVSAT--------------HGDMDQNTRDIIMRE 323
                        +D     +   +   S                H  + +  R ++   
Sbjct: 276 KMSATLSDDEKIVLDEGASPILIPETPTSEDEELAELVLRGVAFHHAGLPREDRQLVEDA 335

Query: 324 FRSGSSRVLITTDLLARGI 342
           FR G  +VL++T  LA G+
Sbjct: 336 FRKGKIKVLVSTPTLAAGV 354

Length = 766

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

 Score = 56.3 bits (136), Expect = 2e-08
 Identities = 28/100 (28%), Positives = 53/100 (53%)

Query: 282 VIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARG 341
           +I+ N+R KV+    +++SR  + +A H  +D + R  +   F+    ++++ T     G
Sbjct: 240 IIYCNSRAKVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMG 299

Query: 342 IDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINF 381
           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 = 52.1 bits (125), Expect = 3e-07
 Identities = 64/336 (19%), Positives = 112/336 (33%), Gaps = 81/336 (24%)

Query: 86  GTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQ-IEKVMRALGDYLGVKVHACVGG 144
           G GKT      I +           LVL PT+EL  Q  E + + L     + +    GG
Sbjct: 65  GAGKTVVAAEAIAELKR------STLVLVPTKELLDQWAEALKKFLLLNDEIGI---YGG 115

Query: 145 TSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLR---PDNIRIFVLDEADEMLSRGFKD- 200
                +         V V T   V  + RRQ L     +   + + DE   + +  ++  
Sbjct: 116 GEKELE------PAKVTVAT---VQTLARRQLLDEFLGNEFGLIIFDEVHHLPAPSYRRI 166

Query: 201 -----------------------QIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKP 237
                                  +I D+F L+ P     V+  +   E   I   +   P
Sbjct: 167 LELLSAAYPRLGLTATPEREDGGRIGDLFDLIGPI----VYEVS-LKEL--IDEGY-LAP 218

Query: 238 VRILVKRDELTLEGIKQ---FHVNVEKEEWKLETLCDLYETLAIT--------------- 279
            + +  +  LT +  ++         +      TL    E   I                
Sbjct: 219 YKYVEIKVTLTEDEEREYAKESARFRELLRARGTLRAENEARRIAIASERKIAAVRGLLL 278

Query: 280 ------QSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLI 333
                 +++IF +       +          V A  G+  +  R+ I+  FR+G  +VL+
Sbjct: 279 KHARGDKTLIFASDVEHAYEIAKLFL-APGIVEAITGETPKEEREAILERFRTGGIKVLV 337

Query: 334 TTDLLARGIDVQQVSLVINYDLPTQ-PENYLHRIGR 368
           T  +L  G+D+    ++I    PT     ++ R+GR
Sbjct: 338 TVKVLDEGVDIPDADVLI-ILRPTGSRRLFIQRLGR 372

Length = 442

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

 Score = 52.2 bits (126), Expect = 3e-07
 Identities = 84/344 (24%), Positives = 128/344 (37%), Gaps = 70/344 (20%)

Query: 82  QAQSGTGKT-ATFCSGILQQLDY------GLVECQALVLAPTRELAQQIEKVMRALGDYL 134
            A +G+GKT A F    L  L        GL     L + P R LA  I + ++A  + L
Sbjct: 34  IAPTGSGKTLAGFL-PSLIDLAGPEKPKKGL---HTLYITPLRALAVDIARNLQAPIEEL 89

Query: 135 GVKVHACV--GGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSL-----RPDNIRIF-- 185
           G+ +      G TS  E  R       +++ TP         +SL      PD  R+F  
Sbjct: 90  GLPIRVETRTGDTSSSERARQRKKPPDILLTTP---------ESLALLLSYPDAARLFKD 140

Query: 186 ----VLDEADEMLS--RGFKDQIYDIFQL-------LPPKIQVGVFSATM--PPEALEIT 230
               V+DE  E+    RG      D  +L       L P ++    SAT+    EA  + 
Sbjct: 141 LRCVVVDEWHELAGSKRG------DQLELALARLRRLAPGLRRWGLSATIGNLEEARRVL 194

Query: 231 RKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWK----LETLCDLYETLAITQSV-IFV 285
                 P  ++  +    +  I     + E+  W     L  L ++Y  +   ++  +F 
Sbjct: 195 LGVGGAPAVLVRGKLPKAIPVISLLPESEERFPWAGHLGLRALPEVYAEIDQARTTLVFT 254

Query: 286 NTRRKVD-WLTDKMRSRD--------HTVSATHGDMDQNTRDIIMREFRSGSSRVLITTD 336
           NTR + + W      +          H     HG +D+  R  +     +G  R ++ T 
Sbjct: 255 NTRSQAELWFQALWEANPEFALPIALH-----HGSLDREQRRWVEAAMAAGRLRAVVCTS 309

Query: 337 LLARGIDVQQVSLVINYDLPTQPENYLHRIGRSG-RFGRKGVAI 379
            L  G+D   V LVI    P      L R GRS  R G    A+
Sbjct: 310 SLDLGVDFGPVDLVIQIGSPKGVARLLQRAGRSNHRPGEPSRAL 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 = 50.8 bits (122), Expect = 8e-07
 Identities = 75/328 (22%), Positives = 129/328 (39%), Gaps = 59/328 (17%)

Query: 82  QAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHAC 141
           Q   G+GKT      +L  ++ G    Q  ++APT  LA+Q    +R L   LG++V   
Sbjct: 262 QGDVGSGKTLVAALAMLAAIEAGY---QVALMAPTEILAEQHYNSLRNLLAPLGIEVALL 318

Query: 142 VGGT------SVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEA----- 190
            G         + E   I S  +H+VVGT   + + +  + L      + ++DE      
Sbjct: 319 TGSLKGKRRKELLET--IASGQIHLVVGTHALIQEKVEFKRLA-----LVIIDEQHRFGV 371

Query: 191 ---DEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDEL 247
               ++  +G       +           V SAT  P  L +T  + +    I+   DEL
Sbjct: 372 EQRKKLREKGQGGFTPHVL----------VMSATPIPRTLALT-VYGDLDTSII---DEL 417

Query: 248 TLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTR----RKVD-------WLTD 296
              G K     + K + K      + E +A  +    V        K+D       +   
Sbjct: 418 PP-GRKPITTVLIKHDEKDIVYEFIEEEIAKGRQAYVVYPLIEESEKLDLKAAEALYERL 476

Query: 297 KMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLP 356
           K     + V   HG M  + ++ +M EFR G   +L+ T ++  G+DV   ++++  D  
Sbjct: 477 KKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPNATVMVIED-- 534

Query: 357 TQPENY----LHRI-GRSGRFGRKGVAI 379
              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 = 47.0 bits (112), Expect = 1e-05
 Identities = 39/138 (28%), Positives = 59/138 (42%), Gaps = 14/138 (10%)

Query: 265 KLETLCDLY-ETLAITQS---VIFVNTRRKVDWLT-------DKMRSRDHTVSATHGD-- 311
           KLE L ++  E L        ++F   R   + +         K R R    ++  GD  
Sbjct: 349 KLEKLREILKEQLEKNGDSRVIVFTEYRDTAEEIVNFLKKIGIKARVRFIGQASREGDKG 408

Query: 312 MDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGR 371
           M Q  +  I+ +FR G   VL+ T +   G+D+ +V LVI Y+        + R GR+GR
Sbjct: 409 MSQKEQKEIIDQFRKGEYNVLVATSVGEEGLDIPEVDLVIFYEPVPSEIRSIQRKGRTGR 468

Query: 372 FGRKGVAINFVTRDDERM 389
             RKG  +  VT      
Sbjct: 469 -KRKGRVVVLVTEGTRDE 485

Length = 542

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

 Score = 45.3 bits (107), Expect = 5e-05
 Identities = 23/94 (24%), Positives = 45/94 (47%)

Query: 282 VIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARG 341
           +I+  +R   + + ++++   H  +  HG MD   R  + +++      ++  T     G
Sbjct: 684 IIYCLSRMDCEKVAERLQEFGHKAAFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGMG 743

Query: 342 IDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRK 375
           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: 309 HGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGR 368
           HG + +  R I  +  +SG  R ++ T  L  GID+  V LVI    P    + L RIGR
Sbjct: 308 HGSVSKEQRAITEQALKSGELRCVVATSSLELGIDMGAVDLVIQVATPLSVASGLQRIGR 367

Query: 369 SG 370
           +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: 287 TRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQ 346
           T++  + LTD ++     V   H ++D   R  I+R+ R G   VL+  +LL  G+D+ +
Sbjct: 451 TKKMAEDLTDYLKELGIKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPE 510

Query: 347 VSLV 350
           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	412
KOG0328	400	consensus Predicted ATP-dependent RNA helicase FAL	100.0
PTZ00110	545	helicase; Provisional	100.0
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	100.0
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	100.0
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	100.0
KOG0331	519	consensus ATP-dependent RNA helicase [RNA processi	100.0
PTZ00424	401	helicase 45; Provisional	100.0
KOG0330	476	consensus ATP-dependent RNA helicase [RNA processi	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
KOG0326	459	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0342	543	consensus ATP-dependent RNA helicase pitchoune [RN	100.0
KOG0338	691	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0335	482	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0327	397	consensus Translation initiation factor 4F, helica	100.0
KOG0345	567	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0340	442	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0343	758	consensus RNA Helicase [RNA processing and modific	100.0
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	100.0
KOG0339	731	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0346	569	consensus RNA helicase [RNA processing and modific	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
KOG0348	708	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0341	610	consensus DEAD-box protein abstrakt [RNA processin	100.0
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	100.0
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	100.0
KOG0334	997	consensus RNA helicase [RNA processing and modific	100.0
PRK02362	737	ski2-like helicase; Provisional	100.0
KOG4284	980	consensus DEAD box protein [Transcription]	100.0
KOG0347	731	consensus RNA helicase [RNA processing and modific	100.0
COG1201	814	Lhr Lhr-like helicases [General function predictio	100.0
PRK13767	876	ATP-dependent helicase; Provisional	100.0
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	100.0
KOG0337	529	consensus ATP-dependent RNA helicase [RNA processi	100.0
PRK00254	720	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
PRK01172	674	ski2-like helicase; Provisional	100.0
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	100.0
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	100.0
PRK10689	1147	transcription-repair coupling factor; Provisional	100.0
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	100.0
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	100.0
COG1202	830	Superfamily II helicase, archaea-specific [General	100.0
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	100.0
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	100.0
PHA02558	501	uvsW UvsW helicase; Provisional	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
PHA02653	675	RNA helicase NPH-II; Provisional	100.0
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	100.0
COG1205	851	Distinct helicase family with a unique C-terminal	100.0
PRK09401	1176	reverse gyrase; Reviewed	100.0
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	100.0
PRK13766	773	Hef nuclease; Provisional	100.0
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	100.0
KOG0354	746	consensus DEAD-box like helicase [General function	100.0
KOG0329	387	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0351	941	consensus ATP-dependent DNA helicase [Replication,	100.0
KOG0352	641	consensus ATP-dependent DNA helicase [Replication,	100.0
PRK14701	1638	reverse gyrase; Provisional	100.0
KOG0353	695	consensus ATP-dependent DNA helicase [General func	100.0
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	100.0
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	100.0
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	100.0
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	100.0
KOG0952	1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	100.0
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	100.0
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	100.0
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	100.0
PRK09200	790	preprotein translocase subunit SecA; Reviewed	100.0
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	100.0
PRK04914	956	ATP-dependent helicase HepA; Validated	100.0
KOG0947	1248	consensus Cytoplasmic exosomal RNA helicase SKI2,	100.0
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	100.0
KOG0948	1041	consensus Nuclear exosomal RNA helicase MTR4, DEAD	100.0
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	100.0
PRK05580	679	primosome assembly protein PriA; Validated	100.0
KOG0349	725	consensus Putative DEAD-box RNA helicase DDX1 [RNA	100.0
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	100.0
PRK09694	878	helicase Cas3; Provisional	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	99.98
TIGR00595	505	priA primosomal protein N'. All proteins in this f	99.98
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	99.98
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	99.97
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	99.97
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	99.97
PRK12904	830	preprotein translocase subunit SecA; Reviewed	99.97
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	99.97
COG4096	875	HsdR Type I site-specific restriction-modification	99.96
KOG0950	1008	consensus DNA polymerase theta/eta, DEAD-box super	99.96
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	99.96
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	99.95
KOG0922	674	consensus DEAH-box RNA helicase [RNA processing an	99.95
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	99.95
PRK13107	908	preprotein translocase subunit SecA; Reviewed	99.95
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	99.95
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	99.94
KOG0385	971	consensus Chromatin remodeling complex WSTF-ISWI,	99.94
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	99.94
KOG1123	776	consensus RNA polymerase II transcription initiati	99.94
KOG0923	902	consensus mRNA splicing factor ATP-dependent RNA h	99.93
KOG0387	923	consensus Transcription-coupled repair protein CSB	99.93
KOG0924	1042	consensus mRNA splicing factor ATP-dependent RNA h	99.93
COG1198	730	PriA Primosomal protein N' (replication factor Y)	99.92
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	99.92
KOG0920	924	consensus ATP-dependent RNA helicase A [RNA proces	99.91
PRK12326	764	preprotein translocase subunit SecA; Reviewed	99.91
KOG0384	1373	consensus Chromodomain-helicase DNA-binding protei	99.91
KOG0390	776	consensus DNA repair protein, SNF2 family [Replica	99.91
KOG0925	699	consensus mRNA splicing factor ATP-dependent RNA h	99.9
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	99.9
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	99.9
COG4889	1518	Predicted helicase [General function prediction on	99.9
KOG1000	689	consensus Chromatin remodeling protein HARP/SMARCA	99.9
KOG0949	1330	consensus Predicted helicase, DEAD-box superfamily	99.9
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	99.89
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	99.89
KOG0926	1172	consensus DEAH-box RNA helicase [RNA processing an	99.88
smart00487	201	DEXDc DEAD-like helicases superfamily.	99.88
KOG0392	1549	consensus SNF2 family DNA-dependent ATPase domain-	99.88
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	99.87
PRK05298	652	excinuclease ABC subunit B; Provisional	99.86
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	99.86
KOG0389	941	consensus SNF2 family DNA-dependent ATPase [Chroma	99.86
CHL00122	870	secA preprotein translocase subunit SecA; Validate	99.84
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	99.84
KOG4150	1034	consensus Predicted ATP-dependent RNA helicase [RN	99.84
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	99.83
cd00079	131	HELICc Helicase superfamily c-terminal domain; ass	99.81
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	99.8
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	99.79
KOG0953	700	consensus Mitochondrial RNA helicase SUV3, DEAD-bo	99.79
KOG0386	1157	consensus Chromatin remodeling complex SWI/SNF, co	99.79
KOG4439	901	consensus RNA polymerase II transcription terminat	99.79
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	99.78
COG0610	962	Type I site-specific restriction-modification syst	99.78
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	99.77
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	99.77
TIGR02562	1110	cas3_yersinia CRISPR-associated helicase Cas3. The	99.76
PF00271	78	Helicase_C: Helicase conserved C-terminal domain;	99.75
KOG1002	791	consensus Nucleotide excision repair protein RAD16	99.74
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	99.73
KOG0388	1185	consensus SNF2 family DNA-dependent ATPase [Replic	99.72
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	99.72
KOG0391	1958	consensus SNF2 family DNA-dependent ATPase [Genera	99.71
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	99.71
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	99.7
PRK14873	665	primosome assembly protein PriA; Provisional	99.65
KOG1015	1567	consensus Transcription regulator XNP/ATRX, DEAD-b	99.64
smart00490	82	HELICc helicase superfamily c-terminal domain.	99.63
COG0553	866	HepA Superfamily II DNA/RNA helicases, SNF2 family	99.57
PF07652	148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	99.57
PF00176	299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	99.53
PF06862	442	DUF1253: Protein of unknown function (DUF1253); In	99.5
COG0653	822	SecA Preprotein translocase subunit SecA (ATPase,	99.45
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	99.3
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	99.3
PRK15483	986	type III restriction-modification system StyLTI en	99.25
KOG1016	1387	consensus Predicted DNA helicase, DEAD-box superfa	99.17
KOG1133	821	consensus Helicase of the DEAD superfamily [Replic	99.15
PF07517	266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	99.06
KOG2340	698	consensus Uncharacterized conserved protein [Funct	99.06
KOG1001	674	consensus Helicase-like transcription factor HLTF/	99.03
KOG0921	1282	consensus Dosage compensation complex, subunit MLE	99.02
COG3587	985	Restriction endonuclease [Defense mechanisms]	98.94
PF13872	303	AAA_34: P-loop containing NTP hydrolase pore-1	98.93
KOG0952	1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	98.86
PF13307	167	Helicase_C_2: Helicase C-terminal domain; PDB: 4A1	98.83
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	98.81
KOG1802	935	consensus RNA helicase nonsense mRNA reducing fact	98.74
KOG1131	755	consensus RNA polymerase II transcription initiati	98.68
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	98.65
TIGR00596	814	rad1 DNA repair protein (rad1). This family is bas	98.6
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	98.6
PRK10536	262	hypothetical protein; Provisional	98.47
KOG1803	649	consensus DNA helicase [Replication, recombination	98.35
KOG1132	945	consensus Helicase of the DEAD superfamily [Replic	98.34
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	98.32
PF13245	76	AAA_19: Part of AAA domain	98.31
PF12340	229	DUF3638: Protein of unknown function (DUF3638); In	98.3
PRK10875	615	recD exonuclease V subunit alpha; Provisional	98.27
TIGR00376	637	DNA helicase, putative. The gene product may repre	98.26
TIGR01447	586	recD exodeoxyribonuclease V, alpha subunit. This f	98.26
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	98.24
COG3421	812	Uncharacterized protein conserved in bacteria [Fun	98.22
smart00492	141	HELICc3 helicase superfamily c-terminal domain.	98.12
COG1875	436	NYN ribonuclease and ATPase of PhoH family domains	98.07
smart00491	142	HELICc2 helicase superfamily c-terminal domain.	98.06
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	98.02
PF00580	315	UvrD-helicase: UvrD/REP helicase N-terminal domain	97.96
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	97.91
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	97.85
KOG0298	1394	consensus DEAD box-containing helicase-like transc	97.84
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	97.84
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	97.77
PRK13889	988	conjugal transfer relaxase TraA; Provisional	97.77
PRK04296	190	thymidine kinase; Provisional	97.76
KOG1805	1100	consensus DNA replication helicase [Replication, r	97.74
PRK08181	269	transposase; Validated	97.64
PF13871	278	Helicase_C_4: Helicase_C-like	97.61
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	97.6
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	97.6
PRK13826	1102	Dtr system oriT relaxase; Provisional	97.58
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	97.57
PRK06526	254	transposase; Provisional	97.55
PRK14974	336	cell division protein FtsY; Provisional	97.54
KOG0383	696	consensus Predicted helicase [General function pre	97.51
smart00382	148	AAA ATPases associated with a variety of cellular	97.51
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	97.38
PF03354	477	Terminase_1: Phage Terminase ; InterPro: IPR005021	97.37
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	97.35
PRK10919	672	ATP-dependent DNA helicase Rep; Provisional	97.26
PHA02533	534	17 large terminase protein; Provisional	97.26
KOG1513	1300	consensus Nuclear helicase MOP-3/SNO (DEAD-box sup	97.23
PRK11054	684	helD DNA helicase IV; Provisional	97.2
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	97.16
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	97.14
PRK05642	234	DNA replication initiation factor; Validated	97.12
PRK00149	450	dnaA chromosomal replication initiation protein; R	97.09
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	97.08
PRK14087	450	dnaA chromosomal replication initiation protein; P	97.07
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	97.06
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	97.03
COG1435	201	Tdk Thymidine kinase [Nucleotide transport and met	97.02
COG4626	546	Phage terminase-like protein, large subunit [Gener	97.01
PRK06921	266	hypothetical protein; Provisional	96.99
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	96.99
TIGR01075	715	uvrD DNA helicase II. Designed to identify uvrD me	96.97
TIGR01074	664	rep ATP-dependent DNA helicase Rep. Designed to id	96.92
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	96.91
PRK06893	229	DNA replication initiation factor; Validated	96.91
PRK11773	721	uvrD DNA-dependent helicase II; Provisional	96.89
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	96.89
PRK08727	233	hypothetical protein; Validated	96.88
PRK12377	248	putative replication protein; Provisional	96.83
PF05127	177	Helicase_RecD: Helicase; InterPro: IPR007807 This	96.8
PHA03368	738	DNA packaging terminase subunit 1; Provisional	96.8
PRK07952	244	DNA replication protein DnaC; Validated	96.79
PRK08084	235	DNA replication initiation factor; Provisional	96.79
TIGR02785	1232	addA_Gpos recombination helicase AddA, Firmicutes	96.79
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	96.79
PRK08116	268	hypothetical protein; Validated	96.75
PRK06731	270	flhF flagellar biosynthesis regulator FlhF; Valida	96.74
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	96.73
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	96.73
TIGR01073	726	pcrA ATP-dependent DNA helicase PcrA. Designed to	96.73
COG2256	436	MGS1 ATPase related to the helicase subunit of the	96.71
PRK06835	329	DNA replication protein DnaC; Validated	96.7
COG1484	254	DnaC DNA replication protein [DNA replication, rec	96.69
PRK08903	227	DnaA regulatory inactivator Hda; Validated	96.66
PRK00771	437	signal recognition particle protein Srp54; Provisi	96.63
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	96.63
PRK14088	440	dnaA chromosomal replication initiation protein; P	96.62
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	96.6
PLN03025	319	replication factor C subunit; Provisional	96.6
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	96.59
PRK08769	319	DNA polymerase III subunit delta'; Validated	96.59
PF13173	128	AAA_14: AAA domain	96.57
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	96.56
PRK09183	259	transposase/IS protein; Provisional	96.56
PRK14712	1623	conjugal transfer nickase/helicase TraI; Provision	96.53
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	96.52
PRK12402	337	replication factor C small subunit 2; Reviewed	96.52
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	96.52
KOG2028	554	consensus ATPase related to the helicase subunit o	96.49
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	96.48
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	96.46
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	96.45
TIGR01547	396	phage_term_2 phage terminase, large subunit, PBSX	96.45
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	96.45
PRK05707	328	DNA polymerase III subunit delta'; Validated	96.44
PRK00411	394	cdc6 cell division control protein 6; Reviewed	96.43
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	96.41
PHA03333	752	putative ATPase subunit of terminase; Provisional	96.4
PRK14086	617	dnaA chromosomal replication initiation protein; P	96.4
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	96.35
PRK12422	445	chromosomal replication initiation protein; Provis	96.35
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	96.35
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	96.34
PTZ00112	1164	origin recognition complex 1 protein; Provisional	96.33
PTZ00293	211	thymidine kinase; Provisional	96.33
PRK13709	1747	conjugal transfer nickase/helicase TraI; Provision	96.31
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	96.31
PF05876	557	Terminase_GpA: Phage terminase large subunit (GpA)	96.25
COG2805	353	PilT Tfp pilus assembly protein, pilus retraction	96.22
PF03969	362	AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654	96.19
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	96.15
TIGR00064	272	ftsY signal recognition particle-docking protein F	96.14
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	96.14
PRK08533	230	flagellar accessory protein FlaH; Reviewed	96.13
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	96.13
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	96.12
COG1444	758	Predicted P-loop ATPase fused to an acetyltransfer	96.09
CHL00181	287	cbbX CbbX; Provisional	96.08
cd03115	173	SRP The signal recognition particle (SRP) mediates	96.07
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	96.05
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	96.02
PRK05986	191	cob(I)alamin adenolsyltransferase/cobinamide ATP-d	96.01
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	96.01
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	96.01
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	95.99
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	95.97
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	95.97
PHA02544	316	44 clamp loader, small subunit; Provisional	95.97
PF14617	252	CMS1: U3-containing 90S pre-ribosomal complex subu	95.96
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	95.94
PRK00440	319	rfc replication factor C small subunit; Reviewed	95.94
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	95.93
COG3972	660	Superfamily I DNA and RNA helicases [General funct	95.91
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	95.9
PF02572	172	CobA_CobO_BtuR: ATP:corrinoid adenosyltransferase	95.89
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	95.89
COG0593	408	DnaA ATPase involved in DNA replication initiation	95.88
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	95.82
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	95.8
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	95.79
COG4962	355	CpaF Flp pilus assembly protein, ATPase CpaF [Intr	95.78
PRK08939	306	primosomal protein DnaI; Reviewed	95.77
PRK13833	323	conjugal transfer protein TrbB; Provisional	95.77
PHA00729	226	NTP-binding motif containing protein	95.74
PRK06871	325	DNA polymerase III subunit delta'; Validated	95.73
PRK09376	416	rho transcription termination factor Rho; Provisio	95.69
TIGR00767	415	rho transcription termination factor Rho. Members	95.69
TIGR00708	173	cobA cob(I)alamin adenosyltransferase. Alternate n	95.65
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	95.65
PRK13342	413	recombination factor protein RarA; Reviewed	95.64
PF00004	132	AAA: ATPase family associated with various cellula	95.63
PRK05580	679	primosome assembly protein PriA; Validated	95.62
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	95.61
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	95.59
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	95.57
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	95.57
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	95.56
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	95.56
PRK10867	433	signal recognition particle protein; Provisional	95.55
PRK04195	482	replication factor C large subunit; Provisional	95.51
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	95.5
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	95.46
PRK11823	446	DNA repair protein RadA; Provisional	95.45
PRK10416	318	signal recognition particle-docking protein FtsY;	95.45
PRK13341	725	recombination factor protein RarA/unknown domain f	95.43
cd01128	249	rho_factor Transcription termination factor rho is	95.38
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	95.37
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	95.35
COG3973	747	Superfamily I DNA and RNA helicases [General funct	95.33
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	95.3
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	95.3
PRK06067	234	flagellar accessory protein FlaH; Validated	95.29
PF05729	166	NACHT: NACHT domain	95.29
PRK12608	380	transcription termination factor Rho; Provisional	95.27
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	95.25
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	95.24
PRK06090	319	DNA polymerase III subunit delta'; Validated	95.24
TIGR00595	505	priA primosomal protein N'. All proteins in this f	95.23
PRK06620	214	hypothetical protein; Validated	95.23
KOG0298	1394	consensus DEAD box-containing helicase-like transc	95.22
PF02456	369	Adeno_IVa2: Adenovirus IVa2 protein; InterPro: IPR	95.19
TIGR00959	428	ffh signal recognition particle protein. This mode	95.16
PRK07471	365	DNA polymerase III subunit delta'; Validated	95.16
PHA00012	361	I assembly protein	95.15
KOG0742	630	consensus AAA+-type ATPase [Posttranslational modi	95.11
PRK07993	334	DNA polymerase III subunit delta'; Validated	95.1
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	95.1
PRK06964	342	DNA polymerase III subunit delta'; Validated	95.09
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	95.08
COG2109	198	BtuR ATP:corrinoid adenosyltransferase [Coenzyme m	95.05
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	95.02
KOG1132	945	consensus Helicase of the DEAD superfamily [Replic	95.01
PRK09112	351	DNA polymerase III subunit delta'; Validated	94.99
COG0552	340	FtsY Signal recognition particle GTPase [Intracell	94.97
COG1485	367	Predicted ATPase [General function prediction only	94.97
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	94.97
PRK05973	237	replicative DNA helicase; Provisional	94.92
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	94.91
PRK08699	325	DNA polymerase III subunit delta'; Validated	94.87
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	94.82
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	94.81
COG1198	730	PriA Primosomal protein N' (replication factor Y)	94.79
PRK07414	178	cob(I)yrinic acid a,c-diamide adenosyltransferase;	94.77
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	94.75
PRK14873	665	primosome assembly protein PriA; Provisional	94.7
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	94.65
PF01443	234	Viral_helicase1: Viral (Superfamily 1) RNA helicas	94.61
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	94.57
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	94.56
PRK04841	903	transcriptional regulator MalT; Provisional	94.54
PRK06904	472	replicative DNA helicase; Validated	94.54
PF03796	259	DnaB_C: DnaB-like helicase C terminal domain; Inte	94.52
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	94.5
TIGR03600	421	phage_DnaB phage replicative helicase, DnaB family	94.48
PF03237	384	Terminase_6: Terminase-like family; InterPro: IPR0	94.46
PRK13851	344	type IV secretion system protein VirB11; Provision	94.44
PRK07940	394	DNA polymerase III subunit delta'; Validated	94.41
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	94.31
KOG0738	491	consensus AAA+-type ATPase [Posttranslational modi	94.31
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	94.29
PHA00350	399	putative assembly protein	94.29
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	94.25
KOG0739	439	consensus AAA+-type ATPase [Posttranslational modi	94.17
COG5008	375	PilU Tfp pilus assembly protein, ATPase PilU [Cell	94.14
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	94.1
PF06733	174	DEAD_2: DEAD_2; InterPro: IPR010614 This represent	94.04
COG0210	655	UvrD Superfamily I DNA and RNA helicases [DNA repl	94.01
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	93.97
KOG0732	1080	consensus AAA+-type ATPase containing the bromodom	93.92
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	93.9
PRK09087	226	hypothetical protein; Validated	93.9
PRK08506	472	replicative DNA helicase; Provisional	93.89
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	93.71
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	93.58
PRK08058	329	DNA polymerase III subunit delta'; Validated	93.55
KOG0737	386	consensus AAA+-type ATPase [Posttranslational modi	93.54
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	93.43
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	93.37
PRK10689	1147	transcription-repair coupling factor; Provisional	93.34
KOG1513	1300	consensus Nuclear helicase MOP-3/SNO (DEAD-box sup	93.32
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	93.3
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	93.27
COG0541	451	Ffh Signal recognition particle GTPase [Intracellu	93.11
PRK08840	464	replicative DNA helicase; Provisional	93.07
PHA03372	668	DNA packaging terminase subunit 1; Provisional	93.02
KOG0780	483	consensus Signal recognition particle, subunit Srp	92.99
PRK07399	314	DNA polymerase III subunit delta'; Validated	92.99
PF12846	304	AAA_10: AAA-like domain	92.98
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	92.98
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	92.98
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	92.97
COG1132	567	MdlB ABC-type multidrug transport system, ATPase a	92.92
TIGR02868	529	CydC thiol reductant ABC exporter, CydC subunit. T	92.92
PRK09165	497	replicative DNA helicase; Provisional	92.92
PRK04328	249	hypothetical protein; Provisional	92.9
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	92.9
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	92.87
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	92.83
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	92.75
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	92.74
KOG0058	716	consensus Peptide exporter, ABC superfamily [Intra	92.56
PRK07004	460	replicative DNA helicase; Provisional	92.54
CHL00176	638	ftsH cell division protein; Validated	92.54
PRK05748	448	replicative DNA helicase; Provisional	92.48
COG1074	1139	RecB ATP-dependent exoDNAse (exonuclease V) beta s	92.31
cd01126	384	TraG_VirD4 The TraG/TraD/VirD4 family are bacteria	92.31
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	92.27
KOG2227	529	consensus Pre-initiation complex, subunit CDC6, AA	92.26
TIGR00665	434	DnaB replicative DNA helicase. This model describe	92.25
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	92.25
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	92.24
KOG0701	1606	consensus dsRNA-specific nuclease Dicer and relate	92.21
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	92.2
KOG0344	593	consensus ATP-dependent RNA helicase [RNA processi	92.1
KOG1806	1320	consensus DEAD box containing helicases [Replicati	92.04
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	92.02
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	91.94
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	91.93
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	91.9
PRK08006	471	replicative DNA helicase; Provisional	91.88
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	91.79
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	91.78
PRK10436	462	hypothetical protein; Provisional	91.77
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	91.76
KOG1807	1025	consensus Helicases [Replication, recombination an	91.74
PRK08760	476	replicative DNA helicase; Provisional	91.72
PF02534	469	T4SS-DNA_transf: Type IV secretory system Conjugat	91.59
TIGR02784	1141	addA_alphas double-strand break repair helicase Ad	91.59
TIGR02237	209	recomb_radB DNA repair and recombination protein R	91.43
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	91.43
PF13555	62	AAA_29: P-loop containing region of AAA domain	91.41
PF01580	205	FtsK_SpoIIIE: FtsK/SpoIIIE family; InterPro: IPR00	91.41
TIGR03880	224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	91.38
PF08423	256	Rad51: Rad51; InterPro: IPR013632 This domain is f	91.27
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	91.15
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	91.15
TIGR02533	486	type_II_gspE general secretory pathway protein E.	91.06
COG5410	305	Uncharacterized protein conserved in bacteria [Fun	91.06
KOG2543	438	consensus Origin recognition complex, subunit 5 [R	90.91
PRK13897	606	type IV secretion system component VirD4; Provisio	90.88
PRK14701	1638	reverse gyrase; Provisional	90.81
PRK05636	505	replicative DNA helicase; Provisional	90.75
PRK06321	472	replicative DNA helicase; Provisional	90.67
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	90.63
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	90.6
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	90.59
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	90.54
PF01935	229	DUF87: Domain of unknown function DUF87; InterPro:	90.34
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	90.29
cd01394	218	radB RadB. The archaeal protein radB shares simila	90.27
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	90.23
PRK05564	313	DNA polymerase III subunit delta'; Validated	90.19
PF10593	239	Z1: Z1 domain; InterPro: IPR018310 This entry repr	90.18
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	90.17

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

Probab=100.00  E-value=1.8e-63  Score=405.89  Aligned_cols=379  Identities=68%  Similarity=1.064  Sum_probs=364.9

Q ss_pred             hhhhccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEE
Q 015158           34 YDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVL  113 (412)
Q Consensus        34 ~~~~~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil  113 (412)
                      .-.+..+|+++++.+++.+.+++.||..|...|+.|++++++|++++.++..|+|||.++...++..+.-.....+++++
T Consensus        22 ~~~v~~~F~~Mgl~edlLrgiY~yGfekPS~IQqrAi~~IlkGrdViaQaqSGTGKTa~~si~vlq~~d~~~r~tQ~lil  101 (400)
T KOG0328|consen   22 KVKVIPTFDDMGLKEDLLRGIYAYGFEKPSAIQQRAIPQILKGRDVIAQAQSGTGKTATFSISVLQSLDISVRETQALIL  101 (400)
T ss_pred             CcccccchhhcCchHHHHHHHHHhccCCchHHHhhhhhhhhcccceEEEecCCCCceEEEEeeeeeecccccceeeEEEe
Confidence            34567899999999999999999999999999999999999999999999999999999988888877766666789999


Q ss_pred             cCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchh
Q 015158          114 APTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEM  193 (412)
Q Consensus       114 ~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~  193 (412)
                      .||++|+.|..+.+..++...++.+..+.|+.+...+.+....+.+++.+||++.+.+.++..+..+.+.++|+||++++
T Consensus       102 sPTRELa~Qi~~vi~alg~~mnvq~hacigg~n~gedikkld~G~hvVsGtPGrv~dmikr~~L~tr~vkmlVLDEaDem  181 (400)
T KOG0328|consen  102 SPTRELAVQIQKVILALGDYMNVQCHACIGGKNLGEDIKKLDYGQHVVSGTPGRVLDMIKRRSLRTRAVKMLVLDEADEM  181 (400)
T ss_pred             cChHHHHHHHHHHHHHhcccccceEEEEecCCccchhhhhhcccceEeeCCCchHHHHHHhccccccceeEEEeccHHHH
Confidence            99999999999999999999999999999999999888888888999999999999999999999999999999999999


Q ss_pred             hccCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhHHHHHHHH
Q 015158          194 LSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLY  273 (412)
Q Consensus       194 ~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~  273 (412)
                      ++.+|..++..++..+|++.|++++|||++.+..+....+..+|+.+...+.+...++++.++..+..++++.+.|.+++
T Consensus       182 L~kgfk~Qiydiyr~lp~~~Qvv~~SATlp~eilemt~kfmtdpvrilvkrdeltlEgIKqf~v~ve~EewKfdtLcdLY  261 (400)
T KOG0328|consen  182 LNKGFKEQIYDIYRYLPPGAQVVLVSATLPHEILEMTEKFMTDPVRILVKRDELTLEGIKQFFVAVEKEEWKFDTLCDLY  261 (400)
T ss_pred             HHhhHHHHHHHHHHhCCCCceEEEEeccCcHHHHHHHHHhcCCceeEEEecCCCchhhhhhheeeechhhhhHhHHHHHh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhcCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEc
Q 015158          274 ETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINY  353 (412)
Q Consensus       274 ~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~  353 (412)
                      ........+|||+++..+..+.+.+++.+..+...||+|..++|++++.+|++|+.+||++|+.+.+|+|+|.++.||.+
T Consensus       262 d~LtItQavIFcnTk~kVdwLtekm~~~nftVssmHGDm~qkERd~im~dFRsg~SrvLitTDVwaRGiDv~qVslviNY  341 (400)
T KOG0328|consen  262 DTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMEQKERDKIMNDFRSGKSRVLITTDVWARGIDVQQVSLVINY  341 (400)
T ss_pred             hhhehheEEEEecccchhhHHHHHHHhhCceeeeccCCcchhHHHHHHHHhhcCCceEEEEechhhccCCcceeEEEEec
Confidence            99988899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHHhccccccCChhhhhcC
Q 015158          354 DLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVADLL  412 (412)
Q Consensus       354 ~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  412 (412)
                      ++|.+...|++|+||.||.|..|.++-|+...+.+.++.++++|+..+.++|.++.+++
T Consensus       342 DLP~nre~YIHRIGRSGRFGRkGvainFVk~~d~~~lrdieq~yst~i~emp~nvad~i  400 (400)
T KOG0328|consen  342 DLPNNRELYIHRIGRSGRFGRKGVAINFVKSDDLRILRDIEQYYSTQIDEMPMNVADLI  400 (400)
T ss_pred             CCCccHHHHhhhhccccccCCcceEEEEecHHHHHHHHHHHHHHhhhcccccchhhhcC
Confidence            99999999999999999999999999999999999999999999999999999998874

>PTZ00110 helicase; Provisional

Probab=100.00  E-value=1.4e-59  Score=448.33  Aligned_cols=376  Identities=33%  Similarity=0.517  Sum_probs=332.2

Q ss_pred             hhhccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccC-----CCcee
Q 015158           35 DEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYG-----LVECQ  109 (412)
Q Consensus        35 ~~~~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~-----~~~~~  109 (412)
                      ..+...|+.+++++.+.+.|...+|.+|+++|.++++.+++|+++++++|||||||++|+++++..+...     ..++.
T Consensus       126 p~p~~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~aip~~l~G~dvI~~ApTGSGKTlaylLP~l~~i~~~~~~~~~~gp~  205 (545)
T PTZ00110        126 PKPVVSFEYTSFPDYILKSLKNAGFTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLPAIVHINAQPLLRYGDGPI  205 (545)
T ss_pred             CcccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEEeCCCChHHHHHHHHHHHHHHhcccccCCCCcE
Confidence            3456789999999999999999999999999999999999999999999999999999999988776432     23568


Q ss_pred             EEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeC
Q 015158          110 ALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDE  189 (412)
Q Consensus       110 ~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE  189 (412)
                      +||++||++|+.|+.+.+..+....++.+..++|+.........+..+++|+|+||++|..++......+.++++||+||
T Consensus       206 ~LIL~PTreLa~Qi~~~~~~~~~~~~i~~~~~~gg~~~~~q~~~l~~~~~IlVaTPgrL~d~l~~~~~~l~~v~~lViDE  285 (545)
T PTZ00110        206 VLVLAPTRELAEQIREQCNKFGASSKIRNTVAYGGVPKRGQIYALRRGVEILIACPGRLIDFLESNVTNLRRVTYLVLDE  285 (545)
T ss_pred             EEEECChHHHHHHHHHHHHHHhcccCccEEEEeCCCCHHHHHHHHHcCCCEEEECHHHHHHHHHcCCCChhhCcEEEeeh
Confidence            99999999999999999999988888888899998887766666777889999999999999988877888999999999


Q ss_pred             CchhhccCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcC-CCeEEEecCCc-cccCCceEEEEEeccchhhHH
Q 015158          190 ADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMN-KPVRILVKRDE-LTLEGIKQFHVNVEKEEWKLE  267 (412)
Q Consensus       190 ~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~-~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~  267 (412)
                      ||++.+++|...+..++..+++..+++++|||++.+.......++. .+..+...... .....+.+.+..+.. ..+..
T Consensus       286 Ad~mld~gf~~~i~~il~~~~~~~q~l~~SAT~p~~v~~l~~~l~~~~~v~i~vg~~~l~~~~~i~q~~~~~~~-~~k~~  364 (545)
T PTZ00110        286 ADRMLDMGFEPQIRKIVSQIRPDRQTLMWSATWPKEVQSLARDLCKEEPVHVNVGSLDLTACHNIKQEVFVVEE-HEKRG  364 (545)
T ss_pred             HHhhhhcchHHHHHHHHHhCCCCCeEEEEEeCCCHHHHHHHHHHhccCCEEEEECCCccccCCCeeEEEEEEec-hhHHH
Confidence            9999999999999999999999999999999999888888777775 45555554333 223445555444433 44666


Q ss_pred             HHHHHHHhc--CCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCC
Q 015158          268 TLCDLYETL--AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQ  345 (412)
Q Consensus       268 ~l~~~~~~~--~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~  345 (412)
                      .+..++...  ..+++||||++++.|+.+++.|+..++.+..+||++++.+|..+++.|++|+.+|||||+++++|+|+|
T Consensus       365 ~L~~ll~~~~~~~~k~LIF~~t~~~a~~l~~~L~~~g~~~~~ihg~~~~~eR~~il~~F~~G~~~ILVaTdv~~rGIDi~  444 (545)
T PTZ00110        365 KLKMLLQRIMRDGDKILIFVETKKGADFLTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKSPIMIATDVASRGLDVK  444 (545)
T ss_pred             HHHHHHHHhcccCCeEEEEecChHHHHHHHHHHHHcCCcEEEEECCCcHHHHHHHHHHHhcCCCcEEEEcchhhcCCCcc
Confidence            677777664  457999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHHhccccccCChhhhhc
Q 015158          346 QVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVADL  411 (412)
Q Consensus       346 ~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  411 (412)
                      ++++||+++.|.+...|+||+||+||.|..|.+++|+++.+...+..+.+.++...+++|+++.++
T Consensus       445 ~v~~VI~~d~P~s~~~yvqRiGRtGR~G~~G~ai~~~~~~~~~~~~~l~~~l~~~~q~vp~~l~~~  510 (545)
T PTZ00110        445 DVKYVINFDFPNQIEDYVHRIGRTGRAGAKGASYTFLTPDKYRLARDLVKVLREAKQPVPPELEKL  510 (545)
T ss_pred             cCCEEEEeCCCCCHHHHHHHhcccccCCCCceEEEEECcchHHHHHHHHHHHHHccCCCCHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999999999988754

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=1.3e-59  Score=440.15  Aligned_cols=367  Identities=32%  Similarity=0.480  Sum_probs=327.8

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccC-------CCceeEE
Q 015158           39 DTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYG-------LVECQAL  111 (412)
Q Consensus        39 ~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~-------~~~~~~l  111 (412)
                      .+|+++++++.+.+.|...||..|+|+|.++++.++.|+++++.+|||||||++|+++++..+...       ..++++|
T Consensus         8 ~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvi~~ApTGsGKTla~llp~l~~l~~~~~~~~~~~~~~~~l   87 (423)
T PRK04837          8 QKFSDFALHPQVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHYLLSHPAPEDRKVNQPRAL   87 (423)
T ss_pred             CCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCcEEEECCCCchHHHHHHHHHHHHHHhcccccccccCCceEE
Confidence            589999999999999999999999999999999999999999999999999999999998876432       1246899


Q ss_pred             EEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCc
Q 015158          112 VLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEAD  191 (412)
Q Consensus       112 il~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h  191 (412)
                      |++|+++|+.|+.+.+..+....++.+..++|+............+++|+|+||+++..++....+.+.+++++|+||||
T Consensus        88 il~PtreLa~Qi~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~l~~~~~IlV~TP~~l~~~l~~~~~~l~~v~~lViDEad  167 (423)
T PRK04837         88 IMAPTRELAVQIHADAEPLAQATGLKLGLAYGGDGYDKQLKVLESGVDILIGTTGRLIDYAKQNHINLGAIQVVVLDEAD  167 (423)
T ss_pred             EECCcHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHhcCCCCEEEECHHHHHHHHHcCCcccccccEEEEecHH
Confidence            99999999999999999998888999999999988777766677788999999999999998888888999999999999


Q ss_pred             hhhccCcHHHHHHHHHhCCC--CceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhHHHH
Q 015158          192 EMLSRGFKDQIYDIFQLLPP--KIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETL  269 (412)
Q Consensus       192 ~~~~~~~~~~~~~i~~~~~~--~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  269 (412)
                      ++.+.+|...+..++..++.  ..+.+++|||++..........+..+..+...........+....... ....+...+
T Consensus       168 ~l~~~~f~~~i~~i~~~~~~~~~~~~~l~SAT~~~~~~~~~~~~~~~p~~i~v~~~~~~~~~i~~~~~~~-~~~~k~~~l  246 (423)
T PRK04837        168 RMFDLGFIKDIRWLFRRMPPANQRLNMLFSATLSYRVRELAFEHMNNPEYVEVEPEQKTGHRIKEELFYP-SNEEKMRLL  246 (423)
T ss_pred             HHhhcccHHHHHHHHHhCCCccceeEEEEeccCCHHHHHHHHHHCCCCEEEEEcCCCcCCCceeEEEEeC-CHHHHHHHH
Confidence            99999999999999988874  445789999999988888888888888777665555445555544433 335677788


Q ss_pred             HHHHHhcCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCE
Q 015158          270 CDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSL  349 (412)
Q Consensus       270 ~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~  349 (412)
                      ..++.....+++||||++++.|+.+++.|.+.++.+..+||+++..+|..+++.|++|+++|||||+++++|+|+|++++
T Consensus       247 ~~ll~~~~~~~~lVF~~t~~~~~~l~~~L~~~g~~v~~lhg~~~~~~R~~~l~~F~~g~~~vLVaTdv~~rGiDip~v~~  326 (423)
T PRK04837        247 QTLIEEEWPDRAIIFANTKHRCEEIWGHLAADGHRVGLLTGDVAQKKRLRILEEFTRGDLDILVATDVAARGLHIPAVTH  326 (423)
T ss_pred             HHHHHhcCCCeEEEEECCHHHHHHHHHHHHhCCCcEEEecCCCChhHHHHHHHHHHcCCCcEEEEechhhcCCCccccCE
Confidence            88888777789999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHHhccccccCCh
Q 015158          350 VINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPA  406 (412)
Q Consensus       350 vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  406 (412)
                      ||+++.|.+...|.||+||+||.|+.|.+++|+++.+...+..+++++...++..+.
T Consensus       327 VI~~d~P~s~~~yiqR~GR~gR~G~~G~ai~~~~~~~~~~~~~i~~~~~~~~~~~~~  383 (423)
T PRK04837        327 VFNYDLPDDCEDYVHRIGRTGRAGASGHSISLACEEYALNLPAIETYIGHSIPVSKY  383 (423)
T ss_pred             EEEeCCCCchhheEeccccccCCCCCeeEEEEeCHHHHHHHHHHHHHhCCCCCCccC
Confidence            999999999999999999999999999999999999999999999999988765543

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=100.00  E-value=7.3e-59  Score=439.80  Aligned_cols=363  Identities=36%  Similarity=0.598  Sum_probs=331.4

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHH
Q 015158           39 DTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRE  118 (412)
Q Consensus        39 ~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  118 (412)
                      .+|+.+++++.+.+.+...||..|+|+|+++++.+++|+++++++|||||||++|+++++..+.......+++|++||++
T Consensus         4 ~~f~~l~l~~~l~~~l~~~g~~~~t~iQ~~ai~~~l~g~dvi~~a~TGsGKT~a~~lpil~~l~~~~~~~~~lil~Ptre   83 (460)
T PRK11776          4 TAFSTLPLPPALLANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQKLDVKRFRVQALVLCPTRE   83 (460)
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHhhhccCCceEEEEeCCHH
Confidence            57999999999999999999999999999999999999999999999999999999999998876555668999999999


Q ss_pred             HHHHHHHHHHHhhccc-CcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccC
Q 015158          119 LAQQIEKVMRALGDYL-GVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRG  197 (412)
Q Consensus       119 L~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~  197 (412)
                      |+.|+.+.++.+.... +..+..++|+.+..........+++|+|+||+.|..++.+..+.+.++++||+||||++.+.+
T Consensus        84 La~Q~~~~~~~~~~~~~~~~v~~~~Gg~~~~~~~~~l~~~~~IvV~Tp~rl~~~l~~~~~~l~~l~~lViDEad~~l~~g  163 (460)
T PRK11776         84 LADQVAKEIRRLARFIPNIKVLTLCGGVPMGPQIDSLEHGAHIIVGTPGRILDHLRKGTLDLDALNTLVLDEADRMLDMG  163 (460)
T ss_pred             HHHHHHHHHHHHHhhCCCcEEEEEECCCChHHHHHHhcCCCCEEEEChHHHHHHHHcCCccHHHCCEEEEECHHHHhCcC
Confidence            9999999999887544 688999999988877777777889999999999999999888888999999999999999999


Q ss_pred             cHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhHHHHHHHHHhcC
Q 015158          198 FKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLA  277 (412)
Q Consensus       198 ~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  277 (412)
                      |...+..++..++...+.+++|||+++........++..+..+...... ....+.+.++.... ..+...+..++....
T Consensus       164 ~~~~l~~i~~~~~~~~q~ll~SAT~~~~~~~l~~~~~~~~~~i~~~~~~-~~~~i~~~~~~~~~-~~k~~~l~~ll~~~~  241 (460)
T PRK11776        164 FQDAIDAIIRQAPARRQTLLFSATYPEGIAAISQRFQRDPVEVKVESTH-DLPAIEQRFYEVSP-DERLPALQRLLLHHQ  241 (460)
T ss_pred             cHHHHHHHHHhCCcccEEEEEEecCcHHHHHHHHHhcCCCEEEEECcCC-CCCCeeEEEEEeCc-HHHHHHHHHHHHhcC
Confidence            9999999999999999999999999998888888888888887776544 33446777776665 347888888888887


Q ss_pred             CCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccCCC
Q 015158          278 ITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPT  357 (412)
Q Consensus       278 ~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~~~  357 (412)
                      .+++||||++++.++.+++.|.+.+..+..+||++++.+|..+++.|++|+.+|||||+++++|+|+|++++||+++.|.
T Consensus       242 ~~~~lVF~~t~~~~~~l~~~L~~~~~~v~~~hg~~~~~eR~~~l~~F~~g~~~vLVaTdv~~rGiDi~~v~~VI~~d~p~  321 (460)
T PRK11776        242 PESCVVFCNTKKECQEVADALNAQGFSALALHGDLEQRDRDQVLVRFANRSCSVLVATDVAARGLDIKALEAVINYELAR  321 (460)
T ss_pred             CCceEEEECCHHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHHcCCCcEEEEecccccccchhcCCeEEEecCCC
Confidence            78999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHHhcccccc
Q 015158          358 QPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEE  403 (412)
Q Consensus       358 s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~  403 (412)
                      +...|+||+||+||.|..|.+++++.+.+...+..+++++...++.
T Consensus       322 ~~~~yiqR~GRtGR~g~~G~ai~l~~~~e~~~~~~i~~~~~~~~~~  367 (460)
T PRK11776        322 DPEVHVHRIGRTGRAGSKGLALSLVAPEEMQRANAIEDYLGRKLNW  367 (460)
T ss_pred             CHhHhhhhcccccCCCCcceEEEEEchhHHHHHHHHHHHhCCCCce
Confidence            9999999999999999999999999999999999999998876554

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=100.00  E-value=1e-58  Score=436.70  Aligned_cols=363  Identities=36%  Similarity=0.607  Sum_probs=327.4

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCC------CceeEEEE
Q 015158           40 TFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGL------VECQALVL  113 (412)
Q Consensus        40 ~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~------~~~~~lil  113 (412)
                      +|+++++++.+.+.|...+|..|+++|.++++.++.++++++.+|||||||++|+++++..+....      ...++||+
T Consensus         2 ~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~ai~~il~g~dvlv~apTGsGKTla~~lpil~~l~~~~~~~~~~~~~~aLil   81 (456)
T PRK10590          2 SFDSLGLSPDILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQHLITRQPHAKGRRPVRALIL   81 (456)
T ss_pred             CHHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHhhhcccccccCCCceEEEE
Confidence            688999999999999999999999999999999999999999999999999999999998875422      22479999


Q ss_pred             cCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchh
Q 015158          114 APTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEM  193 (412)
Q Consensus       114 ~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~  193 (412)
                      +||++|+.|+.+.+..+....++.+..++|+.........+...++|+|+||++|..++......++++++||+||||++
T Consensus        82 ~PtreLa~Qi~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~IiV~TP~rL~~~~~~~~~~l~~v~~lViDEah~l  161 (456)
T PRK10590         82 TPTRELAAQIGENVRDYSKYLNIRSLVVFGGVSINPQMMKLRGGVDVLVATPGRLLDLEHQNAVKLDQVEILVLDEADRM  161 (456)
T ss_pred             eCcHHHHHHHHHHHHHHhccCCCEEEEEECCcCHHHHHHHHcCCCcEEEEChHHHHHHHHcCCcccccceEEEeecHHHH
Confidence            99999999999999999888888999999998877766667778899999999999998887778899999999999999


Q ss_pred             hccCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhHHHHHHHH
Q 015158          194 LSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLY  273 (412)
Q Consensus       194 ~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~  273 (412)
                      .+++|...+..++..++...+.+++|||++.+.......++..+..+...........+...+..... ..+...+..++
T Consensus       162 l~~~~~~~i~~il~~l~~~~q~l~~SAT~~~~~~~l~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~-~~k~~~l~~l~  240 (456)
T PRK10590        162 LDMGFIHDIRRVLAKLPAKRQNLLFSATFSDDIKALAEKLLHNPLEIEVARRNTASEQVTQHVHFVDK-KRKRELLSQMI  240 (456)
T ss_pred             hccccHHHHHHHHHhCCccCeEEEEeCCCcHHHHHHHHHHcCCCeEEEEecccccccceeEEEEEcCH-HHHHHHHHHHH
Confidence            99999999999999999999999999999998888888888888877766655555566666555543 45666777777


Q ss_pred             HhcCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEc
Q 015158          274 ETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINY  353 (412)
Q Consensus       274 ~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~  353 (412)
                      ......++||||++++.++.+++.|.+.++.+..+||+++..+|..+++.|++|+++|||||+++++|+|+|++++||++
T Consensus       241 ~~~~~~~~lVF~~t~~~~~~l~~~L~~~g~~~~~lhg~~~~~~R~~~l~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~~  320 (456)
T PRK10590        241 GKGNWQQVLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALADFKSGDIRVLVATDIAARGLDIEELPHVVNY  320 (456)
T ss_pred             HcCCCCcEEEEcCcHHHHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHcCCCcEEEEccHHhcCCCcccCCEEEEe
Confidence            77767899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHHhcccccc
Q 015158          354 DLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEE  403 (412)
Q Consensus       354 ~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~  403 (412)
                      +.|.+..+|+||+||+||.|..|.+++|+...+...++.+++.++.+++.
T Consensus       321 ~~P~~~~~yvqR~GRaGR~g~~G~ai~l~~~~d~~~~~~ie~~l~~~~~~  370 (456)
T PRK10590        321 ELPNVPEDYVHRIGRTGRAAATGEALSLVCVDEHKLLRDIEKLLKKEIPR  370 (456)
T ss_pred             CCCCCHHHhhhhccccccCCCCeeEEEEecHHHHHHHHHHHHHhcCCCcc
Confidence            99999999999999999999999999999999999999999999887743

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

Probab=100.00  E-value=2.6e-59  Score=423.65  Aligned_cols=370  Identities=38%  Similarity=0.617  Sum_probs=342.0

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhcc------CCCceeEEEE
Q 015158           40 TFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY------GLVECQALVL  113 (412)
Q Consensus        40 ~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~------~~~~~~~lil  113 (412)
                      .|+.+++++.....++..+|..|+|.|.+.|+.++.|++++..+.||||||++|+++++.++..      ...++++||+
T Consensus        92 ~f~~~~ls~~~~~~lk~~g~~~PtpIQaq~wp~~l~GrD~v~iA~TGSGKTLay~lP~i~~l~~~~~~~~~~~~P~vLVL  171 (519)
T KOG0331|consen   92 AFQELGLSEELMKALKEQGFEKPTPIQAQGWPIALSGRDLVGIARTGSGKTLAYLLPAIVHLNNEQGKLSRGDGPIVLVL  171 (519)
T ss_pred             hhhcccccHHHHHHHHhcCCCCCchhhhcccceeccCCceEEEeccCCcchhhhhhHHHHHHHhccccccCCCCCeEEEE
Confidence            8899999999999999999999999999999999999999999999999999999999998875      2346789999


Q ss_pred             cCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchh
Q 015158          114 APTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEM  193 (412)
Q Consensus       114 ~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~  193 (412)
                      +||++|+.|..+.+.++....++...+++|+.+...+...+..+.+|+|+||.++..+++.....++.+.++|+|||+++
T Consensus       172 ~PTRELA~QV~~~~~~~~~~~~~~~~cvyGG~~~~~Q~~~l~~gvdiviaTPGRl~d~le~g~~~l~~v~ylVLDEADrM  251 (519)
T KOG0331|consen  172 APTRELAVQVQAEAREFGKSLRLRSTCVYGGAPKGPQLRDLERGVDVVIATPGRLIDLLEEGSLNLSRVTYLVLDEADRM  251 (519)
T ss_pred             cCcHHHHHHHHHHHHHHcCCCCccEEEEeCCCCccHHHHHHhcCCcEEEeCChHHHHHHHcCCccccceeEEEeccHHhh
Confidence            99999999999999999998888899999999999999999999999999999999999999999999999999999999


Q ss_pred             hccCcHHHHHHHHHhCC-CCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCc--cccCCceEEEEEeccchhhHHHHH
Q 015158          194 LSRGFKDQIYDIFQLLP-PKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDE--LTLEGIKQFHVNVEKEEWKLETLC  270 (412)
Q Consensus       194 ~~~~~~~~~~~i~~~~~-~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~l~  270 (412)
                      ++.+|..++.+|+..++ +..|.++.|||++..+..+...+++++..+.+....  ....++.+....++ ...+...+.
T Consensus       252 ldmGFe~qI~~Il~~i~~~~rQtlm~saTwp~~v~~lA~~fl~~~~~i~ig~~~~~~a~~~i~qive~~~-~~~K~~~l~  330 (519)
T KOG0331|consen  252 LDMGFEPQIRKILSQIPRPDRQTLMFSATWPKEVRQLAEDFLNNPIQINVGNKKELKANHNIRQIVEVCD-ETAKLRKLG  330 (519)
T ss_pred             hccccHHHHHHHHHhcCCCcccEEEEeeeccHHHHHHHHHHhcCceEEEecchhhhhhhcchhhhhhhcC-HHHHHHHHH
Confidence            99999999999999994 455799999999999999999999998888776543  45566777776666 455666666


Q ss_pred             HHHHhc---CCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCC
Q 015158          271 DLYETL---AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQV  347 (412)
Q Consensus       271 ~~~~~~---~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~  347 (412)
                      .++...   ..+|+||||++++.|+++...|+..++++..+||+.++.+|+.+++.|++|+..|||||+++++|+|+|++
T Consensus       331 ~lL~~~~~~~~~KvIIFc~tkr~~~~l~~~l~~~~~~a~~iHGd~sQ~eR~~~L~~FreG~~~vLVATdVAaRGLDi~dV  410 (519)
T KOG0331|consen  331 KLLEDISSDSEGKVIIFCETKRTCDELARNLRRKGWPAVAIHGDKSQSERDWVLKGFREGKSPVLVATDVAARGLDVPDV  410 (519)
T ss_pred             HHHHHHhccCCCcEEEEecchhhHHHHHHHHHhcCcceeeecccccHHHHHHHHHhcccCCcceEEEcccccccCCCccc
Confidence            666665   45799999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHHhccccccCChhhhh
Q 015158          348 SLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVAD  410 (412)
Q Consensus       348 ~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  410 (412)
                      ++||++++|.+..+|+||+||.||+|+.|.+++|++..+......+.+.+....+.+++.+..
T Consensus       411 ~lVInydfP~~vEdYVHRiGRTGRa~~~G~A~tfft~~~~~~a~~l~~~l~e~~q~v~~~l~~  473 (519)
T KOG0331|consen  411 DLVINYDFPNNVEDYVHRIGRTGRAGKKGTAITFFTSDNAKLARELIKVLREAGQTVPPDLLE  473 (519)
T ss_pred             cEEEeCCCCCCHHHHHhhcCccccCCCCceEEEEEeHHHHHHHHHHHHHHHHccCCCChHHHH
Confidence            999999999999999999999999999999999999999999999999999999999987644

>PTZ00424 helicase 45; Provisional

Probab=100.00  E-value=1.7e-58  Score=432.24  Aligned_cols=382  Identities=71%  Similarity=1.124  Sum_probs=342.5

Q ss_pred             CCCChhhhccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCcee
Q 015158           30 FFTSYDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQ  109 (412)
Q Consensus        30 ~~~~~~~~~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~  109 (412)
                      ..+.+.+...+|+++++++.+.+.+..++|..|+|+|.++++.++.++++++.+|||||||++|+++++..+.....+.+
T Consensus        19 ~~~~~~~~~~~~~~l~l~~~~~~~l~~~~~~~~~~~Q~~ai~~i~~~~d~ii~apTGsGKT~~~~l~~l~~~~~~~~~~~   98 (401)
T PTZ00424         19 IESNYDEIVDSFDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQLIDYDLNACQ   98 (401)
T ss_pred             cccccccccCCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhcCCCCCce
Confidence            33444556788999999999999999999999999999999999999999999999999999999999988765555678


Q ss_pred             EEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeC
Q 015158          110 ALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDE  189 (412)
Q Consensus       110 ~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE  189 (412)
                      +||++|+++|+.|+.+.+..+....+..+..+.|+.....+......+.+|+|+||+++...+.+....++++++||+||
T Consensus        99 ~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~l~~i~lvViDE  178 (401)
T PTZ00424         99 ALILAPTRELAQQIQKVVLALGDYLKVRCHACVGGTVVRDDINKLKAGVHMVVGTPGRVYDMIDKRHLRVDDLKLFILDE  178 (401)
T ss_pred             EEEECCCHHHHHHHHHHHHHHhhhcCceEEEEECCcCHHHHHHHHcCCCCEEEECcHHHHHHHHhCCcccccccEEEEec
Confidence            99999999999999999999887777888888888876666666667789999999999998888777788999999999


Q ss_pred             CchhhccCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhHHHH
Q 015158          190 ADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETL  269 (412)
Q Consensus       190 ~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  269 (412)
                      +|++.+.++...+..++..++++.+++++|||+++........+...+..+...........+..++........+...+
T Consensus       179 ah~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  258 (401)
T PTZ00424        179 ADEMLSRGFKGQIYDVFKKLPPDVQVALFSATMPNEILELTTKFMRDPKRILVKKDELTLEGIRQFYVAVEKEEWKFDTL  258 (401)
T ss_pred             HHHHHhcchHHHHHHHHhhCCCCcEEEEEEecCCHHHHHHHHHHcCCCEEEEeCCCCcccCCceEEEEecChHHHHHHHH
Confidence            99999988888899999999999999999999998888888888888877766666666667777777776656677777


Q ss_pred             HHHHHhcCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCE
Q 015158          270 CDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSL  349 (412)
Q Consensus       270 ~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~  349 (412)
                      ..++......++||||++++.++.+++.|.+.+..+..+||+++..+|..+++.|++|+++|||||+++++|+|+|++++
T Consensus       259 ~~~~~~~~~~~~ivF~~t~~~~~~l~~~l~~~~~~~~~~h~~~~~~~R~~i~~~f~~g~~~vLvaT~~l~~GiDip~v~~  338 (401)
T PTZ00424        259 CDLYETLTITQAIIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSL  338 (401)
T ss_pred             HHHHHhcCCCeEEEEecCcHHHHHHHHHHHHCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEEcccccCCcCcccCCE
Confidence            78887777789999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHHhccccccCChhhhhc
Q 015158          350 VINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVADL  411 (412)
Q Consensus       350 vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  411 (412)
                      ||+++.|.|...|.||+||+||.|..|.|++++++.+...++.+++.+..++++.++...+.
T Consensus       339 VI~~~~p~s~~~y~qr~GRagR~g~~G~~i~l~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~  400 (401)
T PTZ00424        339 VINYDLPASPENYIHRIGRSGRFGRKGVAINFVTPDDIEQLKEIERHYNTQIEEMPMEVADY  400 (401)
T ss_pred             EEEECCCCCHHHEeecccccccCCCCceEEEEEcHHHHHHHHHHHHHHCCcccccCcchhhc
Confidence            99999999999999999999999999999999999999999999999999999888776554

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

Probab=100.00  E-value=2.8e-59  Score=397.63  Aligned_cols=369  Identities=34%  Similarity=0.547  Sum_probs=349.8

Q ss_pred             hhhhccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEE
Q 015158           34 YDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVL  113 (412)
Q Consensus        34 ~~~~~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil  113 (412)
                      ..+...+|.++++.+.+.++....++..|++.|+++++.++.|++++..+.||||||.+|++|+++.+........++|+
T Consensus        56 ~~e~~~sf~dLgv~~~L~~ac~~l~~~~PT~IQ~~aiP~~L~g~dvIglAeTGSGKT~afaLPIl~~LL~~p~~~~~lVL  135 (476)
T KOG0330|consen   56 TDESFKSFADLGVHPELLEACQELGWKKPTKIQSEAIPVALGGRDVIGLAETGSGKTGAFALPILQRLLQEPKLFFALVL  135 (476)
T ss_pred             hhhhhcchhhcCcCHHHHHHHHHhCcCCCchhhhhhcchhhCCCcEEEEeccCCCchhhhHHHHHHHHHcCCCCceEEEe
Confidence            35667899999999999999999999999999999999999999999999999999999999999999888778899999


Q ss_pred             cCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHH-cCCCCCCCceEEEEeCCch
Q 015158          114 APTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLR-RQSLRPDNIRIFVLDEADE  192 (412)
Q Consensus       114 ~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~-~~~~~~~~~~~iiiDE~h~  192 (412)
                      +|+++|+.|+.+.+..++...|+.+..+.|+.............++|+|+||+.|..++. ...+....++++|+|||++
T Consensus       136 tPtRELA~QI~e~fe~Lg~~iglr~~~lvGG~~m~~q~~~L~kkPhilVaTPGrL~dhl~~Tkgf~le~lk~LVlDEADr  215 (476)
T KOG0330|consen  136 TPTRELAQQIAEQFEALGSGIGLRVAVLVGGMDMMLQANQLSKKPHILVATPGRLWDHLENTKGFSLEQLKFLVLDEADR  215 (476)
T ss_pred             cCcHHHHHHHHHHHHHhccccCeEEEEEecCchHHHHHHHhhcCCCEEEeCcHHHHHHHHhccCccHHHhHHHhhchHHh
Confidence            999999999999999999999999999999999888877888899999999999999998 5677888999999999999


Q ss_pred             hhccCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhHHHHHHH
Q 015158          193 MLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDL  272 (412)
Q Consensus       193 ~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  272 (412)
                      +++.+|...+..|+..+|...+.+++|||++..........+..|..+.........+.+.+.+..++. .++...|..+
T Consensus       216 lLd~dF~~~ld~ILk~ip~erqt~LfsATMt~kv~kL~rasl~~p~~v~~s~ky~tv~~lkQ~ylfv~~-k~K~~yLV~l  294 (476)
T KOG0330|consen  216 LLDMDFEEELDYILKVIPRERQTFLFSATMTKKVRKLQRASLDNPVKVAVSSKYQTVDHLKQTYLFVPG-KDKDTYLVYL  294 (476)
T ss_pred             hhhhhhHHHHHHHHHhcCccceEEEEEeecchhhHHHHhhccCCCeEEeccchhcchHHhhhheEeccc-cccchhHHHH
Confidence            999999999999999999999999999999999988888889999999988888888888888888876 5688889999


Q ss_pred             HHhcCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEE
Q 015158          273 YETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVIN  352 (412)
Q Consensus       273 ~~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~  352 (412)
                      ++......+||||++...+..++-.|+..|+.+..+||.|++..|-..++.|++|..+||+||+..++|+|+|.+++||.
T Consensus       295 l~e~~g~s~iVF~~t~~tt~~la~~L~~lg~~a~~LhGqmsq~~Rlg~l~~Fk~~~r~iLv~TDVaSRGLDip~Vd~VVN  374 (476)
T KOG0330|consen  295 LNELAGNSVIVFCNTCNTTRFLALLLRNLGFQAIPLHGQMSQSKRLGALNKFKAGARSILVCTDVASRGLDIPHVDVVVN  374 (476)
T ss_pred             HHhhcCCcEEEEEeccchHHHHHHHHHhcCcceecccchhhHHHHHHHHHHHhccCCcEEEecchhcccCCCCCceEEEe
Confidence            99998899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHHhcccccc
Q 015158          353 YDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEE  403 (412)
Q Consensus       353 ~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~  403 (412)
                      |+.|.+..+|++|+||.+|.|.+|.++.+++..|.+.+.+++..+++..+.
T Consensus       375 yDiP~~skDYIHRvGRtaRaGrsG~~ItlVtqyDve~~qrIE~~~gkkl~~  425 (476)
T KOG0330|consen  375 YDIPTHSKDYIHRVGRTARAGRSGKAITLVTQYDVELVQRIEHALGKKLPE  425 (476)
T ss_pred             cCCCCcHHHHHHHcccccccCCCcceEEEEehhhhHHHHHHHHHHhcCCCc
Confidence            999999999999999999999999999999999999999999999987654

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=100.00  E-value=5.1e-58  Score=431.62  Aligned_cols=364  Identities=34%  Similarity=0.537  Sum_probs=331.3

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccC----CCceeEEEEcC
Q 015158           40 TFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYG----LVECQALVLAP  115 (412)
Q Consensus        40 ~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~----~~~~~~lil~P  115 (412)
                      +|+.+++++.+.+.|...||.+|+++|.++++.++.|+++++.+|||+|||++|+++++..+...    ....++||++|
T Consensus         2 ~f~~l~l~~~l~~~l~~~g~~~p~~iQ~~ai~~~~~g~d~l~~apTGsGKT~~~~lp~l~~l~~~~~~~~~~~~~lil~P   81 (434)
T PRK11192          2 TFSELELDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQHLLDFPRRKSGPPRILILTP   81 (434)
T ss_pred             CHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhhccccCCCCceEEEECC
Confidence            68999999999999999999999999999999999999999999999999999999999876432    12358999999


Q ss_pred             CHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhc
Q 015158          116 TRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLS  195 (412)
Q Consensus       116 ~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~  195 (412)
                      +++|+.|+.+.+..+....++.+..++|+............+++|+|+||++|...+....+..+++++||+||||++.+
T Consensus        82 t~eLa~Q~~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~l~~~~~IlV~Tp~rl~~~~~~~~~~~~~v~~lViDEah~~l~  161 (434)
T PRK11192         82 TRELAMQVADQARELAKHTHLDIATITGGVAYMNHAEVFSENQDIVVATPGRLLQYIKEENFDCRAVETLILDEADRMLD  161 (434)
T ss_pred             cHHHHHHHHHHHHHHHccCCcEEEEEECCCCHHHHHHHhcCCCCEEEEChHHHHHHHHcCCcCcccCCEEEEECHHHHhC
Confidence            99999999999999988889999999999888777777778889999999999999998888889999999999999999


Q ss_pred             cCcHHHHHHHHHhCCCCceEEEEeecCChH-HHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhHHHHHHHHH
Q 015158          196 RGFKDQIYDIFQLLPPKIQVGVFSATMPPE-ALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYE  274 (412)
Q Consensus       196 ~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  274 (412)
                      ++|...+..+...++...+.+++|||++.. .......++..+..+...........+.+.+...+....+...+..++.
T Consensus       162 ~~~~~~~~~i~~~~~~~~q~~~~SAT~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~  241 (434)
T PRK11192        162 MGFAQDIETIAAETRWRKQTLLFSATLEGDAVQDFAERLLNDPVEVEAEPSRRERKKIHQWYYRADDLEHKTALLCHLLK  241 (434)
T ss_pred             CCcHHHHHHHHHhCccccEEEEEEeecCHHHHHHHHHHHccCCEEEEecCCcccccCceEEEEEeCCHHHHHHHHHHHHh
Confidence            999999999999998889999999999754 6666777778888877776666666777777777766778888888888


Q ss_pred             hcCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEcc
Q 015158          275 TLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYD  354 (412)
Q Consensus       275 ~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~  354 (412)
                      ....+++||||++++.++.+++.|++.++.+..+||+++..+|..+++.|++|+++|||||+++++|+|+|++++||+++
T Consensus       242 ~~~~~~~lVF~~s~~~~~~l~~~L~~~~~~~~~l~g~~~~~~R~~~l~~f~~G~~~vLVaTd~~~~GiDip~v~~VI~~d  321 (434)
T PRK11192        242 QPEVTRSIVFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATDVAARGIDIDDVSHVINFD  321 (434)
T ss_pred             cCCCCeEEEEeCChHHHHHHHHHHHhCCCCEEEecCCCCHHHHHHHHHHHhCCCCcEEEEccccccCccCCCCCEEEEEC
Confidence            76778999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHHhcccccc
Q 015158          355 LPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEE  403 (412)
Q Consensus       355 ~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~  403 (412)
                      .|.|...|+||+||+||.|..|.++++++..+...+..+++++...+..
T Consensus       322 ~p~s~~~yiqr~GR~gR~g~~g~ai~l~~~~d~~~~~~i~~~~~~~~~~  370 (434)
T PRK11192        322 MPRSADTYLHRIGRTGRAGRKGTAISLVEAHDHLLLGKIERYIEEPLKA  370 (434)
T ss_pred             CCCCHHHHhhcccccccCCCCceEEEEecHHHHHHHHHHHHHHhccccc
Confidence            9999999999999999999999999999999999999999988876543

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=100.00  E-value=3.2e-58  Score=442.54  Aligned_cols=366  Identities=39%  Similarity=0.606  Sum_probs=333.5

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHH
Q 015158           39 DTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRE  118 (412)
Q Consensus        39 ~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  118 (412)
                      .+|+++++++.+.++|..+||.+|+|+|.++++.+++++++++.+|||||||.+|.++++..+......+++||++||++
T Consensus         6 ~~f~~l~L~~~ll~al~~~G~~~ptpiQ~~ai~~ll~g~dvl~~ApTGsGKT~af~lpll~~l~~~~~~~~~LIL~PTre   85 (629)
T PRK11634          6 TTFADLGLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLHNLDPELKAPQILVLAPTRE   85 (629)
T ss_pred             CCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHHHhhhccCCCeEEEEeCcHH
Confidence            46899999999999999999999999999999999999999999999999999999999988766555678999999999


Q ss_pred             HHHHHHHHHHHhhccc-CcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccC
Q 015158          119 LAQQIEKVMRALGDYL-GVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRG  197 (412)
Q Consensus       119 L~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~  197 (412)
                      |+.|+++.+..+.... ++.+..++|+.....+...+...++|+|+||+++..++.+..+.++++++||+||||++++.+
T Consensus        86 La~Qv~~~l~~~~~~~~~i~v~~~~gG~~~~~q~~~l~~~~~IVVgTPgrl~d~l~r~~l~l~~l~~lVlDEAd~ml~~g  165 (629)
T PRK11634         86 LAVQVAEAMTDFSKHMRGVNVVALYGGQRYDVQLRALRQGPQIVVGTPGRLLDHLKRGTLDLSKLSGLVLDEADEMLRMG  165 (629)
T ss_pred             HHHHHHHHHHHHHhhcCCceEEEEECCcCHHHHHHHhcCCCCEEEECHHHHHHHHHcCCcchhhceEEEeccHHHHhhcc
Confidence            9999999999886554 788889999988777777777788999999999999998888888999999999999999999


Q ss_pred             cHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhHHHHHHHHHhcC
Q 015158          198 FKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLA  277 (412)
Q Consensus       198 ~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  277 (412)
                      |...+..++..++...+.+++|||++.........++..+..+.........+.+.+.+..+.. ..+...+..++....
T Consensus       166 f~~di~~Il~~lp~~~q~llfSAT~p~~i~~i~~~~l~~~~~i~i~~~~~~~~~i~q~~~~v~~-~~k~~~L~~~L~~~~  244 (629)
T PRK11634        166 FIEDVETIMAQIPEGHQTALFSATMPEAIRRITRRFMKEPQEVRIQSSVTTRPDISQSYWTVWG-MRKNEALVRFLEAED  244 (629)
T ss_pred             cHHHHHHHHHhCCCCCeEEEEEccCChhHHHHHHHHcCCCeEEEccCccccCCceEEEEEEech-hhHHHHHHHHHHhcC
Confidence            9999999999999999999999999998888888888888888777666666666666665554 457778888888777


Q ss_pred             CCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccCCC
Q 015158          278 ITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPT  357 (412)
Q Consensus       278 ~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~~~  357 (412)
                      ..++||||+++..++.+++.|.+.++.+..+||++++.+|..++++|++|+++|||||+++++|+|+|++++||+++.|.
T Consensus       245 ~~~~IVF~~tk~~a~~l~~~L~~~g~~~~~lhgd~~q~~R~~il~~Fr~G~~~ILVATdv~arGIDip~V~~VI~~d~P~  324 (629)
T PRK11634        245 FDAAIIFVRTKNATLEVAEALERNGYNSAALNGDMNQALREQTLERLKDGRLDILIATDVAARGLDVERISLVVNYDIPM  324 (629)
T ss_pred             CCCEEEEeccHHHHHHHHHHHHhCCCCEEEeeCCCCHHHHHHHHHHHhCCCCCEEEEcchHhcCCCcccCCEEEEeCCCC
Confidence            78999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHHhccccccCC
Q 015158          358 QPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELP  405 (412)
Q Consensus       358 s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  405 (412)
                      +...|+||+||+||.|+.|.+++|+++.+...++.+++.++..++++.
T Consensus       325 ~~e~yvqRiGRtGRaGr~G~ai~~v~~~e~~~l~~ie~~~~~~i~~~~  372 (629)
T PRK11634        325 DSESYVHRIGRTGRAGRAGRALLFVENRERRLLRNIERTMKLTIPEVE  372 (629)
T ss_pred             CHHHHHHHhccccCCCCcceEEEEechHHHHHHHHHHHHhCCCcceec
Confidence            999999999999999999999999999999999999999998877654

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

Probab=100.00  E-value=4.3e-58  Score=437.23  Aligned_cols=374  Identities=32%  Similarity=0.535  Sum_probs=330.5

Q ss_pred             hhhccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhcc-------CCCc
Q 015158           35 DEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY-------GLVE  107 (412)
Q Consensus        35 ~~~~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~-------~~~~  107 (412)
                      ..+..+|+.+++++.+.+.|...||..|+|+|.++++.++.|+++++.+|||||||++|+++++..+..       ...+
T Consensus       117 p~pi~~f~~~~l~~~l~~~L~~~g~~~ptpiQ~~aip~il~g~dviv~ApTGSGKTlayllPil~~l~~~~~~~~~~~~~  196 (518)
T PLN00206        117 PPPILSFSSCGLPPKLLLNLETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPIISRCCTIRSGHPSEQRN  196 (518)
T ss_pred             CchhcCHHhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEEecCCCCccHHHHHHHHHHHHhhccccccccCC
Confidence            367788999999999999999999999999999999999999999999999999999999999876532       1245


Q ss_pred             eeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEE
Q 015158          108 CQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVL  187 (412)
Q Consensus       108 ~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iii  187 (412)
                      +++||++||++|+.|+.+.++.+....++.+..+.|+.........+..+++|+|+||++|..++.+....++++++||+
T Consensus       197 ~~aLIL~PTreLa~Qi~~~~~~l~~~~~~~~~~~~gG~~~~~q~~~l~~~~~IiV~TPgrL~~~l~~~~~~l~~v~~lVi  276 (518)
T PLN00206        197 PLAMVLTPTRELCVQVEDQAKVLGKGLPFKTALVVGGDAMPQQLYRIQQGVELIVGTPGRLIDLLSKHDIELDNVSVLVL  276 (518)
T ss_pred             ceEEEEeCCHHHHHHHHHHHHHHhCCCCceEEEEECCcchHHHHHHhcCCCCEEEECHHHHHHHHHcCCccchheeEEEe
Confidence            68999999999999999999998877788888888888776666666677899999999999999888888899999999


Q ss_pred             eCCchhhccCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhHH
Q 015158          188 DEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLE  267 (412)
Q Consensus       188 DE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  267 (412)
                      ||||++.+++|...+..++..++ +.+++++|||++.........+...+..+...........+.+....... ..+..
T Consensus       277 DEad~ml~~gf~~~i~~i~~~l~-~~q~l~~SATl~~~v~~l~~~~~~~~~~i~~~~~~~~~~~v~q~~~~~~~-~~k~~  354 (518)
T PLN00206        277 DEVDCMLERGFRDQVMQIFQALS-QPQVLLFSATVSPEVEKFASSLAKDIILISIGNPNRPNKAVKQLAIWVET-KQKKQ  354 (518)
T ss_pred             ecHHHHhhcchHHHHHHHHHhCC-CCcEEEEEeeCCHHHHHHHHHhCCCCEEEEeCCCCCCCcceeEEEEeccc-hhHHH
Confidence            99999999999999999988885 67899999999998888888888888877776655555556666555554 34556


Q ss_pred             HHHHHHHhcC--CCcEEEEEcchhHHHHHHHHHhc-CCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCC
Q 015158          268 TLCDLYETLA--ITQSVIFVNTRRKVDWLTDKMRS-RDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDV  344 (412)
Q Consensus       268 ~l~~~~~~~~--~~k~lif~~~~~~~~~~~~~L~~-~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~  344 (412)
                      .+.+++....  ..++||||+++..++.+++.|.. .++.+..+||+++..+|..+++.|++|+.+|||||+++++|+|+
T Consensus       355 ~l~~~l~~~~~~~~~~iVFv~s~~~a~~l~~~L~~~~g~~~~~~Hg~~~~~eR~~il~~Fr~G~~~ILVaTdvl~rGiDi  434 (518)
T PLN00206        355 KLFDILKSKQHFKPPAVVFVSSRLGADLLANAITVVTGLKALSIHGEKSMKERREVMKSFLVGEVPVIVATGVLGRGVDL  434 (518)
T ss_pred             HHHHHHHhhcccCCCEEEEcCCchhHHHHHHHHhhccCcceEEeeCCCCHHHHHHHHHHHHCCCCCEEEEecHhhccCCc
Confidence            6667766543  36899999999999999999975 58899999999999999999999999999999999999999999


Q ss_pred             CCCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHHhccccccCChhhhh
Q 015158          345 QQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVAD  410 (412)
Q Consensus       345 ~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  410 (412)
                      |++++||+++.|.+..+|+||+||+||.|..|.+++|+++.+...+..+.+.++...+.+|.++.+
T Consensus       435 p~v~~VI~~d~P~s~~~yihRiGRaGR~g~~G~ai~f~~~~~~~~~~~l~~~l~~~~~~vp~~l~~  500 (518)
T PLN00206        435 LRVRQVIIFDMPNTIKEYIHQIGRASRMGEKGTAIVFVNEEDRNLFPELVALLKSSGAAIPRELAN  500 (518)
T ss_pred             ccCCEEEEeCCCCCHHHHHHhccccccCCCCeEEEEEEchhHHHHHHHHHHHHHHcCCCCCHHHHh
Confidence            999999999999999999999999999999999999999999999999999999999999988754

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=1.2e-57  Score=436.43  Aligned_cols=363  Identities=33%  Similarity=0.524  Sum_probs=323.3

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccC-------CCceeEEE
Q 015158           40 TFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYG-------LVECQALV  112 (412)
Q Consensus        40 ~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~-------~~~~~~li  112 (412)
                      +|+.+++++.+.+.|...||..|+|+|.++++.+++|+++++.+|||||||++|+++++..+...       ...+++||
T Consensus        10 ~f~~l~l~~~l~~~L~~~g~~~ptpiQ~~~ip~~l~G~Dvi~~ApTGSGKTlafllpil~~l~~~~~~~~~~~~~~raLI   89 (572)
T PRK04537         10 TFSSFDLHPALLAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMNRLLSRPALADRKPEDPRALI   89 (572)
T ss_pred             ChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEEcCCCCcHHHHHHHHHHHHHHhcccccccccCCceEEE
Confidence            69999999999999999999999999999999999999999999999999999999999876432       12468999


Q ss_pred             EcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcC-CCCCCCceEEEEeCCc
Q 015158          113 LAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQ-SLRPDNIRIFVLDEAD  191 (412)
Q Consensus       113 l~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~-~~~~~~~~~iiiDE~h  191 (412)
                      ++|+++|+.|+.+.+..+....++.+..++|+.....+...+..+++|+|+||++|.+++.+. .+.+..+++||+||||
T Consensus        90 l~PTreLa~Qi~~~~~~l~~~~~i~v~~l~Gg~~~~~q~~~l~~~~dIiV~TP~rL~~~l~~~~~~~l~~v~~lViDEAh  169 (572)
T PRK04537         90 LAPTRELAIQIHKDAVKFGADLGLRFALVYGGVDYDKQRELLQQGVDVIIATPGRLIDYVKQHKVVSLHACEICVLDEAD  169 (572)
T ss_pred             EeCcHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHHhCCCCEEEECHHHHHHHHHhccccchhheeeeEecCHH
Confidence            999999999999999999888899999999998877776777778899999999999988764 3567789999999999


Q ss_pred             hhhccCcHHHHHHHHHhCCC--CceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhHHHH
Q 015158          192 EMLSRGFKDQIYDIFQLLPP--KIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETL  269 (412)
Q Consensus       192 ~~~~~~~~~~~~~i~~~~~~--~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  269 (412)
                      ++.+.+|...+..++..++.  ..+++++|||++.........++..+..+...........+.+.+... ....+...+
T Consensus       170 ~lld~gf~~~i~~il~~lp~~~~~q~ll~SATl~~~v~~l~~~~l~~p~~i~v~~~~~~~~~i~q~~~~~-~~~~k~~~L  248 (572)
T PRK04537        170 RMFDLGFIKDIRFLLRRMPERGTRQTLLFSATLSHRVLELAYEHMNEPEKLVVETETITAARVRQRIYFP-ADEEKQTLL  248 (572)
T ss_pred             HHhhcchHHHHHHHHHhcccccCceEEEEeCCccHHHHHHHHHHhcCCcEEEeccccccccceeEEEEec-CHHHHHHHH
Confidence            99999999999999998876  678999999999988888888888877666655554445555554443 335577778


Q ss_pred             HHHHHhcCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCE
Q 015158          270 CDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSL  349 (412)
Q Consensus       270 ~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~  349 (412)
                      ..++......++||||++++.++.+++.|.+.++.+..+||+++..+|..+++.|++|+++|||||+++++|+|+|++++
T Consensus       249 ~~ll~~~~~~k~LVF~nt~~~ae~l~~~L~~~g~~v~~lhg~l~~~eR~~il~~Fr~G~~~VLVaTdv~arGIDip~V~~  328 (572)
T PRK04537        249 LGLLSRSEGARTMVFVNTKAFVERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQKGQLEILVATDVAARGLHIDGVKY  328 (572)
T ss_pred             HHHHhcccCCcEEEEeCCHHHHHHHHHHHHHcCCCEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEehhhhcCCCccCCCE
Confidence            88887777789999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHHhcccccc
Q 015158          350 VINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEE  403 (412)
Q Consensus       350 vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~  403 (412)
                      ||+++.|.+...|+||+||+||.|..|.+++|+++.+...+..+++++...++.
T Consensus       329 VInyd~P~s~~~yvqRiGRaGR~G~~G~ai~~~~~~~~~~l~~i~~~~~~~~~~  382 (572)
T PRK04537        329 VYNYDLPFDAEDYVHRIGRTARLGEEGDAISFACERYAMSLPDIEAYIEQKIPV  382 (572)
T ss_pred             EEEcCCCCCHHHHhhhhcccccCCCCceEEEEecHHHHHHHHHHHHHHcCCCCc
Confidence            999999999999999999999999999999999999999999999998876643

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

Probab=100.00  E-value=2.2e-57  Score=429.11  Aligned_cols=369  Identities=45%  Similarity=0.705  Sum_probs=341.4

Q ss_pred             hhhhccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhcc-CCCcee-EE
Q 015158           34 YDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY-GLVECQ-AL  111 (412)
Q Consensus        34 ~~~~~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~-~~~~~~-~l  111 (412)
                      .......|+.+++++.+.+++...||..|+|.|..+++.++.|++++..++||||||.+|++++++.+.. ...... +|
T Consensus        24 ~~~~~~~F~~l~l~~~ll~~l~~~gf~~pt~IQ~~~IP~~l~g~Dvi~~A~TGsGKT~Af~lP~l~~l~~~~~~~~~~aL  103 (513)
T COG0513          24 EEKTPPEFASLGLSPELLQALKDLGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFLLPLLQKILKSVERKYVSAL  103 (513)
T ss_pred             cccccCCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhcccccCCCceE
Confidence            3333467999999999999999999999999999999999999999999999999999999999999773 222222 99


Q ss_pred             EEcCCHHHHHHHHHHHHHhhccc-CcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCC
Q 015158          112 VLAPTRELAQQIEKVMRALGDYL-GVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEA  190 (412)
Q Consensus       112 il~P~~~L~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~  190 (412)
                      |++||++|+.|+.+.+..+.... ++.+..++|+.....+...+..+++|+|+||.++..++.+..+.+.++.++|+|||
T Consensus       104 il~PTRELA~Qi~~~~~~~~~~~~~~~~~~i~GG~~~~~q~~~l~~~~~ivVaTPGRllD~i~~~~l~l~~v~~lVlDEA  183 (513)
T COG0513         104 ILAPTRELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQIEALKRGVDIVVATPGRLLDLIKRGKLDLSGVETLVLDEA  183 (513)
T ss_pred             EECCCHHHHHHHHHHHHHHHhhcCCccEEEEECCCCHHHHHHHHhcCCCEEEECccHHHHHHHcCCcchhhcCEEEeccH
Confidence            99999999999999999999888 78999999999988887777777999999999999999999999999999999999


Q ss_pred             chhhccCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCcc--ccCCceEEEEEeccchhhHHH
Q 015158          191 DEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDEL--TLEGIKQFHVNVEKEEWKLET  268 (412)
Q Consensus       191 h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~  268 (412)
                      +++++.+|...+..+...++.+.|.+++|||++.........++.+|..+.......  ....+.+.++.+.....+...
T Consensus       184 DrmLd~Gf~~~i~~I~~~~p~~~qtllfSAT~~~~i~~l~~~~l~~p~~i~v~~~~~~~~~~~i~q~~~~v~~~~~k~~~  263 (513)
T COG0513         184 DRMLDMGFIDDIEKILKALPPDRQTLLFSATMPDDIRELARRYLNDPVEIEVSVEKLERTLKKIKQFYLEVESEEEKLEL  263 (513)
T ss_pred             hhhhcCCCHHHHHHHHHhCCcccEEEEEecCCCHHHHHHHHHHccCCcEEEEccccccccccCceEEEEEeCCHHHHHHH
Confidence            999999999999999999999999999999999999999999999998888775555  778899999999876679999


Q ss_pred             HHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCC
Q 015158          269 LCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVS  348 (412)
Q Consensus       269 l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~  348 (412)
                      +..++.....+++||||++++.++.++..|...|+.+..+||++++.+|.++++.|++|+.+|||||+++++|+|+|+++
T Consensus       264 L~~ll~~~~~~~~IVF~~tk~~~~~l~~~l~~~g~~~~~lhG~l~q~~R~~~l~~F~~g~~~vLVaTDvaaRGiDi~~v~  343 (513)
T COG0513         264 LLKLLKDEDEGRVIVFVRTKRLVEELAESLRKRGFKVAALHGDLPQEERDRALEKFKDGELRVLVATDVAARGLDIPDVS  343 (513)
T ss_pred             HHHHHhcCCCCeEEEEeCcHHHHHHHHHHHHHCCCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEEechhhccCCccccc
Confidence            99999998888999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccC-cHHHHHHHHHHhccccc
Q 015158          349 LVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRD-DERMLFDIQKFYNVVIE  402 (412)
Q Consensus       349 ~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~-~~~~~~~~~~~~~~~~~  402 (412)
                      +||+++.|.++..|+||+||+||.|..|.++.|+.+. +...+..+++.+....+
T Consensus       344 ~VinyD~p~~~e~yvHRiGRTgRaG~~G~ai~fv~~~~e~~~l~~ie~~~~~~~~  398 (513)
T COG0513         344 HVINYDLPLDPEDYVHRIGRTGRAGRKGVAISFVTEEEEVKKLKRIEKRLERKLP  398 (513)
T ss_pred             eeEEccCCCCHHHheeccCccccCCCCCeEEEEeCcHHHHHHHHHHHHHHhcccc
Confidence            9999999999999999999999999999999999986 89999999999876643

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=2.5e-56  Score=423.46  Aligned_cols=363  Identities=33%  Similarity=0.522  Sum_probs=322.9

Q ss_pred             ccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCC-------CceeE
Q 015158           38 YDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGL-------VECQA  110 (412)
Q Consensus        38 ~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~-------~~~~~  110 (412)
                      ...|..+++++.+.++|...||..|+++|.++++.+++|+++++.+|||||||++|+++++..+....       ...++
T Consensus        86 ~~~f~~~~l~~~l~~~l~~~g~~~~~~iQ~~ai~~~~~G~dvi~~apTGSGKTlay~lpil~~l~~~~~~~~~~~~~~~a  165 (475)
T PRK01297         86 KTRFHDFNLAPELMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQLLQTPPPKERYMGEPRA  165 (475)
T ss_pred             CCCHhHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhcCcccccccCCceE
Confidence            34688899999999999999999999999999999999999999999999999999999998875432       14689


Q ss_pred             EEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHh-cCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeC
Q 015158          111 LVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL-SSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDE  189 (412)
Q Consensus       111 lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE  189 (412)
                      ||++||++|+.|+.+.+..+....++.+..++|+.......... ...++|+|+||++|..+..++...++++++||+||
T Consensus       166 Lil~PtreLa~Q~~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~~~~~~~~Iiv~TP~~Ll~~~~~~~~~l~~l~~lViDE  245 (475)
T PRK01297        166 LIIAPTRELVVQIAKDAAALTKYTGLNVMTFVGGMDFDKQLKQLEARFCDILVATPGRLLDFNQRGEVHLDMVEVMVLDE  245 (475)
T ss_pred             EEEeCcHHHHHHHHHHHHHhhccCCCEEEEEEccCChHHHHHHHhCCCCCEEEECHHHHHHHHHcCCcccccCceEEech
Confidence            99999999999999999999888889999999987655544333 45689999999999998888888889999999999


Q ss_pred             CchhhccCcHHHHHHHHHhCCC--CceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhHH
Q 015158          190 ADEMLSRGFKDQIYDIFQLLPP--KIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLE  267 (412)
Q Consensus       190 ~h~~~~~~~~~~~~~i~~~~~~--~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  267 (412)
                      +|.+.+.++...+..++..++.  ..+++++|||++.+.......+...+..+...........+...+..... ..+..
T Consensus       246 ah~l~~~~~~~~l~~i~~~~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~-~~k~~  324 (475)
T PRK01297        246 ADRMLDMGFIPQVRQIIRQTPRKEERQTLLFSATFTDDVMNLAKQWTTDPAIVEIEPENVASDTVEQHVYAVAG-SDKYK  324 (475)
T ss_pred             HHHHHhcccHHHHHHHHHhCCCCCCceEEEEEeecCHHHHHHHHHhccCCEEEEeccCcCCCCcccEEEEEecc-hhHHH
Confidence            9999999999999999888864  56899999999988888888888888887776666555555555555443 45667


Q ss_pred             HHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCC
Q 015158          268 TLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQV  347 (412)
Q Consensus       268 ~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~  347 (412)
                      .+..++.....+++||||++++.++.+++.|.+.++.+..+||+++..+|.++++.|++|++++||||+++++|+|+|++
T Consensus       325 ~l~~ll~~~~~~~~IVF~~s~~~~~~l~~~L~~~~~~~~~~~g~~~~~~R~~~~~~Fr~G~~~vLvaT~~l~~GIDi~~v  404 (475)
T PRK01297        325 LLYNLVTQNPWERVMVFANRKDEVRRIEERLVKDGINAAQLSGDVPQHKRIKTLEGFREGKIRVLVATDVAGRGIHIDGI  404 (475)
T ss_pred             HHHHHHHhcCCCeEEEEeCCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHhCCCCcEEEEccccccCCcccCC
Confidence            78888887777899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHHhcccc
Q 015158          348 SLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVI  401 (412)
Q Consensus       348 ~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~  401 (412)
                      ++||+++.|.|...|.||+||+||.|.+|.+++|+++.|...+..++++++..+
T Consensus       405 ~~VI~~~~P~s~~~y~Qr~GRaGR~g~~g~~i~~~~~~d~~~~~~~~~~~~~~~  458 (475)
T PRK01297        405 SHVINFTLPEDPDDYVHRIGRTGRAGASGVSISFAGEDDAFQLPEIEELLGRKI  458 (475)
T ss_pred             CEEEEeCCCCCHHHHHHhhCccCCCCCCceEEEEecHHHHHHHHHHHHHhCCCC
Confidence            999999999999999999999999999999999999999999999999998876

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

Probab=100.00  E-value=9.3e-54  Score=376.79  Aligned_cols=367  Identities=34%  Similarity=0.540  Sum_probs=338.8

Q ss_pred             CCChhhhccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhcc-------
Q 015158           31 FTSYDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY-------  103 (412)
Q Consensus        31 ~~~~~~~~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~-------  103 (412)
                      -...+++..+|+..+++..+++.+...||..|+|.|+.+++..++++++|.++.||||||.+|+++++..+..       
T Consensus       237 g~~lpnplrnwEE~~~P~e~l~~I~~~~y~eptpIqR~aipl~lQ~rD~igvaETgsGktaaf~ipLl~~IsslP~~~~~  316 (673)
T KOG0333|consen  237 GGRLPNPLRNWEESGFPLELLSVIKKPGYKEPTPIQRQAIPLGLQNRDPIGVAETGSGKTAAFLIPLLIWISSLPPMARL  316 (673)
T ss_pred             CCCCCccccChhhcCCCHHHHHHHHhcCCCCCchHHHhhccchhccCCeeeEEeccCCccccchhhHHHHHHcCCCcchh
Confidence            3446678889999999999999999999999999999999999999999999999999999999988876532       


Q ss_pred             --CCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCC
Q 015158          104 --GLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDN  181 (412)
Q Consensus       104 --~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~  181 (412)
                        ...++.++++.||+.|++|+.++-.++....++.+..+.|+...+...-.+..++.|+|+||..|...+.+..+.+..
T Consensus       317 en~~~gpyaiilaptReLaqqIeeEt~kf~~~lg~r~vsvigg~s~EEq~fqls~gceiviatPgrLid~Lenr~lvl~q  396 (673)
T KOG0333|consen  317 ENNIEGPYAIILAPTRELAQQIEEETNKFGKPLGIRTVSVIGGLSFEEQGFQLSMGCEIVIATPGRLIDSLENRYLVLNQ  396 (673)
T ss_pred             hhcccCceeeeechHHHHHHHHHHHHHHhcccccceEEEEecccchhhhhhhhhccceeeecCchHHHHHHHHHHHHhcc
Confidence              234678999999999999999999999999999999999999987776677889999999999999999999888899


Q ss_pred             ceEEEEeCCchhhccCcHHHHHHHHHhCCC-------------------------CceEEEEeecCChHHHHHHHHhcCC
Q 015158          182 IRIFVLDEADEMLSRGFKDQIYDIFQLLPP-------------------------KIQVGVFSATMPPEALEITRKFMNK  236 (412)
Q Consensus       182 ~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~-------------------------~~~~i~~SAT~~~~~~~~~~~~~~~  236 (412)
                      ..++|+|||+++.+.+|...+..++..+|.                         -.+.+.+|||+++....+...++..
T Consensus       397 ctyvvldeadrmiDmgfE~dv~~iL~~mPssn~k~~tde~~~~~~~~~~~~~~k~yrqT~mftatm~p~verlar~ylr~  476 (673)
T KOG0333|consen  397 CTYVVLDEADRMIDMGFEPDVQKILEQMPSSNAKPDTDEKEGEERVRKNFSSSKKYRQTVMFTATMPPAVERLARSYLRR  476 (673)
T ss_pred             CceEeccchhhhhcccccHHHHHHHHhCCccccCCCccchhhHHHHHhhcccccceeEEEEEecCCChHHHHHHHHHhhC
Confidence            999999999999999999999999999873                         1467999999999999999999999


Q ss_pred             CeEEEecCCccccCCceEEEEEeccchhhHHHHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHH
Q 015158          237 PVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNT  316 (412)
Q Consensus       237 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~  316 (412)
                      |+.+.+.......+-+.+.+..+.. +.+...|.+++......++|||+|.++.|+.+++.|.+.|+.+..+||+-++++
T Consensus       477 pv~vtig~~gk~~~rveQ~v~m~~e-d~k~kkL~eil~~~~~ppiIIFvN~kk~~d~lAk~LeK~g~~~~tlHg~k~qeQ  555 (673)
T KOG0333|consen  477 PVVVTIGSAGKPTPRVEQKVEMVSE-DEKRKKLIEILESNFDPPIIIFVNTKKGADALAKILEKAGYKVTTLHGGKSQEQ  555 (673)
T ss_pred             CeEEEeccCCCCccchheEEEEecc-hHHHHHHHHHHHhCCCCCEEEEEechhhHHHHHHHHhhccceEEEeeCCccHHH
Confidence            9999999988888888888888876 456899999999988899999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHH
Q 015158          317 RDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKF  396 (412)
Q Consensus       317 r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~  396 (412)
                      |+.+++.|++|..+|+|||+++++|+|+|++.+||.++.+.|..+|.+||||.||+|+.|.++.|+++.+...++.+.+.
T Consensus       556 Re~aL~~fr~~t~dIlVaTDvAgRGIDIpnVSlVinydmaksieDYtHRIGRTgRAGk~GtaiSflt~~dt~v~ydLkq~  635 (673)
T KOG0333|consen  556 RENALADFREGTGDILVATDVAGRGIDIPNVSLVINYDMAKSIEDYTHRIGRTGRAGKSGTAISFLTPADTAVFYDLKQA  635 (673)
T ss_pred             HHHHHHHHHhcCCCEEEEecccccCCCCCccceeeecchhhhHHHHHHHhccccccccCceeEEEeccchhHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999998777777766


Q ss_pred             hc
Q 015158          397 YN  398 (412)
Q Consensus       397 ~~  398 (412)
                      +.
T Consensus       636 l~  637 (673)
T KOG0333|consen  636 LR  637 (673)
T ss_pred             HH
Confidence            65

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

Probab=100.00  E-value=1.7e-54  Score=359.24  Aligned_cols=370  Identities=40%  Similarity=0.664  Sum_probs=347.5

Q ss_pred             ccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCH
Q 015158           38 YDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTR  117 (412)
Q Consensus        38 ~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~  117 (412)
                      -..|+++.+..++...+.+.||..|+|.|.++++..+.|++++..+..|+|||-+|.+++++.+......-+.++++|++
T Consensus        84 G~efEd~~Lkr~LLmgIfe~G~ekPSPiQeesIPiaLtGrdiLaRaKNGTGKT~a~~IP~Lekid~~~~~IQ~~ilVPtr  163 (459)
T KOG0326|consen   84 GNEFEDYCLKRELLMGIFEKGFEKPSPIQEESIPIALTGRDILARAKNGTGKTAAYCIPVLEKIDPKKNVIQAIILVPTR  163 (459)
T ss_pred             CccHHHhhhhHHHHHHHHHhccCCCCCccccccceeecchhhhhhccCCCCCccceechhhhhcCccccceeEEEEeecc
Confidence            45788899999999999999999999999999999999999999999999999999999999998877777899999999


Q ss_pred             HHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccC
Q 015158          118 ELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRG  197 (412)
Q Consensus       118 ~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~  197 (412)
                      +|+-|..+.++.++...++.+...+|+++...+.-.+.+..+++|+||++++.+..+.-..+++..++|+|||+.+++..
T Consensus       164 elALQtSqvc~~lskh~~i~vmvttGGT~lrDDI~Rl~~~VH~~vgTPGRIlDL~~KgVa~ls~c~~lV~DEADKlLs~~  243 (459)
T KOG0326|consen  164 ELALQTSQVCKELSKHLGIKVMVTTGGTSLRDDIMRLNQTVHLVVGTPGRILDLAKKGVADLSDCVILVMDEADKLLSVD  243 (459)
T ss_pred             hhhHHHHHHHHHHhcccCeEEEEecCCcccccceeeecCceEEEEcCChhHHHHHhcccccchhceEEEechhhhhhchh
Confidence            99999999999999999999999999999888877778889999999999999999988888899999999999999999


Q ss_pred             cHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhHHHHHHHHHhcC
Q 015158          198 FKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLA  277 (412)
Q Consensus       198 ~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  277 (412)
                      |...+..++..+|++.|+++.|||.+-....++...+.+|..+. -.++....++.++|..+.. ..+..-+..+..+..
T Consensus       244 F~~~~e~li~~lP~~rQillySATFP~tVk~Fm~~~l~kPy~IN-LM~eLtl~GvtQyYafV~e-~qKvhCLntLfskLq  321 (459)
T KOG0326|consen  244 FQPIVEKLISFLPKERQILLYSATFPLTVKGFMDRHLKKPYEIN-LMEELTLKGVTQYYAFVEE-RQKVHCLNTLFSKLQ  321 (459)
T ss_pred             hhhHHHHHHHhCCccceeeEEecccchhHHHHHHHhccCcceee-hhhhhhhcchhhheeeech-hhhhhhHHHHHHHhc
Confidence            99999999999999999999999999999999999999998665 4556677788888877766 558888888888888


Q ss_pred             CCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccCCC
Q 015158          278 ITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPT  357 (412)
Q Consensus       278 ~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~~~  357 (412)
                      ....||||||...++-+++.+.+.|+.+.++|+.|.++.|..++..|++|..+.||||+.+.+|+|++.+++||.++.|.
T Consensus       322 INQsIIFCNS~~rVELLAkKITelGyscyyiHakM~Q~hRNrVFHdFr~G~crnLVctDL~TRGIDiqavNvVINFDfpk  401 (459)
T KOG0326|consen  322 INQSIIFCNSTNRVELLAKKITELGYSCYYIHAKMAQEHRNRVFHDFRNGKCRNLVCTDLFTRGIDIQAVNVVINFDFPK  401 (459)
T ss_pred             ccceEEEeccchHhHHHHHHHHhccchhhHHHHHHHHhhhhhhhhhhhccccceeeehhhhhcccccceeeEEEecCCCC
Confidence            88999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHHhccccccCChhhh
Q 015158          358 QPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVA  409 (412)
Q Consensus       358 s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  409 (412)
                      ++..|.+|+||.||.|-.|.++-+++..|...+..+++.++.+++++|..+.
T Consensus       402 ~aEtYLHRIGRsGRFGhlGlAInLityedrf~L~~IE~eLGtEI~pip~~iD  453 (459)
T KOG0326|consen  402 NAETYLHRIGRSGRFGHLGLAINLITYEDRFNLYRIEQELGTEIKPIPSNID  453 (459)
T ss_pred             CHHHHHHHccCCccCCCcceEEEEEehhhhhhHHHHHHHhccccccCCCcCC
Confidence            9999999999999999999999999999999999999999999999998764

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

Probab=100.00  E-value=6.6e-53  Score=369.35  Aligned_cols=356  Identities=31%  Similarity=0.485  Sum_probs=319.0

Q ss_pred             ccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCC----CceeEEEE
Q 015158           38 YDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGL----VECQALVL  113 (412)
Q Consensus        38 ~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~----~~~~~lil  113 (412)
                      -..|+...+++...++++.+||..+++.|...++.++.|++++..|-||+|||+++++++...+...+    .+-.++|+
T Consensus        81 ~~~f~~~~LS~~t~kAi~~~GF~~MT~VQ~~ti~pll~gkDvl~~AKTGtGKTlAFLiPaie~l~k~~~~~r~~~~vlIi  160 (543)
T KOG0342|consen   81 TFRFEEGSLSPLTLKAIKEMGFETMTPVQQKTIPPLLEGKDVLAAAKTGTGKTLAFLLPAIELLRKLKFKPRNGTGVLII  160 (543)
T ss_pred             hhHhhccccCHHHHHHHHhcCccchhHHHHhhcCccCCCccceeeeccCCCceeeehhHHHHHHHhcccCCCCCeeEEEe
Confidence            45678889999999999999999999999999999999999999999999999999999998876543    34469999


Q ss_pred             cCCHHHHHHHHHHHHHhhccc-CcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCC-CCCCCceEEEEeCCc
Q 015158          114 APTRELAQQIEKVMRALGDYL-GVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQS-LRPDNIRIFVLDEAD  191 (412)
Q Consensus       114 ~P~~~L~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~-~~~~~~~~iiiDE~h  191 (412)
                      |||++|+.|.+.+++++.... +..+....|+.+.....+....++.|+|+||++|..++++.. +..++.+++|+|||+
T Consensus       161 ~PTRELA~Q~~~eak~Ll~~h~~~~v~~viGG~~~~~e~~kl~k~~niliATPGRLlDHlqNt~~f~~r~~k~lvlDEAD  240 (543)
T KOG0342|consen  161 CPTRELAMQIFAEAKELLKYHESITVGIVIGGNNFSVEADKLVKGCNILIATPGRLLDHLQNTSGFLFRNLKCLVLDEAD  240 (543)
T ss_pred             cccHHHHHHHHHHHHHHHhhCCCcceEEEeCCccchHHHHHhhccccEEEeCCchHHhHhhcCCcchhhccceeEeecch
Confidence            999999999999999988777 889999999999887777777799999999999999998854 446777899999999


Q ss_pred             hhhccCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCC-CeEEEecCCc--cccCCceEEEEEeccchhhHHH
Q 015158          192 EMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNK-PVRILVKRDE--LTLEGIKQFHVNVEKEEWKLET  268 (412)
Q Consensus       192 ~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~-~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~  268 (412)
                      ++++.+|...+..|...+|...|.+++|||.++.+.+.....+.. +..+......  ..-..+.+.+...+.. .....
T Consensus       241 rlLd~GF~~di~~Ii~~lpk~rqt~LFSAT~~~kV~~l~~~~L~~d~~~v~~~d~~~~~The~l~Qgyvv~~~~-~~f~l  319 (543)
T KOG0342|consen  241 RLLDIGFEEDVEQIIKILPKQRQTLLFSATQPSKVKDLARGALKRDPVFVNVDDGGERETHERLEQGYVVAPSD-SRFSL  319 (543)
T ss_pred             hhhhcccHHHHHHHHHhccccceeeEeeCCCcHHHHHHHHHhhcCCceEeecCCCCCcchhhcccceEEecccc-chHHH
Confidence            999999999999999999999999999999999888877766554 6666655433  2334566666666654 34788


Q ss_pred             HHHHHHhcCC-CcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCC
Q 015158          269 LCDLYETLAI-TQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQV  347 (412)
Q Consensus       269 l~~~~~~~~~-~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~  347 (412)
                      +..+++++.. .|+||||++...+..+++.|+..++++..+||+.++..|..+..+|.+.+..|||||++..+|+|+|++
T Consensus       320 l~~~LKk~~~~~KiiVF~sT~~~vk~~~~lL~~~dlpv~eiHgk~~Q~kRT~~~~~F~kaesgIL~cTDVaARGlD~P~V  399 (543)
T KOG0342|consen  320 LYTFLKKNIKRYKIIVFFSTCMSVKFHAELLNYIDLPVLEIHGKQKQNKRTSTFFEFCKAESGILVCTDVAARGLDIPDV  399 (543)
T ss_pred             HHHHHHHhcCCceEEEEechhhHHHHHHHHHhhcCCchhhhhcCCcccccchHHHHHhhcccceEEecchhhccCCCCCc
Confidence            8889988866 899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHH
Q 015158          348 SLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQ  394 (412)
Q Consensus       348 ~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~  394 (412)
                      ++|+.+++|.++.+|++|+||.+|.|..|++++++.+.+..+++.+.
T Consensus       400 ~~VvQ~~~P~d~~~YIHRvGRTaR~gk~G~alL~l~p~El~Flr~LK  446 (543)
T KOG0342|consen  400 DWVVQYDPPSDPEQYIHRVGRTAREGKEGKALLLLAPWELGFLRYLK  446 (543)
T ss_pred             eEEEEeCCCCCHHHHHHHhccccccCCCceEEEEeChhHHHHHHHHh
Confidence            99999999999999999999999999999999999999999888877

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

Probab=100.00  E-value=2.6e-53  Score=372.72  Aligned_cols=359  Identities=35%  Similarity=0.563  Sum_probs=332.4

Q ss_pred             ccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCC---CceeEEEEc
Q 015158           38 YDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGL---VECQALVLA  114 (412)
Q Consensus        38 ~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~---~~~~~lil~  114 (412)
                      ..+|.+++|+-.+.+++...||..|+|.|...++..+-|++++-++.||||||.+|++|++.++....   ...++||+|
T Consensus       180 ~~sF~~mNLSRPlLka~~~lGy~~PTpIQ~a~IPvallgkDIca~A~TGsGKTAAF~lPiLERLlYrPk~~~~TRVLVL~  259 (691)
T KOG0338|consen  180 NESFQSMNLSRPLLKACSTLGYKKPTPIQVATIPVALLGKDICACAATGSGKTAAFALPILERLLYRPKKVAATRVLVLV  259 (691)
T ss_pred             hhhHHhcccchHHHHHHHhcCCCCCCchhhhcccHHhhcchhhheecccCCchhhhHHHHHHHHhcCcccCcceeEEEEe
Confidence            56899999999999999999999999999999999999999999999999999999999999986543   345899999


Q ss_pred             CCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHc-CCCCCCCceEEEEeCCchh
Q 015158          115 PTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRR-QSLRPDNIRIFVLDEADEM  193 (412)
Q Consensus       115 P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~-~~~~~~~~~~iiiDE~h~~  193 (412)
                      ||++|+.|.....++++...++.+.+..||.....+...+...++|+|+||++|..++.+ ..+.++++.++|+|||+++
T Consensus       260 PTRELaiQv~sV~~qlaqFt~I~~~L~vGGL~lk~QE~~LRs~PDIVIATPGRlIDHlrNs~sf~ldsiEVLvlDEADRM  339 (691)
T KOG0338|consen  260 PTRELAIQVHSVTKQLAQFTDITVGLAVGGLDLKAQEAVLRSRPDIVIATPGRLIDHLRNSPSFNLDSIEVLVLDEADRM  339 (691)
T ss_pred             ccHHHHHHHHHHHHHHHhhccceeeeeecCccHHHHHHHHhhCCCEEEecchhHHHHhccCCCccccceeEEEechHHHH
Confidence            999999999999999999999999999999999999999999999999999999999987 5677899999999999999


Q ss_pred             hccCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEec--cchhhHHHHHH
Q 015158          194 LSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVE--KEEWKLETLCD  271 (412)
Q Consensus       194 ~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~l~~  271 (412)
                      ++.+|..++..++..|+.+.|.+++|||+...+.++..--+++|+.+.+.......+.+.+-+..+.  ....+...+..
T Consensus       340 LeegFademnEii~lcpk~RQTmLFSATMteeVkdL~slSL~kPvrifvd~~~~~a~~LtQEFiRIR~~re~dRea~l~~  419 (691)
T KOG0338|consen  340 LEEGFADEMNEIIRLCPKNRQTMLFSATMTEEVKDLASLSLNKPVRIFVDPNKDTAPKLTQEFIRIRPKREGDREAMLAS  419 (691)
T ss_pred             HHHHHHHHHHHHHHhccccccceeehhhhHHHHHHHHHhhcCCCeEEEeCCccccchhhhHHHheeccccccccHHHHHH
Confidence            9999999999999999999999999999999999999999999999999888777777666555443  33446667777


Q ss_pred             HHHhcCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEE
Q 015158          272 LYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVI  351 (412)
Q Consensus       272 ~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi  351 (412)
                      ++.......++||+.+++.|..+.-.|-=.|..+.-+||.+++.+|-..++.|++++++|||||+..++|+|++++.+||
T Consensus       420 l~~rtf~~~~ivFv~tKk~AHRl~IllGLlgl~agElHGsLtQ~QRlesL~kFk~~eidvLiaTDvAsRGLDI~gV~tVI  499 (691)
T KOG0338|consen  420 LITRTFQDRTIVFVRTKKQAHRLRILLGLLGLKAGELHGSLTQEQRLESLEKFKKEEIDVLIATDVASRGLDIEGVQTVI  499 (691)
T ss_pred             HHHHhcccceEEEEehHHHHHHHHHHHHHhhchhhhhcccccHHHHHHHHHHHHhccCCEEEEechhhccCCccceeEEE
Confidence            88877788999999999999999999988899999999999999999999999999999999999999999999999999


Q ss_pred             EccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHH
Q 015158          352 NYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKF  396 (412)
Q Consensus       352 ~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~  396 (412)
                      .+..|.+...|++|+||..|+|..|.++.|..+++-+.++.+.+.
T Consensus       500 Ny~mP~t~e~Y~HRVGRTARAGRaGrsVtlvgE~dRkllK~iik~  544 (691)
T KOG0338|consen  500 NYAMPKTIEHYLHRVGRTARAGRAGRSVTLVGESDRKLLKEIIKS  544 (691)
T ss_pred             eccCchhHHHHHHHhhhhhhcccCcceEEEeccccHHHHHHHHhh
Confidence            999999999999999999999999999999999999998888766

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

Probab=100.00  E-value=1.2e-52  Score=373.65  Aligned_cols=372  Identities=35%  Similarity=0.514  Sum_probs=339.8

Q ss_pred             ccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCC----------c
Q 015158           38 YDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLV----------E  107 (412)
Q Consensus        38 ~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~----------~  107 (412)
                      +..|..-.+.+.+..+++..++..|+|+|+.+++.+..|++++++|+||+|||.+|+++++..+.....          .
T Consensus        73 i~~f~~~~l~~~l~~ni~~~~~~~ptpvQk~sip~i~~Grdl~acAqTGsGKT~aFLiPii~~~~~~~~~~~~~~~~~~~  152 (482)
T KOG0335|consen   73 IPTFDEAILGEALAGNIKRSGYTKPTPVQKYSIPIISGGRDLMACAQTGSGKTAAFLIPIISYLLDEGPEDRGESGGGVY  152 (482)
T ss_pred             cccccccchhHHHhhccccccccCCCcceeeccceeecCCceEEEccCCCcchHHHHHHHHHHHHhcCcccCcccCCCCC
Confidence            447887788999999999999999999999999999999999999999999999999999998765422          4


Q ss_pred             eeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEE
Q 015158          108 CQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVL  187 (412)
Q Consensus       108 ~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iii  187 (412)
                      ++++|++||++|+.|.+++.+++....+......+|+.+...+......+++|+++||.+|..++++..+.+++++++|+
T Consensus       153 P~~lIlapTReL~~Qi~nea~k~~~~s~~~~~~~ygg~~~~~q~~~~~~gcdIlvaTpGrL~d~~e~g~i~l~~~k~~vL  232 (482)
T KOG0335|consen  153 PRALILAPTRELVDQIYNEARKFSYLSGMKSVVVYGGTDLGAQLRFIKRGCDILVATPGRLKDLIERGKISLDNCKFLVL  232 (482)
T ss_pred             CceEEEeCcHHHhhHHHHHHHhhcccccceeeeeeCCcchhhhhhhhccCccEEEecCchhhhhhhcceeehhhCcEEEe
Confidence            78999999999999999999999988899999999998888888888899999999999999999999999999999999


Q ss_pred             eCCchhhc-cCcHHHHHHHHHhCCC----CceEEEEeecCChHHHHHHHHhcCC-CeEEEecCCccccCCceEEEEEecc
Q 015158          188 DEADEMLS-RGFKDQIYDIFQLLPP----KIQVGVFSATMPPEALEITRKFMNK-PVRILVKRDELTLEGIKQFHVNVEK  261 (412)
Q Consensus       188 DE~h~~~~-~~~~~~~~~i~~~~~~----~~~~i~~SAT~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~  261 (412)
                      |||+.+.+ .+|...+..++.....    +.|-+++|||.+.+.......++.+ .....+........++.+....+..
T Consensus       233 DEADrMlD~mgF~p~Ir~iv~~~~~~~~~~~qt~mFSAtfp~~iq~l~~~fl~~~yi~laV~rvg~~~~ni~q~i~~V~~  312 (482)
T KOG0335|consen  233 DEADRMLDEMGFEPQIRKIVEQLGMPPKNNRQTLLFSATFPKEIQRLAADFLKDNYIFLAVGRVGSTSENITQKILFVNE  312 (482)
T ss_pred             cchHHhhhhccccccHHHHhcccCCCCccceeEEEEeccCChhhhhhHHHHhhccceEEEEeeeccccccceeEeeeecc
Confidence            99999999 8999999999988743    6789999999999988888877776 6777788888888899998888887


Q ss_pred             chhhHHHHHHHHHhcC----CC-----cEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEE
Q 015158          262 EEWKLETLCDLYETLA----IT-----QSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVL  332 (412)
Q Consensus       262 ~~~~~~~l~~~~~~~~----~~-----k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vl  332 (412)
                      .. +...+.+++....    .+     +++|||.+++.+..+...|...++....+||+-++.+|.+.+..|++|...++
T Consensus       313 ~~-kr~~Lldll~~~~~~~~~~~~~~e~tlvFvEt~~~~d~l~~~l~~~~~~~~sIhg~~tq~er~~al~~Fr~g~~pvl  391 (482)
T KOG0335|consen  313 ME-KRSKLLDLLNKDDGPPSDGEPKWEKTLVFVETKRGADELAAFLSSNGYPAKSIHGDRTQIEREQALNDFRNGKAPVL  391 (482)
T ss_pred             hh-hHHHHHHHhhcccCCcccCCcccceEEEEeeccchhhHHHHHHhcCCCCceeecchhhhhHHHHHHHHhhcCCcceE
Confidence            44 5556666655332    23     89999999999999999999999999999999999999999999999999999


Q ss_pred             EEcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHHhccccccCChhhhh
Q 015158          333 ITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVAD  410 (412)
Q Consensus       333 v~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  410 (412)
                      |+|++.++|+|+|+++|||.++.|.+..+|++|+||+||.|+.|.+..|++..+....+.+.+.+....+.+|.|+.+
T Consensus       392 VaT~VaaRGlDi~~V~hVInyDmP~d~d~YvHRIGRTGR~Gn~G~atsf~n~~~~~i~~~L~~~l~ea~q~vP~wl~~  469 (482)
T KOG0335|consen  392 VATNVAARGLDIPNVKHVINYDMPADIDDYVHRIGRTGRVGNGGRATSFFNEKNQNIAKALVEILTEANQEVPQWLSE  469 (482)
T ss_pred             EEehhhhcCCCCCCCceeEEeecCcchhhHHHhccccccCCCCceeEEEeccccchhHHHHHHHHHHhcccCcHHHHh
Confidence            999999999999999999999999999999999999999999999999999999999999999999999999999976

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

Probab=100.00  E-value=9.4e-53  Score=358.63  Aligned_cols=383  Identities=72%  Similarity=1.084  Sum_probs=361.3

Q ss_pred             CCCCCCChhhhccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCC
Q 015158           27 GQDFFTSYDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLV  106 (412)
Q Consensus        27 ~~~~~~~~~~~~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~  106 (412)
                      +..+.++|.+..++|++++|.+++.+.++..||.+|+..|+.|+..+.+|.++.+.+.+|+|||.++..+++..+.....
T Consensus        14 ~~~iesn~~evvdsfddm~L~e~LLrgiy~yGFekPSaIQqraI~p~i~G~dv~~qaqsgTgKt~af~i~iLq~iD~~~k   93 (397)
T KOG0327|consen   14 EGVIESNWNEVVDSFDDMNLKESLLRGIYAYGFEKPSAIQQRAILPCIKGHDVIAQAQSGTGKTAAFLISILQQIDMSVK   93 (397)
T ss_pred             cccccccHHHHhhhhhhcCCCHHHHhHHHhhccCCchHHHhccccccccCCceeEeeeccccchhhhHHHHHhhcCcchH
Confidence            67788899999999999999999999999999999999999999999999999999999999999999999998877666


Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHH-HHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEE
Q 015158          107 ECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQ-RILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIF  185 (412)
Q Consensus       107 ~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~i  185 (412)
                      ...+++++|+++|+.|..+....++...+..+..+.|+....... ......++|+++||+.....+....+..+.+.++
T Consensus        94 e~qalilaPtreLa~qi~~v~~~lg~~~~~~v~~~igg~~~~~~~~~i~~~~~hivvGTpgrV~dml~~~~l~~~~iKmf  173 (397)
T KOG0327|consen   94 ETQALILAPTRELAQQIQKVVRALGDHMDVSVHACIGGTNVRREDQALLKDKPHIVVGTPGRVFDMLNRGSLSTDGIKMF  173 (397)
T ss_pred             HHHHHHhcchHHHHHHHHHHHHhhhcccceeeeeecCcccchhhhhhhhccCceeecCCchhHHHhhccccccccceeEE
Confidence            678999999999999999999999998899999999988877444 4445568999999999999998888888889999


Q ss_pred             EEeCCchhhccCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhh
Q 015158          186 VLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWK  265 (412)
Q Consensus       186 iiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  265 (412)
                      |+||++++...+|...+..+...+|++.|++++|||.+.+.....+.+..+|+.+.....+...+.+++++..+.... +
T Consensus       174 vlDEaDEmLs~gfkdqI~~if~~lp~~vQv~l~SAT~p~~vl~vt~~f~~~pv~i~vkk~~ltl~gikq~~i~v~k~~-k  252 (397)
T KOG0327|consen  174 VLDEADEMLSRGFKDQIYDIFQELPSDVQVVLLSATMPSDVLEVTKKFMREPVRILVKKDELTLEGIKQFYINVEKEE-K  252 (397)
T ss_pred             eecchHhhhccchHHHHHHHHHHcCcchhheeecccCcHHHHHHHHHhccCceEEEecchhhhhhheeeeeeeccccc-c
Confidence            999999999999999999999999999999999999999999999999999999999999999999999999988855 8


Q ss_pred             HHHHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCC
Q 015158          266 LETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQ  345 (412)
Q Consensus       266 ~~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~  345 (412)
                      ...+..+..  .....+||||+++.+..+...|..++..+..+|+++.+.+|+.+.+.|+.|..+|||+|+.+++|+|+.
T Consensus       253 ~~~l~dl~~--~~~q~~if~nt~r~v~~l~~~L~~~~~~~s~~~~d~~q~~R~~~~~ef~~gssrvlIttdl~argidv~  330 (397)
T KOG0327|consen  253 LDTLCDLYR--RVTQAVIFCNTRRKVDNLTDKLRAHGFTVSAIHGDMEQNERDTLMREFRSGSSRVLITTDLLARGIDVQ  330 (397)
T ss_pred             ccHHHHHHH--hhhcceEEecchhhHHHHHHHHhhCCceEEEeecccchhhhhHHHHHhhcCCceEEeeccccccccchh
Confidence            888888888  446899999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHHhccccccCChhhhhcC
Q 015158          346 QVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVADLL  412 (412)
Q Consensus       346 ~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  412 (412)
                      .+..|+.++.|.....|.+|+||+||.|.+|.++.++.+.+...+++++++|...++++|.++.+|+
T Consensus       331 ~~slvinydlP~~~~~yihR~gr~gr~grkg~~in~v~~~d~~~lk~ie~~y~~~i~e~p~~~~~l~  397 (397)
T KOG0327|consen  331 QVSLVVNYDLPARKENYIHRIGRAGRFGRKGVAINFVTEEDVRDLKDIEKFYNTPIEELPSNFADLL  397 (397)
T ss_pred             hcceeeeeccccchhhhhhhcccccccCCCceeeeeehHhhHHHHHhHHHhcCCcceecccchhhcC
Confidence            9999999999999999999999999999999999999999999999999999999999999998875

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

Probab=100.00  E-value=8.9e-52  Score=359.94  Aligned_cols=356  Identities=33%  Similarity=0.544  Sum_probs=315.1

Q ss_pred             ccccCC--CCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccC--C--Cc-eeEEE
Q 015158           40 TFDAMG--LQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYG--L--VE-CQALV  112 (412)
Q Consensus        40 ~f~~~~--l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~--~--~~-~~~li  112 (412)
                      .|++++  +++++...+...||...+|+|..+++.+++++++++.++||||||++|++|++..+...  .  ++ --++|
T Consensus         5 ~~~~l~~~L~~~l~~~l~~~GF~~mTpVQa~tIPlll~~KDVvveavTGSGKTlAFllP~le~i~rr~~~~~~~~vgalI   84 (567)
T KOG0345|consen    5 SFSSLAPPLSPWLLEALDESGFEKMTPVQAATIPLLLKNKDVVVEAVTGSGKTLAFLLPMLEIIYRREAKTPPGQVGALI   84 (567)
T ss_pred             chhhcCCCccHHHHHHHHhcCCcccCHHHHhhhHHHhcCCceEEEcCCCCCchhhHHHHHHHHHHhhccCCCccceeEEE
Confidence            466664  56999999999999999999999999999999999999999999999999999988322  1  11 25899


Q ss_pred             EcCCHHHHHHHHHHHHHhhcc-cCcEEEEEEcCcchHHHHHHhc-CCCcEEEeChHHHHHHHHcCC--CCCCCceEEEEe
Q 015158          113 LAPTRELAQQIEKVMRALGDY-LGVKVHACVGGTSVREDQRILS-SGVHVVVGTPGRVFDMLRRQS--LRPDNIRIFVLD  188 (412)
Q Consensus       113 l~P~~~L~~q~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~-~~~~iii~T~~~l~~~~~~~~--~~~~~~~~iiiD  188 (412)
                      |+||++|+.|+.+....+... .+++..++.|+.+...+...+. .++.|+|+||++|..++.+..  ++.+++.++|+|
T Consensus        85 IsPTRELa~QI~~V~~~F~~~l~~l~~~l~vGG~~v~~Di~~fkee~~nIlVgTPGRL~di~~~~~~~l~~rsLe~LVLD  164 (567)
T KOG0345|consen   85 ISPTRELARQIREVAQPFLEHLPNLNCELLVGGRSVEEDIKTFKEEGPNILVGTPGRLLDILQREAEKLSFRSLEILVLD  164 (567)
T ss_pred             ecCcHHHHHHHHHHHHHHHHhhhccceEEEecCccHHHHHHHHHHhCCcEEEeCchhHHHHHhchhhhccccccceEEec
Confidence            999999999999998887655 5889999999998888766654 567899999999999998743  445699999999


Q ss_pred             CCchhhccCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCcc--ccCCceEEEEEeccchhhH
Q 015158          189 EADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDEL--TLEGIKQFHVNVEKEEWKL  266 (412)
Q Consensus       189 E~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~  266 (412)
                      ||+++.+.+|...++.|++.+|++.+.=++|||......++....+.+++.+.+.....  .+......+..+.. ..+.
T Consensus       165 EADrLldmgFe~~~n~ILs~LPKQRRTGLFSATq~~~v~dL~raGLRNpv~V~V~~k~~~~tPS~L~~~Y~v~~a-~eK~  243 (567)
T KOG0345|consen  165 EADRLLDMGFEASVNTILSFLPKQRRTGLFSATQTQEVEDLARAGLRNPVRVSVKEKSKSATPSSLALEYLVCEA-DEKL  243 (567)
T ss_pred             chHhHhcccHHHHHHHHHHhcccccccccccchhhHHHHHHHHhhccCceeeeecccccccCchhhcceeeEecH-HHHH
Confidence            99999999999999999999999999999999999999999999999999988876665  66667777777765 6789


Q ss_pred             HHHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcC--CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCC
Q 015158          267 ETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSR--DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDV  344 (412)
Q Consensus       267 ~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~--~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~  344 (412)
                      ..+.+++.....+|.|||+++...++.++..+...  +..+..+||.++...|..+++.|.+..-.+++||+++.+|+|+
T Consensus       244 ~~lv~~L~~~~~kK~iVFF~TCasVeYf~~~~~~~l~~~~i~~iHGK~~q~~R~k~~~~F~~~~~~vl~~TDVaARGlDi  323 (567)
T KOG0345|consen  244 SQLVHLLNNNKDKKCIVFFPTCASVEYFGKLFSRLLKKREIFSIHGKMSQKARAKVLEAFRKLSNGVLFCTDVAARGLDI  323 (567)
T ss_pred             HHHHHHHhccccccEEEEecCcchHHHHHHHHHHHhCCCcEEEecchhcchhHHHHHHHHHhccCceEEeehhhhccCCC
Confidence            99999999999999999999999999999998765  6689999999999999999999999888899999999999999


Q ss_pred             CCCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHHhccc
Q 015158          345 QQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVV  400 (412)
Q Consensus       345 ~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~  400 (412)
                      |++++||++++|.++..|.+|.||++|.|..|.+++|+.+.+..    +..|++..
T Consensus       324 p~iD~VvQ~DpP~~~~~FvHR~GRTaR~gr~G~Aivfl~p~E~a----YveFl~i~  375 (567)
T KOG0345|consen  324 PGIDLVVQFDPPKDPSSFVHRCGRTARAGREGNAIVFLNPREEA----YVEFLRIK  375 (567)
T ss_pred             CCceEEEecCCCCChhHHHhhcchhhhccCccceEEEecccHHH----HHHHHHhc
Confidence            99999999999999999999999999999999999999995553    45555544

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

Probab=100.00  E-value=5.1e-52  Score=355.51  Aligned_cols=373  Identities=33%  Similarity=0.516  Sum_probs=338.1

Q ss_pred             hhhhccccccC-CCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhcc------CCC
Q 015158           34 YDEVYDTFDAM-GLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY------GLV  106 (412)
Q Consensus        34 ~~~~~~~f~~~-~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~------~~~  106 (412)
                      ..+|.-+|++. .-.+++...+...||.+|+|.|.+|++.+++|.+++-++.||+|||++++++.+..+..      ...
T Consensus       214 IPnP~ctFddAFq~~pevmenIkK~GFqKPtPIqSQaWPI~LQG~DliGVAQTgtgKtL~~L~pg~ihi~aqp~~~~qr~  293 (629)
T KOG0336|consen  214 IPNPVCTFDDAFQCYPEVMENIKKTGFQKPTPIQSQAWPILLQGIDLIGVAQTGTGKTLAFLLPGFIHIDAQPKRREQRN  293 (629)
T ss_pred             CCCCcCcHHHHHhhhHHHHHHHHhccCCCCCcchhcccceeecCcceEEEEecCCCcCHHHhccceeeeeccchhhhccC
Confidence            45566677764 67899999999999999999999999999999999999999999999999988766543      245


Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEE
Q 015158          107 ECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFV  186 (412)
Q Consensus       107 ~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~ii  186 (412)
                      ++.+|+++||++|+.|+.-++.++. ..+....+++|+.+.......+..+.+|+++||.+|..+.-..-.++..+.++|
T Consensus       294 ~p~~lvl~ptreLalqie~e~~kys-yng~ksvc~ygggnR~eqie~lkrgveiiiatPgrlndL~~~n~i~l~siTYlV  372 (629)
T KOG0336|consen  294 GPGVLVLTPTRELALQIEGEVKKYS-YNGLKSVCVYGGGNRNEQIEDLKRGVEIIIATPGRLNDLQMDNVINLASITYLV  372 (629)
T ss_pred             CCceEEEeccHHHHHHHHhHHhHhh-hcCcceEEEecCCCchhHHHHHhcCceEEeeCCchHhhhhhcCeeeeeeeEEEE
Confidence            6789999999999999988888764 347888888888888888888899999999999999999888888889999999


Q ss_pred             EeCCchhhccCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccC-CceEEEEEeccchhh
Q 015158          187 LDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLE-GIKQFHVNVEKEEWK  265 (412)
Q Consensus       187 iDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~  265 (412)
                      +|||+++++.+|..++.+++-..++..+.+..|||+++.+..+.+.++.+|..+.....+...- ++.+.+ .+....++
T Consensus       373 lDEADrMLDMgFEpqIrkilldiRPDRqtvmTSATWP~~VrrLa~sY~Kep~~v~vGsLdL~a~~sVkQ~i-~v~~d~~k  451 (629)
T KOG0336|consen  373 LDEADRMLDMGFEPQIRKILLDIRPDRQTVMTSATWPEGVRRLAQSYLKEPMIVYVGSLDLVAVKSVKQNI-IVTTDSEK  451 (629)
T ss_pred             ecchhhhhcccccHHHHHHhhhcCCcceeeeecccCchHHHHHHHHhhhCceEEEecccceeeeeeeeeeE-EecccHHH
Confidence            9999999999999999999999999999999999999999999999999999998887766543 444444 66666778


Q ss_pred             HHHHHHHHHhc-CCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCC
Q 015158          266 LETLCDLYETL-AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDV  344 (412)
Q Consensus       266 ~~~l~~~~~~~-~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~  344 (412)
                      ...+..+++.+ ..+|+||||.++..|+.+..-|.-.|+....+||+-.+.+|+..++.|+.|+.+|||+|+.+++|+|+
T Consensus       452 ~~~~~~f~~~ms~ndKvIiFv~~K~~AD~LSSd~~l~gi~~q~lHG~r~Q~DrE~al~~~ksG~vrILvaTDlaSRGlDv  531 (629)
T KOG0336|consen  452 LEIVQFFVANMSSNDKVIIFVSRKVMADHLSSDFCLKGISSQSLHGNREQSDREMALEDFKSGEVRILVATDLASRGLDV  531 (629)
T ss_pred             HHHHHHHHHhcCCCceEEEEEechhhhhhccchhhhcccchhhccCChhhhhHHHHHHhhhcCceEEEEEechhhcCCCc
Confidence            88888888887 45899999999999999999998889999999999999999999999999999999999999999999


Q ss_pred             CCCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHHhccccccCChhh
Q 015158          345 QQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANV  408 (412)
Q Consensus       345 ~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  408 (412)
                      +++.||+.++.|.+..+|++|+||.||+|..|.++.|++..|-.....+.+.+....+++|+++
T Consensus       532 ~DiTHV~NyDFP~nIeeYVHRvGrtGRaGr~G~sis~lt~~D~~~a~eLI~ILe~aeQevPdeL  595 (629)
T KOG0336|consen  532 PDITHVYNYDFPRNIEEYVHRVGRTGRAGRTGTSISFLTRNDWSMAEELIQILERAEQEVPDEL  595 (629)
T ss_pred             hhcceeeccCCCccHHHHHHHhcccccCCCCcceEEEEehhhHHHHHHHHHHHHHhhhhCcHHH
Confidence            9999999999999999999999999999999999999999999999999999999999999876

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

Probab=100.00  E-value=2.9e-51  Score=344.77  Aligned_cols=366  Identities=37%  Similarity=0.509  Sum_probs=317.5

Q ss_pred             ccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCH
Q 015158           38 YDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTR  117 (412)
Q Consensus        38 ~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~  117 (412)
                      ..+|+.+|+++++.+.+...++.+|+|.|...++.+++|++++=++.||||||.++.+++++.+.....+..++|++||+
T Consensus         6 ~~~F~~LGl~~Wlve~l~~l~i~~pTpiQ~~cIpkILeGrdcig~AkTGsGKT~AFaLPil~rLsedP~giFalvlTPTr   85 (442)
T KOG0340|consen    6 AKPFSILGLSPWLVEQLKALGIKKPTPIQQACIPKILEGRDCIGCAKTGSGKTAAFALPILNRLSEDPYGIFALVLTPTR   85 (442)
T ss_pred             cCchhhcCccHHHHHHHHHhcCCCCCchHhhhhHHHhcccccccccccCCCcchhhhHHHHHhhccCCCcceEEEecchH
Confidence            46899999999999999999999999999999999999999999999999999999999999999988889999999999


Q ss_pred             HHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcC----CCCCCCceEEEEeCCchh
Q 015158          118 ELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQ----SLRPDNIRIFVLDEADEM  193 (412)
Q Consensus       118 ~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~----~~~~~~~~~iiiDE~h~~  193 (412)
                      +|+-|..++|..++...++.+..+.|+...-.....+...++++++||+++..++...    .+-++++.++|+|||+.+
T Consensus        86 ELA~QiaEQF~alGk~l~lK~~vivGG~d~i~qa~~L~~rPHvVvatPGRlad~l~sn~~~~~~~~~rlkflVlDEADrv  165 (442)
T KOG0340|consen   86 ELALQIAEQFIALGKLLNLKVSVIVGGTDMIMQAAILSDRPHVVVATPGRLADHLSSNLGVCSWIFQRLKFLVLDEADRV  165 (442)
T ss_pred             HHHHHHHHHHHHhcccccceEEEEEccHHHhhhhhhcccCCCeEecCccccccccccCCccchhhhhceeeEEecchhhh
Confidence            9999999999999999999999999999877777778888999999999999888764    233578899999999999


Q ss_pred             hccCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCC--CeEEEecCCccccCCceEEEEEeccchhhHHHHHH
Q 015158          194 LSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNK--PVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCD  271 (412)
Q Consensus       194 ~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  271 (412)
                      .+..|...+..+.+.+|...|.+++|||+..........-...  .............+....-+..++. ..+...+..
T Consensus       166 L~~~f~d~L~~i~e~lP~~RQtLlfSATitd~i~ql~~~~i~k~~a~~~e~~~~vstvetL~q~yI~~~~-~vkdaYLv~  244 (442)
T KOG0340|consen  166 LAGCFPDILEGIEECLPKPRQTLLFSATITDTIKQLFGCPITKSIAFELEVIDGVSTVETLYQGYILVSI-DVKDAYLVH  244 (442)
T ss_pred             hccchhhHHhhhhccCCCccceEEEEeehhhHHHHhhcCCcccccceEEeccCCCCchhhhhhheeecch-hhhHHHHHH
Confidence            9999999999999999999899999999975443332222222  1222223333334444444554444 445555666


Q ss_pred             HHHhc---CCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCC
Q 015158          272 LYETL---AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVS  348 (412)
Q Consensus       272 ~~~~~---~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~  348 (412)
                      +++..   ..+.++||+++...|+.++..|+..++++..+|+.|++.+|-..+.+|+++..++||||+.+++|+|+|.++
T Consensus       245 ~Lr~~~~~~~~simIFvnttr~cQ~l~~~l~~le~r~~~lHs~m~Q~eR~~aLsrFrs~~~~iliaTDVAsRGLDIP~V~  324 (442)
T KOG0340|consen  245 LLRDFENKENGSIMIFVNTTRECQLLSMTLKNLEVRVVSLHSQMPQKERLAALSRFRSNAARILIATDVASRGLDIPTVE  324 (442)
T ss_pred             HHhhhhhccCceEEEEeehhHHHHHHHHHHhhhceeeeehhhcchHHHHHHHHHHHhhcCccEEEEechhhcCCCCCcee
Confidence            66554   347899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHHhccccccC
Q 015158          349 LVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEEL  404 (412)
Q Consensus       349 ~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~  404 (412)
                      .|+.++.|.++.+|++|+||..|+|..|.++.|+++.|.+.+..+++-.++...+-
T Consensus       325 LVvN~diPr~P~~yiHRvGRtARAGR~G~aiSivt~rDv~l~~aiE~~igkKl~e~  380 (442)
T KOG0340|consen  325 LVVNHDIPRDPKDYIHRVGRTARAGRKGMAISIVTQRDVELLQAIEEEIGKKLTEY  380 (442)
T ss_pred             EEEecCCCCCHHHHHHhhcchhcccCCcceEEEechhhHHHHHHHHHHHhcccccc
Confidence            99999999999999999999999999999999999999999999998877755443

>KOG0343 consensus RNA Helicase [RNA processing and modification]

Probab=100.00  E-value=1.5e-50  Score=358.56  Aligned_cols=357  Identities=31%  Similarity=0.465  Sum_probs=323.1

Q ss_pred             ccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCC----CceeEEEE
Q 015158           38 YDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGL----VECQALVL  113 (412)
Q Consensus        38 ~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~----~~~~~lil  113 (412)
                      ...|.+++++....+.|...+|..++..|+++++..+.|++++=.+-||||||++++.+++..+...+    .+--+|||
T Consensus        68 ~~kF~dlpls~~t~kgLke~~fv~~teiQ~~~Ip~aL~G~DvlGAAkTGSGKTLAFlvPvlE~L~r~kWs~~DGlGalII  147 (758)
T KOG0343|consen   68 IKKFADLPLSQKTLKGLKEAKFVKMTEIQRDTIPMALQGHDVLGAAKTGSGKTLAFLVPVLEALYRLKWSPTDGLGALII  147 (758)
T ss_pred             hhhHHhCCCchHHHHhHhhcCCccHHHHHHhhcchhccCcccccccccCCCceeeehHHHHHHHHHcCCCCCCCceeEEe
Confidence            34899999999999999999999999999999999999999999999999999999999999886543    23469999


Q ss_pred             cCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHc-CCCCCCCceEEEEeCCch
Q 015158          114 APTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRR-QSLRPDNIRIFVLDEADE  192 (412)
Q Consensus       114 ~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~-~~~~~~~~~~iiiDE~h~  192 (412)
                      .||++|+.|+++.+.+.+...++...++.||.......... +...|+||||++|+.++.. ..+...++.++|+|||++
T Consensus       148 SPTRELA~QtFevL~kvgk~h~fSaGLiiGG~~~k~E~eRi-~~mNILVCTPGRLLQHmde~~~f~t~~lQmLvLDEADR  226 (758)
T KOG0343|consen  148 SPTRELALQTFEVLNKVGKHHDFSAGLIIGGKDVKFELERI-SQMNILVCTPGRLLQHMDENPNFSTSNLQMLVLDEADR  226 (758)
T ss_pred             cchHHHHHHHHHHHHHHhhccccccceeecCchhHHHHHhh-hcCCeEEechHHHHHHhhhcCCCCCCcceEEEeccHHH
Confidence            99999999999999999999999999999998866554433 4568999999999888765 566678899999999999


Q ss_pred             hhccCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecC--CccccCCceEEEEEeccchhhHHHHH
Q 015158          193 MLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKR--DELTLEGIKQFHVNVEKEEWKLETLC  270 (412)
Q Consensus       193 ~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~l~  270 (412)
                      +++.+|...+..|+..+|+..|.+++|||....+.++..--+.+|.++.+..  ....+.+..++++.++. ..++..|.
T Consensus       227 ~LDMGFk~tL~~Ii~~lP~~RQTLLFSATqt~svkdLaRLsL~dP~~vsvhe~a~~atP~~L~Q~y~~v~l-~~Ki~~L~  305 (758)
T KOG0343|consen  227 MLDMGFKKTLNAIIENLPKKRQTLLFSATQTKSVKDLARLSLKDPVYVSVHENAVAATPSNLQQSYVIVPL-EDKIDMLW  305 (758)
T ss_pred             HHHHhHHHHHHHHHHhCChhheeeeeecccchhHHHHHHhhcCCCcEEEEeccccccChhhhhheEEEEeh-hhHHHHHH
Confidence            9999999999999999999999999999999999999988889998887763  34567778888888876 66999999


Q ss_pred             HHHHhcCCCcEEEEEcchhHHHHHHHHHhcC--CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCC
Q 015158          271 DLYETLAITQSVIFVNTRRKVDWLTDKMRSR--DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVS  348 (412)
Q Consensus       271 ~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~--~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~  348 (412)
                      .+++.+...|+|||+.|.+++..+++.+++.  |..+..+||.|++..|..+..+|....--||+||+++++|+|+|.++
T Consensus       306 sFI~shlk~K~iVF~SscKqvkf~~e~F~rlrpg~~l~~L~G~~~Q~~R~ev~~~F~~~~~~vLF~TDv~aRGLDFpaVd  385 (758)
T KOG0343|consen  306 SFIKSHLKKKSIVFLSSCKQVKFLYEAFCRLRPGIPLLALHGTMSQKKRIEVYKKFVRKRAVVLFCTDVAARGLDFPAVD  385 (758)
T ss_pred             HHHHhccccceEEEEehhhHHHHHHHHHHhcCCCCceeeeccchhHHHHHHHHHHHHHhcceEEEeehhhhccCCCcccc
Confidence            9999999999999999999999999999875  77899999999999999999999998888999999999999999999


Q ss_pred             EEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCc-HHHHHHHHHH
Q 015158          349 LVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDD-ERMLFDIQKF  396 (412)
Q Consensus       349 ~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~-~~~~~~~~~~  396 (412)
                      +||.++.|-+..+|++|+||..|.+..|.+++++.+.+ +.++..+++.
T Consensus       386 wViQ~DCPedv~tYIHRvGRtAR~~~~G~sll~L~psEeE~~l~~Lq~k  434 (758)
T KOG0343|consen  386 WVIQVDCPEDVDTYIHRVGRTARYKERGESLLMLTPSEEEAMLKKLQKK  434 (758)
T ss_pred             eEEEecCchhHHHHHHHhhhhhcccCCCceEEEEcchhHHHHHHHHHHc
Confidence            99999999999999999999999999999999999998 6666666654

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

Probab=100.00  E-value=7.8e-50  Score=391.90  Aligned_cols=361  Identities=20%  Similarity=0.252  Sum_probs=281.2

Q ss_pred             ChhhhccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEE
Q 015158           33 SYDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALV  112 (412)
Q Consensus        33 ~~~~~~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~li  112 (412)
                      .....+.+|.. .+++.+.+.|...||.+|+++|.++++.+++|+++++.+|||||||++|+++++..+... ++.++||
T Consensus         9 ~~~a~~~~~~~-~l~~~l~~~L~~~g~~~p~~~Q~~ai~~il~G~nvvv~apTGSGKTla~~LPiL~~l~~~-~~~~aL~   86 (742)
T TIGR03817         9 ARAGRTAPWPA-WAHPDVVAALEAAGIHRPWQHQARAAELAHAGRHVVVATGTASGKSLAYQLPVLSALADD-PRATALY   86 (742)
T ss_pred             CCCcccCCCCC-cCCHHHHHHHHHcCCCcCCHHHHHHHHHHHCCCCEEEECCCCCcHHHHHHHHHHHHHhhC-CCcEEEE
Confidence            33444444433 378999999999999999999999999999999999999999999999999999988653 4568999


Q ss_pred             EcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcC----CCCCCCceEEEEe
Q 015158          113 LAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQ----SLRPDNIRIFVLD  188 (412)
Q Consensus       113 l~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~----~~~~~~~~~iiiD  188 (412)
                      ++|+++|+.|+.+.++++. ..++.+..+.|+...... .....+++|+++||+++...+...    ...++++++||+|
T Consensus        87 l~PtraLa~q~~~~l~~l~-~~~i~v~~~~Gdt~~~~r-~~i~~~~~IivtTPd~L~~~~L~~~~~~~~~l~~l~~vViD  164 (742)
T TIGR03817        87 LAPTKALAADQLRAVRELT-LRGVRPATYDGDTPTEER-RWAREHARYVLTNPDMLHRGILPSHARWARFLRRLRYVVID  164 (742)
T ss_pred             EcChHHHHHHHHHHHHHhc-cCCeEEEEEeCCCCHHHH-HHHhcCCCEEEEChHHHHHhhccchhHHHHHHhcCCEEEEe
Confidence            9999999999999999986 447788888888764433 344556899999999987533221    1225789999999


Q ss_pred             CCchhhccCcHHHHHHH-------HHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEecc
Q 015158          189 EADEMLSRGFKDQIYDI-------FQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEK  261 (412)
Q Consensus       189 E~h~~~~~~~~~~~~~i-------~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  261 (412)
                      |+|.+.+ .|...+..+       ....+.+.|++++|||+++.. +....+++.+..+. ..... +.....+....+.
T Consensus       165 Eah~~~g-~fg~~~~~il~rL~ri~~~~g~~~q~i~~SATi~n~~-~~~~~l~g~~~~~i-~~~~~-~~~~~~~~~~~p~  240 (742)
T TIGR03817       165 ECHSYRG-VFGSHVALVLRRLRRLCARYGASPVFVLASATTADPA-AAASRLIGAPVVAV-TEDGS-PRGARTVALWEPP  240 (742)
T ss_pred             ChhhccC-ccHHHHHHHHHHHHHHHHhcCCCCEEEEEecCCCCHH-HHHHHHcCCCeEEE-CCCCC-CcCceEEEEecCC
Confidence            9999865 354443333       333456789999999998764 45667777775443 22221 1222222222111


Q ss_pred             ----------------chhhHHHHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcC--------CCeeEEecCCCCHHHH
Q 015158          262 ----------------EEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSR--------DHTVSATHGDMDQNTR  317 (412)
Q Consensus       262 ----------------~~~~~~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~--------~~~~~~~~~~~~~~~r  317 (412)
                                      ...+...+..++..  ..++||||+|++.++.++..|++.        +..+..+||++++++|
T Consensus       241 ~~~~~~~~~~~~r~~~~~~~~~~l~~l~~~--~~~~IVF~~sr~~ae~l~~~l~~~l~~~~~~l~~~v~~~hgg~~~~eR  318 (742)
T TIGR03817       241 LTELTGENGAPVRRSASAEAADLLADLVAE--GARTLTFVRSRRGAELVAAIARRLLGEVDPDLAERVAAYRAGYLPEDR  318 (742)
T ss_pred             ccccccccccccccchHHHHHHHHHHHHHC--CCCEEEEcCCHHHHHHHHHHHHHHHHhhccccccchhheecCCCHHHH
Confidence                            11234455555553  469999999999999999988753        5678899999999999


Q ss_pred             HHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEec--cCcHHHHHHHHH
Q 015158          318 DIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVT--RDDERMLFDIQK  395 (412)
Q Consensus       318 ~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~--~~~~~~~~~~~~  395 (412)
                      .+++++|++|++++||||+++++|+|++++++||+++.|.+...|.||+||+||.|+.|.++++..  +.|...+..+++
T Consensus       319 ~~ie~~f~~G~i~vLVaTd~lerGIDI~~vd~VI~~~~P~s~~~y~qRiGRaGR~G~~g~ai~v~~~~~~d~~~~~~~~~  398 (742)
T TIGR03817       319 RELERALRDGELLGVATTNALELGVDISGLDAVVIAGFPGTRASLWQQAGRAGRRGQGALVVLVARDDPLDTYLVHHPEA  398 (742)
T ss_pred             HHHHHHHHcCCceEEEECchHhccCCcccccEEEEeCCCCCHHHHHHhccccCCCCCCcEEEEEeCCChHHHHHHhCHHH
Confidence            999999999999999999999999999999999999999999999999999999999999999886  446667777888


Q ss_pred             Hhcccccc
Q 015158          396 FYNVVIEE  403 (412)
Q Consensus       396 ~~~~~~~~  403 (412)
                      +++...+.
T Consensus       399 ~~~~~~e~  406 (742)
T TIGR03817       399 LFDRPVEA  406 (742)
T ss_pred             HhcCCCcc
Confidence            88876554

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.

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

Probab=100.00  E-value=7.5e-50  Score=350.69  Aligned_cols=380  Identities=32%  Similarity=0.476  Sum_probs=353.4

Q ss_pred             CChhhhccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccC-----CC
Q 015158           32 TSYDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYG-----LV  106 (412)
Q Consensus        32 ~~~~~~~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~-----~~  106 (412)
                      .+...+...|+.+++++.+..++..-.|.+|+|.|.++++..+.|++++=.+.||||||-+++.+++..+...     ..
T Consensus       216 ~s~~rpvtsfeh~gfDkqLm~airk~Ey~kptpiq~qalptalsgrdvigIAktgSgktaAfi~pm~~himdq~eL~~g~  295 (731)
T KOG0339|consen  216 SSPPRPVTSFEHFGFDKQLMTAIRKSEYEKPTPIQCQALPTALSGRDVIGIAKTGSGKTAAFIWPMIVHIMDQPELKPGE  295 (731)
T ss_pred             CCCCCCcchhhhcCchHHHHHHHhhhhcccCCcccccccccccccccchheeeccCcchhHHHHHHHHHhcchhhhcCCC
Confidence            3455667899999999999999999999999999999999999999999999999999999999998877543     24


Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEE
Q 015158          107 ECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFV  186 (412)
Q Consensus       107 ~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~ii  186 (412)
                      ++..+|+|||++|+.|++.++++|+...++++..++|+.+...+.+-+..++.||||||++|..++.-...++.++.++|
T Consensus       296 gPi~vilvPTrela~Qi~~eaKkf~K~ygl~~v~~ygGgsk~eQ~k~Lk~g~EivVaTPgRlid~VkmKatn~~rvS~LV  375 (731)
T KOG0339|consen  296 GPIGVILVPTRELASQIFSEAKKFGKAYGLRVVAVYGGGSKWEQSKELKEGAEIVVATPGRLIDMVKMKATNLSRVSYLV  375 (731)
T ss_pred             CCeEEEEeccHHHHHHHHHHHHHhhhhccceEEEeecCCcHHHHHHhhhcCCeEEEechHHHHHHHHhhcccceeeeEEE
Confidence            67899999999999999999999999999999999999998888777888999999999999999998888899999999


Q ss_pred             EeCCchhhccCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhH
Q 015158          187 LDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKL  266 (412)
Q Consensus       187 iDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  266 (412)
                      +||++++.+.+|..+++.|....++..|.+++|||....+....+.++..|+.+-..........+.+.+..+.+...+.
T Consensus       376 ~DEadrmfdmGfe~qVrSI~~hirpdrQtllFsaTf~~kIe~lard~L~dpVrvVqg~vgean~dITQ~V~V~~s~~~Kl  455 (731)
T KOG0339|consen  376 LDEADRMFDMGFEPQVRSIKQHIRPDRQTLLFSATFKKKIEKLARDILSDPVRVVQGEVGEANEDITQTVSVCPSEEKKL  455 (731)
T ss_pred             EechhhhhccccHHHHHHHHhhcCCcceEEEeeccchHHHHHHHHHHhcCCeeEEEeehhccccchhheeeeccCcHHHH
Confidence            99999999999999999999999999999999999999999999999999999888877777788999999999888888


Q ss_pred             HHHHHHHHh-cCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCC
Q 015158          267 ETLCDLYET-LAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQ  345 (412)
Q Consensus       267 ~~l~~~~~~-~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~  345 (412)
                      .++..-+.. ...+++|+|+.-+..++.+...|+-.++++..+||++.+.+|.+++..|+.+...|+++|+...+|+|++
T Consensus       456 ~wl~~~L~~f~S~gkvlifVTKk~~~e~i~a~Lklk~~~v~llhgdkdqa~rn~~ls~fKkk~~~VlvatDvaargldI~  535 (731)
T KOG0339|consen  456 NWLLRHLVEFSSEGKVLIFVTKKADAEEIAANLKLKGFNVSLLHGDKDQAERNEVLSKFKKKRKPVLVATDVAARGLDIP  535 (731)
T ss_pred             HHHHHHhhhhccCCcEEEEEeccCCHHHHHHHhccccceeeeecCchhhHHHHHHHHHHhhcCCceEEEeeHhhcCCCcc
Confidence            776655544 4668999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHHhccccccCChhhhhc
Q 015158          346 QVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVADL  411 (412)
Q Consensus       346 ~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  411 (412)
                      .+++|+.++...+...+.||+||.||.|.+|.+|+++++.|..+.-.+.+.+.-..+.||+++.+|
T Consensus       536 ~ikTVvnyD~ardIdththrigrtgRag~kGvayTlvTeKDa~fAG~LVnnLe~agQnVP~~l~dl  601 (731)
T KOG0339|consen  536 SIKTVVNYDFARDIDTHTHRIGRTGRAGEKGVAYTLVTEKDAEFAGHLVNNLEGAGQNVPDELMDL  601 (731)
T ss_pred             ccceeecccccchhHHHHHHhhhcccccccceeeEEechhhHHHhhHHHHHHhhccccCChHHHHH
Confidence            999999999999999999999999999999999999999999999999999999999999987654

>KOG0346 consensus RNA helicase [RNA processing and modification]

Probab=100.00  E-value=6.7e-50  Score=345.36  Aligned_cols=361  Identities=30%  Similarity=0.449  Sum_probs=316.4

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccC------CCceeEEE
Q 015158           39 DTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYG------LVECQALV  112 (412)
Q Consensus        39 ~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~------~~~~~~li  112 (412)
                      .+|+.+++++.+.+++...|+.+|+-.|..|++.+++|++++..|.||||||.+|++++++.+...      ..+..++|
T Consensus        19 ktFe~~gLD~RllkAi~~lG~ekpTlIQs~aIplaLEgKDvvarArTGSGKT~AYliPllqkll~~k~t~~~e~~~sa~i   98 (569)
T KOG0346|consen   19 KTFEEFGLDSRLLKAITKLGWEKPTLIQSSAIPLALEGKDVVARARTGSGKTAAYLIPLLQKLLAEKKTNDGEQGPSAVI   98 (569)
T ss_pred             ccHHHhCCCHHHHHHHHHhCcCCcchhhhcccchhhcCcceeeeeccCCCchHHHHHHHHHHHHHhhhcccccccceeEE
Confidence            699999999999999999999999999999999999999999999999999999999999876432      34568999


Q ss_pred             EcCCHHHHHHHHHHHHHhhcccC--cEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCC-CCCCCceEEEEeC
Q 015158          113 LAPTRELAQQIEKVMRALGDYLG--VKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQS-LRPDNIRIFVLDE  189 (412)
Q Consensus       113 l~P~~~L~~q~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~-~~~~~~~~iiiDE  189 (412)
                      ++||++|++|.+..+.++....+  +.+.-+..+.+.......+.+.++|+|+||..+..++.... .....+.++|+||
T Consensus        99 LvPTkEL~qQvy~viekL~~~c~k~lr~~nl~s~~sdsv~~~~L~d~pdIvV~TP~~ll~~~~~~~~~~~~~l~~LVvDE  178 (569)
T KOG0346|consen   99 LVPTKELAQQVYKVIEKLVEYCSKDLRAINLASSMSDSVNSVALMDLPDIVVATPAKLLRHLAAGVLEYLDSLSFLVVDE  178 (569)
T ss_pred             EechHHHHHHHHHHHHHHHHHHHHhhhhhhhhcccchHHHHHHHccCCCeEEeChHHHHHHHhhccchhhhheeeEEech
Confidence            99999999999998888654433  33434443444444456677889999999999999998766 5567899999999


Q ss_pred             CchhhccCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCcccc-CCceEEEEEeccchhhHHH
Q 015158          190 ADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTL-EGIKQFHVNVEKEEWKLET  268 (412)
Q Consensus       190 ~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~  268 (412)
                      |+.+++.+|...+..+...+|+..|.++||||+..++..+-..++.+|+.......+... ..+.+++..+. ..++...
T Consensus       179 ADLllsfGYeedlk~l~~~LPr~~Q~~LmSATl~dDv~~LKkL~l~nPviLkl~e~el~~~dqL~Qy~v~cs-e~DKfll  257 (569)
T KOG0346|consen  179 ADLLLSFGYEEDLKKLRSHLPRIYQCFLMSATLSDDVQALKKLFLHNPVILKLTEGELPNPDQLTQYQVKCS-EEDKFLL  257 (569)
T ss_pred             hhhhhhcccHHHHHHHHHhCCchhhheeehhhhhhHHHHHHHHhccCCeEEEeccccCCCcccceEEEEEec-cchhHHH
Confidence            999999999999999999999999999999999999999888899999998777666553 45666666666 5677777


Q ss_pred             HHHHHHhc-CCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCC----------
Q 015158          269 LCDLYETL-AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDL----------  337 (412)
Q Consensus       269 l~~~~~~~-~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~----------  337 (412)
                      +..+++-. -.+|.|||+|++..+..+.-.|++.|+...+++|+++.+.|-.++++|+.|-++++|+|+.          
T Consensus       258 lyallKL~LI~gKsliFVNtIdr~YrLkLfLeqFGiksciLNseLP~NSR~Hii~QFNkG~YdivIAtD~s~~~~~~eee  337 (569)
T KOG0346|consen  258 LYALLKLRLIRGKSLIFVNTIDRCYRLKLFLEQFGIKSCILNSELPANSRCHIIEQFNKGLYDIVIATDDSADGDKLEEE  337 (569)
T ss_pred             HHHHHHHHHhcCceEEEEechhhhHHHHHHHHHhCcHhhhhcccccccchhhHHHHhhCcceeEEEEccCccchhhhhcc
Confidence            77777664 5589999999999999999999999999999999999999999999999999999999991          


Q ss_pred             -------------------------CcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHH
Q 015158          338 -------------------------LARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFD  392 (412)
Q Consensus       338 -------------------------~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~  392 (412)
                                               ..+|+|+..+.+|+.++.|.+...|++|+||.+|.+++|.++.|+.+.+......
T Consensus       338 ~kgk~~e~~~kndkkskkK~D~E~GVsRGIDF~~V~~VlNFD~P~t~~sYIHRvGRTaRg~n~GtalSfv~P~e~~g~~~  417 (569)
T KOG0346|consen  338 VKGKSDEKNPKNDKKSKKKLDKESGVSRGIDFHHVSNVLNFDFPETVTSYIHRVGRTARGNNKGTALSFVSPKEEFGKES  417 (569)
T ss_pred             ccccccccCCCCccccccccCchhchhccccchheeeeeecCCCCchHHHHHhccccccCCCCCceEEEecchHHhhhhH
Confidence                                     2389999999999999999999999999999999999999999999999988888


Q ss_pred             HHHHhccc
Q 015158          393 IQKFYNVV  400 (412)
Q Consensus       393 ~~~~~~~~  400 (412)
                      ++.+++..
T Consensus       418 le~~~~d~  425 (569)
T KOG0346|consen  418 LESILKDE  425 (569)
T ss_pred             HHHHHhhH
Confidence            88887764

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

Probab=100.00  E-value=1.6e-49  Score=336.30  Aligned_cols=368  Identities=41%  Similarity=0.687  Sum_probs=329.8

Q ss_pred             ccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcC--ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcC
Q 015158           38 YDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKG--LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAP  115 (412)
Q Consensus        38 ~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~--~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P  115 (412)
                      ...|+.+.|.+++.+.++.++|..|+..|..|++.++..  ++.+-++..|+|||.+|.+.++.++......++++.++|
T Consensus        89 ~ksFeeL~LkPellkgly~M~F~kPskIQe~aLPlll~~Pp~nlIaQsqsGtGKTaaFvL~MLsrvd~~~~~PQ~iCLaP  168 (477)
T KOG0332|consen   89 AKSFEELRLKPELLKGLYAMKFQKPSKIQETALPLLLAEPPQNLIAQSQSGTGKTAAFVLTMLSRVDPDVVVPQCICLAP  168 (477)
T ss_pred             cccHHhhCCCHHHHhHHHHhccCCcchHHHhhcchhhcCCchhhhhhhcCCCchhHHHHHHHHHhcCccccCCCceeeCc
Confidence            468999999999999999999999999999999999986  789999999999999999999999988777889999999


Q ss_pred             CHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHc-CCCCCCCceEEEEeCCchhh
Q 015158          116 TRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRR-QSLRPDNIRIFVLDEADEML  194 (412)
Q Consensus       116 ~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~-~~~~~~~~~~iiiDE~h~~~  194 (412)
                      +++|+.|+.+.+.+.+...++.......+.....-   ..-..+|+|+||..+..+... ..+....+..+|+|||+.+.
T Consensus       169 trELA~Q~~eVv~eMGKf~~ita~yair~sk~~rG---~~i~eqIviGTPGtv~Dlm~klk~id~~kikvfVlDEAD~Mi  245 (477)
T KOG0332|consen  169 TRELAPQTGEVVEEMGKFTELTASYAIRGSKAKRG---NKLTEQIVIGTPGTVLDLMLKLKCIDLEKIKVFVLDEADVMI  245 (477)
T ss_pred             hHHHHHHHHHHHHHhcCceeeeEEEEecCcccccC---CcchhheeeCCCccHHHHHHHHHhhChhhceEEEecchhhhh
Confidence            99999999999999988777777666655421111   112347999999999998877 66777899999999999877


Q ss_pred             c-cCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhHHHHHHHH
Q 015158          195 S-RGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLY  273 (412)
Q Consensus       195 ~-~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~  273 (412)
                      + .+|...-..+...+|++.|++++|||.......+......++..+...+++....++.+++..+.....+...+.+++
T Consensus       246 ~tqG~~D~S~rI~~~lP~~~QllLFSATf~e~V~~Fa~kivpn~n~i~Lk~eel~L~~IkQlyv~C~~~~~K~~~l~~ly  325 (477)
T KOG0332|consen  246 DTQGFQDQSIRIMRSLPRNQQLLLFSATFVEKVAAFALKIVPNANVIILKREELALDNIKQLYVLCACRDDKYQALVNLY  325 (477)
T ss_pred             hcccccccchhhhhhcCCcceEEeeechhHHHHHHHHHHhcCCCceeeeehhhccccchhhheeeccchhhHHHHHHHHH
Confidence            4 568888899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhcCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEc
Q 015158          274 ETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINY  353 (412)
Q Consensus       274 ~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~  353 (412)
                      .....+..||||.++..|..+++.+.+.|..+..+||++...+|..++++|+.|..+|||+|+.+.+|+|++.++.||.+
T Consensus       326 g~~tigqsiIFc~tk~ta~~l~~~m~~~Gh~V~~l~G~l~~~~R~~ii~~Fr~g~~kVLitTnV~ARGiDv~qVs~VvNy  405 (477)
T KOG0332|consen  326 GLLTIGQSIIFCHTKATAMWLYEEMRAEGHQVSLLHGDLTVEQRAAIIDRFREGKEKVLITTNVCARGIDVAQVSVVVNY  405 (477)
T ss_pred             hhhhhhheEEEEeehhhHHHHHHHHHhcCceeEEeeccchhHHHHHHHHHHhcCcceEEEEechhhcccccceEEEEEec
Confidence            99888999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCC------CChhhHHHhhhhcccCCCCceEEEEecc-CcHHHHHHHHHHhccccccC-Chhh
Q 015158          354 DLP------TQPENYLHRIGRSGRFGRKGVAINFVTR-DDERMLFDIQKFYNVVIEEL-PANV  408 (412)
Q Consensus       354 ~~~------~s~~~~~Q~~GR~~R~g~~g~~~~~~~~-~~~~~~~~~~~~~~~~~~~~-~~~~  408 (412)
                      ++|      .+...|++|+||+||.|+.|.++-+++. .....++.+++++...+..+ |+++
T Consensus       406 dlP~~~~~~pD~etYlHRiGRtGRFGkkG~a~n~v~~~~s~~~mn~iq~~F~~~i~~~~~~d~  468 (477)
T KOG0332|consen  406 DLPVKYTGEPDYETYLHRIGRTGRFGKKGLAINLVDDKDSMNIMNKIQKHFNMKIKRLDPDDL  468 (477)
T ss_pred             CCccccCCCCCHHHHHHHhcccccccccceEEEeecccCcHHHHHHHHHHHhhcceecCCccH
Confidence            998      4688999999999999999999988866 57778889999996654443 3443

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=100.00  E-value=1.3e-48  Score=369.08  Aligned_cols=324  Identities=21%  Similarity=0.289  Sum_probs=254.8

Q ss_pred             HCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccC
Q 015158           56 AYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLG  135 (412)
Q Consensus        56 ~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~  135 (412)
                      .+||..|+|+|.++++.+++|+++++.+|||+|||++|+++++..      .+.+||++|+++|+.|+.+.+..+    +
T Consensus         6 ~~g~~~~r~~Q~~ai~~~l~g~dvlv~apTGsGKTl~y~lp~l~~------~~~~lVi~P~~~L~~dq~~~l~~~----g   75 (470)
T TIGR00614         6 VFGLSSFRPVQLEVINAVLLGRDCFVVMPTGGGKSLCYQLPALCS------DGITLVISPLISLMEDQVLQLKAS----G   75 (470)
T ss_pred             hcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHhHHHHHHHHHc------CCcEEEEecHHHHHHHHHHHHHHc----C
Confidence            479999999999999999999999999999999999999988752      247999999999999999988765    6


Q ss_pred             cEEEEEEcCcchHHHH----HHhcCCCcEEEeChHHHHHHH-HcCCC-CCCCceEEEEeCCchhhccC--cHHHHHH---
Q 015158          136 VKVHACVGGTSVREDQ----RILSSGVHVVVGTPGRVFDML-RRQSL-RPDNIRIFVLDEADEMLSRG--FKDQIYD---  204 (412)
Q Consensus       136 ~~~~~~~~~~~~~~~~----~~~~~~~~iii~T~~~l~~~~-~~~~~-~~~~~~~iiiDE~h~~~~~~--~~~~~~~---  204 (412)
                      +.+..+.++.......    ....+.++|+++||+.+.... ....+ ...++++||+||||++.+|+  |...+..   
T Consensus        76 i~~~~l~~~~~~~~~~~i~~~~~~~~~~il~~TPe~l~~~~~~~~~l~~~~~i~~iViDEaH~i~~~g~~fr~~~~~l~~  155 (470)
T TIGR00614        76 IPATFLNSSQSKEQQKNVLTDLKDGKIKLLYVTPEKCSASNRLLQTLEERKGITLIAVDEAHCISQWGHDFRPDYKALGS  155 (470)
T ss_pred             CcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHcCchhHHHHHHhcCCcCEEEEeCCcccCccccccHHHHHHHHH
Confidence            7777787776644322    223456899999999875321 00111 34688999999999998876  4444443   


Q ss_pred             HHHhCCCCceEEEEeecCChHHHHHHHHhcC--CCeEEEecCCccccCCceEEEEEeccchhhHHHHHHHHH-hcCCCcE
Q 015158          205 IFQLLPPKIQVGVFSATMPPEALEITRKFMN--KPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYE-TLAITQS  281 (412)
Q Consensus       205 i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~-~~~~~k~  281 (412)
                      +...+ ++.+++++|||+++.....+...++  .+..+..   ....+++.....  .........+..++. ....+++
T Consensus       156 l~~~~-~~~~~l~lTAT~~~~~~~di~~~l~l~~~~~~~~---s~~r~nl~~~v~--~~~~~~~~~l~~~l~~~~~~~~~  229 (470)
T TIGR00614       156 LKQKF-PNVPIMALTATASPSVREDILRQLNLKNPQIFCT---SFDRPNLYYEVR--RKTPKILEDLLRFIRKEFKGKSG  229 (470)
T ss_pred             HHHHc-CCCceEEEecCCCHHHHHHHHHHcCCCCCcEEeC---CCCCCCcEEEEE--eCCccHHHHHHHHHHHhcCCCce
Confidence            34444 4778999999999877666665543  3332222   122233322222  222234455666665 4455667


Q ss_pred             EEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccCCCChhh
Q 015158          282 VIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPEN  361 (412)
Q Consensus       282 lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~~~s~~~  361 (412)
                      ||||++++.++.+++.|++.++.+..+||+++..+|..+++.|.+|+.+|||||+++++|+|+|++++||+++.|.|...
T Consensus       230 IIF~~s~~~~e~la~~L~~~g~~~~~~H~~l~~~eR~~i~~~F~~g~~~vLVaT~~~~~GID~p~V~~VI~~~~P~s~~~  309 (470)
T TIGR00614       230 IIYCPSRKKSEQVTASLQNLGIAAGAYHAGLEISARDDVHHKFQRDEIQVVVATVAFGMGINKPDVRFVIHYSLPKSMES  309 (470)
T ss_pred             EEEECcHHHHHHHHHHHHhcCCCeeEeeCCCCHHHHHHHHHHHHcCCCcEEEEechhhccCCcccceEEEEeCCCCCHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhhhcccCCCCceEEEEeccCcHHHHHHHHH
Q 015158          362 YLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQK  395 (412)
Q Consensus       362 ~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~  395 (412)
                      |.||+||+||.|.+|.|++++++.|...++.+..
T Consensus       310 y~Qr~GRaGR~G~~~~~~~~~~~~d~~~~~~~~~  343 (470)
T TIGR00614       310 YYQESGRAGRDGLPSECHLFYAPADINRLRRLLM  343 (470)
T ss_pred             HHhhhcCcCCCCCCceEEEEechhHHHHHHHHHh
Confidence            9999999999999999999999988876665543

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=3.9e-48  Score=377.87  Aligned_cols=338  Identities=21%  Similarity=0.257  Sum_probs=262.6

Q ss_pred             CCCCHHHHHHHHH-CCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHH
Q 015158           44 MGLQENLLRGIYA-YGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQ  122 (412)
Q Consensus        44 ~~l~~~~~~~l~~-~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q  122 (412)
                      ++....+...++. +|+..++|.|+++++.++.|+++++.+|||+|||+||+++++..      .+.+|||+|+++|+.+
T Consensus       442 fpw~~~L~~~lk~~FG~~sFRp~Q~eaI~aiL~GrDVLVimPTGSGKSLcYQLPAL~~------~GiTLVISPLiSLmqD  515 (1195)
T PLN03137        442 FPWTKKLEVNNKKVFGNHSFRPNQREIINATMSGYDVFVLMPTGGGKSLTYQLPALIC------PGITLVISPLVSLIQD  515 (1195)
T ss_pred             CCchHHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHHHHHHHHHHHc------CCcEEEEeCHHHHHHH
Confidence            4455566666654 79999999999999999999999999999999999999999853      2479999999999987


Q ss_pred             HHHHHHHhhcccCcEEEEEEcCcchHHHHHHhc------CCCcEEEeChHHHHH--HHHcC--CC-CCCCceEEEEeCCc
Q 015158          123 IEKVMRALGDYLGVKVHACVGGTSVREDQRILS------SGVHVVVGTPGRVFD--MLRRQ--SL-RPDNIRIFVLDEAD  191 (412)
Q Consensus       123 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~iii~T~~~l~~--~~~~~--~~-~~~~~~~iiiDE~h  191 (412)
                      +...+...    ++.+..+.++.........+.      +.++|+++||+++..  .+.+.  .+ ....+.+|||||||
T Consensus       516 QV~~L~~~----GI~Aa~L~s~~s~~eq~~ilr~l~s~~g~~~ILyvTPERL~~~d~ll~~L~~L~~~~~LslIVIDEAH  591 (1195)
T PLN03137        516 QIMNLLQA----NIPAASLSAGMEWAEQLEILQELSSEYSKYKLLYVTPEKVAKSDSLLRHLENLNSRGLLARFVIDEAH  591 (1195)
T ss_pred             HHHHHHhC----CCeEEEEECCCCHHHHHHHHHHHHhcCCCCCEEEEChHHhhcchHHHHHHHhhhhccccceeccCcch
Confidence            77766654    788888888876554433221      568999999999752  11111  11 12457899999999


Q ss_pred             hhhccC--cHHHHHHH--HHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhHH
Q 015158          192 EMLSRG--FKDQIYDI--FQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLE  267 (412)
Q Consensus       192 ~~~~~~--~~~~~~~i--~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  267 (412)
                      ++++|+  |+..+..+  +....++.+++++|||++......+...++....... ......+++...  ..........
T Consensus       592 cVSqWGhDFRpdYr~L~~Lr~~fp~vPilALTATAT~~V~eDI~~~L~l~~~~vf-r~Sf~RpNL~y~--Vv~k~kk~le  668 (1195)
T PLN03137        592 CVSQWGHDFRPDYQGLGILKQKFPNIPVLALTATATASVKEDVVQALGLVNCVVF-RQSFNRPNLWYS--VVPKTKKCLE  668 (1195)
T ss_pred             hhhhcccchHHHHHHHHHHHHhCCCCCeEEEEecCCHHHHHHHHHHcCCCCcEEe-ecccCccceEEE--EeccchhHHH
Confidence            999887  66655543  2233347789999999998888777666543222211 122233333222  2222222345


Q ss_pred             HHHHHHHhc-CCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCC
Q 015158          268 TLCDLYETL-AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQ  346 (412)
Q Consensus       268 ~l~~~~~~~-~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~  346 (412)
                      .+..++... ..+++||||.+++.++.+++.|++.|+.+..+||+|++.+|..++++|.+|+++|||||.++++|||+|+
T Consensus       669 ~L~~~I~~~~~~esgIIYC~SRke~E~LAe~L~~~Gika~~YHAGLs~eeR~~vqe~F~~Gei~VLVATdAFGMGIDkPD  748 (1195)
T PLN03137        669 DIDKFIKENHFDECGIIYCLSRMDCEKVAERLQEFGHKAAFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGMGINKPD  748 (1195)
T ss_pred             HHHHHHHhcccCCCceeEeCchhHHHHHHHHHHHCCCCeeeeeCCCCHHHHHHHHHHHhcCCCcEEEEechhhcCCCccC
Confidence            566666543 3578999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHH
Q 015158          347 VSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQ  394 (412)
Q Consensus       347 ~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~  394 (412)
                      +++||+++.|.|...|.|++||+||.|.+|.|++|+...|...+..+.
T Consensus       749 VR~VIHydlPkSiEsYyQriGRAGRDG~~g~cILlys~~D~~~~~~lI  796 (1195)
T PLN03137        749 VRFVIHHSLPKSIEGYHQECGRAGRDGQRSSCVLYYSYSDYIRVKHMI  796 (1195)
T ss_pred             CcEEEEcCCCCCHHHHHhhhcccCCCCCCceEEEEecHHHHHHHHHHH
Confidence            999999999999999999999999999999999999887776555544

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

Probab=100.00  E-value=1.4e-48  Score=344.84  Aligned_cols=358  Identities=29%  Similarity=0.478  Sum_probs=298.2

Q ss_pred             ccccccCCCCHHHHHHHHH-CCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhcc------CCCceeE
Q 015158           38 YDTFDAMGLQENLLRGIYA-YGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY------GLVECQA  110 (412)
Q Consensus        38 ~~~f~~~~l~~~~~~~l~~-~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~------~~~~~~~  110 (412)
                      ...|..+++++.+...|+. +++..|+..|+++++.+++|++++|.++||||||++|++++...+..      ...+..+
T Consensus       135 s~~f~~LGL~~~lv~~L~~~m~i~~pTsVQkq~IP~lL~grD~lV~aQTGSGKTLAYllPiVq~Lq~m~~ki~Rs~G~~A  214 (708)
T KOG0348|consen  135 SAAFASLGLHPHLVSHLNTKMKISAPTSVQKQAIPVLLEGRDALVRAQTGSGKTLAYLLPIVQSLQAMEPKIQRSDGPYA  214 (708)
T ss_pred             cccchhcCCCHHHHHHHHHHhccCccchHhhcchhhhhcCcceEEEcCCCCcccHHHHHHHHHHHHhcCccccccCCceE
Confidence            3578899999999999987 79999999999999999999999999999999999999999987743      2346789


Q ss_pred             EEEcCCHHHHHHHHHHHHHhhcccC-cEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHc-CCCCCCCceEEEEe
Q 015158          111 LVLAPTRELAQQIEKVMRALGDYLG-VKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRR-QSLRPDNIRIFVLD  188 (412)
Q Consensus       111 lil~P~~~L~~q~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~-~~~~~~~~~~iiiD  188 (412)
                      ||++||++|+.|.++.+.++...+. +....+.||...+.....+..+..|+|+||++|..++.+ ..+.+..++++|+|
T Consensus       215 LVivPTREL~~Q~y~~~qKLl~~~hWIVPg~lmGGEkkKSEKARLRKGiNILIgTPGRLvDHLknT~~i~~s~LRwlVlD  294 (708)
T KOG0348|consen  215 LVIVPTRELALQIYETVQKLLKPFHWIVPGVLMGGEKKKSEKARLRKGINILIGTPGRLVDHLKNTKSIKFSRLRWLVLD  294 (708)
T ss_pred             EEEechHHHHHHHHHHHHHHhcCceEEeeceeecccccccHHHHHhcCceEEEcCchHHHHHHhccchheeeeeeEEEec
Confidence            9999999999999999999876654 345567788888777888889999999999999999987 45667889999999


Q ss_pred             CCchhhccCcHHHHHHHHHhCC-------------CCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCc---------
Q 015158          189 EADEMLSRGFKDQIYDIFQLLP-------------PKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDE---------  246 (412)
Q Consensus       189 E~h~~~~~~~~~~~~~i~~~~~-------------~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~---------  246 (412)
                      |++++.+.+|...+..|+..+.             ...+.+++|||+...+..+...-+.+|+.+..+...         
T Consensus       295 EaDrlleLGfekdit~Il~~v~~~~~~e~~~~~lp~q~q~mLlSATLtd~V~rLa~~sLkDpv~I~ld~s~~~~~p~~~a  374 (708)
T KOG0348|consen  295 EADRLLELGFEKDITQILKAVHSIQNAECKDPKLPHQLQNMLLSATLTDGVNRLADLSLKDPVYISLDKSHSQLNPKDKA  374 (708)
T ss_pred             chhHHHhccchhhHHHHHHHHhhccchhcccccccHHHHhHhhhhhhHHHHHHHhhccccCceeeeccchhhhcCcchhh
Confidence            9999999999999988887762             236789999999888877777778888877622111         


Q ss_pred             ----------------cccCCceEEEEEeccchhhHHHHHHHH----HhcCCCcEEEEEcchhHHHHHHHHHhcC-----
Q 015158          247 ----------------LTLEGIKQFHVNVEKEEWKLETLCDLY----ETLAITQSVIFVNTRRKVDWLTDKMRSR-----  301 (412)
Q Consensus       247 ----------------~~~~~~~~~~~~~~~~~~~~~~l~~~~----~~~~~~k~lif~~~~~~~~~~~~~L~~~-----  301 (412)
                                      ..+++..+.+..++... ..-.|..++    +.....|+|||+.+.+.++.=+..|.+.     
T Consensus       375 ~~ev~~~~~~~~l~~~~iPeqL~qry~vVPpKL-RLV~Laa~L~~~~k~~~~qk~iVF~S~~d~VeFHy~lf~~~l~~~~  453 (708)
T KOG0348|consen  375 VQEVDDGPAGDKLDSFAIPEQLLQRYTVVPPKL-RLVALAALLLNKVKFEEKQKMIVFFSCSDSVEFHYSLFSEALLSHL  453 (708)
T ss_pred             hhhcCCcccccccccccCcHHhhhceEecCCch-hHHHHHHHHHHHhhhhhhceeEEEEechhHHHHHHHHHHhhhhccc
Confidence                            11223344455555432 333333333    3334568999999999999888877642     


Q ss_pred             -----------------CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccCCCChhhHHH
Q 015158          302 -----------------DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLH  364 (412)
Q Consensus       302 -----------------~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q  364 (412)
                                       +..+..+||+|.+++|..+++.|...+-.||+||++.++|+|+|.+.+||.++.|.+.++|++
T Consensus       454 e~~s~~~~s~g~~~l~~~~k~~rLHGsm~QeeRts~f~~Fs~~~~~VLLcTDVAaRGLDlP~V~~vVQYd~P~s~adylH  533 (708)
T KOG0348|consen  454 EGSSGAPDSEGLPPLFMDLKFYRLHGSMEQEERTSVFQEFSHSRRAVLLCTDVAARGLDLPHVGLVVQYDPPFSTADYLH  533 (708)
T ss_pred             ccccCCcccCCChhhhhcceEEEecCchhHHHHHHHHHhhccccceEEEehhhhhccCCCCCcCeEEEeCCCCCHHHHHH
Confidence                             456889999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhcccCCCCceEEEEeccCcHHHHHHHHHH
Q 015158          365 RIGRSGRFGRKGVAINFVTRDDERMLFDIQKF  396 (412)
Q Consensus       365 ~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~  396 (412)
                      |+||..|.|..|.+++|+.+.+.++++.++..
T Consensus       534 RvGRTARaG~kG~alLfL~P~Eaey~~~l~~~  565 (708)
T KOG0348|consen  534 RVGRTARAGEKGEALLFLLPSEAEYVNYLKKH  565 (708)
T ss_pred             HhhhhhhccCCCceEEEecccHHHHHHHHHhh
Confidence            99999999999999999999999877666544

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

Probab=100.00  E-value=1.6e-49  Score=338.09  Aligned_cols=374  Identities=33%  Similarity=0.555  Sum_probs=324.1

Q ss_pred             hhccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhc--------cCCCc
Q 015158           36 EVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLD--------YGLVE  107 (412)
Q Consensus        36 ~~~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~--------~~~~~  107 (412)
                      +|..+|..+.++..+.+.|+..|+..|+|.|.+.++.+++|++.+=.+-||||||++|.+++.....        ....+
T Consensus       167 PPIksF~eMKFP~~~L~~lk~KGI~~PTpIQvQGlPvvLsGRDmIGIAfTGSGKTlvFvLP~imf~LeqE~~lPf~~~EG  246 (610)
T KOG0341|consen  167 PPIKSFKEMKFPKPLLRGLKKKGIVHPTPIQVQGLPVVLSGRDMIGIAFTGSGKTLVFVLPVIMFALEQEMMLPFARGEG  246 (610)
T ss_pred             CchhhhhhccCCHHHHHHHHhcCCCCCCceeecCcceEeecCceeeEEeecCCceEEEeHHHHHHHHHHHhcCccccCCC
Confidence            4566899999999999999999999999999999999999999999999999999999887764431        22356


Q ss_pred             eeEEEEcCCHHHHHHHHHHHHHhhccc------CcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCC
Q 015158          108 CQALVLAPTRELAQQIEKVMRALGDYL------GVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDN  181 (412)
Q Consensus       108 ~~~lil~P~~~L~~q~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~  181 (412)
                      +..||+||+++|+.|+.+.+..+....      .+....+.|+............+.+|+|+||.+|..++.+....++-
T Consensus       247 P~gLiicPSRELArQt~~iie~~~~~L~e~g~P~lRs~LciGG~~v~eql~~v~~GvHivVATPGRL~DmL~KK~~sLd~  326 (610)
T KOG0341|consen  247 PYGLIICPSRELARQTHDIIEQYVAALQEAGYPELRSLLCIGGVPVREQLDVVRRGVHIVVATPGRLMDMLAKKIMSLDA  326 (610)
T ss_pred             CeeEEEcCcHHHHHHHHHHHHHHHHHHHhcCChhhhhhhhhcCccHHHHHHHHhcCeeEEEcCcchHHHHHHHhhccHHH
Confidence            789999999999999999887765433      35566788888888888888899999999999999999988888888


Q ss_pred             ceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEecc
Q 015158          182 IRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEK  261 (412)
Q Consensus       182 ~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  261 (412)
                      .+++.+|||+++.+.+|...++.++..+..+.|.+++|||++.....+...-+-+|+.+.+.+.....-++.+-...+. 
T Consensus       327 CRyL~lDEADRmiDmGFEddir~iF~~FK~QRQTLLFSATMP~KIQ~FAkSALVKPvtvNVGRAGAAsldViQevEyVk-  405 (610)
T KOG0341|consen  327 CRYLTLDEADRMIDMGFEDDIRTIFSFFKGQRQTLLFSATMPKKIQNFAKSALVKPVTVNVGRAGAASLDVIQEVEYVK-  405 (610)
T ss_pred             HHHhhhhhHHHHhhccchhhHHHHHHHHhhhhheeeeeccccHHHHHHHHhhcccceEEecccccccchhHHHHHHHHH-
Confidence            8999999999999999999999999999999999999999999999999999999999988876655543322222221 


Q ss_pred             chhhHHHHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCC
Q 015158          262 EEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARG  341 (412)
Q Consensus       262 ~~~~~~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G  341 (412)
                      .+.+.-.+.+.+++.. .++||||..+..++.++++|--.|..++.+||+-.+++|...++.|+.|+.+|||+|+..+.|
T Consensus       406 qEaKiVylLeCLQKT~-PpVLIFaEkK~DVD~IhEYLLlKGVEavaIHGGKDQedR~~ai~afr~gkKDVLVATDVASKG  484 (610)
T KOG0341|consen  406 QEAKIVYLLECLQKTS-PPVLIFAEKKADVDDIHEYLLLKGVEAVAIHGGKDQEDRHYAIEAFRAGKKDVLVATDVASKG  484 (610)
T ss_pred             hhhhhhhHHHHhccCC-CceEEEeccccChHHHHHHHHHccceeEEeecCcchhHHHHHHHHHhcCCCceEEEecchhcc
Confidence            2345555566666544 689999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccC-cHHHHHHHHHHhccccccCChhhhhc
Q 015158          342 IDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRD-DERMLFDIQKFYNVVIEELPANVADL  411 (412)
Q Consensus       342 ~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~l  411 (412)
                      +|+|++.|||.++.|.....|++|+||.||.|+.|.+.+|+... +...+-.+...+...-+++|+-++.|
T Consensus       485 LDFp~iqHVINyDMP~eIENYVHRIGRTGRsg~~GiATTfINK~~~esvLlDLK~LL~EakQ~vP~~L~~L  555 (610)
T KOG0341|consen  485 LDFPDIQHVINYDMPEEIENYVHRIGRTGRSGKTGIATTFINKNQEESVLLDLKHLLQEAKQEVPPVLAEL  555 (610)
T ss_pred             CCCccchhhccCCChHHHHHHHHHhcccCCCCCcceeeeeecccchHHHHHHHHHHHHHhhccCCHHHHHh
Confidence            99999999999999999999999999999999999999999875 56667777778877778888766554

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=100.00  E-value=3.6e-47  Score=368.23  Aligned_cols=328  Identities=20%  Similarity=0.276  Sum_probs=257.5

Q ss_pred             HHHHHHH-CCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHH
Q 015158           50 LLRGIYA-YGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMR  128 (412)
Q Consensus        50 ~~~~l~~-~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~  128 (412)
                      ....|+. +||..++|.|.++++.++.|+++++.+|||+|||++|+++++..      .+.+||++|+++|+.|+.+.+.
T Consensus        13 ~~~~l~~~fG~~~~r~~Q~~ai~~il~g~dvlv~apTGsGKTl~y~lpal~~------~g~tlVisPl~sL~~dqv~~l~   86 (607)
T PRK11057         13 AKQVLQETFGYQQFRPGQQEIIDAVLSGRDCLVVMPTGGGKSLCYQIPALVL------DGLTLVVSPLISLMKDQVDQLL   86 (607)
T ss_pred             HHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCchHHHHHHHHHHHc------CCCEEEEecHHHHHHHHHHHHH
Confidence            3344443 69999999999999999999999999999999999999888753      2369999999999999999888


Q ss_pred             HhhcccCcEEEEEEcCcchHHHH----HHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccC--cHHH-
Q 015158          129 ALGDYLGVKVHACVGGTSVREDQ----RILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRG--FKDQ-  201 (412)
Q Consensus       129 ~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~--~~~~-  201 (412)
                      ..    ++.+..+.+........    ....+..+++++||+.+........+...++++||+||||++.+|+  |... 
T Consensus        87 ~~----gi~~~~~~s~~~~~~~~~~~~~~~~g~~~il~~tPe~l~~~~~~~~l~~~~l~~iVIDEaH~i~~~G~~fr~~y  162 (607)
T PRK11057         87 AN----GVAAACLNSTQTREQQLEVMAGCRTGQIKLLYIAPERLMMDNFLEHLAHWNPALLAVDEAHCISQWGHDFRPEY  162 (607)
T ss_pred             Hc----CCcEEEEcCCCCHHHHHHHHHHHhCCCCcEEEEChHHhcChHHHHHHhhCCCCEEEEeCccccccccCcccHHH
Confidence            75    67777777766544332    2234567899999999864222223334578999999999998876  4433 


Q ss_pred             --HHHHHHhCCCCceEEEEeecCChHHHHHHHHhcC--CCeEEEecCCccccCCceEEEEEeccchhhHHHHHHHHHhcC
Q 015158          202 --IYDIFQLLPPKIQVGVFSATMPPEALEITRKFMN--KPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLA  277 (412)
Q Consensus       202 --~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  277 (412)
                        +..+...+ ++.+++++|||+++.....+...+.  .+.... .  ....+++.....   ........+..++....
T Consensus       163 ~~L~~l~~~~-p~~~~v~lTAT~~~~~~~di~~~l~l~~~~~~~-~--~~~r~nl~~~v~---~~~~~~~~l~~~l~~~~  235 (607)
T PRK11057        163 AALGQLRQRF-PTLPFMALTATADDTTRQDIVRLLGLNDPLIQI-S--SFDRPNIRYTLV---EKFKPLDQLMRYVQEQR  235 (607)
T ss_pred             HHHHHHHHhC-CCCcEEEEecCCChhHHHHHHHHhCCCCeEEEE-C--CCCCCcceeeee---eccchHHHHHHHHHhcC
Confidence              33444444 4788999999999877665555443  332222 1  112233322221   11234556667777777


Q ss_pred             CCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccCCC
Q 015158          278 ITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPT  357 (412)
Q Consensus       278 ~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~~~  357 (412)
                      .+++||||++++.++.+++.|++.++.+..+|++++..+|..+++.|.+|+.+|||+|+++++|+|+|++++||+++.|.
T Consensus       236 ~~~~IIFc~tr~~~e~la~~L~~~g~~v~~~Ha~l~~~~R~~i~~~F~~g~~~VLVaT~a~~~GIDip~V~~VI~~d~P~  315 (607)
T PRK11057        236 GKSGIIYCNSRAKVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPR  315 (607)
T ss_pred             CCCEEEEECcHHHHHHHHHHHHhCCCCEEEecCCCCHHHHHHHHHHHHCCCCCEEEEechhhccCCCCCcCEEEEeCCCC
Confidence            78999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHH
Q 015158          358 QPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQ  394 (412)
Q Consensus       358 s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~  394 (412)
                      |...|.|++||+||.|.+|.|++|+++.|...++.+.
T Consensus       316 s~~~y~Qr~GRaGR~G~~~~~ill~~~~d~~~~~~~~  352 (607)
T PRK11057        316 NIESYYQETGRAGRDGLPAEAMLFYDPADMAWLRRCL  352 (607)
T ss_pred             CHHHHHHHhhhccCCCCCceEEEEeCHHHHHHHHHHH
Confidence            9999999999999999999999999998876655443

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=100.00  E-value=2.1e-46  Score=364.26  Aligned_cols=323  Identities=22%  Similarity=0.303  Sum_probs=258.1

Q ss_pred             CCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCc
Q 015158           57 YGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGV  136 (412)
Q Consensus        57 ~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~  136 (412)
                      +||..++|.|.++++.++.|+++++.+|||+|||++|+++++..      .+.++|++|+++|+.|+.+.+..+    ++
T Consensus         9 fg~~~fr~~Q~~~i~~il~g~dvlv~~PTG~GKTl~y~lpal~~------~g~~lVisPl~sL~~dq~~~l~~~----gi   78 (591)
T TIGR01389         9 FGYDDFRPGQEEIISHVLDGRDVLVVMPTGGGKSLCYQVPALLL------KGLTVVISPLISLMKDQVDQLRAA----GV   78 (591)
T ss_pred             cCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHhHHHHHHHHHc------CCcEEEEcCCHHHHHHHHHHHHHc----CC
Confidence            79999999999999999999999999999999999999888742      236899999999999999988885    67


Q ss_pred             EEEEEEcCcchHHHH----HHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccC--cHHHHHH---HHH
Q 015158          137 KVHACVGGTSVREDQ----RILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRG--FKDQIYD---IFQ  207 (412)
Q Consensus       137 ~~~~~~~~~~~~~~~----~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~--~~~~~~~---i~~  207 (412)
                      .+..++++.......    ....+..+|+++||+++........+...++++||+||||++..|+  |...+..   +..
T Consensus        79 ~~~~~~s~~~~~~~~~~~~~l~~~~~~il~~tpe~l~~~~~~~~l~~~~l~~iViDEaH~i~~~g~~frp~y~~l~~l~~  158 (591)
T TIGR01389        79 AAAYLNSTLSAKEQQDIEKALVNGELKLLYVAPERLEQDYFLNMLQRIPIALVAVDEAHCVSQWGHDFRPEYQRLGSLAE  158 (591)
T ss_pred             cEEEEeCCCCHHHHHHHHHHHhCCCCCEEEEChhHhcChHHHHHHhcCCCCEEEEeCCcccccccCccHHHHHHHHHHHH
Confidence            788888776654432    2344678999999999865333333445689999999999998876  5544443   344


Q ss_pred             hCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhHHHHHHHHHhcCCCcEEEEEcc
Q 015158          208 LLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNT  287 (412)
Q Consensus       208 ~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lif~~~  287 (412)
                      .++ +.+++++|||+++.....+...++........ .....+++.....   ....+...+.+++.....+++||||++
T Consensus       159 ~~~-~~~vi~lTAT~~~~~~~~i~~~l~~~~~~~~~-~~~~r~nl~~~v~---~~~~~~~~l~~~l~~~~~~~~IIf~~s  233 (591)
T TIGR01389       159 RFP-QVPRIALTATADAETRQDIRELLRLADANEFI-TSFDRPNLRFSVV---KKNNKQKFLLDYLKKHRGQSGIIYASS  233 (591)
T ss_pred             hCC-CCCEEEEEeCCCHHHHHHHHHHcCCCCCCeEe-cCCCCCCcEEEEE---eCCCHHHHHHHHHHhcCCCCEEEEECc
Confidence            454 44599999999988777777665422111111 1122233322222   223456677777877777899999999


Q ss_pred             hhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhh
Q 015158          288 RRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIG  367 (412)
Q Consensus       288 ~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~G  367 (412)
                      ++.++.+++.|...++.+..+||+++.++|..+++.|.+|+++|||+|+++++|+|+|++++||+++.|.|...|.|++|
T Consensus       234 r~~~e~la~~L~~~g~~~~~~H~~l~~~~R~~i~~~F~~g~~~vlVaT~a~~~GID~p~v~~VI~~~~p~s~~~y~Q~~G  313 (591)
T TIGR01389       234 RKKVEELAERLESQGISALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMGIDKPNVRFVIHYDMPGNLESYYQEAG  313 (591)
T ss_pred             HHHHHHHHHHHHhCCCCEEEEECCCCHHHHHHHHHHHHcCCCcEEEEechhhccCcCCCCCEEEEcCCCCCHHHHhhhhc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hcccCCCCceEEEEeccCcHHHHHHHH
Q 015158          368 RSGRFGRKGVAINFVTRDDERMLFDIQ  394 (412)
Q Consensus       368 R~~R~g~~g~~~~~~~~~~~~~~~~~~  394 (412)
                      |+||.|.++.|++++++.|...++.+.
T Consensus       314 RaGR~G~~~~~il~~~~~d~~~~~~~i  340 (591)
T TIGR01389       314 RAGRDGLPAEAILLYSPADIALLKRRI  340 (591)
T ss_pred             cccCCCCCceEEEecCHHHHHHHHHHH
Confidence            999999999999999888766544433

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.

>KOG0334 consensus RNA helicase [RNA processing and modification]

Probab=100.00  E-value=1e-46  Score=359.09  Aligned_cols=382  Identities=34%  Similarity=0.545  Sum_probs=350.8

Q ss_pred             CCCChhhhccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccC-----
Q 015158           30 FFTSYDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYG-----  104 (412)
Q Consensus        30 ~~~~~~~~~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~-----  104 (412)
                      .-.....+...|.+.+++..++.-++.++|..|+|.|.+||++++.|+++|.++-||||||++|+++++.+....     
T Consensus       356 ~g~~~pkpv~sW~q~gl~~~il~tlkkl~y~k~~~IQ~qAiP~ImsGrdvIgvakTgSGKT~af~LPmirhi~dQr~~~~  435 (997)
T KOG0334|consen  356 KGKECPKPVTSWTQCGLSSKILETLKKLGYEKPTPIQAQAIPAIMSGRDVIGVAKTGSGKTLAFLLPMIRHIKDQRPLEE  435 (997)
T ss_pred             ccCCCCcccchHhhCCchHHHHHHHHHhcCCCCcchhhhhcchhccCcceEEeeccCCccchhhhcchhhhhhcCCChhh
Confidence            344456778899999999999999999999999999999999999999999999999999999999999766433     


Q ss_pred             CCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCce-
Q 015158          105 LVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIR-  183 (412)
Q Consensus       105 ~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~-  183 (412)
                      ..++.++|++||++|+.|+.++++.|+...++.+.+.+|+.........+..++.|+||||.++...+........+++ 
T Consensus       436 gdGPi~li~aPtrela~QI~r~~~kf~k~l~ir~v~vygg~~~~~qiaelkRg~eIvV~tpGRmiD~l~~n~grvtnlrR  515 (997)
T KOG0334|consen  436 GDGPIALILAPTRELAMQIHREVRKFLKLLGIRVVCVYGGSGISQQIAELKRGAEIVVCTPGRMIDILCANSGRVTNLRR  515 (997)
T ss_pred             CCCceEEEEcCCHHHHHHHHHHHHHHHhhcCceEEEecCCccHHHHHHHHhcCCceEEeccchhhhhHhhcCCccccccc
Confidence            2367899999999999999999999999999999999999999998888888899999999999888766554444554 


Q ss_pred             --EEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEecc
Q 015158          184 --IFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEK  261 (412)
Q Consensus       184 --~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  261 (412)
                        ++|+||++++++.+|..+...|+..+++..|.+.+|||.+..+.......+..|+.+.+.........+...+.....
T Consensus       516 ~t~lv~deaDrmfdmgfePq~~~Ii~nlrpdrQtvlfSatfpr~m~~la~~vl~~Pveiiv~~~svV~k~V~q~v~V~~~  595 (997)
T KOG0334|consen  516 VTYLVLDEADRMFDMGFEPQITRILQNLRPDRQTVLFSATFPRSMEALARKVLKKPVEIIVGGRSVVCKEVTQVVRVCAI  595 (997)
T ss_pred             cceeeechhhhhheeccCcccchHHhhcchhhhhhhhhhhhhHHHHHHHHHhhcCCeeEEEccceeEeccceEEEEEecC
Confidence              999999999999999999999999999999999999999999888888999999998888888888888888888887


Q ss_pred             chhhHHHHHHHHHhc-CCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcC
Q 015158          262 EEWKLETLCDLYETL-AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLAR  340 (412)
Q Consensus       262 ~~~~~~~l~~~~~~~-~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~  340 (412)
                      ...+...|.+++... ..+++||||.+.+.|..+.+.|.+.++.+..+||+.+..+|+..++.|+++...+||+|+.+.+
T Consensus       596 e~eKf~kL~eLl~e~~e~~~tiiFv~~qe~~d~l~~~L~~ag~~~~slHGgv~q~dR~sti~dfK~~~~~LLvaTsvvar  675 (997)
T KOG0334|consen  596 ENEKFLKLLELLGERYEDGKTIIFVDKQEKADALLRDLQKAGYNCDSLHGGVDQHDRSSTIEDFKNGVVNLLVATSVVAR  675 (997)
T ss_pred             chHHHHHHHHHHHHHhhcCCEEEEEcCchHHHHHHHHHHhcCcchhhhcCCCchHHHHhHHHHHhccCceEEEehhhhhc
Confidence            788888888888776 4589999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHHhccccccCChhhhhc
Q 015158          341 GIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVADL  411 (412)
Q Consensus       341 G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  411 (412)
                      |+|++.+..||+++.|....+|++|.||+||.|..|.|++|.++.+.++...+.++|...-+++|+.+..+
T Consensus       676 GLdv~~l~Lvvnyd~pnh~edyvhR~gRTgragrkg~AvtFi~p~q~~~a~dl~~al~~~~~~~P~~l~~l  746 (997)
T KOG0334|consen  676 GLDVKELILVVNYDFPNHYEDYVHRVGRTGRAGRKGAAVTFITPDQLKYAGDLCKALELSKQPVPKLLQAL  746 (997)
T ss_pred             ccccccceEEEEcccchhHHHHHHHhcccccCCccceeEEEeChHHhhhHHHHHHHHHhccCCCchHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999877654

>PRK02362 ski2-like helicase; Provisional

Probab=100.00  E-value=3.4e-46  Score=370.41  Aligned_cols=352  Identities=22%  Similarity=0.316  Sum_probs=261.4

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHHhhhhh-hhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHH
Q 015158           40 TFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVP-FCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRE  118 (412)
Q Consensus        40 ~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~-~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  118 (412)
                      .|+++++++.+.+.+...|+.+|+|+|.++++. +..|+++++++|||||||+++.++++..+..   +.+++|++|+++
T Consensus         2 ~~~~l~lp~~~~~~l~~~g~~~l~p~Q~~ai~~~~~~g~nvlv~APTGSGKTlia~lail~~l~~---~~kal~i~P~ra   78 (737)
T PRK02362          2 KIAELPLPEGVIEFYEAEGIEELYPPQAEAVEAGLLDGKNLLAAIPTASGKTLIAELAMLKAIAR---GGKALYIVPLRA   78 (737)
T ss_pred             ChhhcCCCHHHHHHHHhCCCCcCCHHHHHHHHHHHhCCCcEEEECCCcchHHHHHHHHHHHHHhc---CCcEEEEeChHH
Confidence            578899999999999999999999999999998 7789999999999999999999999988753   358999999999


Q ss_pred             HHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCc
Q 015158          119 LAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGF  198 (412)
Q Consensus       119 L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~  198 (412)
                      |+.|+.+.++.+.. .++.+..++|+......   ....++|+|+||+++..++.+.....++++++|+||+|.+.+.++
T Consensus        79 La~q~~~~~~~~~~-~g~~v~~~tGd~~~~~~---~l~~~~IiV~Tpek~~~llr~~~~~l~~v~lvViDE~H~l~d~~r  154 (737)
T PRK02362         79 LASEKFEEFERFEE-LGVRVGISTGDYDSRDE---WLGDNDIIVATSEKVDSLLRNGAPWLDDITCVVVDEVHLIDSANR  154 (737)
T ss_pred             HHHHHHHHHHHhhc-CCCEEEEEeCCcCcccc---ccCCCCEEEECHHHHHHHHhcChhhhhhcCEEEEECccccCCCcc
Confidence            99999999998643 47889999987654321   224579999999999888876555567899999999999888777


Q ss_pred             HHHHHHHHHhC---CCCceEEEEeecCChHHHHHHHHhcCCCeEE----------Eec-CCccccCCceEEEEEeccchh
Q 015158          199 KDQIYDIFQLL---PPKIQVGVFSATMPPEALEITRKFMNKPVRI----------LVK-RDELTLEGIKQFHVNVEKEEW  264 (412)
Q Consensus       199 ~~~~~~i~~~~---~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~----------~~~-~~~~~~~~~~~~~~~~~~~~~  264 (412)
                      +..+..++..+   .++.|++++|||+++. .+.. .+++.....          ... ........ ............
T Consensus       155 g~~le~il~rl~~~~~~~qii~lSATl~n~-~~la-~wl~~~~~~~~~rpv~l~~~v~~~~~~~~~~-~~~~~~~~~~~~  231 (737)
T PRK02362        155 GPTLEVTLAKLRRLNPDLQVVALSATIGNA-DELA-DWLDAELVDSEWRPIDLREGVFYGGAIHFDD-SQREVEVPSKDD  231 (737)
T ss_pred             hHHHHHHHHHHHhcCCCCcEEEEcccCCCH-HHHH-HHhCCCcccCCCCCCCCeeeEecCCeecccc-ccccCCCccchH
Confidence            77776665443   4678999999999752 2333 333221100          000 00000000 000000001111


Q ss_pred             hHHHHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcC------------------------------------CCeeEEe
Q 015158          265 KLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSR------------------------------------DHTVSAT  308 (412)
Q Consensus       265 ~~~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~------------------------------------~~~~~~~  308 (412)
                      ....+.+.+.  ..+++||||++++.++.+++.|.+.                                    ...+.++
T Consensus       232 ~~~~~~~~~~--~~~~~LVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~L~~~l~~gva~h  309 (737)
T PRK02362        232 TLNLVLDTLE--EGGQCLVFVSSRRNAEGFAKRAASALKKTLTAAERAELAELAEEIREVSDTETSKDLADCVAKGAAFH  309 (737)
T ss_pred             HHHHHHHHHH--cCCCeEEEEeCHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHhccCccccHHHHHHHHhCEEee
Confidence            2223333332  4579999999999999888887543                                    1368899


Q ss_pred             cCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEE----cc-----CCCChhhHHHhhhhcccCCCC--ce
Q 015158          309 HGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVIN----YD-----LPTQPENYLHRIGRSGRFGRK--GV  377 (412)
Q Consensus       309 ~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~----~~-----~~~s~~~~~Q~~GR~~R~g~~--g~  377 (412)
                      |++++..+|..+++.|++|.++|||||+++++|+|+|..++||.    ++     .|.+..+|.||+||+||.|.+  |.
T Consensus       310 Hagl~~~eR~~ve~~Fr~G~i~VLvaT~tla~GvnlPa~~VVI~~~~~yd~~~g~~~~s~~~y~Qm~GRAGR~g~d~~G~  389 (737)
T PRK02362        310 HAGLSREHRELVEDAFRDRLIKVISSTPTLAAGLNLPARRVIIRDYRRYDGGAGMQPIPVLEYHQMAGRAGRPGLDPYGE  389 (737)
T ss_pred             cCCCCHHHHHHHHHHHHcCCCeEEEechhhhhhcCCCceEEEEecceeecCCCCceeCCHHHHHHHhhcCCCCCCCCCce
Confidence            99999999999999999999999999999999999999988885    33     578999999999999999865  88


Q ss_pred             EEEEeccCcHHHHHHHHHHhccccccC
Q 015158          378 AINFVTRDDERMLFDIQKFYNVVIEEL  404 (412)
Q Consensus       378 ~~~~~~~~~~~~~~~~~~~~~~~~~~~  404 (412)
                      ++++....+. ...-+.+|+....+++
T Consensus       390 ~ii~~~~~~~-~~~~~~~~l~~~~~~i  415 (737)
T PRK02362        390 AVLLAKSYDE-LDELFERYIWADPEDV  415 (737)
T ss_pred             EEEEecCchh-HHHHHHHHHhCCCCce
Confidence            8888865432 2222445554344343

>KOG4284 consensus DEAD box protein [Transcription]

Probab=100.00  E-value=5.8e-46  Score=334.93  Aligned_cols=350  Identities=33%  Similarity=0.572  Sum_probs=324.0

Q ss_pred             hccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCC
Q 015158           37 VYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPT  116 (412)
Q Consensus        37 ~~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~  116 (412)
                      ...+|+.+.+...+...|...+|..|++.|..|++.++.+-+.||++..|+|||++|...+...+........++|++||
T Consensus        23 ~~~~fe~l~l~r~vl~glrrn~f~~ptkiQaaAIP~~~~kmDliVQaKSGTGKTlVfsv~av~sl~~~~~~~q~~Iv~PT  102 (980)
T KOG4284|consen   23 CTPGFEQLALWREVLLGLRRNAFALPTKIQAAAIPAIFSKMDLIVQAKSGTGKTLVFSVLAVESLDSRSSHIQKVIVTPT  102 (980)
T ss_pred             CCCCHHHHHHHHHHHHHHHhhcccCCCchhhhhhhhhhcccceEEEecCCCCceEEEEeeeehhcCcccCcceeEEEecc
Confidence            34588999999999999999999999999999999999999999999999999999988888888777677889999999


Q ss_pred             HHHHHHHHHHHHHhhccc-CcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhc
Q 015158          117 RELAQQIEKVMRALGDYL-GVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLS  195 (412)
Q Consensus       117 ~~L~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~  195 (412)
                      ++++.|+.+.+.+++..+ |..+..+.||+....+...+. .++|+|+||+++..+++...++..+++++|+|||+.+.+
T Consensus       103 REiaVQI~~tv~~v~~sf~g~~csvfIGGT~~~~d~~rlk-~~rIvIGtPGRi~qL~el~~~n~s~vrlfVLDEADkL~~  181 (980)
T KOG4284|consen  103 REIAVQIKETVRKVAPSFTGARCSVFIGGTAHKLDLIRLK-QTRIVIGTPGRIAQLVELGAMNMSHVRLFVLDEADKLMD  181 (980)
T ss_pred             hhhhhHHHHHHHHhcccccCcceEEEecCchhhhhhhhhh-hceEEecCchHHHHHHHhcCCCccceeEEEeccHHhhhc
Confidence            999999999999998755 889999999998776655444 458999999999999999999999999999999999997


Q ss_pred             -cCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccch-------hhHH
Q 015158          196 -RGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEE-------WKLE  267 (412)
Q Consensus       196 -~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~  267 (412)
                       ..|...+..++..+|...|++++|||.+.++...+..++.+|..+.........-+++++++......       .+..
T Consensus       182 t~sfq~~In~ii~slP~~rQv~a~SATYp~nLdn~Lsk~mrdp~lVr~n~~d~~L~GikQyv~~~~s~nnsveemrlklq  261 (980)
T KOG4284|consen  182 TESFQDDINIIINSLPQIRQVAAFSATYPRNLDNLLSKFMRDPALVRFNADDVQLFGIKQYVVAKCSPNNSVEEMRLKLQ  261 (980)
T ss_pred             hhhHHHHHHHHHHhcchhheeeEEeccCchhHHHHHHHHhcccceeecccCCceeechhheeeeccCCcchHHHHHHHHH
Confidence             66999999999999999999999999999999999999999999999999999999999998887652       3567


Q ss_pred             HHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCC
Q 015158          268 TLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQV  347 (412)
Q Consensus       268 ~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~  347 (412)
                      .|.++++..+-...||||+....|+-++.+|...|+++-+++|.|++.+|-.+++.+++-..+|||+|+.-.+|+|-+.+
T Consensus       262 ~L~~vf~~ipy~QAlVF~~~~sra~~~a~~L~ssG~d~~~ISgaM~Q~~Rl~a~~~lr~f~~rILVsTDLtaRGIDa~~v  341 (980)
T KOG4284|consen  262 KLTHVFKSIPYVQALVFCDQISRAEPIATHLKSSGLDVTFISGAMSQKDRLLAVDQLRAFRVRILVSTDLTARGIDADNV  341 (980)
T ss_pred             HHHHHHhhCchHHHHhhhhhhhhhhHHHHHhhccCCCeEEeccccchhHHHHHHHHhhhceEEEEEecchhhccCCcccc
Confidence            77788888888899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcH
Q 015158          348 SLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDE  387 (412)
Q Consensus       348 ~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~  387 (412)
                      +.||.++.|-+...|.+||||+||.|..|.+++|+....+
T Consensus       342 NLVVNiD~p~d~eTY~HRIGRAgRFG~~G~aVT~~~~~~e  381 (980)
T KOG4284|consen  342 NLVVNIDAPADEETYFHRIGRAGRFGAHGAAVTLLEDERE  381 (980)
T ss_pred             ceEEecCCCcchHHHHHHhhhcccccccceeEEEeccchh
Confidence            9999999999999999999999999999999999987655

>KOG0347 consensus RNA helicase [RNA processing and modification]

Probab=100.00  E-value=7.3e-47  Score=335.04  Aligned_cols=362  Identities=28%  Similarity=0.428  Sum_probs=297.1

Q ss_pred             hhccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcC-ccEEEECCCCCCchhHhHHHHHHhhccC----------
Q 015158           36 EVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKG-LDVIQQAQSGTGKTATFCSGILQQLDYG----------  104 (412)
Q Consensus        36 ~~~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~-~~~lv~~~tGsGKT~~~~~~~~~~~~~~----------  104 (412)
                      .-...|..+.++..+.++|...||..|++.|...++.+..| .+++=.|.||||||++|-++++..+...          
T Consensus       178 ~DvsAW~~l~lp~~iL~aL~~~gFs~Pt~IQsl~lp~ai~gk~DIlGaAeTGSGKTLAFGIPiv~~l~~~s~~s~e~~~~  257 (731)
T KOG0347|consen  178 VDVSAWKNLFLPMEILRALSNLGFSRPTEIQSLVLPAAIRGKVDILGAAETGSGKTLAFGIPIVERLLESSDDSQELSNT  257 (731)
T ss_pred             cChHHHhcCCCCHHHHHHHHhcCCCCCccchhhcccHhhccchhcccccccCCCceeeecchhhhhhhhccchHhhhhhH
Confidence            34567889999999999999999999999999999999998 7899999999999999999999844221          


Q ss_pred             -CCce--eEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCC---C
Q 015158          105 -LVEC--QALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSL---R  178 (412)
Q Consensus       105 -~~~~--~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~---~  178 (412)
                       ...+  -.||++||++|+.|+.+.+...+..+++.+..++||.....+...+...++|||+||++|..++.....   +
T Consensus       258 ~~k~~k~~~LV~tPTRELa~QV~~Hl~ai~~~t~i~v~si~GGLavqKQqRlL~~~p~IVVATPGRlweli~e~n~~l~~  337 (731)
T KOG0347|consen  258 SAKYVKPIALVVTPTRELAHQVKQHLKAIAEKTQIRVASITGGLAVQKQQRLLNQRPDIVVATPGRLWELIEEDNTHLGN  337 (731)
T ss_pred             HhccCcceeEEecChHHHHHHHHHHHHHhccccCeEEEEeechhHHHHHHHHHhcCCCEEEecchHHHHHHHhhhhhhhh
Confidence             1123  499999999999999999999999999999999999999888888988999999999999998876543   3


Q ss_pred             CCCceEEEEeCCchhhccCcHHHHHHHHHhCC-----CCceEEEEeecCChHH---------------------HHHHHH
Q 015158          179 PDNIRIFVLDEADEMLSRGFKDQIYDIFQLLP-----PKIQVGVFSATMPPEA---------------------LEITRK  232 (412)
Q Consensus       179 ~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~-----~~~~~i~~SAT~~~~~---------------------~~~~~~  232 (412)
                      +..+.++|+||+++++..++...+..++..+.     ...|.+.+|||+.-..                     ..++..
T Consensus       338 ~k~vkcLVlDEaDRmvekghF~Els~lL~~L~e~~~~~qrQTlVFSATlt~~~~~~~~~~~k~~~k~~~~~~kiq~Lmk~  417 (731)
T KOG0347|consen  338 FKKVKCLVLDEADRMVEKGHFEELSKLLKHLNEEQKNRQRQTLVFSATLTLVLQQPLSSSRKKKDKEDELNAKIQHLMKK  417 (731)
T ss_pred             hhhceEEEEccHHHHhhhccHHHHHHHHHHhhhhhcccccceEEEEEEeehhhcChhHHhhhccchhhhhhHHHHHHHHH
Confidence            56788999999999999999999998888775     3568899999985211                     111111


Q ss_pred             --hcCCCeEEEecCCccccCCceEEEEEeccchhhHHHHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecC
Q 015158          233 --FMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHG  310 (412)
Q Consensus       233 --~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~  310 (412)
                        +.++|..+...+.......+......++. ..+.-.++.++..++ |++|||||++..+.+++-+|+..++....+|+
T Consensus       418 ig~~~kpkiiD~t~q~~ta~~l~Es~I~C~~-~eKD~ylyYfl~ryP-GrTlVF~NsId~vKRLt~~L~~L~i~p~~LHA  495 (731)
T KOG0347|consen  418 IGFRGKPKIIDLTPQSATASTLTESLIECPP-LEKDLYLYYFLTRYP-GRTLVFCNSIDCVKRLTVLLNNLDIPPLPLHA  495 (731)
T ss_pred             hCccCCCeeEecCcchhHHHHHHHHhhcCCc-cccceeEEEEEeecC-CceEEEechHHHHHHHHHHHhhcCCCCchhhH
Confidence              22444444443333322222222222211 112222222333333 79999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHHHH
Q 015158          311 DMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERML  390 (412)
Q Consensus       311 ~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~  390 (412)
                      .|.+.+|-+.+++|++....|||||+++.+|+|+|++.|||||-.|.+...|++|.||..|++..|..++++.+.+...+
T Consensus       496 ~M~QKqRLknLEkF~~~~~~VLiaTDVAARGLDIp~V~HVIHYqVPrtseiYVHRSGRTARA~~~Gvsvml~~P~e~~~~  575 (731)
T KOG0347|consen  496 SMIQKQRLKNLEKFKQSPSGVLIATDVAARGLDIPGVQHVIHYQVPRTSEIYVHRSGRTARANSEGVSVMLCGPQEVGPL  575 (731)
T ss_pred             HHHHHHHHHhHHHHhcCCCeEEEeehhhhccCCCCCcceEEEeecCCccceeEecccccccccCCCeEEEEeChHHhHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             HHHHHHhcc
Q 015158          391 FDIQKFYNV  399 (412)
Q Consensus       391 ~~~~~~~~~  399 (412)
                      .++.+-++.
T Consensus       576 ~KL~ktL~k  584 (731)
T KOG0347|consen  576 KKLCKTLKK  584 (731)
T ss_pred             HHHHHHHhh
Confidence            888887775

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

Probab=100.00  E-value=3.6e-45  Score=350.12  Aligned_cols=333  Identities=21%  Similarity=0.286  Sum_probs=271.8

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccC-----CCceeEEEEcCCHHHH
Q 015158           46 LQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYG-----LVECQALVLAPTRELA  120 (412)
Q Consensus        46 l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~-----~~~~~~lil~P~~~L~  120 (412)
                      +++.+.+++... |.+|+|.|++|++.+.+|+|+++.+|||||||.++++++++.+...     ..+-.+|||+|.++|.
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            678899999887 8889999999999999999999999999999999999999988665     2245799999999999


Q ss_pred             HHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCC--CCCCceEEEEeCCchhhccCc
Q 015158          121 QQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSL--RPDNIRIFVLDEADEMLSRGF  198 (412)
Q Consensus       121 ~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~--~~~~~~~iiiDE~h~~~~~~~  198 (412)
                      +++.+.+..+....|+++...+|+++.........++++|+++|||+|.-++....+  .+.++.+||+||+|.+.+...
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            999999999999999999999999998888888889999999999999877655332  357899999999999886654


Q ss_pred             H----HHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCC--eEEEecCCccccCCceEEEEEec------cchhhH
Q 015158          199 K----DQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKP--VRILVKRDELTLEGIKQFHVNVE------KEEWKL  266 (412)
Q Consensus       199 ~----~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~  266 (412)
                      +    -.+.++....+ ..|.|++|||..+ .....+.+.+..  ..+.... ......+........      ......
T Consensus       167 G~~Lsl~LeRL~~l~~-~~qRIGLSATV~~-~~~varfL~g~~~~~~Iv~~~-~~k~~~i~v~~p~~~~~~~~~~~~~~~  243 (814)
T COG1201         167 GVQLALSLERLRELAG-DFQRIGLSATVGP-PEEVAKFLVGFGDPCEIVDVS-AAKKLEIKVISPVEDLIYDEELWAALY  243 (814)
T ss_pred             chhhhhhHHHHHhhCc-ccEEEeehhccCC-HHHHHHHhcCCCCceEEEEcc-cCCcceEEEEecCCccccccchhHHHH
Confidence            4    34455555555 8999999999974 345555555543  2222222 211222222211111      112345


Q ss_pred             HHHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcCC-CeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCC
Q 015158          267 ETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRD-HTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQ  345 (412)
Q Consensus       267 ~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~-~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~  345 (412)
                      ..+.++++++.  .+|||+|++..++.++..|++.+ ..+..+||.++.+.|..++++|++|+++++|||+.++-|+|+.
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            56666777765  89999999999999999999987 8999999999999999999999999999999999999999999


Q ss_pred             CCCEEEEccCCCChhhHHHhhhhcccC-CCCceEEEEecc
Q 015158          346 QVSLVINYDLPTQPENYLHRIGRSGRF-GRKGVAINFVTR  384 (412)
Q Consensus       346 ~~~~vi~~~~~~s~~~~~Q~~GR~~R~-g~~g~~~~~~~~  384 (412)
                      +++.||+++.|.+.+.+.||+||+|+. |...+++++...
T Consensus       322 ~vdlVIq~~SP~sV~r~lQRiGRsgHr~~~~Skg~ii~~~  361 (814)
T COG1201         322 DIDLVIQLGSPKSVNRFLQRIGRAGHRLGEVSKGIIIAED  361 (814)
T ss_pred             CceEEEEeCCcHHHHHHhHhccccccccCCcccEEEEecC
Confidence            999999999999999999999999986 555677766666

>PRK13767 ATP-dependent helicase; Provisional

Probab=100.00  E-value=2.4e-44  Score=360.16  Aligned_cols=334  Identities=22%  Similarity=0.313  Sum_probs=246.2

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccC------CCceeEEEEcCCHHH
Q 015158           46 LQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYG------LVECQALVLAPTREL  119 (412)
Q Consensus        46 l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~------~~~~~~lil~P~~~L  119 (412)
                      +++.+.+.+.. +|..|+|+|.++++.+++|+++++++|||||||++++++++..+...      ..+.++||++|+++|
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            45777777765 78889999999999999999999999999999999999999876531      234579999999999


Q ss_pred             HHHHHHHHHH-------hh----ccc-CcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCC--CCCCceEE
Q 015158          120 AQQIEKVMRA-------LG----DYL-GVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSL--RPDNIRIF  185 (412)
Q Consensus       120 ~~q~~~~~~~-------~~----~~~-~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~--~~~~~~~i  185 (412)
                      +.|+.+.+..       +.    ... ++.+...+|+............+++|+|+||++|..++....+  .+.++++|
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            9999876653       22    122 6788899999887776666777889999999999877655433  35789999


Q ss_pred             EEeCCchhhccCcHHH----HHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCC-------CeEEEecCCccccCCceE
Q 015158          186 VLDEADEMLSRGFKDQ----IYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNK-------PVRILVKRDELTLEGIKQ  254 (412)
Q Consensus       186 iiDE~h~~~~~~~~~~----~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~  254 (412)
                      |+||+|.+.+..+...    +.++....+...+++++|||+++. ......+.+.       +..+. .........+..
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 IVDEIHSLAENKRGVHLSLSLERLEELAGGEFVRIGLSATIEPL-EEVAKFLVGYEDDGEPRDCEIV-DARFVKPFDIKV  254 (876)
T ss_pred             EEechhhhccCccHHHHHHHHHHHHHhcCCCCeEEEEecccCCH-HHHHHHhcCccccCCCCceEEE-ccCCCccceEEE
Confidence            9999999887654443    344444444678999999999752 2333323221       11111 111100000100


Q ss_pred             EE-----EEeccc---hhhHHHHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcC------CCeeEEecCCCCHHHHHHH
Q 015158          255 FH-----VNVEKE---EWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSR------DHTVSATHGDMDQNTRDII  320 (412)
Q Consensus       255 ~~-----~~~~~~---~~~~~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~------~~~~~~~~~~~~~~~r~~~  320 (412)
                      ..     ......   ......+.++++.  .+++||||++++.|+.++..|++.      +..+..+||+++.++|..+
T Consensus       255 ~~p~~~l~~~~~~~~~~~l~~~L~~~i~~--~~~~LVF~nTr~~ae~la~~L~~~~~~~~~~~~i~~hHg~ls~~~R~~v  332 (876)
T PRK13767        255 ISPVDDLIHTPAEEISEALYETLHELIKE--HRTTLIFTNTRSGAERVLYNLRKRFPEEYDEDNIGAHHSSLSREVRLEV  332 (876)
T ss_pred             eccCccccccccchhHHHHHHHHHHHHhc--CCCEEEEeCCHHHHHHHHHHHHHhchhhccccceeeeeCCCCHHHHHHH
Confidence            00     000000   1112233333333  468999999999999999999873      4679999999999999999


Q ss_pred             HHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccC-CCCceEEEEecc
Q 015158          321 MREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRF-GRKGVAINFVTR  384 (412)
Q Consensus       321 ~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~-g~~g~~~~~~~~  384 (412)
                      ++.|++|++++||||++++.|+|+|++++||+++.|.|...|+||+||+||. |..+.++++...
T Consensus       333 e~~fk~G~i~vLVaTs~Le~GIDip~Vd~VI~~~~P~sv~~ylQRiGRaGR~~g~~~~g~ii~~~  397 (876)
T PRK13767        333 EEKLKRGELKVVVSSTSLELGIDIGYIDLVVLLGSPKSVSRLLQRIGRAGHRLGEVSKGRIIVVD  397 (876)
T ss_pred             HHHHHcCCCeEEEECChHHhcCCCCCCcEEEEeCCCCCHHHHHHhcccCCCCCCCCCcEEEEEcC
Confidence            9999999999999999999999999999999999999999999999999997 444555555543

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

Probab=100.00  E-value=6.4e-45  Score=336.37  Aligned_cols=327  Identities=23%  Similarity=0.287  Sum_probs=261.2

Q ss_pred             CCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCc
Q 015158           57 YGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGV  136 (412)
Q Consensus        57 ~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~  136 (412)
                      +|+..+++-|.+++..++.++++++.+|||+|||+||.+|++-.  .    +-+|||.|..+|++++.+.+...    |+
T Consensus        13 fGy~~FR~gQ~evI~~~l~g~d~lvvmPTGgGKSlCyQiPAll~--~----G~TLVVSPLiSLM~DQV~~l~~~----Gi   82 (590)
T COG0514          13 FGYASFRPGQQEIIDALLSGKDTLVVMPTGGGKSLCYQIPALLL--E----GLTLVVSPLISLMKDQVDQLEAA----GI   82 (590)
T ss_pred             hCccccCCCHHHHHHHHHcCCcEEEEccCCCCcchHhhhHHHhc--C----CCEEEECchHHHHHHHHHHHHHc----Cc
Confidence            68999999999999999999999999999999999999988754  2    36999999999999999999886    77


Q ss_pred             EEEEEEcCcchHHHH----HHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccC--cHHHHHHH---HH
Q 015158          137 KVHACVGGTSVREDQ----RILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRG--FKDQIYDI---FQ  207 (412)
Q Consensus       137 ~~~~~~~~~~~~~~~----~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~--~~~~~~~i---~~  207 (412)
                      .+..+.+..+.....    ....+..++++.+||.+........+....+.+++|||||+++.|+  |+..+..+   ..
T Consensus        83 ~A~~lnS~l~~~e~~~v~~~l~~g~~klLyisPErl~~~~f~~~L~~~~i~l~vIDEAHCiSqWGhdFRP~Y~~lg~l~~  162 (590)
T COG0514          83 RAAYLNSTLSREERQQVLNQLKSGQLKLLYISPERLMSPRFLELLKRLPISLVAIDEAHCISQWGHDFRPDYRRLGRLRA  162 (590)
T ss_pred             eeehhhcccCHHHHHHHHHHHhcCceeEEEECchhhcChHHHHHHHhCCCceEEechHHHHhhcCCccCHhHHHHHHHHh
Confidence            888887775554443    3334568999999999865433333334578999999999999997  76655554   45


Q ss_pred             hCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhHHHHHHHHHhcCCCcEEEEEcc
Q 015158          208 LLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNT  287 (412)
Q Consensus       208 ~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lif~~~  287 (412)
                      .++ +.+++++|||.++.+...+...++-.... ......+++++............+...+.+ ......+..||||.|
T Consensus       163 ~~~-~~p~~AlTATA~~~v~~DI~~~L~l~~~~-~~~~sfdRpNi~~~v~~~~~~~~q~~fi~~-~~~~~~~~GIIYc~s  239 (590)
T COG0514         163 GLP-NPPVLALTATATPRVRDDIREQLGLQDAN-IFRGSFDRPNLALKVVEKGEPSDQLAFLAT-VLPQLSKSGIIYCLT  239 (590)
T ss_pred             hCC-CCCEEEEeCCCChHHHHHHHHHhcCCCcc-eEEecCCCchhhhhhhhcccHHHHHHHHHh-hccccCCCeEEEEee
Confidence            555 78899999999998888887766533311 111122334444333333322223333332 224455779999999


Q ss_pred             hhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhh
Q 015158          288 RRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIG  367 (412)
Q Consensus       288 ~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~G  367 (412)
                      ++.++.+++.|.+.|+.+..||++|+.++|..+.++|.+++.+|+|||.++++|||-|+++.|||++.|.|...|.|-+|
T Consensus       240 Rk~~E~ia~~L~~~g~~a~~YHaGl~~~eR~~~q~~f~~~~~~iiVAT~AFGMGIdKpdVRfViH~~lP~s~EsYyQE~G  319 (590)
T COG0514         240 RKKVEELAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKVMVATNAFGMGIDKPDVRFVIHYDLPGSIESYYQETG  319 (590)
T ss_pred             HHhHHHHHHHHHHCCCceEEecCCCCHHHHHHHHHHHhcCCCcEEEEeccccCccCCCCceEEEEecCCCCHHHHHHHHh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hcccCCCCceEEEEeccCcHHHHHHHHHH
Q 015158          368 RSGRFGRKGVAINFVTRDDERMLFDIQKF  396 (412)
Q Consensus       368 R~~R~g~~g~~~~~~~~~~~~~~~~~~~~  396 (412)
                      ||||.|.+..|++++++.|....+.+.+.
T Consensus       320 RAGRDG~~a~aill~~~~D~~~~~~~i~~  348 (590)
T COG0514         320 RAGRDGLPAEAILLYSPEDIRWQRYLIEQ  348 (590)
T ss_pred             hccCCCCcceEEEeeccccHHHHHHHHHh
Confidence            99999999999999999997655544443

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

Probab=100.00  E-value=8e-46  Score=318.56  Aligned_cols=364  Identities=32%  Similarity=0.513  Sum_probs=335.8

Q ss_pred             ccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccC-CCceeEEEEcCC
Q 015158           38 YDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYG-LVECQALVLAPT  116 (412)
Q Consensus        38 ~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~-~~~~~~lil~P~  116 (412)
                      .+.|+.++|+..+.+++...||..|+|.|++-++.++++++++-.+-||||||.+++++++..+... ..+.+++++.|+
T Consensus        20 ~g~fqsmgL~~~v~raI~kkg~~~ptpiqRKTipliLe~~dvv~martgsgktaaf~ipm~e~Lk~~s~~g~Ralilspt   99 (529)
T KOG0337|consen   20 SGGFQSMGLDYKVLRAIHKKGFNTPTPIQRKTIPLILEGRDVVGMARTGSGKTAAFLIPMIEKLKSHSQTGLRALILSPT   99 (529)
T ss_pred             CCCccccCCCHHHHHHHHHhhcCCCCchhcccccceeeccccceeeecCCcchhhHHHHHHHHHhhccccccceeeccCc
Confidence            5789999999999999999999999999999999999999999999999999999999999988654 345699999999


Q ss_pred             HHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhcc
Q 015158          117 RELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSR  196 (412)
Q Consensus       117 ~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~  196 (412)
                      +.|+.|..+.++.++..++....++.|+...+.++..+..++|||++||.++.+......+.++.+.+||+||++.++..
T Consensus       100 reLa~qtlkvvkdlgrgt~lr~s~~~ggD~~eeqf~~l~~npDii~ATpgr~~h~~vem~l~l~sveyVVfdEadrlfem  179 (529)
T KOG0337|consen  100 RELALQTLKVVKDLGRGTKLRQSLLVGGDSIEEQFILLNENPDIIIATPGRLLHLGVEMTLTLSSVEYVVFDEADRLFEM  179 (529)
T ss_pred             HHHHHHHHHHHHHhccccchhhhhhcccchHHHHHHHhccCCCEEEecCceeeeeehheeccccceeeeeehhhhHHHhh
Confidence            99999999999999999999999999999999998888888999999999999888877788899999999999999999


Q ss_pred             CcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhHHHHHHHHHhc
Q 015158          197 GFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETL  276 (412)
Q Consensus       197 ~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  276 (412)
                      +|..++.+++..++...|.+++|||++..+.+..+..+..|..+..+.+..-.+.....+..+.. .++...|..++...
T Consensus       180 gfqeql~e~l~rl~~~~QTllfSatlp~~lv~fakaGl~~p~lVRldvetkise~lk~~f~~~~~-a~K~aaLl~il~~~  258 (529)
T KOG0337|consen  180 GFQEQLHEILSRLPESRQTLLFSATLPRDLVDFAKAGLVPPVLVRLDVETKISELLKVRFFRVRK-AEKEAALLSILGGR  258 (529)
T ss_pred             hhHHHHHHHHHhCCCcceEEEEeccCchhhHHHHHccCCCCceEEeehhhhcchhhhhheeeecc-HHHHHHHHHHHhcc
Confidence            99999999999999999999999999999999999999999999877766666666666665555 56777777777775


Q ss_pred             C-CCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccC
Q 015158          277 A-ITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDL  355 (412)
Q Consensus       277 ~-~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~  355 (412)
                      . .+.++||+.+..+++.+...|++.|+.+..++|.+.+..|..-..+|..++..++|+|+...+|+|+|-.+.||.++.
T Consensus       259 ~~~~~t~vf~~tk~hve~~~~ll~~~g~~~s~iysslD~~aRk~~~~~F~~~k~~~lvvTdvaaRG~diplldnvinyd~  338 (529)
T KOG0337|consen  259 IKDKQTIVFVATKHHVEYVRGLLRDFGGEGSDIYSSLDQEARKINGRDFRGRKTSILVVTDVAARGLDIPLLDNVINYDF  338 (529)
T ss_pred             ccccceeEEecccchHHHHHHHHHhcCCCccccccccChHhhhhccccccCCccceEEEehhhhccCCCccccccccccC
Confidence            3 468999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHHhccccc
Q 015158          356 PTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIE  402 (412)
Q Consensus       356 ~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~  402 (412)
                      |.+...|++|+||+.|+|..|.+|.++.+.+..++-.+.-++...+.
T Consensus       339 p~~~klFvhRVgr~aragrtg~aYs~V~~~~~~yl~DL~lflgr~~~  385 (529)
T KOG0337|consen  339 PPDDKLFVHRVGRVARAGRTGRAYSLVASTDDPYLLDLQLFLGRPLI  385 (529)
T ss_pred             CCCCceEEEEecchhhccccceEEEEEecccchhhhhhhhhcCCcee
Confidence            99999999999999999999999999999999999999999887553

>PRK00254 ski2-like helicase; Provisional

Probab=100.00  E-value=1.3e-44  Score=358.29  Aligned_cols=349  Identities=19%  Similarity=0.246  Sum_probs=261.8

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHHhhhhh-hhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHH
Q 015158           40 TFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVP-FCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRE  118 (412)
Q Consensus        40 ~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~-~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  118 (412)
                      +|+++++++.+.+.+...|+.+|+|+|.++++. +..|+++++++|||||||.++.++++..+..  .+.+++|++|+++
T Consensus         2 ~~~~l~l~~~~~~~l~~~g~~~l~~~Q~~ai~~~~~~g~nvlv~apTGsGKT~~~~l~il~~l~~--~~~~~l~l~P~~a   79 (720)
T PRK00254          2 KVDELRVDERIKRVLKERGIEELYPPQAEALKSGVLEGKNLVLAIPTASGKTLVAEIVMVNKLLR--EGGKAVYLVPLKA   79 (720)
T ss_pred             cHHHcCCCHHHHHHHHhCCCCCCCHHHHHHHHHHHhCCCcEEEECCCCcHHHHHHHHHHHHHHHh--cCCeEEEEeChHH
Confidence            577889999999999999999999999999986 7889999999999999999999999887653  2458999999999


Q ss_pred             HHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCc
Q 015158          119 LAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGF  198 (412)
Q Consensus       119 L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~  198 (412)
                      |+.|+.+.+..+. ..+..+..++|+......   ....++|+|+||+++..++.+.....+++++||+||+|.+.+.++
T Consensus        80 La~q~~~~~~~~~-~~g~~v~~~~Gd~~~~~~---~~~~~~IiV~Tpe~~~~ll~~~~~~l~~l~lvViDE~H~l~~~~r  155 (720)
T PRK00254         80 LAEEKYREFKDWE-KLGLRVAMTTGDYDSTDE---WLGKYDIIIATAEKFDSLLRHGSSWIKDVKLVVADEIHLIGSYDR  155 (720)
T ss_pred             HHHHHHHHHHHHh-hcCCEEEEEeCCCCCchh---hhccCCEEEEcHHHHHHHHhCCchhhhcCCEEEEcCcCccCCccc
Confidence            9999999998764 358889999988764322   234679999999999888876555578899999999999988888


Q ss_pred             HHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCce--EEEEEeccc-----hhhHHHHHH
Q 015158          199 KDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIK--QFHVNVEKE-----EWKLETLCD  271 (412)
Q Consensus       199 ~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~-----~~~~~~l~~  271 (412)
                      ...+..++..+....|++++|||+++. .+.. .+++........+.......+.  .........     ......+.+
T Consensus       156 g~~le~il~~l~~~~qiI~lSATl~n~-~~la-~wl~~~~~~~~~rpv~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  233 (720)
T PRK00254        156 GATLEMILTHMLGRAQILGLSATVGNA-EELA-EWLNAELVVSDWRPVKLRKGVFYQGFLFWEDGKIERFPNSWESLVYD  233 (720)
T ss_pred             hHHHHHHHHhcCcCCcEEEEEccCCCH-HHHH-HHhCCccccCCCCCCcceeeEecCCeeeccCcchhcchHHHHHHHHH
Confidence            889999999888899999999999753 3333 3444322111111000000000  000000000     111223334


Q ss_pred             HHHhcCCCcEEEEEcchhHHHHHHHHHhcC---------------------------------CCeeEEecCCCCHHHHH
Q 015158          272 LYETLAITQSVIFVNTRRKVDWLTDKMRSR---------------------------------DHTVSATHGDMDQNTRD  318 (412)
Q Consensus       272 ~~~~~~~~k~lif~~~~~~~~~~~~~L~~~---------------------------------~~~~~~~~~~~~~~~r~  318 (412)
                      .++  .++++||||++++.++.++..|...                                 ...+..+|+++++++|.
T Consensus       234 ~i~--~~~~vLVF~~sr~~~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~gv~~hHagl~~~eR~  311 (720)
T PRK00254        234 AVK--KGKGALVFVNTRRSAEKEALELAKKIKRFLTKPELRALKELADSLEENPTNEKLKKALRGGVAFHHAGLGRTERV  311 (720)
T ss_pred             HHH--hCCCEEEEEcChHHHHHHHHHHHHHHHHhcCchhHHHHHHHHHHHhcCCCcHHHHHHHhhCEEEeCCCCCHHHHH
Confidence            443  3468999999999998777666321                                 23589999999999999


Q ss_pred             HHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEE-------ccC-CCChhhHHHhhhhcccCC--CCceEEEEeccCcHH
Q 015158          319 IIMREFRSGSSRVLITTDLLARGIDVQQVSLVIN-------YDL-PTQPENYLHRIGRSGRFG--RKGVAINFVTRDDER  388 (412)
Q Consensus       319 ~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~-------~~~-~~s~~~~~Q~~GR~~R~g--~~g~~~~~~~~~~~~  388 (412)
                      .+++.|++|.++|||||++++.|+|+|..++||.       ++. +.+..+|.||+||+||.|  ..|.++++....+.+
T Consensus       312 ~ve~~F~~G~i~VLvaT~tLa~Gvnipa~~vVI~~~~~~~~~~~~~~~~~~~~Qm~GRAGR~~~d~~G~~ii~~~~~~~~  391 (720)
T PRK00254        312 LIEDAFREGLIKVITATPTLSAGINLPAFRVIIRDTKRYSNFGWEDIPVLEIQQMMGRAGRPKYDEVGEAIIVATTEEPS  391 (720)
T ss_pred             HHHHHHHCCCCeEEEeCcHHhhhcCCCceEEEECCceEcCCCCceeCCHHHHHHhhhccCCCCcCCCceEEEEecCcchH
Confidence            9999999999999999999999999999998884       222 235679999999999975  568999888765432


Q ss_pred             HHHHHHHHhccc
Q 015158          389 MLFDIQKFYNVV  400 (412)
Q Consensus       389 ~~~~~~~~~~~~  400 (412)
                      .  -+++|+...
T Consensus       392 ~--~~~~~~~~~  401 (720)
T PRK00254        392 K--LMERYIFGK  401 (720)
T ss_pred             H--HHHHHHhCC
Confidence            2  244555443

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

Probab=100.00  E-value=7.1e-45  Score=319.06  Aligned_cols=360  Identities=28%  Similarity=0.445  Sum_probs=290.2

Q ss_pred             ccccccCCCCHHHHHH----------HHHCCCCCChHHHHhhhhhhhc---------CccEEEECCCCCCchhHhHHHHH
Q 015158           38 YDTFDAMGLQENLLRG----------IYAYGFEKPSAIQQRGIVPFCK---------GLDVIQQAQSGTGKTATFCSGIL   98 (412)
Q Consensus        38 ~~~f~~~~l~~~~~~~----------l~~~~~~~l~~~Q~~a~~~~~~---------~~~~lv~~~tGsGKT~~~~~~~~   98 (412)
                      ...|+.+++++.....          +..+++..+.|.|..+++.++.         +++++|.+|||||||++|.+++.
T Consensus       126 lq~~s~l~~se~k~~~d~lea~~~q~l~k~~is~~FPVQ~aVlp~ll~~~~~p~~~r~rDIcV~ApTGSGKTLaY~iPIV  205 (620)
T KOG0350|consen  126 LQIFSVLGKSEMKNLEDTLEATIDQLLVKMAISRLFPVQYAVLPSLLEEIRSPPPSRPRDICVNAPTGSGKTLAYVIPIV  205 (620)
T ss_pred             eeeeeccchhHHHHHHHHHHHHHHHHHHHhhcccccchHHHHHHHHHHhhcCCCCCCCCceEEecCCCCCceeeehhHHH
Confidence            3456666666555444          8888999999999999999863         47999999999999999999999


Q ss_pred             HhhccC-CCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhc-CCC----cEEEeChHHHHHHH
Q 015158           99 QQLDYG-LVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILS-SGV----HVVVGTPGRVFDML  172 (412)
Q Consensus        99 ~~~~~~-~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~----~iii~T~~~l~~~~  172 (412)
                      +.+... ...-+++||+|++.|+.|.++.|..++...++.|..+.|....+.....+. ...    +|+|+||++|..++
T Consensus       206 Q~L~~R~v~~LRavVivPtr~L~~QV~~~f~~~~~~tgL~V~~~sgq~sl~~E~~qL~~~~~~~~~DIlVaTPGRLVDHl  285 (620)
T KOG0350|consen  206 QLLSSRPVKRLRAVVIVPTRELALQVYDTFKRLNSGTGLAVCSLSGQNSLEDEARQLASDPPECRIDILVATPGRLVDHL  285 (620)
T ss_pred             HHHccCCccceEEEEEeeHHHHHHHHHHHHHHhccCCceEEEecccccchHHHHHHHhcCCCccccceEEcCchHHHHhc
Confidence            988765 344689999999999999999999999999999999999888776655444 334    89999999999999


Q ss_pred             Hc-CCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCC----------------------------------CCceEEE
Q 015158          173 RR-QSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLP----------------------------------PKIQVGV  217 (412)
Q Consensus       173 ~~-~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~----------------------------------~~~~~i~  217 (412)
                      .+ ..+++++++++|+|||+++.+..|..-+..+...+.                                  +....++
T Consensus       286 ~~~k~f~Lk~LrfLVIDEADRll~qsfQ~Wl~~v~~~~~~~k~~~~~~nii~~~~~~~pt~~~e~~t~~~~~~~~l~kL~  365 (620)
T KOG0350|consen  286 NNTKSFDLKHLRFLVIDEADRLLDQSFQEWLDTVMSLCKTMKRVACLDNIIRQRQAPQPTVLSELLTKLGKLYPPLWKLV  365 (620)
T ss_pred             cCCCCcchhhceEEEechHHHHHHHHHHHHHHHHHHHhCCchhhcChhhhhhhcccCCchhhHHHHhhcCCcCchhHhhh
Confidence            84 678899999999999999987665544444443332                                  2234677


Q ss_pred             EeecCChHHHHHHHHhcCCCeEEEecC----CccccCCceEEEEEeccchhhHHHHHHHHHhcCCCcEEEEEcchhHHHH
Q 015158          218 FSATMPPEALEITRKFMNKPVRILVKR----DELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDW  293 (412)
Q Consensus       218 ~SAT~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lif~~~~~~~~~  293 (412)
                      +|||+..+......--++.|..+....    ....+..+.+....... ..+...+..++......++|||++|.+.+.+
T Consensus       366 ~satLsqdP~Kl~~l~l~~Prl~~v~~~~~~ryslp~~l~~~~vv~~~-~~kpl~~~~lI~~~k~~r~lcf~~S~~sa~R  444 (620)
T KOG0350|consen  366 FSATLSQDPSKLKDLTLHIPRLFHVSKPLIGRYSLPSSLSHRLVVTEP-KFKPLAVYALITSNKLNRTLCFVNSVSSANR  444 (620)
T ss_pred             cchhhhcChHHHhhhhcCCCceEEeecccceeeecChhhhhceeeccc-ccchHhHHHHHHHhhcceEEEEecchHHHHH
Confidence            888877665566665566665444442    22333444444444433 4466778888888888999999999999999


Q ss_pred             HHHHHh----cCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhc
Q 015158          294 LTDKMR----SRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRS  369 (412)
Q Consensus       294 ~~~~L~----~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~  369 (412)
                      ++..|+    .....+-.++|.++...|.+.++.|..|++.+|||++++.+|+|+.++++||.+++|.+...|++|+||.
T Consensus       445 l~~~L~v~~~~~~~~~s~~t~~l~~k~r~k~l~~f~~g~i~vLIcSD~laRGiDv~~v~~VINYd~P~~~ktyVHR~GRT  524 (620)
T KOG0350|consen  445 LAHVLKVEFCSDNFKVSEFTGQLNGKRRYKMLEKFAKGDINVLICSDALARGIDVNDVDNVINYDPPASDKTYVHRAGRT  524 (620)
T ss_pred             HHHHHHHHhccccchhhhhhhhhhHHHHHHHHHHHhcCCceEEEehhhhhcCCcccccceEeecCCCchhhHHHHhhccc
Confidence            999987    3355667789999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCceEEEEeccCcHHHHHHHHHHhc
Q 015158          370 GRFGRKGVAINFVTRDDERMLFDIQKFYN  398 (412)
Q Consensus       370 ~R~g~~g~~~~~~~~~~~~~~~~~~~~~~  398 (412)
                      +|+|+.|.|+.+++..+...+.++.+...
T Consensus       525 ARAgq~G~a~tll~~~~~r~F~klL~~~~  553 (620)
T KOG0350|consen  525 ARAGQDGYAITLLDKHEKRLFSKLLKKTN  553 (620)
T ss_pred             ccccCCceEEEeeccccchHHHHHHHHhc
Confidence            99999999999999998887766654443

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

Probab=100.00  E-value=1.6e-44  Score=324.03  Aligned_cols=373  Identities=32%  Similarity=0.455  Sum_probs=324.5

Q ss_pred             hcccccc----CCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccC-----CCc
Q 015158           37 VYDTFDA----MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYG-----LVE  107 (412)
Q Consensus        37 ~~~~f~~----~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~-----~~~  107 (412)
                      +..+|..    ......+++.+...+|..|+|.|++|++.++++++++.++|||+|||++|.++++..+...     ..+
T Consensus       130 ~l~~f~~lt~~~~~~~~ll~nl~~~~F~~Pt~iq~~aipvfl~~r~~lAcapTGsgKtlaf~~Pil~~L~~~~~~~~~~g  209 (593)
T KOG0344|consen  130 PLLSFSDLTYDYSMNKRLLENLQELGFDEPTPIQKQAIPVFLEKRDVLACAPTGSGKTLAFNLPILQHLKDLSQEKHKVG  209 (593)
T ss_pred             ccccccccchhhhhcHHHHHhHhhCCCCCCCcccchhhhhhhcccceEEeccCCCcchhhhhhHHHHHHHHhhcccCccc
Confidence            3445554    3467888999999999999999999999999999999999999999999999999887543     345


Q ss_pred             eeEEEEcCCHHHHHHHHHHHHHhh--cccCcEEEEEEcCcchHHHH-HHhcCCCcEEEeChHHHHHHHHcCC--CCCCCc
Q 015158          108 CQALVLAPTRELAQQIEKVMRALG--DYLGVKVHACVGGTSVREDQ-RILSSGVHVVVGTPGRVFDMLRRQS--LRPDNI  182 (412)
Q Consensus       108 ~~~lil~P~~~L~~q~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~-~~~~~~~~iii~T~~~l~~~~~~~~--~~~~~~  182 (412)
                      -+++|+.|+++|+.|.++++.++.  ...+..+..+.......... ......++|++.||..+...+....  ..+.++
T Consensus       210 l~a~Il~ptreLa~Qi~re~~k~~~~~~t~~~a~~~~~~~~~~qk~a~~~~~k~dili~TP~ri~~~~~~~~~~idl~~V  289 (593)
T KOG0344|consen  210 LRALILSPTRELAAQIYREMRKYSIDEGTSLRAAQFSKPAYPSQKPAFLSDEKYDILISTPMRIVGLLGLGKLNIDLSKV  289 (593)
T ss_pred             eEEEEecchHHHHHHHHHHHHhcCCCCCCchhhhhcccccchhhccchhHHHHHHHHhcCHHHHHHHhcCCCccchhhee
Confidence            689999999999999999999998  55555555544432221111 1112347899999999988887665  567889


Q ss_pred             eEEEEeCCchhhcc-CcHHHHHHHHHhCC-CCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEec
Q 015158          183 RIFVLDEADEMLSR-GFKDQIYDIFQLLP-PKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVE  260 (412)
Q Consensus       183 ~~iiiDE~h~~~~~-~~~~~~~~i~~~~~-~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  260 (412)
                      .++|+||++.+... .|..++..++..+. ++..+-++|||.+....+.+......+..+.+...+.....+.+-...+.
T Consensus       290 ~~lV~dEaD~lfe~~~f~~Qla~I~sac~s~~i~~a~FSat~~~~VEE~~~~i~~~~~~vivg~~~sa~~~V~QelvF~g  369 (593)
T KOG0344|consen  290 EWLVVDEADLLFEPEFFVEQLADIYSACQSPDIRVALFSATISVYVEEWAELIKSDLKRVIVGLRNSANETVDQELVFCG  369 (593)
T ss_pred             eeEeechHHhhhChhhHHHHHHHHHHHhcCcchhhhhhhccccHHHHHHHHHhhccceeEEEecchhHhhhhhhhheeee
Confidence            99999999999988 89999999998875 46677889999999999999999999998888887777777777777788


Q ss_pred             cchhhHHHHHHHHHhcCCCcEEEEEcchhHHHHHHHHH-hcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCc
Q 015158          261 KEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKM-RSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLA  339 (412)
Q Consensus       261 ~~~~~~~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L-~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~  339 (412)
                      ....+.-.+.+++...-..+++||+++.+.|..+...| .-.++++.++||+.+..+|+..+++|+.|++++|+||+.++
T Consensus       370 se~~K~lA~rq~v~~g~~PP~lIfVQs~eRak~L~~~L~~~~~i~v~vIh~e~~~~qrde~~~~FR~g~IwvLicTdll~  449 (593)
T KOG0344|consen  370 SEKGKLLALRQLVASGFKPPVLIFVQSKERAKQLFEELEIYDNINVDVIHGERSQKQRDETMERFRIGKIWVLICTDLLA  449 (593)
T ss_pred             cchhHHHHHHHHHhccCCCCeEEEEecHHHHHHHHHHhhhccCcceeeEecccchhHHHHHHHHHhccCeeEEEehhhhh
Confidence            88889999999999988889999999999999999999 56688999999999999999999999999999999999999


Q ss_pred             CCCCCCCCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHHhccccccCChhhh
Q 015158          340 RGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVA  409 (412)
Q Consensus       340 ~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  409 (412)
                      +|+|+.+++.||.++.|.+...|++|+||.||.|+.|.+++||+..|...++.+...+...--++|.++-
T Consensus       450 RGiDf~gvn~VInyD~p~s~~syihrIGRtgRag~~g~Aitfytd~d~~~ir~iae~~~~sG~evpe~~m  519 (593)
T KOG0344|consen  450 RGIDFKGVNLVINYDFPQSDLSYIHRIGRTGRAGRSGKAITFYTDQDMPRIRSIAEVMEQSGCEVPEKIM  519 (593)
T ss_pred             ccccccCcceEEecCCCchhHHHHHHhhccCCCCCCcceEEEeccccchhhhhHHHHHHHcCCcchHHHH
Confidence            9999999999999999999999999999999999999999999999999999999999999889998764

>PRK01172 ski2-like helicase; Provisional

Probab=100.00  E-value=7.4e-44  Score=351.57  Aligned_cols=345  Identities=19%  Similarity=0.268  Sum_probs=254.6

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHH
Q 015158           40 TFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTREL  119 (412)
Q Consensus        40 ~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L  119 (412)
                      .|+++++++.+.+.+...++. |+++|.++++.+.+++++++++|||||||+++.++++..+..+   .+++|++|+++|
T Consensus         2 ~~~~~~l~~~~~~~~~~~~~~-l~~~Q~~ai~~l~~~~nvlv~apTGSGKTl~a~lail~~l~~~---~k~v~i~P~raL   77 (674)
T PRK01172          2 KISDLGYDDEFLNLFTGNDFE-LYDHQRMAIEQLRKGENVIVSVPTAAGKTLIAYSAIYETFLAG---LKSIYIVPLRSL   77 (674)
T ss_pred             cHhhcCCCHHHHHHHhhCCCC-CCHHHHHHHHHHhcCCcEEEECCCCchHHHHHHHHHHHHHHhC---CcEEEEechHHH
Confidence            467889999999999999998 9999999999999999999999999999999999998877643   489999999999


Q ss_pred             HHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcH
Q 015158          120 AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFK  199 (412)
Q Consensus       120 ~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~  199 (412)
                      +.|+++++.++. ..+..+...+|+......   ....++|+|+||+++..++.++...++++++||+||+|.+.+.++.
T Consensus        78 a~q~~~~~~~l~-~~g~~v~~~~G~~~~~~~---~~~~~dIiv~Tpek~~~l~~~~~~~l~~v~lvViDEaH~l~d~~rg  153 (674)
T PRK01172         78 AMEKYEELSRLR-SLGMRVKISIGDYDDPPD---FIKRYDVVILTSEKADSLIHHDPYIINDVGLIVADEIHIIGDEDRG  153 (674)
T ss_pred             HHHHHHHHHHHh-hcCCeEEEEeCCCCCChh---hhccCCEEEECHHHHHHHHhCChhHHhhcCEEEEecchhccCCCcc
Confidence            999999998764 357888888887654322   2245799999999999888776666788999999999998877766


Q ss_pred             HHHHHHHH---hCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEE-----EeccchhhHHHHHH
Q 015158          200 DQIYDIFQ---LLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHV-----NVEKEEWKLETLCD  271 (412)
Q Consensus       200 ~~~~~i~~---~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~l~~  271 (412)
                      ..+..++.   ..+++.+++++|||+++. .+.. .+++......    ...+..+.....     ...........+..
T Consensus       154 ~~le~ll~~~~~~~~~~riI~lSATl~n~-~~la-~wl~~~~~~~----~~r~vpl~~~i~~~~~~~~~~~~~~~~~~~~  227 (674)
T PRK01172        154 PTLETVLSSARYVNPDARILALSATVSNA-NELA-QWLNASLIKS----NFRPVPLKLGILYRKRLILDGYERSQVDINS  227 (674)
T ss_pred             HHHHHHHHHHHhcCcCCcEEEEeCccCCH-HHHH-HHhCCCccCC----CCCCCCeEEEEEecCeeeecccccccccHHH
Confidence            66666544   345678999999999652 3333 3443222110    001111110000     00000101111223


Q ss_pred             HHHh--cCCCcEEEEEcchhHHHHHHHHHhcC-------------------------CCeeEEecCCCCHHHHHHHHHHH
Q 015158          272 LYET--LAITQSVIFVNTRRKVDWLTDKMRSR-------------------------DHTVSATHGDMDQNTRDIIMREF  324 (412)
Q Consensus       272 ~~~~--~~~~k~lif~~~~~~~~~~~~~L~~~-------------------------~~~~~~~~~~~~~~~r~~~~~~f  324 (412)
                      ++..  ...+++||||++++.++.+++.|.+.                         ...+..+|++++.++|..+++.|
T Consensus       228 ~i~~~~~~~~~vLVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~gv~~~hagl~~~eR~~ve~~f  307 (674)
T PRK01172        228 LIKETVNDGGQVLVFVSSRKNAEDYAEMLIQHFPEFNDFKVSSENNNVYDDSLNEMLPHGVAFHHAGLSNEQRRFIEEMF  307 (674)
T ss_pred             HHHHHHhCCCcEEEEeccHHHHHHHHHHHHHhhhhcccccccccccccccHHHHHHHhcCEEEecCCCCHHHHHHHHHHH
Confidence            3332  24578999999999999999888653                         12478899999999999999999


Q ss_pred             hcCCCcEEEEcCCCcCCCCCCCCCEEEEcc---------CCCChhhHHHhhhhcccCCC--CceEEEEeccCcHHHHHHH
Q 015158          325 RSGSSRVLITTDLLARGIDVQQVSLVINYD---------LPTQPENYLHRIGRSGRFGR--KGVAINFVTRDDERMLFDI  393 (412)
Q Consensus       325 ~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~---------~~~s~~~~~Q~~GR~~R~g~--~g~~~~~~~~~~~~~~~~~  393 (412)
                      ++|.++|||||+++++|+|+|...+|| .+         .|.|..+|.||+||+||.|.  .|.++++....+.  ...+
T Consensus       308 ~~g~i~VLvaT~~la~Gvnipa~~VII-~~~~~~~~~~~~~~s~~~~~Qm~GRAGR~g~d~~g~~~i~~~~~~~--~~~~  384 (674)
T PRK01172        308 RNRYIKVIVATPTLAAGVNLPARLVIV-RDITRYGNGGIRYLSNMEIKQMIGRAGRPGYDQYGIGYIYAASPAS--YDAA  384 (674)
T ss_pred             HcCCCeEEEecchhhccCCCcceEEEE-cCceEeCCCCceeCCHHHHHHHhhcCCCCCCCCcceEEEEecCccc--HHHH
Confidence            999999999999999999999765444 33         25688899999999999985  5678877654432  2235


Q ss_pred             HHHhcccc
Q 015158          394 QKFYNVVI  401 (412)
Q Consensus       394 ~~~~~~~~  401 (412)
                      .+++....
T Consensus       385 ~~~l~~~~  392 (674)
T PRK01172        385 KKYLSGEP  392 (674)
T ss_pred             HHHHcCCC
Confidence            56664433

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=100.00  E-value=1.9e-42  Score=342.77  Aligned_cols=318  Identities=20%  Similarity=0.264  Sum_probs=245.5

Q ss_pred             HHHHHH-HHCCCCCChHHHHhhhhhhhcC------ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHH
Q 015158           49 NLLRGI-YAYGFEKPSAIQQRGIVPFCKG------LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQ  121 (412)
Q Consensus        49 ~~~~~l-~~~~~~~l~~~Q~~a~~~~~~~------~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~  121 (412)
                      ...+.+ ..++|. |++.|.+|++.+..+      .+.+++++||+|||.+++.+++..+..+   .+++|++||++|+.
T Consensus       439 ~~~~~~~~~~~f~-~T~~Q~~aI~~I~~d~~~~~~~d~Ll~adTGsGKT~val~a~l~al~~g---~qvlvLvPT~~LA~  514 (926)
T TIGR00580       439 EWQQEFEDSFPFE-ETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVLDG---KQVAVLVPTTLLAQ  514 (926)
T ss_pred             HHHHHHHHhCCCC-CCHHHHHHHHHHHhhhcccCcCCEEEECCCCccHHHHHHHHHHHHHHhC---CeEEEEeCcHHHHH
Confidence            333434 446886 999999999999875      6899999999999999999998887654   58999999999999


Q ss_pred             HHHHHHHHhhcccCcEEEEEEcCcchHHHHH----HhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccC
Q 015158          122 QIEKVMRALGDYLGVKVHACVGGTSVREDQR----ILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRG  197 (412)
Q Consensus       122 q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~  197 (412)
                      |+++.+.++....++.+..+++.........    ...++++|+|+||..+     .....+++++++|+||+|++    
T Consensus       515 Q~~~~f~~~~~~~~i~v~~Lsg~~~~~e~~~~~~~l~~g~~dIVIGTp~ll-----~~~v~f~~L~llVIDEahrf----  585 (926)
T TIGR00580       515 QHFETFKERFANFPVTIELLSRFRSAKEQNEILKELASGKIDILIGTHKLL-----QKDVKFKDLGLLIIDEEQRF----  585 (926)
T ss_pred             HHHHHHHHHhccCCcEEEEEeccccHHHHHHHHHHHHcCCceEEEchHHHh-----hCCCCcccCCEEEeeccccc----
Confidence            9999999988777888888888765443322    2345689999998533     23456788999999999984    


Q ss_pred             cHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhHHHHHHHHHhcC
Q 015158          198 FKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLA  277 (412)
Q Consensus       198 ~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  277 (412)
                       .......+..++.+.+++++||||.+...........++..+......  ...+...+..... ......+...+  ..
T Consensus       586 -gv~~~~~L~~~~~~~~vL~~SATpiprtl~~~l~g~~d~s~I~~~p~~--R~~V~t~v~~~~~-~~i~~~i~~el--~~  659 (926)
T TIGR00580       586 -GVKQKEKLKELRTSVDVLTLSATPIPRTLHMSMSGIRDLSIIATPPED--RLPVRTFVMEYDP-ELVREAIRREL--LR  659 (926)
T ss_pred             -chhHHHHHHhcCCCCCEEEEecCCCHHHHHHHHhcCCCcEEEecCCCC--ccceEEEEEecCH-HHHHHHHHHHH--Hc
Confidence             233445556677789999999999876655544444444444433222  2223433332221 11112222222  24


Q ss_pred             CCcEEEEEcchhHHHHHHHHHhcC--CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccC
Q 015158          278 ITQSVIFVNTRRKVDWLTDKMRSR--DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDL  355 (412)
Q Consensus       278 ~~k~lif~~~~~~~~~~~~~L~~~--~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~  355 (412)
                      +++++|||++++.++.+++.|++.  +..+..+||+|+..+|.+++++|.+|+.+|||||+++++|+|+|++++||+.+.
T Consensus       660 g~qv~if~n~i~~~e~l~~~L~~~~p~~~v~~lHG~m~~~eRe~im~~F~~Gk~~ILVaT~iie~GIDIp~v~~VIi~~a  739 (926)
T TIGR00580       660 GGQVFYVHNRIESIEKLATQLRELVPEARIAIAHGQMTENELEEVMLEFYKGEFQVLVCTTIIETGIDIPNANTIIIERA  739 (926)
T ss_pred             CCeEEEEECCcHHHHHHHHHHHHhCCCCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEECChhhcccccccCCEEEEecC
Confidence            578999999999999999999985  678999999999999999999999999999999999999999999999998877


Q ss_pred             C-CChhhHHHhhhhcccCCCCceEEEEeccC
Q 015158          356 P-TQPENYLHRIGRSGRFGRKGVAINFVTRD  385 (412)
Q Consensus       356 ~-~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~  385 (412)
                      + .+..++.|++||+||.|+.|.|++++++.
T Consensus       740 ~~~gls~l~Qr~GRvGR~g~~g~aill~~~~  770 (926)
T TIGR00580       740 DKFGLAQLYQLRGRVGRSKKKAYAYLLYPHQ  770 (926)
T ss_pred             CCCCHHHHHHHhcCCCCCCCCeEEEEEECCc
Confidence            5 46789999999999999999999998653

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.

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=100.00  E-value=2.2e-41  Score=331.18  Aligned_cols=316  Identities=19%  Similarity=0.260  Sum_probs=236.6

Q ss_pred             HHHHHHCCCCCChHHHHhhhhhhhcC------ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHH
Q 015158           51 LRGIYAYGFEKPSAIQQRGIVPFCKG------LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIE  124 (412)
Q Consensus        51 ~~~l~~~~~~~l~~~Q~~a~~~~~~~------~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~  124 (412)
                      .......+|. |++.|+++++.+..+      .+.++++|||||||.+++++++..+..+   .+++|++||++|+.|++
T Consensus       252 ~~~~~~l~f~-lt~~Q~~ai~~I~~d~~~~~~~~~Ll~~~TGSGKT~va~~~il~~~~~g---~q~lilaPT~~LA~Q~~  327 (681)
T PRK10917        252 KKFLASLPFE-LTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIEAG---YQAALMAPTEILAEQHY  327 (681)
T ss_pred             HHHHHhCCCC-CCHHHHHHHHHHHHhhhccCCceEEEECCCCCcHHHHHHHHHHHHHHcC---CeEEEEeccHHHHHHHH
Confidence            3344557886 999999999999886      3789999999999999999998877643   58999999999999999


Q ss_pred             HHHHHhhcccCcEEEEEEcCcchHHHHH----HhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHH
Q 015158          125 KVMRALGDYLGVKVHACVGGTSVREDQR----ILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKD  200 (412)
Q Consensus       125 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~  200 (412)
                      +.++++....++++..++|+.+......    ...+.++|+|+|+..+..     ...+.+++++|+||+|++...    
T Consensus       328 ~~l~~l~~~~~i~v~ll~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~-----~v~~~~l~lvVIDE~Hrfg~~----  398 (681)
T PRK10917        328 ENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQD-----DVEFHNLGLVIIDEQHRFGVE----  398 (681)
T ss_pred             HHHHHHHhhcCcEEEEEcCCCCHHHHHHHHHHHhCCCCCEEEchHHHhcc-----cchhcccceEEEechhhhhHH----
Confidence            9999998888899999999987544332    334568999999877643     334578999999999986322    


Q ss_pred             HHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhHHHHHHHHHhcCCCc
Q 015158          201 QIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQ  280 (412)
Q Consensus       201 ~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k  280 (412)
                       ....+.......++++|||||.+.......  ++................+...+............+.+.+  ....+
T Consensus       399 -qr~~l~~~~~~~~iL~~SATp~prtl~~~~--~g~~~~s~i~~~p~~r~~i~~~~~~~~~~~~~~~~i~~~~--~~g~q  473 (681)
T PRK10917        399 -QRLALREKGENPHVLVMTATPIPRTLAMTA--YGDLDVSVIDELPPGRKPITTVVIPDSRRDEVYERIREEI--AKGRQ  473 (681)
T ss_pred             -HHHHHHhcCCCCCEEEEeCCCCHHHHHHHH--cCCCceEEEecCCCCCCCcEEEEeCcccHHHHHHHHHHHH--HcCCc
Confidence             222333344567899999999775544332  2322211111111112223333332222111122222222  24468


Q ss_pred             EEEEEcch--------hHHHHHHHHHhcC--CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEE
Q 015158          281 SVIFVNTR--------RKVDWLTDKMRSR--DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLV  350 (412)
Q Consensus       281 ~lif~~~~--------~~~~~~~~~L~~~--~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~v  350 (412)
                      ++|||+.+        ..++.+++.|.+.  +..+..+||+|+..+|..++++|++|+.+|||||+++++|+|+|++++|
T Consensus       474 ~~v~~~~ie~s~~l~~~~~~~~~~~L~~~~~~~~v~~lHG~m~~~eR~~i~~~F~~g~~~ILVaT~vie~GiDip~v~~V  553 (681)
T PRK10917        474 AYVVCPLIEESEKLDLQSAEETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGVDVPNATVM  553 (681)
T ss_pred             EEEEEcccccccchhHHHHHHHHHHHHHHCCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEECcceeeCcccCCCcEE
Confidence            99999954        3456777777765  4689999999999999999999999999999999999999999999999


Q ss_pred             EEccCCC-ChhhHHHhhhhcccCCCCceEEEEecc
Q 015158          351 INYDLPT-QPENYLHRIGRSGRFGRKGVAINFVTR  384 (412)
Q Consensus       351 i~~~~~~-s~~~~~Q~~GR~~R~g~~g~~~~~~~~  384 (412)
                      |+++.|. +...+.|++||+||.|..|.|++++..
T Consensus       554 Ii~~~~r~gls~lhQ~~GRvGR~g~~g~~ill~~~  588 (681)
T PRK10917        554 VIENAERFGLAQLHQLRGRVGRGAAQSYCVLLYKD  588 (681)
T ss_pred             EEeCCCCCCHHHHHHHhhcccCCCCceEEEEEECC
Confidence            9998875 678999999999999999999999953

>PRK10689 transcription-repair coupling factor; Provisional

Probab=100.00  E-value=1.5e-41  Score=343.47  Aligned_cols=318  Identities=18%  Similarity=0.226  Sum_probs=249.4

Q ss_pred             HHHHHHHHCCCCCChHHHHhhhhhhhcC------ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHH
Q 015158           49 NLLRGIYAYGFEKPSAIQQRGIVPFCKG------LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQ  122 (412)
Q Consensus        49 ~~~~~l~~~~~~~l~~~Q~~a~~~~~~~------~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q  122 (412)
                      ...+....++|. |++.|.++++.+..+      .+.+++++||+|||.+++.+++..+..   +.+++|++||++|+.|
T Consensus       589 ~~~~~~~~~~~~-~T~~Q~~aI~~il~d~~~~~~~d~Ll~a~TGsGKT~val~aa~~~~~~---g~qvlvLvPT~eLA~Q  664 (1147)
T PRK10689        589 QYQLFCDSFPFE-TTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVEN---HKQVAVLVPTTLLAQQ  664 (1147)
T ss_pred             HHHHHHHhCCCC-CCHHHHHHHHHHHHHhhcCCCCCEEEEcCCCcCHHHHHHHHHHHHHHc---CCeEEEEeCcHHHHHH
Confidence            344555678885 999999999999986      789999999999999998877766543   3589999999999999


Q ss_pred             HHHHHHHhhcccCcEEEEEEcCcchHHHHHHh----cCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCc
Q 015158          123 IEKVMRALGDYLGVKVHACVGGTSVREDQRIL----SSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGF  198 (412)
Q Consensus       123 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~  198 (412)
                      +++.+.+.....++.+..+++..+.......+    .+..+|+|+||+.+.     ....+.+++++|+||+|++   ++
T Consensus       665 ~~~~f~~~~~~~~v~i~~l~g~~s~~e~~~il~~l~~g~~dIVVgTp~lL~-----~~v~~~~L~lLVIDEahrf---G~  736 (1147)
T PRK10689        665 HYDNFRDRFANWPVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLLQ-----SDVKWKDLGLLIVDEEHRF---GV  736 (1147)
T ss_pred             HHHHHHHhhccCCceEEEEECCCCHHHHHHHHHHHHhCCCCEEEECHHHHh-----CCCCHhhCCEEEEechhhc---ch
Confidence            99999987666678888888877765554432    356899999997542     2345578999999999996   22


Q ss_pred             HHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhHHHHHHHHHhcCC
Q 015158          199 KDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAI  278 (412)
Q Consensus       199 ~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  278 (412)
                        .....+..++.+.+++++||||.+....+....+.++..+......  ...+............+...+.++.   ..
T Consensus       737 --~~~e~lk~l~~~~qvLl~SATpiprtl~l~~~gl~d~~~I~~~p~~--r~~v~~~~~~~~~~~~k~~il~el~---r~  809 (1147)
T PRK10689        737 --RHKERIKAMRADVDILTLTATPIPRTLNMAMSGMRDLSIIATPPAR--RLAVKTFVREYDSLVVREAILREIL---RG  809 (1147)
T ss_pred             --hHHHHHHhcCCCCcEEEEcCCCCHHHHHHHHhhCCCcEEEecCCCC--CCCceEEEEecCcHHHHHHHHHHHh---cC
Confidence              2234456677899999999999887777666666677666543332  2234444443332222222233332   34


Q ss_pred             CcEEEEEcchhHHHHHHHHHhcC--CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccC-
Q 015158          279 TQSVIFVNTRRKVDWLTDKMRSR--DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDL-  355 (412)
Q Consensus       279 ~k~lif~~~~~~~~~~~~~L~~~--~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~-  355 (412)
                      ++++|||++++.++.+++.|++.  +..+..+||+|+..+|.+++.+|.+|+++|||||+++++|+|+|++++||+... 
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  678999999999999999999999999999999999999999999999996543 


Q ss_pred             CCChhhHHHhhhhcccCCCCceEEEEeccC
Q 015158          356 PTQPENYLHRIGRSGRFGRKGVAINFVTRD  385 (412)
Q Consensus       356 ~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~  385 (412)
                      .++..+|.|++||+||.|+.|.|++++.+.
T Consensus       890 ~fglaq~~Qr~GRvGR~g~~g~a~ll~~~~  919 (1147)
T PRK10689        890 HFGLAQLHQLRGRVGRSHHQAYAWLLTPHP  919 (1147)
T ss_pred             CCCHHHHHHHhhccCCCCCceEEEEEeCCC
Confidence            356788999999999999999999988653

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

Probab=100.00  E-value=2e-41  Score=299.63  Aligned_cols=323  Identities=21%  Similarity=0.238  Sum_probs=247.1

Q ss_pred             CCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcE
Q 015158           58 GFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVK  137 (412)
Q Consensus        58 ~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~  137 (412)
                      +..++|.||.......+.+ |++|+.|||-|||.++++.+...+.... + ++|+++||+.|+.|+++.+.+........
T Consensus        12 ~~ie~R~YQ~~i~a~al~~-NtLvvlPTGLGKT~IA~~V~~~~l~~~~-~-kvlfLAPTKPLV~Qh~~~~~~v~~ip~~~   88 (542)
T COG1111          12 NTIEPRLYQLNIAAKALFK-NTLVVLPTGLGKTFIAAMVIANRLRWFG-G-KVLFLAPTKPLVLQHAEFCRKVTGIPEDE   88 (542)
T ss_pred             ccccHHHHHHHHHHHHhhc-CeEEEecCCccHHHHHHHHHHHHHHhcC-C-eEEEecCCchHHHHHHHHHHHHhCCChhh
Confidence            3446999999999888876 8999999999999999999988887643 3 89999999999999999999988777778


Q ss_pred             EEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEE
Q 015158          138 VHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGV  217 (412)
Q Consensus       138 ~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~  217 (412)
                      +..++|...+......... ..|+++||+.+.+-+..+.++...+.++|+||||+......+..+.+.......++.+++
T Consensus        89 i~~ltGev~p~~R~~~w~~-~kVfvaTPQvveNDl~~Grid~~dv~~lifDEAHRAvGnyAYv~Va~~y~~~~k~~~ilg  167 (542)
T COG1111          89 IAALTGEVRPEEREELWAK-KKVFVATPQVVENDLKAGRIDLDDVSLLIFDEAHRAVGNYAYVFVAKEYLRSAKNPLILG  167 (542)
T ss_pred             eeeecCCCChHHHHHHHhh-CCEEEeccHHHHhHHhcCccChHHceEEEechhhhccCcchHHHHHHHHHHhccCceEEE
Confidence            8999998887766555544 489999999999999999999999999999999997755444555554555556888999


Q ss_pred             EeecCChHHHHH---HHHhcCCCeEEEecCCccccCCc---eEEE-----------------------------------
Q 015158          218 FSATMPPEALEI---TRKFMNKPVRILVKRDELTLEGI---KQFH-----------------------------------  256 (412)
Q Consensus       218 ~SAT~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~---~~~~-----------------------------------  256 (412)
                      +||||+.+....   +..+.-..+.+....+.-..+.+   +..+                                   
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            999997443221   11111111111111000000000   0000                                   


Q ss_pred             --------------------------------------------------------------------------------
Q 015158          257 --------------------------------------------------------------------------------  256 (412)
Q Consensus       257 --------------------------------------------------------------------------------  256 (412)
                                                                                                      
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             -------------EEeccchhhHHHHHHHH----HhcCCCcEEEEEcchhHHHHHHHHHhcCCCeeE--Ee-------cC
Q 015158          257 -------------VNVEKEEWKLETLCDLY----ETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVS--AT-------HG  310 (412)
Q Consensus       257 -------------~~~~~~~~~~~~l~~~~----~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~--~~-------~~  310 (412)
                                   ......+.++..+.+++    ++....++|||++.+..++.+.+.|.+.+..+.  ++       ..
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                         00000122344444443    334556899999999999999999999887764  22       24


Q ss_pred             CCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccC
Q 015158          311 DMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRD  385 (412)
Q Consensus       311 ~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~  385 (412)
                      +|++.++.+++++|++|+++|||+|++.++|+|+|.++.||++++..|+..++||.||+||. ..|.++++++.+
T Consensus       408 GMsQkeQ~eiI~~Fr~Ge~nVLVaTSVgEEGLDIp~vDlVifYEpvpSeIR~IQR~GRTGR~-r~Grv~vLvt~g  481 (542)
T COG1111         408 GMSQKEQKEIIDQFRKGEYNVLVATSVGEEGLDIPEVDLVIFYEPVPSEIRSIQRKGRTGRK-RKGRVVVLVTEG  481 (542)
T ss_pred             ccCHHHHHHHHHHHhcCCceEEEEcccccccCCCCcccEEEEecCCcHHHHHHHhhCccccC-CCCeEEEEEecC
Confidence            69999999999999999999999999999999999999999999999999999999999999 789999999887

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=100.00  E-value=1.6e-40  Score=323.20  Aligned_cols=315  Identities=21%  Similarity=0.293  Sum_probs=234.3

Q ss_pred             HHHHHHHCCCCCChHHHHhhhhhhhcC------ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHH
Q 015158           50 LLRGIYAYGFEKPSAIQQRGIVPFCKG------LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQI  123 (412)
Q Consensus        50 ~~~~l~~~~~~~l~~~Q~~a~~~~~~~------~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~  123 (412)
                      +...+...+|. |++.|+++++.+..+      .+.++++|||||||.+++++++..+..+   .+++|++||++|+.|+
T Consensus       225 ~~~~~~~lpf~-lt~~Q~~ai~~I~~~~~~~~~~~~Ll~g~TGSGKT~va~l~il~~~~~g---~qvlilaPT~~LA~Q~  300 (630)
T TIGR00643       225 LTKFLASLPFK-LTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEAG---YQVALMAPTEILAEQH  300 (630)
T ss_pred             HHHHHHhCCCC-CCHHHHHHHHHHHHHhccCCCccEEEECCCCCcHHHHHHHHHHHHHHcC---CcEEEECCHHHHHHHH
Confidence            44566677885 999999999999876      3579999999999999999998887654   5899999999999999


Q ss_pred             HHHHHHhhcccCcEEEEEEcCcchHHHH----HHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcH
Q 015158          124 EKVMRALGDYLGVKVHACVGGTSVREDQ----RILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFK  199 (412)
Q Consensus       124 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~  199 (412)
                      ++.+.++....++.+..++|+.......    ....++++|+|+|+..+..     ...+.++++||+||+|++...   
T Consensus       301 ~~~~~~l~~~~gi~v~lltg~~~~~~r~~~~~~i~~g~~~IiVgT~~ll~~-----~~~~~~l~lvVIDEaH~fg~~---  372 (630)
T TIGR00643       301 YNSLRNLLAPLGIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQE-----KVEFKRLALVIIDEQHRFGVE---  372 (630)
T ss_pred             HHHHHHHhcccCcEEEEEecCCCHHHHHHHHHHHhCCCCCEEEecHHHHhc-----cccccccceEEEechhhccHH---
Confidence            9999999887889999999988765432    2334568999999987753     344678999999999985322   


Q ss_pred             HHHHHHHHhCC--CCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhHHHHHHHHHh--
Q 015158          200 DQIYDIFQLLP--PKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYET--  275 (412)
Q Consensus       200 ~~~~~i~~~~~--~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~--  275 (412)
                       +...+.....  ...++++|||||.+......  .++................+.......   ... ..+...+..  
T Consensus       373 -qr~~l~~~~~~~~~~~~l~~SATp~prtl~l~--~~~~l~~~~i~~~p~~r~~i~~~~~~~---~~~-~~~~~~i~~~l  445 (630)
T TIGR00643       373 -QRKKLREKGQGGFTPHVLVMSATPIPRTLALT--VYGDLDTSIIDELPPGRKPITTVLIKH---DEK-DIVYEFIEEEI  445 (630)
T ss_pred             -HHHHHHHhcccCCCCCEEEEeCCCCcHHHHHH--hcCCcceeeeccCCCCCCceEEEEeCc---chH-HHHHHHHHHHH
Confidence             1222223222  26789999999876543332  222211111111111112222222211   112 233333332  


Q ss_pred             cCCCcEEEEEcch--------hHHHHHHHHHhcC--CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCC
Q 015158          276 LAITQSVIFVNTR--------RKVDWLTDKMRSR--DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQ  345 (412)
Q Consensus       276 ~~~~k~lif~~~~--------~~~~~~~~~L~~~--~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~  345 (412)
                      ....+++|||+..        ..++.+++.|.+.  +..+..+||+|+..+|..++++|++|+.+|||||+++++|+|+|
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            2446899999875        4566777777753  67899999999999999999999999999999999999999999


Q ss_pred             CCCEEEEccCCC-ChhhHHHhhhhcccCCCCceEEEEec
Q 015158          346 QVSLVINYDLPT-QPENYLHRIGRSGRFGRKGVAINFVT  383 (412)
Q Consensus       346 ~~~~vi~~~~~~-s~~~~~Q~~GR~~R~g~~g~~~~~~~  383 (412)
                      ++++||+++.+. +...+.|++||+||.|..|.|++++.
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            999999998875 68899999999999999999999993

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

Probab=100.00  E-value=1.2e-41  Score=303.79  Aligned_cols=340  Identities=20%  Similarity=0.238  Sum_probs=270.5

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHHhhhhh-hhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCH
Q 015158           39 DTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVP-FCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTR  117 (412)
Q Consensus        39 ~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~-~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~  117 (412)
                      -+.+.+++++.+.+-|+..|+.++.|.|..++.. +++|.|.+|+.+|+||||++.-++-+..+..  .+++.|+++|..
T Consensus       194 ~~vdeLdipe~fk~~lk~~G~~eLlPVQ~laVe~GLLeG~nllVVSaTasGKTLIgElAGi~~~l~--~g~KmlfLvPLV  271 (830)
T COG1202         194 VPVDELDIPEKFKRMLKREGIEELLPVQVLAVEAGLLEGENLLVVSATASGKTLIGELAGIPRLLS--GGKKMLFLVPLV  271 (830)
T ss_pred             ccccccCCcHHHHHHHHhcCcceecchhhhhhhhccccCCceEEEeccCCCcchHHHhhCcHHHHh--CCCeEEEEehhH
Confidence            4677889999999999999999999999999998 8899999999999999999998877776654  246899999999


Q ss_pred             HHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHH----HHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchh
Q 015158          118 ELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQ----RILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEM  193 (412)
Q Consensus       118 ~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~  193 (412)
                      +|++|.+++|+.-+...++.+..-.|........    ......+||||+||+-+..++... -.+.+++.||+||+|.+
T Consensus       272 ALANQKy~dF~~rYs~LglkvairVG~srIk~~~~pv~~~t~~dADIIVGTYEGiD~lLRtg-~~lgdiGtVVIDEiHtL  350 (830)
T COG1202         272 ALANQKYEDFKERYSKLGLKVAIRVGMSRIKTREEPVVVDTSPDADIIVGTYEGIDYLLRTG-KDLGDIGTVVIDEIHTL  350 (830)
T ss_pred             HhhcchHHHHHHHhhcccceEEEEechhhhcccCCccccCCCCCCcEEEeechhHHHHHHcC-CcccccceEEeeeeeec
Confidence            9999999999998888899888888776655442    223456899999999998888765 56789999999999988


Q ss_pred             hccCcHHHHHHHH---HhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhHHHHH
Q 015158          194 LSRGFKDQIYDIF---QLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLC  270 (412)
Q Consensus       194 ~~~~~~~~~~~i~---~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  270 (412)
                      .+...+..+..++   ..+-+..|+|++|||..++ .+....+.-+.+.+...     +..+............+.+.+.
T Consensus       351 ~deERG~RLdGLI~RLr~l~~~AQ~i~LSATVgNp-~elA~~l~a~lV~y~~R-----PVplErHlvf~~~e~eK~~ii~  424 (830)
T COG1202         351 EDEERGPRLDGLIGRLRYLFPGAQFIYLSATVGNP-EELAKKLGAKLVLYDER-----PVPLERHLVFARNESEKWDIIA  424 (830)
T ss_pred             cchhcccchhhHHHHHHHhCCCCeEEEEEeecCCh-HHHHHHhCCeeEeecCC-----CCChhHeeeeecCchHHHHHHH
Confidence            7755444443333   3334589999999999754 45566555554433322     2234444555555566777766


Q ss_pred             HHHHhc--------CCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCC
Q 015158          271 DLYETL--------AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGI  342 (412)
Q Consensus       271 ~~~~~~--------~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~  342 (412)
                      .+.+.-        -.+.+|||++|+..|..+++.|..+|++...||++++-.+|..+...|.++++.++|+|.+++.|+
T Consensus       425 ~L~k~E~~~~sskg~rGQtIVFT~SRrr~h~lA~~L~~kG~~a~pYHaGL~y~eRk~vE~~F~~q~l~~VVTTAAL~AGV  504 (830)
T COG1202         425 RLVKREFSTESSKGYRGQTIVFTYSRRRCHELADALTGKGLKAAPYHAGLPYKERKSVERAFAAQELAAVVTTAALAAGV  504 (830)
T ss_pred             HHHHHHHhhhhccCcCCceEEEecchhhHHHHHHHhhcCCcccccccCCCcHHHHHHHHHHHhcCCcceEeehhhhhcCC
Confidence            665432        237899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCEEE---Ecc-CCCChhhHHHhhhhcccCC--CCceEEEEeccCcH
Q 015158          343 DVQQVSLVI---NYD-LPTQPENYLHRIGRSGRFG--RKGVAINFVTRDDE  387 (412)
Q Consensus       343 d~~~~~~vi---~~~-~~~s~~~~~Q~~GR~~R~g--~~g~~~~~~~~~~~  387 (412)
                      |+|.-.+++   -++ -..|+.+|.||.||+||.+  ..|++|++..+...
T Consensus       505 DFPASQVIFEsLaMG~~WLs~~EF~QM~GRAGRp~yHdrGkVyllvepg~~  555 (830)
T COG1202         505 DFPASQVIFESLAMGIEWLSVREFQQMLGRAGRPDYHDRGKVYLLVEPGKK  555 (830)
T ss_pred             CCchHHHHHHHHHcccccCCHHHHHHHhcccCCCCcccCceEEEEecCChh
Confidence            999544432   122 2458999999999999974  56899998877543

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

Probab=100.00  E-value=1.1e-39  Score=314.18  Aligned_cols=315  Identities=21%  Similarity=0.249  Sum_probs=233.9

Q ss_pred             CCCCCChHHHHhhhhhhhcCc-cEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccc-
Q 015158           57 YGFEKPSAIQQRGIVPFCKGL-DVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYL-  134 (412)
Q Consensus        57 ~~~~~l~~~Q~~a~~~~~~~~-~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~-  134 (412)
                      .||. |+|+|.++++.++.|+ +.++.+|||||||.++..+++..........+.++++|+++|+.|.++.+.++.... 
T Consensus        12 ~G~~-PtpiQ~~~i~~il~G~~~v~~~apTGSGKTaa~aafll~~~~~~~~~~rLv~~vPtReLa~Qi~~~~~~~~k~l~   90 (844)
T TIGR02621        12 HGYS-PFPWQLSLAERFVAGQPPESCSTPTGLGKTSIIAAWLLAVEIGAKVPRRLVYVVNRRTVVDQVTEEAEKIGERLP   90 (844)
T ss_pred             hCCC-CCHHHHHHHHHHHcCCCcceEecCCCCcccHHHHHhhccccccccccceEEEeCchHHHHHHHHHHHHHHHHHhc
Confidence            4888 9999999999999998 577789999999986654444222212122356668899999999999999887643 


Q ss_pred             ----------------------CcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHc---------CCC---CCC
Q 015158          135 ----------------------GVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRR---------QSL---RPD  180 (412)
Q Consensus       135 ----------------------~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~---------~~~---~~~  180 (412)
                                            ++.+..++|+.....+......+++|+|+|++.+.+-...         +.+   .+.
T Consensus        91 ~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~GG~~~~~q~~~l~~~p~IIVgT~D~i~sr~L~~gYg~~~~~~pi~ag~L~  170 (844)
T TIGR02621        91 DVPEVEAALWALCSTRPEKKDRPLAISTLRGQFADNDEWMLDPHRPAVIVGTVDMIGSRLLFSGYGCGFKSRPLHAGFLG  170 (844)
T ss_pred             ccchhhhhhhhhhccccccccCCeEEEEEECCCChHHHHHhcCCCCcEEEECHHHHcCCccccccccccccccchhhhhc
Confidence                                  4788899999988888887888899999997655332110         001   146


Q ss_pred             CceEEEEeCCchhhccCcHHHHHHHHHhC--CC---CceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEE
Q 015158          181 NIRIFVLDEADEMLSRGFKDQIYDIFQLL--PP---KIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQF  255 (412)
Q Consensus       181 ~~~~iiiDE~h~~~~~~~~~~~~~i~~~~--~~---~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  255 (412)
                      ++.++|+||||  .+.+|...+..+...+  ++   +.|+++||||++.+.......+..++..+...........+.+.
T Consensus       171 ~v~~LVLDEAD--Ld~gF~~~l~~Il~~l~rp~~~rprQtLLFSAT~p~ei~~l~~~~~~~p~~i~V~~~~l~a~ki~q~  248 (844)
T TIGR02621       171 QDALIVHDEAH--LEPAFQELLKQIMNEQQRPPDFLPLRVVELTATSRTDGPDRTTLLSAEDYKHPVLKKRLAAKKIVKL  248 (844)
T ss_pred             cceEEEEehhh--hccccHHHHHHHHHhcccCcccccceEEEEecCCCccHHHHHHHHccCCceeecccccccccceEEE
Confidence            78999999999  5778999999999864  33   26899999999887766666666666655554444444444443


Q ss_pred             EEEeccchhhHHHHH----HHHHhcCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHH-----HHHHHHhc
Q 015158          256 HVNVEKEEWKLETLC----DLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRD-----IIMREFRS  326 (412)
Q Consensus       256 ~~~~~~~~~~~~~l~----~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~-----~~~~~f~~  326 (412)
                       +.... ..+...+.    .++. ...+++|||||+++.++.+++.|++.+.  ..+||++++.+|.     .++++|++
T Consensus       249 -v~v~~-e~Kl~~lv~~L~~ll~-e~g~~vLVF~NTv~~Aq~L~~~L~~~g~--~lLHG~m~q~dR~~~~~~~il~~Fk~  323 (844)
T TIGR02621       249 -VPPSD-EKFLSTMVKELNLLMK-DSGGAILVFCRTVKHVRKVFAKLPKEKF--ELLTGTLRGAERDDLVKKEIFNRFLP  323 (844)
T ss_pred             -EecCh-HHHHHHHHHHHHHHHh-hCCCcEEEEECCHHHHHHHHHHHHhcCC--eEeeCCCCHHHHhhHHHHHHHHHHhc
Confidence             22222 22322222    2222 3457899999999999999999998876  8999999999999     78899987


Q ss_pred             ----CC-------CcEEEEcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccCCCCc-eEEEEe
Q 015158          327 ----GS-------SRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKG-VAINFV  382 (412)
Q Consensus       327 ----g~-------~~vlv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g-~~~~~~  382 (412)
                          |+       ..|||+|+++++|+|++. ++||....|  ...|+||+||+||.|..+ ..+.++
T Consensus       324 ~~~~g~~~~~~~g~~ILVATdVaerGLDId~-d~VI~d~aP--~esyIQRiGRtgR~G~~~~~~i~vv  388 (844)
T TIGR02621       324 QMLSGSRARPQQGTVYLVCTSAGEVGVNISA-DHLVCDLAP--FESMQQRFGRVNRFGELQACQIAVV  388 (844)
T ss_pred             cccccccccccccceEEeccchhhhcccCCc-ceEEECCCC--HHHHHHHhcccCCCCCCCCceEEEE
Confidence                43       679999999999999986 777765544  689999999999998754 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.

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=100.00  E-value=6.4e-40  Score=333.31  Aligned_cols=321  Identities=20%  Similarity=0.290  Sum_probs=231.3

Q ss_pred             EECCCCCCchhHhHHHHHHhhccC----------CCceeEEEEcCCHHHHHHHHHHHHHhh------------cccCcEE
Q 015158           81 QQAQSGTGKTATFCSGILQQLDYG----------LVECQALVLAPTRELAQQIEKVMRALG------------DYLGVKV  138 (412)
Q Consensus        81 v~~~tGsGKT~~~~~~~~~~~~~~----------~~~~~~lil~P~~~L~~q~~~~~~~~~------------~~~~~~~  138 (412)
                      |++|||||||++|+++++..+...          ..+.++|||+|+++|+.|+.+.++...            ...++.+
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          134689999999999999999886521            1236889


Q ss_pred             EEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcC-CCCCCCceEEEEeCCchhhccC----cHHHHHHHHHhCCCCc
Q 015158          139 HACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQ-SLRPDNIRIFVLDEADEMLSRG----FKDQIYDIFQLLPPKI  213 (412)
Q Consensus       139 ~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~-~~~~~~~~~iiiDE~h~~~~~~----~~~~~~~i~~~~~~~~  213 (412)
                      ...+|+.+.....+...++++|+|+||++|..++.+. ...++++++||+||+|.+.+..    +...+.++...++.+.
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            9999999887776677778899999999998876543 2357889999999999998654    3345666767777789


Q ss_pred             eEEEEeecCChHHHHHHHHhcCC-CeEEEecCCccccCCceEEEEEeccch-------------------hhH-HHHHHH
Q 015158          214 QVGVFSATMPPEALEITRKFMNK-PVRILVKRDELTLEGIKQFHVNVEKEE-------------------WKL-ETLCDL  272 (412)
Q Consensus       214 ~~i~~SAT~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~-------------------~~~-~~l~~~  272 (412)
                      |+|++|||+.+. .+....+.+. +..+.. ........+... .......                   ... .....+
T Consensus       161 QrIgLSATI~n~-eevA~~L~g~~pv~Iv~-~~~~r~~~l~v~-vp~~d~~~~~~~~~~~~~~~~~~r~~~i~~~v~~~i  237 (1490)
T PRK09751        161 QRIGLSATVRSA-SDVAAFLGGDRPVTVVN-PPAMRHPQIRIV-VPVANMDDVSSVASGTGEDSHAGREGSIWPYIETGI  237 (1490)
T ss_pred             eEEEEEeeCCCH-HHHHHHhcCCCCEEEEC-CCCCcccceEEE-EecCchhhccccccccccccchhhhhhhhHHHHHHH
Confidence            999999999763 4444444332 444432 222222222211 1111100                   000 111122


Q ss_pred             HHh-cCCCcEEEEEcchhHHHHHHHHHhcCC---------------------------------CeeEEecCCCCHHHHH
Q 015158          273 YET-LAITQSVIFVNTRRKVDWLTDKMRSRD---------------------------------HTVSATHGDMDQNTRD  318 (412)
Q Consensus       273 ~~~-~~~~k~lif~~~~~~~~~~~~~L~~~~---------------------------------~~~~~~~~~~~~~~r~  318 (412)
                      +.. ....++||||||++.|+.++..|++..                                 ..+..+||++++++|.
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 234789999999999999999997641                                 1256899999999999


Q ss_pred             HHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccC-CCCceEEEEeccCcHHHH---HHHH
Q 015158          319 IIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRF-GRKGVAINFVTRDDERML---FDIQ  394 (412)
Q Consensus       319 ~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~-g~~g~~~~~~~~~~~~~~---~~~~  394 (412)
                      .+++.|++|++++||||++++.|||++.+++||+++.|.|..+|+||+||+||. |..+.++++... ..+.+   ..++
T Consensus       318 ~IE~~fK~G~LrvLVATssLELGIDIg~VDlVIq~gsP~sVas~LQRiGRAGR~~gg~s~gli~p~~-r~dlle~~~~ve  396 (1490)
T PRK09751        318 ITEQALKSGELRCVVATSSLELGIDMGAVDLVIQVATPLSVASGLQRIGRAGHQVGGVSKGLFFPRT-RRDLVDSAVIVE  396 (1490)
T ss_pred             HHHHHHHhCCceEEEeCcHHHccCCcccCCEEEEeCCCCCHHHHHHHhCCCCCCCCCccEEEEEeCc-HHHHHhhHHHHH
Confidence            999999999999999999999999999999999999999999999999999997 333445533332 22222   2366


Q ss_pred             HHhccccccCC
Q 015158          395 KFYNVVIEELP  405 (412)
Q Consensus       395 ~~~~~~~~~~~  405 (412)
                      .+++..++++.
T Consensus       397 ~~l~g~iE~~~  407 (1490)
T PRK09751        397 CMFAGRLENLT  407 (1490)
T ss_pred             HHhcCCCCccC
Confidence            67776666544

>PHA02558 uvsW UvsW helicase; Provisional

Probab=100.00  E-value=9e-40  Score=310.38  Aligned_cols=306  Identities=15%  Similarity=0.132  Sum_probs=218.7

Q ss_pred             CCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEE
Q 015158           60 EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVH  139 (412)
Q Consensus        60 ~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~  139 (412)
                      ..|+++|.+++..++.++++++++|||+|||.++...+...+..  ...++||++|+++|+.||.+.+.++.......+.
T Consensus       113 ~~~r~~Q~~av~~~l~~~~~il~apTGsGKT~i~~~l~~~~~~~--~~~~vLilvpt~eL~~Q~~~~l~~~~~~~~~~~~  190 (501)
T PHA02558        113 IEPHWYQYDAVYEGLKNNRRLLNLPTSAGKSLIQYLLSRYYLEN--YEGKVLIIVPTTSLVTQMIDDFVDYRLFPREAMH  190 (501)
T ss_pred             CCCCHHHHHHHHHHHhcCceEEEeCCCCCHHHHHHHHHHHHHhc--CCCeEEEEECcHHHHHHHHHHHHHhcccccccee
Confidence            46999999999999999999999999999998765433222222  2338999999999999999999998654344444


Q ss_pred             EEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEe
Q 015158          140 ACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFS  219 (412)
Q Consensus       140 ~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~S  219 (412)
                      .+.++....       .+.+|+|+|++++.+...   ..++++++||+||||++....    +..++..+++..+++++|
T Consensus       191 ~i~~g~~~~-------~~~~I~VaT~qsl~~~~~---~~~~~~~~iIvDEaH~~~~~~----~~~il~~~~~~~~~lGLT  256 (501)
T PHA02558        191 KIYSGTAKD-------TDAPIVVSTWQSAVKQPK---EWFDQFGMVIVDECHLFTGKS----LTSIITKLDNCKFKFGLT  256 (501)
T ss_pred             EEecCcccC-------CCCCEEEeeHHHHhhchh---hhccccCEEEEEchhcccchh----HHHHHHhhhccceEEEEe
Confidence            555544321       346899999999875432   134689999999999986543    456666666677899999


Q ss_pred             ecCChHHHHH--HHHhcCCCeEEEecCCcc------ccCCceEEEEE--------------------eccchhhHHHHHH
Q 015158          220 ATMPPEALEI--TRKFMNKPVRILVKRDEL------TLEGIKQFHVN--------------------VEKEEWKLETLCD  271 (412)
Q Consensus       220 AT~~~~~~~~--~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~--------------------~~~~~~~~~~l~~  271 (412)
                      |||.......  +..+++. +.......+.      ....+......                    ......+...+..
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  1222332 1111111000      00000000000                    0011122233333


Q ss_pred             HHHhc--CCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEc-CCCcCCCCCCCCC
Q 015158          272 LYETL--AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITT-DLLARGIDVQQVS  348 (412)
Q Consensus       272 ~~~~~--~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t-~~~~~G~d~~~~~  348 (412)
                      ++...  .+.+++|||.+.++++.+++.|++.+.++..+||+++..+|..+++.|++|+..+||+| +.+++|+|+|+++
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            33322  34689999999999999999999999999999999999999999999999999999998 8999999999999


Q ss_pred             EEEEccCCCChhhHHHhhhhcccCCCCceEEEEe
Q 015158          349 LVINYDLPTQPENYLHRIGRSGRFGRKGVAINFV  382 (412)
Q Consensus       349 ~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~  382 (412)
                      +||++.++.|...|+|++||++|.+..+...+++
T Consensus       416 ~vIl~~p~~s~~~~~QriGR~~R~~~~K~~~~i~  449 (501)
T PHA02558        416 HVIFAHPSKSKIIVLQSIGRVLRKHGSKSIATVW  449 (501)
T ss_pred             EEEEecCCcchhhhhhhhhccccCCCCCceEEEE
Confidence            9999999999999999999999997665433333

>COG1204 Superfamily II helicase [General function prediction only]

Probab=100.00  E-value=1.4e-39  Score=316.14  Aligned_cols=331  Identities=23%  Similarity=0.299  Sum_probs=248.4

Q ss_pred             CCCHHHHHHHHHCCCCCChHHHHhhhhhhhc-CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHH
Q 015158           45 GLQENLLRGIYAYGFEKPSAIQQRGIVPFCK-GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQI  123 (412)
Q Consensus        45 ~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~-~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~  123 (412)
                      .+++.+...++..++.++++.|+.++..... ++|++|++|||||||++++++++..+..+  +.+++|+||+++|+++.
T Consensus        15 ~~~~~v~~i~~~~~~~el~~~qq~av~~~~~~~~N~li~aPTgsGKTlIA~lai~~~l~~~--~~k~vYivPlkALa~Ek   92 (766)
T COG1204          15 KLDDRVLEILKGDGIDELFNPQQEAVEKGLLSDENVLISAPTGSGKTLIALLAILSTLLEG--GGKVVYIVPLKALAEEK   92 (766)
T ss_pred             cccHHHHHHhccCChHHhhHHHHHHhhccccCCCcEEEEcCCCCchHHHHHHHHHHHHHhc--CCcEEEEeChHHHHHHH
Confidence            4678888888888998999999999988665 49999999999999999999999998864  45899999999999999


Q ss_pred             HHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHH
Q 015158          124 EKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIY  203 (412)
Q Consensus       124 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~  203 (412)
                      +++++.+ ...|+++...+|+......   ....++|+|+|||+|....++.......+++||+||+|.+.+...+..+.
T Consensus        93 ~~~~~~~-~~~GirV~~~TgD~~~~~~---~l~~~~ViVtT~EK~Dsl~R~~~~~~~~V~lvViDEiH~l~d~~RG~~lE  168 (766)
T COG1204          93 YEEFSRL-EELGIRVGISTGDYDLDDE---RLARYDVIVTTPEKLDSLTRKRPSWIEEVDLVVIDEIHLLGDRTRGPVLE  168 (766)
T ss_pred             HHHhhhH-HhcCCEEEEecCCcccchh---hhccCCEEEEchHHhhHhhhcCcchhhcccEEEEeeeeecCCcccCceeh
Confidence            9999933 4569999999998874442   33567999999999999988877677889999999999988775566666


Q ss_pred             HHHHhCC---CCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCc-eEEEEEec--c----chhhHHHHHHHH
Q 015158          204 DIFQLLP---PKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGI-KQFHVNVE--K----EEWKLETLCDLY  273 (412)
Q Consensus       204 ~i~~~~~---~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~--~----~~~~~~~l~~~~  273 (412)
                      .+....+   ...+++++|||+++ ..+...++..++............+.. ...+....  .    .......+...+
T Consensus       169 ~iv~r~~~~~~~~rivgLSATlpN-~~evA~wL~a~~~~~~~rp~~l~~~v~~~~~~~~~~~~~k~~~~~~~~~~~~~v~  247 (766)
T COG1204         169 SIVARMRRLNELIRIVGLSATLPN-AEEVADWLNAKLVESDWRPVPLRRGVPYVGAFLGADGKKKTWPLLIDNLALELVL  247 (766)
T ss_pred             hHHHHHHhhCcceEEEEEeeecCC-HHHHHHHhCCcccccCCCCcccccCCccceEEEEecCccccccccchHHHHHHHH
Confidence            6655443   34799999999975 345555444444421222222211111 11111111  1    011222333333


Q ss_pred             Hhc-CCCcEEEEEcchhHHHHHHHHHhcC-------------------------------------CCeeEEecCCCCHH
Q 015158          274 ETL-AITQSVIFVNTRRKVDWLTDKMRSR-------------------------------------DHTVSATHGDMDQN  315 (412)
Q Consensus       274 ~~~-~~~k~lif~~~~~~~~~~~~~L~~~-------------------------------------~~~~~~~~~~~~~~  315 (412)
                      ... .++.+||||+|+..+...++.+...                                     ...+.++|++++.+
T Consensus       248 ~~~~~~~qvLvFv~sR~~a~~~A~~l~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~l~e~v~~GvafHhAGL~~~  327 (766)
T COG1204         248 ESLAEGGQVLVFVHSRKEAEKTAKKLRIKMSATLSDDEKIVLDEGASPILIPETPTSEDEELAELVLRGVAFHHAGLPRE  327 (766)
T ss_pred             HHHhcCCeEEEEEecCchHHHHHHHHHHHHhhcCChhhhhhccccccccccccccccchHHHHHHHHhCccccccCCCHH
Confidence            333 4479999999999999998888731                                     12478999999999


Q ss_pred             HHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEE----Ecc-----CCCChhhHHHhhhhcccCCC--CceEEEEe
Q 015158          316 TRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVI----NYD-----LPTQPENYLHRIGRSGRFGR--KGVAINFV  382 (412)
Q Consensus       316 ~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi----~~~-----~~~s~~~~~Q~~GR~~R~g~--~g~~~~~~  382 (412)
                      +|..+.+.|+.|+++||+||+++..|+|+|.-+++|    .++     .+.+.-++.||+||+||.|-  .|.++++.
T Consensus       328 ~R~~vE~~Fr~g~ikVlv~TpTLA~GVNLPA~~VIIk~~~~y~~~~g~~~i~~~dv~QM~GRAGRPg~d~~G~~~i~~  405 (766)
T COG1204         328 DRQLVEDAFRKGKIKVLVSTPTLAAGVNLPARTVIIKDTRRYDPKGGIVDIPVLDVLQMAGRAGRPGYDDYGEAIILA  405 (766)
T ss_pred             HHHHHHHHHhcCCceEEEechHHhhhcCCcceEEEEeeeEEEcCCCCeEECchhhHhhccCcCCCCCcCCCCcEEEEe
Confidence            999999999999999999999999999999555554    233     34568899999999999874  46677666

>TIGR00603 rad25 DNA repair helicase rad25

Probab=100.00  E-value=3.3e-38  Score=301.09  Aligned_cols=317  Identities=14%  Similarity=0.127  Sum_probs=225.1

Q ss_pred             CCChHHHHhhhhhhhcC---ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCc
Q 015158           60 EKPSAIQQRGIVPFCKG---LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGV  136 (412)
Q Consensus        60 ~~l~~~Q~~a~~~~~~~---~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~  136 (412)
                      ..|||||++|+..+..+   +++++++|||+|||++++.++...      ..++||+||+..|++||.+++.++......
T Consensus       254 ~~LRpYQ~eAl~~~~~~gr~r~GIIvLPtGaGKTlvai~aa~~l------~k~tLILvps~~Lv~QW~~ef~~~~~l~~~  327 (732)
T TIGR00603       254 TQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGVTAACTV------KKSCLVLCTSAVSVEQWKQQFKMWSTIDDS  327 (732)
T ss_pred             CCcCHHHHHHHHHHHhcCCCCCcEEEeCCCCChHHHHHHHHHHh------CCCEEEEeCcHHHHHHHHHHHHHhcCCCCc
Confidence            35999999999998753   478999999999999987665532      236999999999999999999998655556


Q ss_pred             EEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHc--------CCCCCCCceEEEEeCCchhhccCcHHHHHHHHHh
Q 015158          137 KVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRR--------QSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQL  208 (412)
Q Consensus       137 ~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~--------~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~  208 (412)
                      .+..++|+....     ......|+|+|++++.+...+        ..+....|++||+||||++...    .+..+...
T Consensus       328 ~I~~~tg~~k~~-----~~~~~~VvVtTYq~l~~~~~r~~~~~~~l~~l~~~~~gLII~DEvH~lpA~----~fr~il~~  398 (732)
T TIGR00603       328 QICRFTSDAKER-----FHGEAGVVVSTYSMVAHTGKRSYESEKVMEWLTNREWGLILLDEVHVVPAA----MFRRVLTI  398 (732)
T ss_pred             eEEEEecCcccc-----cccCCcEEEEEHHHhhcccccchhhhHHHHHhccccCCEEEEEccccccHH----HHHHHHHh
Confidence            677777754321     123468999999988643221        1233357899999999997543    34445555


Q ss_pred             CCCCceEEEEeecCChHH--HHHHHHhcCCCeEEEecC------CccccCCceEEEEEecc-------------------
Q 015158          209 LPPKIQVGVFSATMPPEA--LEITRKFMNKPVRILVKR------DELTLEGIKQFHVNVEK-------------------  261 (412)
Q Consensus       209 ~~~~~~~i~~SAT~~~~~--~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~-------------------  261 (412)
                      +. ....+++||||..+.  ...+..+++... +....      ....+......++.+..                   
T Consensus       399 l~-a~~RLGLTATP~ReD~~~~~L~~LiGP~v-ye~~~~eLi~~G~LA~~~~~ev~v~~t~~~~~~yl~~~~~~k~~l~~  476 (732)
T TIGR00603       399 VQ-AHCKLGLTATLVREDDKITDLNFLIGPKL-YEANWMELQKKGFIANVQCAEVWCPMTPEFYREYLRENSRKRMLLYV  476 (732)
T ss_pred             cC-cCcEEEEeecCcccCCchhhhhhhcCCee-eecCHHHHHhCCccccceEEEEEecCCHHHHHHHHHhcchhhhHHhh
Confidence            54 334799999996432  122333444332 22211      11111111122222211                   


Q ss_pred             -chhhHHHHHHHHHhc--CCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcC-CCcEEEEcCC
Q 015158          262 -EEWKLETLCDLYETL--AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSG-SSRVLITTDL  337 (412)
Q Consensus       262 -~~~~~~~l~~~~~~~--~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g-~~~vlv~t~~  337 (412)
                       ...+...+..+++.+  ..+++||||.+...++.+++.|.     +..+||+++..+|.+++++|++| .+++||+|++
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             123445555566655  56899999999999999998883     46689999999999999999875 7899999999


Q ss_pred             CcCCCCCCCCCEEEEccCC-CChhhHHHhhhhcccCCCCceE-------EEEeccCcHH--HHHHHHHHhc
Q 015158          338 LARGIDVQQVSLVINYDLP-TQPENYLHRIGRSGRFGRKGVA-------INFVTRDDER--MLFDIQKFYN  398 (412)
Q Consensus       338 ~~~G~d~~~~~~vi~~~~~-~s~~~~~Q~~GR~~R~g~~g~~-------~~~~~~~~~~--~~~~~~~~~~  398 (412)
                      +.+|+|+|.+++||+++.| .|..+|+||+||++|.++.|.+       |.+++.+..+  ...+-++|+.
T Consensus       552 gdeGIDlP~a~vvI~~s~~~gS~~q~iQRlGRilR~~~~~~~~~~~A~fY~lVs~dT~E~~~s~~Rq~fl~  622 (732)
T TIGR00603       552 GDTSIDLPEANVLIQISSHYGSRRQEAQRLGRILRAKKGSDAEEYNAFFYSLVSKDTQEMYYSTKRQRFLV  622 (732)
T ss_pred             cccccCCCCCCEEEEeCCCCCCHHHHHHHhcccccCCCCCccccccceEEEEecCCchHHHHHHHHHHHHH
Confidence            9999999999999999887 4999999999999999776654       7777776444  3345555554

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).

>PHA02653 RNA helicase NPH-II; Provisional

Probab=100.00  E-value=9.5e-38  Score=299.39  Aligned_cols=316  Identities=18%  Similarity=0.207  Sum_probs=227.5

Q ss_pred             hHHHHhhhhhhhcCccEEEECCCCCCchhHhH---------HHHHHhhc---cCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 015158           63 SAIQQRGIVPFCKGLDVIQQAQSGTGKTATFC---------SGILQQLD---YGLVECQALVLAPTRELAQQIEKVMRAL  130 (412)
Q Consensus        63 ~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~---------~~~~~~~~---~~~~~~~~lil~P~~~L~~q~~~~~~~~  130 (412)
                      -..|.++++.+.++++++++|+||||||.+..         ++.+..+.   ......++++++|+++|+.|+...+.+.
T Consensus       166 ~~iQ~qil~~i~~gkdvIv~A~TGSGKTtqvPq~l~~~~flf~~l~~l~~~~~~~~~~~ilvt~PrreLa~qi~~~i~~~  245 (675)
T PHA02653        166 PDVQLKIFEAWISRKPVVLTGGTGVGKTSQVPKLLLWFNYLFGGFDNLDKIDPNFIERPIVLSLPRVALVRLHSITLLKS  245 (675)
T ss_pred             HHHHHHHHHHHHhCCCEEEECCCCCCchhHHHHHHHHhhhccchhhhhhhcccccCCcEEEEECcHHHHHHHHHHHHHHH
Confidence            34789999999999999999999999998732         22233221   1223458999999999999999988775


Q ss_pred             hcc---cCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHH
Q 015158          131 GDY---LGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQ  207 (412)
Q Consensus       131 ~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~  207 (412)
                      ...   .+..+....|+... ..........+|+++|+....       ..++++++||+||||+....+  ..+..++.
T Consensus       246 vg~~~~~g~~v~v~~Gg~~~-~~~~t~~k~~~Ilv~T~~L~l-------~~L~~v~~VVIDEaHEr~~~~--DllL~llk  315 (675)
T PHA02653        246 LGFDEIDGSPISLKYGSIPD-ELINTNPKPYGLVFSTHKLTL-------NKLFDYGTVIIDEVHEHDQIG--DIIIAVAR  315 (675)
T ss_pred             hCccccCCceEEEEECCcch-HHhhcccCCCCEEEEeCcccc-------cccccCCEEEccccccCccch--hHHHHHHH
Confidence            432   35677888888762 211222235689999965211       135689999999999976654  44444444


Q ss_pred             hC-CCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEecc---------chhhHHHHHHHHHh--
Q 015158          208 LL-PPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEK---------EEWKLETLCDLYET--  275 (412)
Q Consensus       208 ~~-~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------~~~~~~~l~~~~~~--  275 (412)
                      .. +...++++||||++.+.... ..+++.+..+.....  ....+.+.+.....         ...+...+..+...  
T Consensus       316 ~~~~~~rq~ILmSATl~~dv~~l-~~~~~~p~~I~I~gr--t~~pV~~~yi~~~~~~~~~~~y~~~~k~~~l~~L~~~~~  392 (675)
T PHA02653        316 KHIDKIRSLFLMTATLEDDRDRI-KEFFPNPAFVHIPGG--TLFPISEVYVKNKYNPKNKRAYIEEEKKNIVTALKKYTP  392 (675)
T ss_pred             HhhhhcCEEEEEccCCcHhHHHH-HHHhcCCcEEEeCCC--cCCCeEEEEeecCcccccchhhhHHHHHHHHHHHHHhhc
Confidence            33 23348999999998776554 677877777766432  22445555543221         01111222222222  


Q ss_pred             cCCCcEEEEEcchhHHHHHHHHHhcC--CCeeEEecCCCCHHHHHHHHHHH-hcCCCcEEEEcCCCcCCCCCCCCCEEEE
Q 015158          276 LAITQSVIFVNTRRKVDWLTDKMRSR--DHTVSATHGDMDQNTRDIIMREF-RSGSSRVLITTDLLARGIDVQQVSLVIN  352 (412)
Q Consensus       276 ~~~~k~lif~~~~~~~~~~~~~L~~~--~~~~~~~~~~~~~~~r~~~~~~f-~~g~~~vlv~t~~~~~G~d~~~~~~vi~  352 (412)
                      ...+++|||++++++++.+++.|++.  +..+..+||++++.  ++.+++| ++|+.+|||+|+++++|+|+|++++||+
T Consensus       393 ~~~g~iLVFlpg~~ei~~l~~~L~~~~~~~~v~~LHG~Lsq~--eq~l~~ff~~gk~kILVATdIAERGIDIp~V~~VID  470 (675)
T PHA02653        393 PKGSSGIVFVASVSQCEEYKKYLEKRLPIYDFYIIHGKVPNI--DEILEKVYSSKNPSIIISTPYLESSVTIRNATHVYD  470 (675)
T ss_pred             ccCCcEEEEECcHHHHHHHHHHHHhhcCCceEEeccCCcCHH--HHHHHHHhccCceeEEeccChhhccccccCeeEEEE
Confidence            23468999999999999999999987  68999999999874  4666776 6899999999999999999999999999


Q ss_pred             cc---CCC---------ChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHH
Q 015158          353 YD---LPT---------QPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQ  394 (412)
Q Consensus       353 ~~---~~~---------s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~  394 (412)
                      ++   .|.         |.+.+.||+||+||. .+|.|+.++++.+...+.++.
T Consensus       471 ~G~~k~p~~~~g~~~~iSkasa~QRaGRAGR~-~~G~c~rLyt~~~~~pI~ri~  523 (675)
T PHA02653        471 TGRVYVPEPFGGKEMFISKSMRTQRKGRVGRV-SPGTYVYFYDLDLLKPIKRID  523 (675)
T ss_pred             CCCccCCCcccCcccccCHHHHHHhccCcCCC-CCCeEEEEECHHHhHHHHHHh
Confidence            98   443         788999999999999 789999999987765444443

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=100.00  E-value=3.3e-37  Score=302.59  Aligned_cols=308  Identities=16%  Similarity=0.267  Sum_probs=234.5

Q ss_pred             hHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHH-hhcccCcEEEEE
Q 015158           63 SAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRA-LGDYLGVKVHAC  141 (412)
Q Consensus        63 ~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~-~~~~~~~~~~~~  141 (412)
                      +.+-.+.+..+..++++++.++||||||+++.++++....   .+++++++.|++.++.|.++.+.+ +....+..+...
T Consensus         4 ~~~~~~i~~~l~~~~~vIi~a~TGSGKTT~vpl~lL~~~~---~~~~ilvlqPrR~aA~qiA~rva~~~~~~~g~~VGy~   80 (819)
T TIGR01970         4 HAVLPALRDALAAHPQVVLEAPPGAGKSTAVPLALLDAPG---IGGKIIMLEPRRLAARSAAQRLASQLGEAVGQTVGYR   80 (819)
T ss_pred             hHHHHHHHHHHHcCCcEEEECCCCCCHHHHHHHHHHHhhc---cCCeEEEEeCcHHHHHHHHHHHHHHhCCCcCcEEEEE
Confidence            3444566777778899999999999999999999987753   235899999999999999998864 434445556555


Q ss_pred             EcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCch-hhccCcHHH-HHHHHHhCCCCceEEEEe
Q 015158          142 VGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADE-MLSRGFKDQ-IYDIFQLLPPKIQVGVFS  219 (412)
Q Consensus       142 ~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~-~~~~~~~~~-~~~i~~~~~~~~~~i~~S  219 (412)
                      .....      ......+|+|+|++.|.+.+.. ...+.++++||+||+|+ ..+.++... +..+...++++.++++||
T Consensus        81 vr~~~------~~s~~t~I~v~T~G~Llr~l~~-d~~L~~v~~VIiDEaHER~L~~Dl~L~ll~~i~~~lr~dlqlIlmS  153 (819)
T TIGR01970        81 VRGEN------KVSRRTRLEVVTEGILTRMIQD-DPELDGVGALIFDEFHERSLDADLGLALALDVQSSLREDLKILAMS  153 (819)
T ss_pred             Ecccc------ccCCCCcEEEECCcHHHHHHhh-CcccccCCEEEEeccchhhhccchHHHHHHHHHHhcCCCceEEEEe
Confidence            44332      1234568999999999998876 34678999999999996 555554433 345566677889999999


Q ss_pred             ecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhh----HHHHHHHHHhcCCCcEEEEEcchhHHHHHH
Q 015158          220 ATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWK----LETLCDLYETLAITQSVIFVNTRRKVDWLT  295 (412)
Q Consensus       220 AT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~l~~~~~~~~~~k~lif~~~~~~~~~~~  295 (412)
                      ||++...   +..++++...+......   ..+...+.........    ...+..++.. ..+++|||+++.++++.++
T Consensus       154 ATl~~~~---l~~~l~~~~vI~~~gr~---~pVe~~y~~~~~~~~~~~~v~~~l~~~l~~-~~g~iLVFlpg~~eI~~l~  226 (819)
T TIGR01970       154 ATLDGER---LSSLLPDAPVVESEGRS---FPVEIRYLPLRGDQRLEDAVSRAVEHALAS-ETGSILVFLPGQAEIRRVQ  226 (819)
T ss_pred             CCCCHHH---HHHHcCCCcEEEecCcc---eeeeeEEeecchhhhHHHHHHHHHHHHHHh-cCCcEEEEECCHHHHHHHH
Confidence            9998643   45566554444433221   1244444444332221    1233334433 3578999999999999999


Q ss_pred             HHHhc---CCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccCCC---------------
Q 015158          296 DKMRS---RDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPT---------------  357 (412)
Q Consensus       296 ~~L~~---~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~~~---------------  357 (412)
                      +.|++   .++.+..+||+++.++|..+++.|.+|+.+|||||+++++|+|+|++++||+++.+.               
T Consensus       227 ~~L~~~~~~~~~v~pLHg~L~~~eq~~~~~~~~~G~rkVlVATnIAErgItIp~V~~VID~Gl~r~~~yd~~~g~~~L~~  306 (819)
T TIGR01970       227 EQLAERLDSDVLICPLYGELSLAAQDRAIKPDPQGRRKVVLATNIAETSLTIEGIRVVIDSGLARVARFDPKTGITRLET  306 (819)
T ss_pred             HHHHhhcCCCcEEEEecCCCCHHHHHHHHhhcccCCeEEEEecchHhhcccccCceEEEEcCcccccccccccCCceeeE
Confidence            99987   478899999999999999999999999999999999999999999999999998764               


Q ss_pred             ---ChhhHHHhhhhcccCCCCceEEEEeccCcHH
Q 015158          358 ---QPENYLHRIGRSGRFGRKGVAINFVTRDDER  388 (412)
Q Consensus       358 ---s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~  388 (412)
                         |.+++.||.||+||. .+|.||.++++.+..
T Consensus       307 ~~iSkasa~QR~GRAGR~-~~G~cyrL~t~~~~~  339 (819)
T TIGR01970       307 VRISQASATQRAGRAGRL-EPGVCYRLWSEEQHQ  339 (819)
T ss_pred             EEECHHHHHhhhhhcCCC-CCCEEEEeCCHHHHH
Confidence               345689999999999 799999999987654

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.

>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=2.5e-37  Score=304.55  Aligned_cols=348  Identities=22%  Similarity=0.317  Sum_probs=271.6

Q ss_pred             CHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHH
Q 015158           47 QENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKV  126 (412)
Q Consensus        47 ~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~  126 (412)
                      ...+...+...++..|++||.+|+..+.+|++++|..|||||||.+|++++++.+...... ++|++.|+++|++++.+.
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            3445777888888889999999999999999999999999999999999999998876433 799999999999999999


Q ss_pred             HHHhhcccC--cEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcC----CCCCCCceEEEEeCCchhhccCcHH
Q 015158          127 MRALGDYLG--VKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQ----SLRPDNIRIFVLDEADEMLSRGFKD  200 (412)
Q Consensus       127 ~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~----~~~~~~~~~iiiDE~h~~~~~~~~~  200 (412)
                      ++++....+  +....++|+...........++++|++|+|++|...+.+.    .+..+++++||+||+|-+-. .++.
T Consensus       135 l~~~~~~~~~~v~~~~y~Gdt~~~~r~~~~~~pp~IllTNpdMLh~~llr~~~~~~~~~~~Lk~lVvDElHtYrG-v~GS  213 (851)
T COG1205         135 LRELISDLPGKVTFGRYTGDTPPEERRAIIRNPPDILLTNPDMLHYLLLRNHDAWLWLLRNLKYLVVDELHTYRG-VQGS  213 (851)
T ss_pred             HHHHHHhCCCcceeeeecCCCChHHHHHHHhCCCCEEEeCHHHHHHHhccCcchHHHHHhcCcEEEEecceeccc-cchh
Confidence            999887776  7888999999887777888899999999999998755443    23356799999999996532 2332


Q ss_pred             -------HHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccc--------hhh
Q 015158          201 -------QIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKE--------EWK  265 (412)
Q Consensus       201 -------~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------~~~  265 (412)
                             .+..++...+.+.++|+.|||..+. .+....+++...... ..+...+.....+....+..        ...
T Consensus       214 ~vA~llRRL~~~~~~~~~~~q~i~~SAT~~np-~e~~~~l~~~~f~~~-v~~~g~~~~~~~~~~~~p~~~~~~~~~r~s~  291 (851)
T COG1205         214 EVALLLRRLLRRLRRYGSPLQIICTSATLANP-GEFAEELFGRDFEVP-VDEDGSPRGLRYFVRREPPIRELAESIRRSA  291 (851)
T ss_pred             HHHHHHHHHHHHHhccCCCceEEEEeccccCh-HHHHHHhcCCcceee-ccCCCCCCCceEEEEeCCcchhhhhhcccch
Confidence                   3333334445688999999999654 567777777766654 33333444445555444411        122


Q ss_pred             HHHHHHHHHhc--CCCcEEEEEcchhHHHHHH----HHHhcCC----CeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEc
Q 015158          266 LETLCDLYETL--AITQSVIFVNTRRKVDWLT----DKMRSRD----HTVSATHGDMDQNTRDIIMREFRSGSSRVLITT  335 (412)
Q Consensus       266 ~~~l~~~~~~~--~~~k~lif~~~~~~~~~~~----~~L~~~~----~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t  335 (412)
                      ...+..++...  ..-++|+|+.+++.++.+.    ..+...+    ..+..+++++...+|..++..|++|++.++++|
T Consensus       292 ~~~~~~~~~~~~~~~~~tL~F~~sr~~~e~~~~~~~~~~~~~~~~l~~~v~~~~~~~~~~er~~ie~~~~~g~~~~~~st  371 (851)
T COG1205         292 LAELATLAALLVRNGIQTLVFFRSRKQVELLYLSPRRRLVREGGKLLDAVSTYRAGLHREERRRIEAEFKEGELLGVIAT  371 (851)
T ss_pred             HHHHHHHHHHHHHcCceEEEEEehhhhhhhhhhchhHHHhhcchhhhhheeeccccCCHHHHHHHHHHHhcCCccEEecc
Confidence            33333333332  3468999999999999886    4444445    578899999999999999999999999999999


Q ss_pred             CCCcCCCCCCCCCEEEEccCCC-ChhhHHHhhhhcccCCCCceEEEEecc--CcHHHHHHHHHHhc
Q 015158          336 DLLARGIDVQQVSLVINYDLPT-QPENYLHRIGRSGRFGRKGVAINFVTR--DDERMLFDIQKFYN  398 (412)
Q Consensus       336 ~~~~~G~d~~~~~~vi~~~~~~-s~~~~~Q~~GR~~R~g~~g~~~~~~~~--~~~~~~~~~~~~~~  398 (412)
                      ++++.|+|+..++.||..+.|. +..++.|+.||+||.++.+..+++...  .+..+....+.++.
T Consensus       372 ~AlelgidiG~ldavi~~g~P~~s~~~~~Q~~GRaGR~~~~~l~~~v~~~~~~d~yy~~~p~~~~~  437 (851)
T COG1205         372 NALELGIDIGSLDAVIAYGYPGVSVLSFRQRAGRAGRRGQESLVLVVLRSDPLDSYYLRHPEELLE  437 (851)
T ss_pred             hhhhhceeehhhhhHhhcCCCCchHHHHHHhhhhccCCCCCceEEEEeCCCccchhhhhCcHhhhh
Confidence            9999999999999999999999 999999999999999977776666653  25555555555555

>PRK09401 reverse gyrase; Reviewed

Probab=100.00  E-value=9.3e-37  Score=309.43  Aligned_cols=284  Identities=22%  Similarity=0.279  Sum_probs=217.4

Q ss_pred             CCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCc
Q 015158           57 YGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGV  136 (412)
Q Consensus        57 ~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~  136 (412)
                      .|+ +|+++|+.+++.++.|+++++++|||+|||..++. ++..+..  .+.+++|++||++|+.|+.+.+..++...+.
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-KPWSLQRTWAKRLLLGESFAIIAPTGVGKTTFGLV-MSLYLAK--KGKKSYIIFPTRLLVEQVVEKLEKFGEKVGC  152 (1176)
T ss_pred             cCC-CCcHHHHHHHHHHHCCCcEEEEcCCCCCHHHHHHH-HHHHHHh--cCCeEEEEeccHHHHHHHHHHHHHHhhhcCc
Confidence            367 59999999999999999999999999999975443 3333322  3568999999999999999999999887788


Q ss_pred             EEEEEEcCcch-----HHHHHH-hcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhc-----------cCcH
Q 015158          137 KVHACVGGTSV-----REDQRI-LSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLS-----------RGFK  199 (412)
Q Consensus       137 ~~~~~~~~~~~-----~~~~~~-~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~-----------~~~~  199 (412)
                      .+..+.++...     ...... ..+.++|+|+||+.+.+.+.  .+....++++|+||||++++           .+|.
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            87777766432     112222 33568999999999998776  34456799999999999885           3453


Q ss_pred             -HHHHHHHHhCCC------------------------CceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceE
Q 015158          200 -DQIYDIFQLLPP------------------------KIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQ  254 (412)
Q Consensus       200 -~~~~~i~~~~~~------------------------~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  254 (412)
                       ..+..++..++.                        ..+.+++|||.++.....  .++.....+..........++.+
T Consensus       231 ~~~i~~i~~~i~~~~~~~~~~~~i~~l~~~i~~~~~~~~q~ilfSAT~~~~~~~~--~l~~~ll~~~v~~~~~~~rnI~~  308 (1176)
T PRK09401        231 EEDIEKAMELIRLKRKYEEIYEKIRELEEKIAELKDKKGVLVVSSATGRPRGNRV--KLFRELLGFEVGSPVFYLRNIVD  308 (1176)
T ss_pred             HHHHHHHHHhcccccccchhhhHHHHHHHhhhhcccCCceEEEEeCCCCccchHH--HHhhccceEEecCcccccCCceE
Confidence             456666665543                        678999999997632211  23334444444444445566777


Q ss_pred             EEEEeccchhhHHHHHHHHHhcCCCcEEEEEcchhH---HHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcE
Q 015158          255 FHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRK---VDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRV  331 (412)
Q Consensus       255 ~~~~~~~~~~~~~~l~~~~~~~~~~k~lif~~~~~~---~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~v  331 (412)
                      .+....   .+...+.++++... .++||||++.+.   ++.+++.|++.|+.+..+||++     .+.+++|++|+.+|
T Consensus       309 ~yi~~~---~k~~~L~~ll~~l~-~~~LIFv~t~~~~~~ae~l~~~L~~~gi~v~~~hg~l-----~~~l~~F~~G~~~V  379 (1176)
T PRK09401        309 SYIVDE---DSVEKLVELVKRLG-DGGLIFVPSDKGKEYAEELAEYLEDLGINAELAISGF-----ERKFEKFEEGEVDV  379 (1176)
T ss_pred             EEEEcc---cHHHHHHHHHHhcC-CCEEEEEecccChHHHHHHHHHHHHCCCcEEEEeCcH-----HHHHHHHHCCCCCE
Confidence            776554   45667777776654 589999999777   9999999999999999999998     23459999999999


Q ss_pred             EEE----cCCCcCCCCCCC-CCEEEEccCCC
Q 015158          332 LIT----TDLLARGIDVQQ-VSLVINYDLPT  357 (412)
Q Consensus       332 lv~----t~~~~~G~d~~~-~~~vi~~~~~~  357 (412)
                      ||+    |+.+++|+|+|+ +++||+++.|.
T Consensus       380 LVatas~tdv~aRGIDiP~~IryVI~y~vP~  410 (1176)
T PRK09401        380 LVGVASYYGVLVRGIDLPERIRYAIFYGVPK  410 (1176)
T ss_pred             EEEecCCCCceeecCCCCcceeEEEEeCCCC
Confidence            999    689999999999 89999988875

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=100.00  E-value=7.9e-37  Score=300.70  Aligned_cols=308  Identities=17%  Similarity=0.283  Sum_probs=234.7

Q ss_pred             hHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHH-hhcccCcEEEEE
Q 015158           63 SAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRA-LGDYLGVKVHAC  141 (412)
Q Consensus        63 ~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~-~~~~~~~~~~~~  141 (412)
                      +.+-.+.+..+.+++++++.++||||||+++.++++.....   .+++++++|++.++.|.++.+.+ +....+..+...
T Consensus         7 ~~~~~~i~~~l~~~~~vvv~A~TGSGKTt~~pl~lL~~~~~---~~~ilvlqPrR~aA~qia~rva~~l~~~~g~~VGy~   83 (812)
T PRK11664          7 AAVLPELLTALKTAPQVLLKAPTGAGKSTWLPLQLLQHGGI---NGKIIMLEPRRLAARNVAQRLAEQLGEKPGETVGYR   83 (812)
T ss_pred             HHHHHHHHHHHHhCCCEEEEcCCCCCHHHHHHHHHHHcCCc---CCeEEEECChHHHHHHHHHHHHHHhCcccCceEEEE
Confidence            44555677778888999999999999999999888875432   24899999999999999998864 444456677766


Q ss_pred             EcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchh-hccCcH-HHHHHHHHhCCCCceEEEEe
Q 015158          142 VGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEM-LSRGFK-DQIYDIFQLLPPKIQVGVFS  219 (412)
Q Consensus       142 ~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~-~~~~~~-~~~~~i~~~~~~~~~~i~~S  219 (412)
                      .++...      .....+|+|+|++.|.+.+.. ...+.++++||+||+|+. .+.++. ..+..+...++++.++++||
T Consensus        84 vr~~~~------~~~~t~I~v~T~G~Llr~l~~-d~~L~~v~~IIlDEaHER~l~~Dl~L~ll~~i~~~lr~~lqlilmS  156 (812)
T PRK11664         84 MRAESK------VGPNTRLEVVTEGILTRMIQR-DPELSGVGLVILDEFHERSLQADLALALLLDVQQGLRDDLKLLIMS  156 (812)
T ss_pred             ecCccc------cCCCCcEEEEChhHHHHHHhh-CCCcCcCcEEEEcCCCccccccchHHHHHHHHHHhCCccceEEEEe
Confidence            655432      123458999999999998875 346789999999999973 333322 23345566677889999999


Q ss_pred             ecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhH----HHHHHHHHhcCCCcEEEEEcchhHHHHHH
Q 015158          220 ATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKL----ETLCDLYETLAITQSVIFVNTRRKVDWLT  295 (412)
Q Consensus       220 AT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~l~~~~~~~~~~k~lif~~~~~~~~~~~  295 (412)
                      ||++.+   .+..+++....+......   ..+...+..........    ..+..++.. ..+.+|||+++.++++.++
T Consensus       157 ATl~~~---~l~~~~~~~~~I~~~gr~---~pV~~~y~~~~~~~~~~~~v~~~l~~~l~~-~~g~iLVFlpg~~ei~~l~  229 (812)
T PRK11664        157 ATLDND---RLQQLLPDAPVIVSEGRS---FPVERRYQPLPAHQRFDEAVARATAELLRQ-ESGSLLLFLPGVGEIQRVQ  229 (812)
T ss_pred             cCCCHH---HHHHhcCCCCEEEecCcc---ccceEEeccCchhhhHHHHHHHHHHHHHHh-CCCCEEEEcCCHHHHHHHH
Confidence            999864   245566655444433221   22455554443322221    133344433 3588999999999999999


Q ss_pred             HHHhc---CCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccCCC---------------
Q 015158          296 DKMRS---RDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPT---------------  357 (412)
Q Consensus       296 ~~L~~---~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~~~---------------  357 (412)
                      +.|++   .++.+..+||+++..+|.++++.|.+|+.+|||||+++++|+|+|++++||+.+.+.               
T Consensus       230 ~~L~~~~~~~~~v~~Lhg~l~~~eq~~~~~~~~~G~rkVlvATnIAErsLtIp~V~~VID~Gl~r~~~yd~~~g~~~L~~  309 (812)
T PRK11664        230 EQLASRVASDVLLCPLYGALSLAEQQKAILPAPAGRRKVVLATNIAETSLTIEGIRLVVDSGLERVARFDPKTGLTRLVT  309 (812)
T ss_pred             HHHHHhccCCceEEEeeCCCCHHHHHHHhccccCCCeEEEEecchHHhcccccCceEEEECCCcccccccccCCcceeEE
Confidence            99987   577899999999999999999999999999999999999999999999999988763               


Q ss_pred             ---ChhhHHHhhhhcccCCCCceEEEEeccCcHH
Q 015158          358 ---QPENYLHRIGRSGRFGRKGVAINFVTRDDER  388 (412)
Q Consensus       358 ---s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~  388 (412)
                         |.+++.||.||+||. .+|.||.++++.+..
T Consensus       310 ~~iSkasa~QR~GRaGR~-~~G~cyrL~t~~~~~  342 (812)
T PRK11664        310 QRISQASMTQRAGRAGRL-EPGICLHLYSKEQAE  342 (812)
T ss_pred             EeechhhhhhhccccCCC-CCcEEEEecCHHHHh
Confidence               446899999999999 699999999987664

>PRK13766 Hef nuclease; Provisional

Probab=100.00  E-value=5.7e-36  Score=301.20  Aligned_cols=322  Identities=21%  Similarity=0.258  Sum_probs=237.4

Q ss_pred             CCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEE
Q 015158           60 EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVH  139 (412)
Q Consensus        60 ~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~  139 (412)
                      -++++||.+++..++.+ ++++++|||+|||.++++.+...+.  ..+.++||++|+++|+.|+.+.++.+....+..+.
T Consensus        14 ~~~r~yQ~~~~~~~l~~-n~lv~~ptG~GKT~~a~~~i~~~l~--~~~~~vLvl~Pt~~L~~Q~~~~~~~~~~~~~~~v~   90 (773)
T PRK13766         14 IEARLYQQLLAATALKK-NTLVVLPTGLGKTAIALLVIAERLH--KKGGKVLILAPTKPLVEQHAEFFRKFLNIPEEKIV   90 (773)
T ss_pred             CCccHHHHHHHHHHhcC-CeEEEcCCCccHHHHHHHHHHHHHH--hCCCeEEEEeCcHHHHHHHHHHHHHHhCCCCceEE
Confidence            35999999999988877 8999999999999999888877663  24568999999999999999999987654455788


Q ss_pred             EEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEe
Q 015158          140 ACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFS  219 (412)
Q Consensus       140 ~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~S  219 (412)
                      .++|+......... ..+++|+|+||+.+.+.+....+...++++||+||||++........+............++++|
T Consensus        91 ~~~g~~~~~~r~~~-~~~~~iiv~T~~~l~~~l~~~~~~~~~~~liVvDEaH~~~~~~~~~~i~~~~~~~~~~~~il~lT  169 (773)
T PRK13766         91 VFTGEVSPEKRAEL-WEKAKVIVATPQVIENDLIAGRISLEDVSLLIFDEAHRAVGNYAYVYIAERYHEDAKNPLVLGLT  169 (773)
T ss_pred             EEeCCCCHHHHHHH-HhCCCEEEECHHHHHHHHHcCCCChhhCcEEEEECCccccccccHHHHHHHHHhcCCCCEEEEEE
Confidence            88887765443333 34569999999999988877777788999999999999775433333434444444567799999


Q ss_pred             ecCChHH---HHHHHHhcCCCeEEEecCCc-----cccCCceE-------------------------------------
Q 015158          220 ATMPPEA---LEITRKFMNKPVRILVKRDE-----LTLEGIKQ-------------------------------------  254 (412)
Q Consensus       220 AT~~~~~---~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~-------------------------------------  254 (412)
                      |||....   ...+..++...+.+......     .....+..                                     
T Consensus       170 aTP~~~~~~i~~~~~~L~i~~v~~~~~~~~~v~~~~~~~~v~~~~v~l~~~~~~i~~~l~~~~~~~l~~l~~~~~~~~~~  249 (773)
T PRK13766        170 ASPGSDEEKIKEVCENLGIEHVEVRTEDDPDVKPYVHKVKIEWVRVELPEELKEIRDLLNEALKDRLKKLKELGVIVSIS  249 (773)
T ss_pred             cCCCCCHHHHHHHHHhCCceEEEEcCCCChhHHhhhccceeEEEEeCCcHHHHHHHHHHHHHHHHHHHHHHHCCCcccCC
Confidence            9985332   11122211111100000000     00000000                                     


Q ss_pred             -----------------EE-------------------------------------------------------------
Q 015158          255 -----------------FH-------------------------------------------------------------  256 (412)
Q Consensus       255 -----------------~~-------------------------------------------------------------  256 (412)
                                       ..                                                             
T Consensus       250 ~~~~~~~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~y~~~l~~~~~~~~~~~~~~~l~~~  329 (773)
T PRK13766        250 PDVSKKELLGLQKKLQQEIANDDSEGYEAISILAEAMKLRHAVELLETQGVEALRRYLERLREEARSSGGSKASKRLVED  329 (773)
T ss_pred             CCcCHHHHHHHHHHHHHHhhcCchHHHHHHHHHHHHHHHHHHHHHHHHhCHHHHHHHHHHHHhhccccCCcHHHHHHHhC
Confidence                             00                                                             


Q ss_pred             ----------EEeccchhhHHHHHHHHHh----cCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCC--------CCH
Q 015158          257 ----------VNVEKEEWKLETLCDLYET----LAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGD--------MDQ  314 (412)
Q Consensus       257 ----------~~~~~~~~~~~~l~~~~~~----~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~--------~~~  314 (412)
                                ..+.....+...+.++++.    ...+++||||+++..++.+++.|...++.+..++|.        ++.
T Consensus       330 ~~~~~~~~~~~~~~~~~pK~~~L~~il~~~~~~~~~~kvlIF~~~~~t~~~L~~~L~~~~~~~~~~~g~~~~~~~~~~~~  409 (773)
T PRK13766        330 PRFRKAVRKAKELDIEHPKLEKLREIVKEQLGKNPDSRIIVFTQYRDTAEKIVDLLEKEGIKAVRFVGQASKDGDKGMSQ  409 (773)
T ss_pred             HHHHHHHHHHHhcccCChHHHHHHHHHHHHHhcCCCCeEEEEeCcHHHHHHHHHHHHhCCCceEEEEccccccccCCCCH
Confidence                      0000112234444555544    456899999999999999999999989988888876        888


Q ss_pred             HHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCc
Q 015158          315 NTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDD  386 (412)
Q Consensus       315 ~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~  386 (412)
                      .+|..++++|++|+.++||+|+++++|+|+|.+++||++++++++..++||+||+||.|. |.+++++..+.
T Consensus       410 ~~r~~~~~~F~~g~~~vLvaT~~~~eGldi~~~~~VI~yd~~~s~~r~iQR~GR~gR~~~-~~v~~l~~~~t  480 (773)
T PRK13766        410 KEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEPVPSEIRSIQRKGRTGRQEE-GRVVVLIAKGT  480 (773)
T ss_pred             HHHHHHHHHHHcCCCCEEEECChhhcCCCcccCCEEEEeCCCCCHHHHHHHhcccCcCCC-CEEEEEEeCCC
Confidence            999999999999999999999999999999999999999999999999999999999865 88888887653

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=100.00  E-value=2.3e-37  Score=284.84  Aligned_cols=302  Identities=16%  Similarity=0.173  Sum_probs=204.7

Q ss_pred             cEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHH--------
Q 015158           78 DVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVRE--------  149 (412)
Q Consensus        78 ~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~--------  149 (412)
                      ++++.+|||||||.+++++++..+... ...+++|++|+++|+.|+.+.+..++.   ..+..++++.....        
T Consensus         1 ~vvi~apTGsGKT~~~~~~~l~~~~~~-~~~~ii~v~P~~~L~~q~~~~l~~~f~---~~~~~~~~~~~~~~~~~~~~~~   76 (358)
T TIGR01587         1 LLVIEAPTGYGKTEAALLWALHSIKSQ-KADRVIIALPTRATINAMYRRAKELFG---SNLGLLHSSSSFKRIKEMGDSE   76 (358)
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHHHhhC-CCCeEEEEeehHHHHHHHHHHHHHHhC---cccEEeeccHHHHHHhccCCch
Confidence            478999999999999999999876543 456899999999999999999999753   23444444332110        


Q ss_pred             ----HHHHh------cCCCcEEEeChHHHHHHHHcCCC----C--CCCceEEEEeCCchhhccCcHHHHHHHHHhCC-CC
Q 015158          150 ----DQRIL------SSGVHVVVGTPGRVFDMLRRQSL----R--PDNIRIFVLDEADEMLSRGFKDQIYDIFQLLP-PK  212 (412)
Q Consensus       150 ----~~~~~------~~~~~iii~T~~~l~~~~~~~~~----~--~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~-~~  212 (412)
                          .....      ....+|+++||+++.+.+.....    .  .-..++||+||+|.+.+..+.. +..++..++ .+
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      12357999999999877664210    0  1123789999999987654333 444444333 47


Q ss_pred             ceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhHHHHHHHHHhc-CCCcEEEEEcchhHH
Q 015158          213 IQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETL-AITQSVIFVNTRRKV  291 (412)
Q Consensus       213 ~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~~~k~lif~~~~~~~  291 (412)
                      .+++++|||++....+..........................+.........+...+..+++.. ..+++||||++++.+
T Consensus       156 ~~~i~~SATlp~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~lVf~~t~~~~  235 (358)
T TIGR01587       156 VPILLMSATLPKFLKEYAEKIGYVEFNEPLDLKEERRFERHRFIKIESDKVGEISSLERLLEFIKKGGKIAIIVNTVDRA  235 (358)
T ss_pred             CCEEEEecCchHHHHHHHhcCCCcccccCCCCccccccccccceeeccccccCHHHHHHHHHHhhCCCeEEEEECCHHHH
Confidence            8899999999865555544432221111111000000001111111222223445555555543 457999999999999


Q ss_pred             HHHHHHHhcCCC--eeEEecCCCCHHHHHH----HHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccCCCChhhHHHh
Q 015158          292 DWLTDKMRSRDH--TVSATHGDMDQNTRDI----IMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHR  365 (412)
Q Consensus       292 ~~~~~~L~~~~~--~~~~~~~~~~~~~r~~----~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~  365 (412)
                      +.+++.|++.+.  .+..+||++++.+|.+    +++.|++|+.++||||+++++|+|++ ++.+|....|  ...|+||
T Consensus       236 ~~~~~~L~~~~~~~~~~~~h~~~~~~~r~~~~~~~~~~f~~~~~~ilvaT~~~~~GiDi~-~~~vi~~~~~--~~~~iqr  312 (358)
T TIGR01587       236 QEFYQQLKENAPEEEIMLLHSRFTEKDRAKKEAELLEEMKKNEKFVIVATQVIEASLDIS-ADVMITELAP--IDSLIQR  312 (358)
T ss_pred             HHHHHHHHhhcCCCeEEEEECCCCHHHHHHHHHHHHHHhcCCCCeEEEECcchhceeccC-CCEEEEcCCC--HHHHHHH
Confidence            999999988765  5999999999999876    48899999999999999999999996 7777776544  7899999


Q ss_pred             hhhcccCCCC----ceEEEEeccCcH
Q 015158          366 IGRSGRFGRK----GVAINFVTRDDE  387 (412)
Q Consensus       366 ~GR~~R~g~~----g~~~~~~~~~~~  387 (412)
                      +||+||.|+.    |.++++....+.
T Consensus       313 ~GR~gR~g~~~~~~~~~~v~~~~~~~  338 (358)
T TIGR01587       313 LGRLHRYGRKNGENFEVYIITIAPEG  338 (358)
T ss_pred             hccccCCCCCCCCCCeEEEEeecCCC
Confidence            9999998753    367777766544

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.

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

Probab=100.00  E-value=6.1e-37  Score=286.81  Aligned_cols=337  Identities=20%  Similarity=0.268  Sum_probs=233.4

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHH
Q 015158           46 LQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEK  125 (412)
Q Consensus        46 l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~  125 (412)
                      +.++....+.-...-.+|.||.+.+...+ |+|++|++|||+|||+++...+.+++... +..++++++|++-|+.|+..
T Consensus        47 ~~~s~~~~~~~p~~~~lR~YQ~eivq~AL-gkNtii~lPTG~GKTfIAa~Vm~nh~rw~-p~~KiVF~aP~~pLv~QQ~a  124 (746)
T KOG0354|consen   47 LDESAAQRWIYPTNLELRNYQEELVQPAL-GKNTIIALPTGSGKTFIAAVIMKNHFEWR-PKGKVVFLAPTRPLVNQQIA  124 (746)
T ss_pred             CChhhhccccccCcccccHHHHHHhHHhh-cCCeEEEeecCCCccchHHHHHHHHHhcC-CcceEEEeeCCchHHHHHHH
Confidence            33444433332233459999999999999 99999999999999999999998888754 45789999999999999997


Q ss_pred             HHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCC-CCceEEEEeCCchhhccC-cHHHHH
Q 015158          126 VMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRP-DNIRIFVLDEADEMLSRG-FKDQIY  203 (412)
Q Consensus       126 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~-~~~~~iiiDE~h~~~~~~-~~~~~~  203 (412)
                      .+..++..  ..+....|+..............+|+++||+.+.+.+.+..... +.|.++|+||||+..... |...+.
T Consensus       125 ~~~~~~~~--~~~T~~l~~~~~~~~r~~i~~s~~vff~TpQil~ndL~~~~~~~ls~fs~iv~DE~Hra~kn~~Y~~Vmr  202 (746)
T KOG0354|consen  125 CFSIYLIP--YSVTGQLGDTVPRSNRGEIVASKRVFFRTPQILENDLKSGLHDELSDFSLIVFDECHRTSKNHPYNNIMR  202 (746)
T ss_pred             HHhhccCc--ccceeeccCccCCCchhhhhcccceEEeChHhhhhhcccccccccceEEEEEEcccccccccccHHHHHH
Confidence            77776543  44555555533333222334456999999999999888766554 789999999999977544 455555


Q ss_pred             HHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEE-------------------------------------------
Q 015158          204 DIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRI-------------------------------------------  240 (412)
Q Consensus       204 ~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~-------------------------------------------  240 (412)
                      .++..-....|++++||||+.+.........+-...+                                           
T Consensus       203 ~~l~~k~~~~qILgLTASpG~~~~~v~~~I~~L~asldvr~~ssi~~~y~~lr~~~~i~v~~~~~~~~~~~~f~~~i~p~  282 (746)
T KOG0354|consen  203 EYLDLKNQGNQILGLTASPGSKLEQVQNVIDNLCASLDVRTESSIKSNYEELREHVQIPVDLSLCERDIEDPFGMIIEPL  282 (746)
T ss_pred             HHHHhhhccccEEEEecCCCccHHHHHHHHHhhheecccchhhhhhhhHHHHhccCcccCcHHHhhhhhhhhHHHHHHHH
Confidence            6665555555999999999843322211110000000                                           


Q ss_pred             ----------EecC------------CccccC--------------------------Cce-------------------
Q 015158          241 ----------LVKR------------DELTLE--------------------------GIK-------------------  253 (412)
Q Consensus       241 ----------~~~~------------~~~~~~--------------------------~~~-------------------  253 (412)
                                ....            .....+                          .++                   
T Consensus       283 l~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~f~~~~~~~~~~~ll~~~gir~~~~l~~~~~f~~e~~~~k  362 (746)
T KOG0354|consen  283 LQQLQEEGLIEISDKSTSYEQWVVQAEKAAAPNGPENQRNCFYALHLRKYNLALLISDGIRFVDALDYLEDFYEEVALKK  362 (746)
T ss_pred             HHHHHhcCccccccccccccchhhhhhhhhccCCCccchhhHHHHHHHHHHHHHHhhcchhhHHHHhhhhhhccccchhH
Confidence                      0000            000000                          000                   


Q ss_pred             ----------------------EEEEEeccchhhHHHHHHHHHh----cCCCcEEEEEcchhHHHHHHHHHhcC---CCe
Q 015158          254 ----------------------QFHVNVEKEEWKLETLCDLYET----LAITQSVIFVNTRRKVDWLTDKMRSR---DHT  304 (412)
Q Consensus       254 ----------------------~~~~~~~~~~~~~~~l~~~~~~----~~~~k~lif~~~~~~~~~~~~~L~~~---~~~  304 (412)
                                            +.....+....+...+.+++..    ....++|||+.+++.|..+.++|.+.   ++.
T Consensus       363 ~~~~~~e~~~~~~~~~~m~~~~~l~~~~~~~npkle~l~~~l~e~f~~~~dsR~IIFve~R~sa~~l~~~l~~~~~~~ir  442 (746)
T KOG0354|consen  363 YLKLELEARLIRNFTENMNELEHLSLDPPKENPKLEKLVEILVEQFEQNPDSRTIIFVETRESALALKKWLLQLHELGIK  442 (746)
T ss_pred             HHHHHhcchhhHHHHHHHHhhhhhhcCCCccChhHHHHHHHHHHHhhcCCCccEEEEEehHHHHHHHHHHHHhhhhcccc
Confidence                                  0000000012233334443333    24468999999999999999999842   222


Q ss_pred             eEEe--------cCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccCCCCc
Q 015158          305 VSAT--------HGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKG  376 (412)
Q Consensus       305 ~~~~--------~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g  376 (412)
                      ...+        ..+|++.++.++++.|++|+++|||||+++++|+|++.|+.||.++...|+..++||.|| ||+ +.|
T Consensus       443 ~~~fiGq~~s~~~~gmtqk~Q~evl~~Fr~G~~NvLVATSV~EEGLDI~ec~lVIcYd~~snpIrmIQrrGR-gRa-~ns  520 (746)
T KOG0354|consen  443 AEIFIGQGKSTQSTGMTQKEQKEVLDKFRDGEINVLVATSVAEEGLDIGECNLVICYDYSSNPIRMVQRRGR-GRA-RNS  520 (746)
T ss_pred             cceeeeccccccccccCHHHHHHHHHHHhCCCccEEEEecchhccCCcccccEEEEecCCccHHHHHHHhcc-ccc-cCC
Confidence            2222        236899999999999999999999999999999999999999999999999999999999 998 678


Q ss_pred             eEEEEeccCcHH
Q 015158          377 VAINFVTRDDER  388 (412)
Q Consensus       377 ~~~~~~~~~~~~  388 (412)
                      .++++.+.....
T Consensus       521 ~~vll~t~~~~~  532 (746)
T KOG0354|consen  521 KCVLLTTGSEVI  532 (746)
T ss_pred             eEEEEEcchhHH
Confidence            898888854433

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

Probab=100.00  E-value=4.7e-38  Score=253.68  Aligned_cols=334  Identities=41%  Similarity=0.700  Sum_probs=290.9

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHH
Q 015158           39 DTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRE  118 (412)
Q Consensus        39 ~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  118 (412)
                      ..|.++-+.+++.+++...||..|...|.+.++...-|-++++++..|.|||.++.++.++.+........++++|.|++
T Consensus        42 sgfrdfllkpellraivdcgfehpsevqhecipqailgmdvlcqaksgmgktavfvl~tlqqiepv~g~vsvlvmchtre  121 (387)
T KOG0329|consen   42 SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQIEPVDGQVSVLVMCHTRE  121 (387)
T ss_pred             cchhhhhcCHHHHHHHHhccCCCchHhhhhhhhHHhhcchhheecccCCCceeeeehhhhhhcCCCCCeEEEEEEeccHH
Confidence            46778889999999999999999999999999999999999999999999999999999998877666678999999999


Q ss_pred             HHHHHHHHHHHhhccc-CcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhc-c
Q 015158          119 LAQQIEKVMRALGDYL-GVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLS-R  196 (412)
Q Consensus       119 L~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~-~  196 (412)
                      |+-|+.+++..++... +.++..+.|+..++.+...+.+.++|+++||+++..+.++..++++++...|+|||+.++. -
T Consensus       122 lafqi~~ey~rfskymP~vkvaVFfGG~~Ikkdee~lk~~PhivVgTPGrilALvr~k~l~lk~vkhFvlDEcdkmle~l  201 (387)
T KOG0329|consen  122 LAFQISKEYERFSKYMPSVKVSVFFGGLFIKKDEELLKNCPHIVVGTPGRILALVRNRSLNLKNVKHFVLDECDKMLEQL  201 (387)
T ss_pred             HHHHHHHHHHHHHhhCCCceEEEEEcceeccccHHHHhCCCeEEEcCcHHHHHHHHhccCchhhcceeehhhHHHHHHHH
Confidence            9999999988887665 6899999999999988888888899999999999999999999999999999999998764 4


Q ss_pred             CcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCc-cccCCceEEEEEeccchhhHHHHHHHHHh
Q 015158          197 GFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDE-LTLEGIKQFHVNVEKEEWKLETLCDLYET  275 (412)
Q Consensus       197 ~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  275 (412)
                      +.++.+.++.+.-|...|++.+|||++.+..-.+..++.+|..+....+. ....+..+.+..+.. ..+...+.+++..
T Consensus       202 DMrRDvQEifr~tp~~KQvmmfsatlskeiRpvC~kFmQdPmEi~vDdE~KLtLHGLqQ~YvkLke-~eKNrkl~dLLd~  280 (387)
T KOG0329|consen  202 DMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCHKFMQDPMEIFVDDEAKLTLHGLQQYYVKLKE-NEKNRKLNDLLDV  280 (387)
T ss_pred             HHHHHHHHHhhcCcccceeeeeeeecchhhHHHHHhhhcCchhhhccchhhhhhhhHHHHHHhhhh-hhhhhhhhhhhhh
Confidence            56788999999999999999999999999999999999998887776543 445666666666554 4567777777777


Q ss_pred             cCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccC
Q 015158          276 LAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDL  355 (412)
Q Consensus       276 ~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~  355 (412)
                      ..-..++||+.|.....                               |   ..+ +|+|+.+++|+|+.+++.++.++.
T Consensus       281 LeFNQVvIFvKsv~Rl~-------------------------------f---~kr-~vat~lfgrgmdiervNi~~NYdm  325 (387)
T KOG0329|consen  281 LEFNQVVIFVKSVQRLS-------------------------------F---QKR-LVATDLFGRGMDIERVNIVFNYDM  325 (387)
T ss_pred             hhhcceeEeeehhhhhh-------------------------------h---hhh-hHHhhhhccccCcccceeeeccCC
Confidence            77788999999876510                               2   122 889999999999999999999999


Q ss_pred             CCChhhHHHhhhhcccCCCCceEEEEecc-CcHHHHHHHHHHhccccccCChhh
Q 015158          356 PTQPENYLHRIGRSGRFGRKGVAINFVTR-DDERMLFDIQKFYNVVIEELPANV  408 (412)
Q Consensus       356 ~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~  408 (412)
                      |.+...|.+|.||+||.|..|.++.|++. .+.+.+..+++-+...+.++|+.+
T Consensus       326 p~~~DtYlHrv~rAgrfGtkglaitfvs~e~da~iLn~vqdRf~v~i~eLpdei  379 (387)
T KOG0329|consen  326 PEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNPVQDRFEVNIKELPDEI  379 (387)
T ss_pred             CCCchHHHHHhhhhhccccccceeehhcchhhHHHhchhhHhhhccHhhcCccc
Confidence            99999999999999999999999999866 577888888888888888888753

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

Probab=100.00  E-value=1.7e-36  Score=296.44  Aligned_cols=331  Identities=18%  Similarity=0.218  Sum_probs=258.6

Q ss_pred             HHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhc
Q 015158           53 GIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGD  132 (412)
Q Consensus        53 ~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~  132 (412)
                      ...-+|...+++-|.+++..++.|++.+|.+|||.||++||.++++-.      ++-.+||.|..+|++++...+...  
T Consensus       256 l~~~Fg~~~FR~~Q~eaI~~~l~Gkd~fvlmpTG~GKSLCYQlPA~l~------~gitvVISPL~SLm~DQv~~L~~~--  327 (941)
T KOG0351|consen  256 LKEVFGHKGFRPNQLEAINATLSGKDCFVLMPTGGGKSLCYQLPALLL------GGVTVVISPLISLMQDQVTHLSKK--  327 (941)
T ss_pred             HHHHhccccCChhHHHHHHHHHcCCceEEEeecCCceeeEeecccccc------CCceEEeccHHHHHHHHHHhhhhc--
Confidence            334579999999999999999999999999999999999997777532      237999999999999888777543  


Q ss_pred             ccCcEEEEEEcCcchHHH----HHHhcC--CCcEEEeChHHHHHHH--HcCCCCCCC---ceEEEEeCCchhhccC--cH
Q 015158          133 YLGVKVHACVGGTSVRED----QRILSS--GVHVVVGTPGRVFDML--RRQSLRPDN---IRIFVLDEADEMLSRG--FK  199 (412)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~----~~~~~~--~~~iii~T~~~l~~~~--~~~~~~~~~---~~~iiiDE~h~~~~~~--~~  199 (412)
                        ++....+.++......    .....+  ..+|++.|||++...-  ......+..   +.++|+||||++..|+  |+
T Consensus       328 --~I~a~~L~s~q~~~~~~~i~q~l~~~~~~ikilYvtPE~v~~~~~l~~~~~~L~~~~~lal~vIDEAHCVSqWgHdFR  405 (941)
T KOG0351|consen  328 --GIPACFLSSIQTAAERLAILQKLANGNPIIKILYVTPEKVVASEGLLESLADLYARGLLALFVIDEAHCVSQWGHDFR  405 (941)
T ss_pred             --CcceeeccccccHHHHHHHHHHHhCCCCeEEEEEeCHHHhhcccchhhHHHhccCCCeeEEEEecHHHHhhhhccccc
Confidence              7888888888776432    233334  5789999999985421  111122223   7899999999999887  55


Q ss_pred             HHHHHH---HHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhHHHHHHHHHhc
Q 015158          200 DQIYDI---FQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETL  276 (412)
Q Consensus       200 ~~~~~i---~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  276 (412)
                      ....++   ....+ ..+++++|||....+...+...++-.... .......+++....+..-.........+...-..+
T Consensus       406 p~Yk~l~~l~~~~~-~vP~iALTATAT~~v~~DIi~~L~l~~~~-~~~~sfnR~NL~yeV~~k~~~~~~~~~~~~~~~~~  483 (941)
T KOG0351|consen  406 PSYKRLGLLRIRFP-GVPFIALTATATERVREDVIRSLGLRNPE-LFKSSFNRPNLKYEVSPKTDKDALLDILEESKLRH  483 (941)
T ss_pred             HHHHHHHHHHhhCC-CCCeEEeehhccHHHHHHHHHHhCCCCcc-eecccCCCCCceEEEEeccCccchHHHHHHhhhcC
Confidence            544444   44444 47899999999888777777665533222 22333344444444433332222333444444455


Q ss_pred             CCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccCC
Q 015158          277 AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLP  356 (412)
Q Consensus       277 ~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~~  356 (412)
                      ..+.+||||.++..|+.+...|+..++....||++|++.+|..+.+.|..++++|+|+|=++++|+|-|+++.|||++.|
T Consensus       484 ~~~s~IIYC~sr~~ce~vs~~L~~~~~~a~~YHAGl~~~~R~~Vq~~w~~~~~~VivATVAFGMGIdK~DVR~ViH~~lP  563 (941)
T KOG0351|consen  484 PDQSGIIYCLSRKECEQVSAVLRSLGKSAAFYHAGLPPKERETVQKAWMSDKIRVIVATVAFGMGIDKPDVRFVIHYSLP  563 (941)
T ss_pred             CCCCeEEEeCCcchHHHHHHHHHHhchhhHhhhcCCCHHHHHHHHHHHhcCCCeEEEEEeeccCCCCCCceeEEEECCCc
Confidence            77899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHH
Q 015158          357 TQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQK  395 (412)
Q Consensus       357 ~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~  395 (412)
                      .|...|.|-+||+||.|.+..|++|+...|...++.+..
T Consensus       564 ks~E~YYQE~GRAGRDG~~s~C~l~y~~~D~~~l~~ll~  602 (941)
T KOG0351|consen  564 KSFEGYYQEAGRAGRDGLPSSCVLLYGYADISELRRLLT  602 (941)
T ss_pred             hhHHHHHHhccccCcCCCcceeEEecchhHHHHHHHHHH
Confidence            999999999999999999999999999998776665543

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

Probab=100.00  E-value=1.2e-36  Score=262.62  Aligned_cols=329  Identities=19%  Similarity=0.233  Sum_probs=243.4

Q ss_pred             HHHHHHH-CCCCCC-hHHHHhhhhhhhcC-ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHH
Q 015158           50 LLRGIYA-YGFEKP-SAIQQRGIVPFCKG-LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKV  126 (412)
Q Consensus        50 ~~~~l~~-~~~~~l-~~~Q~~a~~~~~~~-~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~  126 (412)
                      +...|+. +|+..+ ++.|+.|+..+.++ +++.|++|||+||++||.++.+..      ++..||+.|..+|..++.+.
T Consensus         7 VreaLKK~FGh~kFKs~LQE~A~~c~VK~k~DVyVsMPTGaGKSLCyQLPaL~~------~gITIV~SPLiALIkDQiDH   80 (641)
T KOG0352|consen    7 VREALKKLFGHKKFKSRLQEQAINCIVKRKCDVYVSMPTGAGKSLCYQLPALVH------GGITIVISPLIALIKDQIDH   80 (641)
T ss_pred             HHHHHHHHhCchhhcChHHHHHHHHHHhccCcEEEeccCCCchhhhhhchHHHh------CCeEEEehHHHHHHHHHHHH
Confidence            3445544 577654 88999999998876 799999999999999999888754      23799999999999999998


Q ss_pred             HHHhhcccCcEEEEEEcCcchHHHHH------HhcCCCcEEEeChHHHHHHHH----cCCCCCCCceEEEEeCCchhhcc
Q 015158          127 MRALGDYLGVKVHACVGGTSVREDQR------ILSSGVHVVVGTPGRVFDMLR----RQSLRPDNIRIFVLDEADEMLSR  196 (412)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~iii~T~~~l~~~~~----~~~~~~~~~~~iiiDE~h~~~~~  196 (412)
                      +..+    .+.+..+.+..+..+...      .......+++.||++......    +...+.+.+.++++||+|+++.|
T Consensus        81 L~~L----KVp~~SLNSKlSt~ER~ri~~DL~~ekp~~K~LYITPE~AAt~~FQ~lLn~L~~r~~L~Y~vVDEAHCVSQW  156 (641)
T KOG0352|consen   81 LKRL----KVPCESLNSKLSTVERSRIMGDLAKEKPTIKMLYITPEGAATDGFQKLLNGLANRDVLRYIVVDEAHCVSQW  156 (641)
T ss_pred             HHhc----CCchhHhcchhhHHHHHHHHHHHHhcCCceeEEEEchhhhhhhhHHHHHHHHhhhceeeeEEechhhhHhhh
Confidence            8886    444444444433333222      223456899999987533221    22222345789999999999988


Q ss_pred             C--cHHH---HHHHHHhCCCCceEEEEeecCChHHHHHHHHh--cCCCeEEEecCCccccCCceEEEEEeccch---hhH
Q 015158          197 G--FKDQ---IYDIFQLLPPKIQVGVFSATMPPEALEITRKF--MNKPVRILVKRDELTLEGIKQFHVNVEKEE---WKL  266 (412)
Q Consensus       197 ~--~~~~---~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~  266 (412)
                      +  |+..   +-.+.+.+ +....+.+|||..+.+.+.+..-  +.+|+.+...+...     ...++.....+   +..
T Consensus       157 GHDFRPDYL~LG~LRS~~-~~vpwvALTATA~~~VqEDi~~qL~L~~PVAiFkTP~FR-----~NLFYD~~~K~~I~D~~  230 (641)
T KOG0352|consen  157 GHDFRPDYLTLGSLRSVC-PGVPWVALTATANAKVQEDIAFQLKLRNPVAIFKTPTFR-----DNLFYDNHMKSFITDCL  230 (641)
T ss_pred             ccccCcchhhhhhHHhhC-CCCceEEeecccChhHHHHHHHHHhhcCcHHhccCcchh-----hhhhHHHHHHHHhhhHh
Confidence            7  4443   34444444 47789999999998887766543  34454333222111     11122111111   112


Q ss_pred             HHHHHHHHhc-------------CCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEE
Q 015158          267 ETLCDLYETL-------------AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLI  333 (412)
Q Consensus       267 ~~l~~~~~~~-------------~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv  333 (412)
                      ..|.++-...             ..+-.||||.+++++++++-.|...|+....||.++...+|..+.+.|.+++..||+
T Consensus       231 ~~LaDF~~~~LG~~~~~~~~~K~~~GCGIVYCRTR~~cEq~AI~l~~~Gi~A~AYHAGLK~~ERTeVQe~WM~~~~PvI~  310 (641)
T KOG0352|consen  231 TVLADFSSSNLGKHEKASQNKKTFTGCGIVYCRTRNECEQVAIMLEIAGIPAMAYHAGLKKKERTEVQEKWMNNEIPVIA  310 (641)
T ss_pred             HhHHHHHHHhcCChhhhhcCCCCcCcceEEEeccHHHHHHHHHHhhhcCcchHHHhcccccchhHHHHHHHhcCCCCEEE
Confidence            2222222111             125689999999999999999999999999999999999999999999999999999


Q ss_pred             EcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHH
Q 015158          334 TTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQ  394 (412)
Q Consensus       334 ~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~  394 (412)
                      +|..+++|+|-|+++.||+++.+.|++-|-|..||+||.|++..|-+++...|...++-+.
T Consensus       311 AT~SFGMGVDKp~VRFViHW~~~qn~AgYYQESGRAGRDGk~SyCRLYYsR~D~~~i~FLi  371 (641)
T KOG0352|consen  311 ATVSFGMGVDKPDVRFVIHWSPSQNLAGYYQESGRAGRDGKRSYCRLYYSRQDKNALNFLV  371 (641)
T ss_pred             EEeccccccCCcceeEEEecCchhhhHHHHHhccccccCCCccceeeeecccchHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999887765443

>PRK14701 reverse gyrase; Provisional

Probab=100.00  E-value=8.9e-36  Score=308.41  Aligned_cols=324  Identities=19%  Similarity=0.177  Sum_probs=243.2

Q ss_pred             HHHHHHHH-CCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHH
Q 015158           49 NLLRGIYA-YGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVM  127 (412)
Q Consensus        49 ~~~~~l~~-~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~  127 (412)
                      ++.+.++. .|| +|++.|+++++.++.|+++++.+|||+|||++++++++....   .+.+++|++||++|+.|+.+.+
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-EFWSIQKTWAKRILRGKSFSIVAPTGMGKSTFGAFIALFLAL---KGKKCYIILPTTLLVKQTVEKI  142 (1638)
T ss_pred             HHHHHHHHhhCC-CCCHHHHHHHHHHHcCCCEEEEEcCCCCHHHHHHHHHHHHHh---cCCeEEEEECHHHHHHHHHHHH
Confidence            44455555 799 499999999999999999999999999999976555544322   3458999999999999999999


Q ss_pred             HHhhccc--CcEEEEEEcCcchHHHHH----HhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhcc-----
Q 015158          128 RALGDYL--GVKVHACVGGTSVREDQR----ILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSR-----  196 (412)
Q Consensus       128 ~~~~~~~--~~~~~~~~~~~~~~~~~~----~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~-----  196 (412)
                      ..++...  +..+..++|+........    ...+.++|+|+||+.+...+... . ..+++++|+||||+++.+     
T Consensus       143 ~~l~~~~~~~v~v~~~~g~~s~~e~~~~~~~l~~g~~dILV~TPgrL~~~~~~l-~-~~~i~~iVVDEAD~ml~~~knid  220 (1638)
T PRK14701        143 ESFCEKANLDVRLVYYHSNLRKKEKEEFLERIENGDFDILVTTAQFLARNFPEM-K-HLKFDFIFVDDVDAFLKASKNID  220 (1638)
T ss_pred             HHHHhhcCCceeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECCchhHHhHHHH-h-hCCCCEEEEECceeccccccccc
Confidence            9987654  456677888877554422    23456899999999988766532 1 267899999999999763     


Q ss_pred             ------CcHHHHHH----HHH----------------------hCCCCce-EEEEeecCChHHHHHHHHhcCCCeEEEec
Q 015158          197 ------GFKDQIYD----IFQ----------------------LLPPKIQ-VGVFSATMPPEALEITRKFMNKPVRILVK  243 (412)
Q Consensus       197 ------~~~~~~~~----i~~----------------------~~~~~~~-~i~~SAT~~~~~~~~~~~~~~~~~~~~~~  243 (412)
                            +|...+..    ++.                      .++...+ .+..|||+++.  .....++..+..+...
T Consensus       221 ~~L~llGF~~e~~~~~~~il~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~ll~~SAT~~~r--~~~~~l~~~~l~f~v~  298 (1638)
T PRK14701        221 RSLQLLGFYEEIIEKAWKIIYLKKQGNIEDAMEKREILNKEIEKIGNKIGCLIVASATGKAK--GDRVKLYRELLGFEVG  298 (1638)
T ss_pred             hhhhcCCChHHHHHHHHHhhhcccccccchhhhhhhhhhhhhhhcCCCccEEEEEecCCCch--hHHHHHhhcCeEEEec
Confidence                  56555543    221                      2334444 57799999753  2223445566666666


Q ss_pred             CCccccCCceEEEEEeccchhhHHHHHHHHHhcCCCcEEEEEcchhH---HHHHHHHHhcCCCeeEEecCCCCHHHHHHH
Q 015158          244 RDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRK---VDWLTDKMRSRDHTVSATHGDMDQNTRDII  320 (412)
Q Consensus       244 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lif~~~~~~---~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~  320 (412)
                      .......++.+.+..... ..+ ..+.++++.. ...+||||++++.   |+.+++.|++.|+.+..+||+     |...
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 SGRSALRNIVDVYLNPEK-IIK-EHVRELLKKL-GKGGLIFVPIDEGAEKAEEIEKYLLEDGFKIELVSAK-----NKKG  370 (1638)
T ss_pred             CCCCCCCCcEEEEEECCH-HHH-HHHHHHHHhC-CCCeEEEEeccccchHHHHHHHHHHHCCCeEEEecch-----HHHH
Confidence            655556667777665433 222 4677777765 4689999999875   589999999999999999985     8899


Q ss_pred             HHHHhcCCCcEEEEcC----CCcCCCCCCC-CCEEEEccCCC---ChhhHHHhh-------------hhcccCCCCceEE
Q 015158          321 MREFRSGSSRVLITTD----LLARGIDVQQ-VSLVINYDLPT---QPENYLHRI-------------GRSGRFGRKGVAI  379 (412)
Q Consensus       321 ~~~f~~g~~~vlv~t~----~~~~G~d~~~-~~~vi~~~~~~---s~~~~~Q~~-------------GR~~R~g~~g~~~  379 (412)
                      +++|++|+.+|||+|.    .+.+|+|+|+ +++||+++.|.   |...+.|..             ||++|.|.++.++
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   776555554             9999999988887


Q ss_pred             EEeccCcHH
Q 015158          380 NFVTRDDER  388 (412)
Q Consensus       380 ~~~~~~~~~  388 (412)
                      ..+...+..
T Consensus       451 ~~~~~~~~~  459 (1638)
T PRK14701        451 LDVFPEDVE  459 (1638)
T ss_pred             HHhHHHHHH
Confidence            444444433

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

Probab=100.00  E-value=1.1e-35  Score=253.34  Aligned_cols=351  Identities=18%  Similarity=0.242  Sum_probs=267.9

Q ss_pred             CCCCCCCCChhhhcccccc--CCCCHHHHHHHHH-CCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhh
Q 015158           25 SDGQDFFTSYDEVYDTFDA--MGLQENLLRGIYA-YGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQL  101 (412)
Q Consensus        25 ~~~~~~~~~~~~~~~~f~~--~~l~~~~~~~l~~-~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~  101 (412)
                      .++......++.....|+.  ++.+....+.|++ +....++|.|..+++..+.+.++++..|||.||++||.++++-. 
T Consensus        55 dsdag~~~eyd~spaawdkd~fpws~e~~~ilk~~f~lekfrplq~~ain~~ma~ed~~lil~tgggkslcyqlpal~a-  133 (695)
T KOG0353|consen   55 DSDAGASNEYDRSPAAWDKDDFPWSDEAKDILKEQFHLEKFRPLQLAAINATMAGEDAFLILPTGGGKSLCYQLPALCA-  133 (695)
T ss_pred             cccccccccccCCccccccCCCCCchHHHHHHHHHhhHHhcChhHHHHhhhhhccCceEEEEeCCCccchhhhhhHHhc-
Confidence            3444455556665556664  4566777777765 67778999999999999999999999999999999999888643 


Q ss_pred             ccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHH------HhcCCCcEEEeChHHHHH-----
Q 015158          102 DYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQR------ILSSGVHVVVGTPGRVFD-----  170 (412)
Q Consensus       102 ~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~iii~T~~~l~~-----  170 (412)
                           .+.+|++||..+|++++.-+++.+    |+....+......+....      ....+..+++.||+++..     
T Consensus       134 -----dg~alvi~plislmedqil~lkql----gi~as~lnansske~~k~v~~~i~nkdse~kliyvtpekiaksk~~m  204 (695)
T KOG0353|consen  134 -----DGFALVICPLISLMEDQILQLKQL----GIDASMLNANSSKEEAKRVEAAITNKDSEFKLIYVTPEKIAKSKKFM  204 (695)
T ss_pred             -----CCceEeechhHHHHHHHHHHHHHh----CcchhhccCcccHHHHHHHHHHHcCCCceeEEEEecHHHHHHHHHHH
Confidence                 247999999999999999888887    666666665555433211      123456899999998753     


Q ss_pred             -HHHcCCCCCCCceEEEEeCCchhhccC--cHH---HHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecC
Q 015158          171 -MLRRQSLRPDNIRIFVLDEADEMLSRG--FKD---QIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKR  244 (412)
Q Consensus       171 -~~~~~~~~~~~~~~iiiDE~h~~~~~~--~~~---~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~  244 (412)
                       .++ ..+....+.+|-+||+|+...|+  |+.   .+.-+.+.+ ++.+++++|||...++....+..++-...+.+..
T Consensus       205 nkle-ka~~~~~~~~iaidevhccsqwghdfr~dy~~l~ilkrqf-~~~~iigltatatn~vl~d~k~il~ie~~~tf~a  282 (695)
T KOG0353|consen  205 NKLE-KALEAGFFKLIAIDEVHCCSQWGHDFRPDYKALGILKRQF-KGAPIIGLTATATNHVLDDAKDILCIEAAFTFRA  282 (695)
T ss_pred             HHHH-HHhhcceeEEEeecceeehhhhCcccCcchHHHHHHHHhC-CCCceeeeehhhhcchhhHHHHHHhHHhhheeec
Confidence             222 23345678999999999999887  433   333333444 5788999999999888887777665433332222


Q ss_pred             CccccCCceEEEEEecc-chhhHHHHHHHHHhc-CCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHH
Q 015158          245 DELTLEGIKQFHVNVEK-EEWKLETLCDLYETL-AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMR  322 (412)
Q Consensus       245 ~~~~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~-~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~  322 (412)
                       ...+++...-+..-+. .++..+.+..+++.. .+...||||-|++.++.++..|+.+|+....+|..+.+.++.-..+
T Consensus       283 -~fnr~nl~yev~qkp~n~dd~~edi~k~i~~~f~gqsgiiyc~sq~d~ekva~alkn~gi~a~~yha~lep~dks~~hq  361 (695)
T KOG0353|consen  283 -GFNRPNLKYEVRQKPGNEDDCIEDIAKLIKGDFAGQSGIIYCFSQKDCEKVAKALKNHGIHAGAYHANLEPEDKSGAHQ  361 (695)
T ss_pred             -ccCCCCceeEeeeCCCChHHHHHHHHHHhccccCCCcceEEEeccccHHHHHHHHHhcCccccccccccCccccccccc
Confidence             2333444443333332 233445555555543 5567899999999999999999999999999999999999999999


Q ss_pred             HHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccCCCChhhHHH--------------------------------------
Q 015158          323 EFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLH--------------------------------------  364 (412)
Q Consensus       323 ~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q--------------------------------------  364 (412)
                      .|..|++.|+|+|-++++|+|-|+++.||+-++|.|...|-|                                      
T Consensus       362 ~w~a~eiqvivatvafgmgidkpdvrfvihhsl~ksienyyqasarillrmtkqknksdtggstqinilevctnfkiffa  441 (695)
T KOG0353|consen  362 GWIAGEIQVIVATVAFGMGIDKPDVRFVIHHSLPKSIENYYQASARILLRMTKQKNKSDTGGSTQINILEVCTNFKIFFA  441 (695)
T ss_pred             cccccceEEEEEEeeecccCCCCCeeEEEecccchhHHHHHHHHHHHHHHHhhhcccccCCCcceeehhhhhccceeeee
Confidence            999999999999999999999999999999999999999999                                      


Q ss_pred             -----hhhhcccCCCCceEEEEeccCcHH
Q 015158          365 -----RIGRSGRFGRKGVAINFVTRDDER  388 (412)
Q Consensus       365 -----~~GR~~R~g~~g~~~~~~~~~~~~  388 (412)
                           ..||+||.+.+..|++++.-.|--
T Consensus       442 vfsekesgragrd~~~a~cilyy~~~dif  470 (695)
T KOG0353|consen  442 VFSEKESGRAGRDDMKADCILYYGFADIF  470 (695)
T ss_pred             eecchhccccccCCCcccEEEEechHHHH
Confidence                 679999999999999998765543

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=100.00  E-value=1.5e-34  Score=262.92  Aligned_cols=289  Identities=16%  Similarity=0.229  Sum_probs=199.5

Q ss_pred             HHHhhhhhhhcCcc--EEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcc----cCcEE
Q 015158           65 IQQRGIVPFCKGLD--VIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDY----LGVKV  138 (412)
Q Consensus        65 ~Q~~a~~~~~~~~~--~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~----~~~~~  138 (412)
                      ||.++++.+.++.+  +++.+|||+|||.+++++++..      ..++++++|+++|++|+.+.+..+...    .+..+
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  7889999999999999888742      236899999999999999999887632    25566


Q ss_pred             EEEEcCcchH--HH------------------HHHhcCCCcEEEeChHHHHHHHHcCCC--------CCCCceEEEEeCC
Q 015158          139 HACVGGTSVR--ED------------------QRILSSGVHVVVGTPGRVFDMLRRQSL--------RPDNIRIFVLDEA  190 (412)
Q Consensus       139 ~~~~~~~~~~--~~------------------~~~~~~~~~iii~T~~~l~~~~~~~~~--------~~~~~~~iiiDE~  190 (412)
                      ..++|.....  ..                  .......+.|+++||+.|..++.....        ...++++||+||+
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            6666653221  00                  011134678999999999766543211        1367899999999


Q ss_pred             chhhccCc-----HHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHh--cCCCeEEEecC-----C------cc-----
Q 015158          191 DEMLSRGF-----KDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKF--MNKPVRILVKR-----D------EL-----  247 (412)
Q Consensus       191 h~~~~~~~-----~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~--~~~~~~~~~~~-----~------~~-----  247 (412)
                      |.+..+..     ......++.......+++++|||+++.....+...  ++.+.......     +      ..     
T Consensus       155 H~~~~~~~~~~~~~l~~~~~~~~~~~~~~~i~lSAT~~~~~~~~l~~~~~~~~~~~~v~g~~~~~~~~~~~~~~~~~~~~  234 (357)
T TIGR03158       155 HLYDAKQLVGMLFLLAYMQLIRFFECRRKFVFLSATPDPALILRLQNAKQAGVKIAPIDGEKYQFPDNPELEADNKTQSF  234 (357)
T ss_pred             cccCcccchhhhhhhHHHHHHHhhhcCCcEEEEecCCCHHHHHHHHhccccCceeeeecCcccccCCChhhhcccccccc
Confidence            98764331     12333344433445789999999998877777765  34333221111     0      00     


Q ss_pred             --ccCCceEEEEEeccchhhHHHHHH-------HHHhcCCCcEEEEEcchhHHHHHHHHHhcCC--CeeEEecCCCCHHH
Q 015158          248 --TLEGIKQFHVNVEKEEWKLETLCD-------LYETLAITQSVIFVNTRRKVDWLTDKMRSRD--HTVSATHGDMDQNT  316 (412)
Q Consensus       248 --~~~~~~~~~~~~~~~~~~~~~l~~-------~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~--~~~~~~~~~~~~~~  316 (412)
                        ..+.+...+..  ....+...+..       .++....+++||||++++.++.+++.|++.+  ..+..+||.+++.+
T Consensus       235 ~~~~~~i~~~~~~--~~~~~~~~l~~l~~~i~~~~~~~~~~k~LIf~nt~~~~~~l~~~L~~~~~~~~~~~l~g~~~~~~  312 (357)
T TIGR03158       235 RPVLPPVELELIP--APDFKEEELSELAEEVIERFRQLPGERGAIILDSLDEVNRLSDLLQQQGLGDDIGRITGFAPKKD  312 (357)
T ss_pred             ceeccceEEEEEe--CCchhHHHHHHHHHHHHHHHhccCCCeEEEEECCHHHHHHHHHHHhhhCCCceEEeeecCCCHHH
Confidence              00123333333  11222222222       2222345799999999999999999999864  57888999999988


Q ss_pred             HHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcc
Q 015158          317 RDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSG  370 (412)
Q Consensus       317 r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~  370 (412)
                      |.+.      ++.++||||+++++|+|++.. +|| ++ |.+...|+||+||+|
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            8644      478899999999999999976 555 34 889999999999987

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.

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

Probab=100.00  E-value=2.6e-34  Score=265.41  Aligned_cols=318  Identities=20%  Similarity=0.258  Sum_probs=245.2

Q ss_pred             HHHHHHCCCCCChHHHHhhhhhhhcC------ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHH
Q 015158           51 LRGIYAYGFEKPSAIQQRGIVPFCKG------LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIE  124 (412)
Q Consensus        51 ~~~l~~~~~~~l~~~Q~~a~~~~~~~------~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~  124 (412)
                      .+.+...+|. |+..|++++..|...      .+-++++..|||||.+++++++..+..+.   ++.+.+||.-|++|.+
T Consensus       253 ~~~~~~LPF~-LT~aQ~~vi~EI~~Dl~~~~~M~RLlQGDVGSGKTvVA~laml~ai~~G~---Q~ALMAPTEILA~QH~  328 (677)
T COG1200         253 AKFLAALPFK-LTNAQKRVIKEILADLASPVPMNRLLQGDVGSGKTVVALLAMLAAIEAGY---QAALMAPTEILAEQHY  328 (677)
T ss_pred             HHHHHhCCCC-ccHHHHHHHHHHHhhhcCchhhHHHhccCcCCCHHHHHHHHHHHHHHcCC---eeEEeccHHHHHHHHH
Confidence            3455667898 999999999999874      35699999999999999999999988764   8999999999999999


Q ss_pred             HHHHHhhcccCcEEEEEEcCcchHHHH----HHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHH
Q 015158          125 KVMRALGDYLGVKVHACVGGTSVREDQ----RILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKD  200 (412)
Q Consensus       125 ~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~  200 (412)
                      +.+.++....++.+..++|..+.....    ....+..+|+|+|+     .+......+++++++|+||=|++     +-
T Consensus       329 ~~~~~~l~~~~i~V~lLtG~~kgk~r~~~l~~l~~G~~~ivVGTH-----ALiQd~V~F~~LgLVIiDEQHRF-----GV  398 (677)
T COG1200         329 ESLRKWLEPLGIRVALLTGSLKGKARKEILEQLASGEIDIVVGTH-----ALIQDKVEFHNLGLVIIDEQHRF-----GV  398 (677)
T ss_pred             HHHHHHhhhcCCeEEEeecccchhHHHHHHHHHhCCCCCEEEEcc-----hhhhcceeecceeEEEEeccccc-----cH
Confidence            999999999999999999988765543    34457799999994     44455566789999999999994     33


Q ss_pred             HHHHHHHhCCC-CceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhHHHHHHHHHhcCCC
Q 015158          201 QIYDIFQLLPP-KIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAIT  279 (412)
Q Consensus       201 ~~~~i~~~~~~-~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  279 (412)
                      .=+..+..... .+.++.|||||-|....+.  .+++...-.+......+..+...+..........+.+.+-+.  .+.
T Consensus       399 ~QR~~L~~KG~~~Ph~LvMTATPIPRTLAlt--~fgDldvS~IdElP~GRkpI~T~~i~~~~~~~v~e~i~~ei~--~Gr  474 (677)
T COG1200         399 HQRLALREKGEQNPHVLVMTATPIPRTLALT--AFGDLDVSIIDELPPGRKPITTVVIPHERRPEVYERIREEIA--KGR  474 (677)
T ss_pred             HHHHHHHHhCCCCCcEEEEeCCCchHHHHHH--HhccccchhhccCCCCCCceEEEEeccccHHHHHHHHHHHHH--cCC
Confidence            33333333334 6789999999988654433  344433333333333334455555544443333444443333  456


Q ss_pred             cEEEEEcchh--------HHHHHHHHHhcC--CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCE
Q 015158          280 QSVIFVNTRR--------KVDWLTDKMRSR--DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSL  349 (412)
Q Consensus       280 k~lif~~~~~--------~~~~~~~~L~~~--~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~  349 (412)
                      ++.+.|+-++        .++..++.|+..  +..+..+||.|+..++++++++|++|+++|||+|..+++|||+|+++.
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            8999998664        456677777754  456999999999999999999999999999999999999999999999


Q ss_pred             EEEccC-CCChhhHHHhhhhcccCCCCceEEEEeccCc
Q 015158          350 VINYDL-PTQPENYLHRIGRSGRFGRKGVAINFVTRDD  386 (412)
Q Consensus       350 vi~~~~-~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~  386 (412)
                      +++.+. .+..+++.|.-||+||.+..+.|++++.+..
T Consensus       555 MVIe~AERFGLaQLHQLRGRVGRG~~qSyC~Ll~~~~~  592 (677)
T COG1200         555 MVIENAERFGLAQLHQLRGRVGRGDLQSYCVLLYKPPL  592 (677)
T ss_pred             EEEechhhhhHHHHHHhccccCCCCcceEEEEEeCCCC
Confidence            987643 4667999999999999999999999998876

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=100.00  E-value=2e-34  Score=272.21  Aligned_cols=317  Identities=20%  Similarity=0.192  Sum_probs=236.8

Q ss_pred             CCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcE
Q 015158           58 GFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVK  137 (412)
Q Consensus        58 ~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~  137 (412)
                      |.. |++.|..++..++.|+  +..+.||+|||+++.++++.....+   +.++|++||..|+.|.++.+..++...++.
T Consensus       101 g~~-p~~VQ~~~~~~ll~G~--Iae~~TGeGKTla~~lp~~~~al~G---~~v~VvTptreLA~qdae~~~~l~~~lGls  174 (656)
T PRK12898        101 GQR-HFDVQLMGGLALLSGR--LAEMQTGEGKTLTATLPAGTAALAG---LPVHVITVNDYLAERDAELMRPLYEALGLT  174 (656)
T ss_pred             CCC-CChHHHHHHHHHhCCC--eeeeeCCCCcHHHHHHHHHHHhhcC---CeEEEEcCcHHHHHHHHHHHHHHHhhcCCE
Confidence            555 9999999999999998  9999999999999999999775544   589999999999999999999999989999


Q ss_pred             EEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCC--------------------------CCCCCceEEEEeCCc
Q 015158          138 VHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQS--------------------------LRPDNIRIFVLDEAD  191 (412)
Q Consensus       138 ~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~--------------------------~~~~~~~~iiiDE~h  191 (412)
                      +..+.|+.+..  ......+++|+++|...|.--+.+..                          ...+.+.+.|+||++
T Consensus       175 v~~i~gg~~~~--~r~~~y~~dIvygT~~e~~FDyLrd~~~~~~~~~~~~~~~~~l~~~~~~~~~~v~r~~~~aIvDEvD  252 (656)
T PRK12898        175 VGCVVEDQSPD--ERRAAYGADITYCTNKELVFDYLRDRLALGQRASDARLALESLHGRSSRSTQLLLRGLHFAIVDEAD  252 (656)
T ss_pred             EEEEeCCCCHH--HHHHHcCCCEEEECCCchhhhhccccccccccccchhhhhhhhccccCchhhhcccccceeEeeccc
Confidence            99999987643  33344678999999988733222211                          113557789999999


Q ss_pred             hhh-ccC-----------------cHHHHHHHHHhCC-------------------------------------------
Q 015158          192 EML-SRG-----------------FKDQIYDIFQLLP-------------------------------------------  210 (412)
Q Consensus       192 ~~~-~~~-----------------~~~~~~~i~~~~~-------------------------------------------  210 (412)
                      .++ +..                 +......+...+.                                           
T Consensus       253 SiLiDeartpliis~~~~~~~~~~~y~~~~~~~~~l~~~~~y~~d~~~~~v~lt~~g~~~~e~~~~~l~~~~~~~~~~~~  332 (656)
T PRK12898        253 SVLIDEARTPLIISAPAKEADEAEVYRQALELAAQLKEGEDYTIDAAEKRIELTEAGRARIAELAESLPPAWRGAVRREE  332 (656)
T ss_pred             ceeeccCCCceEEECCCCCCchhHHHHHHHHHHHhcCCCCceEEECCCCeEEEcHHHHHHHHHHhCcchhhcccchHHHH
Confidence            643 100                 0000000100000                                           


Q ss_pred             --------------------------------------------------------------------------CCceEE
Q 015158          211 --------------------------------------------------------------------------PKIQVG  216 (412)
Q Consensus       211 --------------------------------------------------------------------------~~~~~i  216 (412)
                                                                                                .-.++.
T Consensus       333 ~i~~Al~A~~l~~~d~dYiV~d~~V~ivD~~TGR~~~gr~w~~GLhQaieaKE~v~i~~e~~t~a~It~q~~Fr~Y~kl~  412 (656)
T PRK12898        333 LVRQALSALHLFRRDEHYIVRDGKVVIVDEFTGRVMPDRSWEDGLHQMIEAKEGCELTDPRETLARITYQRFFRRYLRLA  412 (656)
T ss_pred             HHHHHHHHHHHHhcCCceEEECCeEEEEECCCCeECCCCCcChHHHHHHHHhcCCCCCcCceeeeeehHHHHHHhhHHHh
Confidence                                                                                      013688


Q ss_pred             EEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhHHHHHHHHHhc--CCCcEEEEEcchhHHHHH
Q 015158          217 VFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETL--AITQSVIFVNTRRKVDWL  294 (412)
Q Consensus       217 ~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~--~~~k~lif~~~~~~~~~~  294 (412)
                      +||||......++...+...++.+........  ...+.++..+ ...+...+.+.+...  ...++||||++++.++.+
T Consensus       413 GmTGTa~~~~~El~~~y~l~vv~IPt~kp~~r--~~~~~~v~~t-~~~K~~aL~~~i~~~~~~~~pvLIft~t~~~se~L  489 (656)
T PRK12898        413 GMTGTAREVAGELWSVYGLPVVRIPTNRPSQR--RHLPDEVFLT-AAAKWAAVAARVRELHAQGRPVLVGTRSVAASERL  489 (656)
T ss_pred             cccCcChHHHHHHHHHHCCCeEEeCCCCCccc--eecCCEEEeC-HHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHH
Confidence            99999987665555555555555444443321  1222233333 355777777777664  246899999999999999


Q ss_pred             HHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCC---CCC-----EEEEccCCCChhhHHHhh
Q 015158          295 TDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQ---QVS-----LVINYDLPTQPENYLHRI  366 (412)
Q Consensus       295 ~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~---~~~-----~vi~~~~~~s~~~~~Q~~  366 (412)
                      ++.|.+.|+.+..+||.+..  ++..+..+..+...|+|||+++++|+|++   .+.     +||.++.|.|...|.|++
T Consensus       490 ~~~L~~~gi~~~~Lhg~~~~--rE~~ii~~ag~~g~VlVATdmAgRGtDI~l~~~V~~~GGLhVI~~d~P~s~r~y~hr~  567 (656)
T PRK12898        490 SALLREAGLPHQVLNAKQDA--EEAAIVARAGQRGRITVATNMAGRGTDIKLEPGVAARGGLHVILTERHDSARIDRQLA  567 (656)
T ss_pred             HHHHHHCCCCEEEeeCCcHH--HHHHHHHHcCCCCcEEEEccchhcccCcCCccchhhcCCCEEEEcCCCCCHHHHHHhc
Confidence            99999999999999998654  44455555656677999999999999999   565     999999999999999999


Q ss_pred             hhcccCCCCceEEEEeccCcH
Q 015158          367 GRSGRFGRKGVAINFVTRDDE  387 (412)
Q Consensus       367 GR~~R~g~~g~~~~~~~~~~~  387 (412)
                      ||+||.|.+|.++.|++..|.
T Consensus       568 GRTGRqG~~G~s~~~is~eD~  588 (656)
T PRK12898        568 GRCGRQGDPGSYEAILSLEDD  588 (656)
T ss_pred             ccccCCCCCeEEEEEechhHH
Confidence            999999999999999998664

>TIGR01054 rgy reverse gyrase

Probab=100.00  E-value=4.6e-34  Score=290.31  Aligned_cols=291  Identities=21%  Similarity=0.260  Sum_probs=211.5

Q ss_pred             HHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHH
Q 015158           49 NLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMR  128 (412)
Q Consensus        49 ~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~  128 (412)
                      ++.+.+.......|+++|+.+++.++.|+++++.+|||+|||..+ +++...+..  .+.+++|++||++|+.|+.+.+.
T Consensus        66 ~f~~~f~~~~g~~p~~iQ~~~i~~il~G~d~vi~ApTGsGKT~f~-l~~~~~l~~--~g~~vLIL~PTreLa~Qi~~~l~  142 (1171)
T TIGR01054        66 EFEEFFKKAVGSEPWSIQKMWAKRVLRGDSFAIIAPTGVGKTTFG-LAMSLFLAK--KGKRCYIILPTTLLVIQVAEKIS  142 (1171)
T ss_pred             HHHHHHHHhcCCCCcHHHHHHHHHHhCCCeEEEECCCCCCHHHHH-HHHHHHHHh--cCCeEEEEeCHHHHHHHHHHHHH
Confidence            344445443334599999999999999999999999999999744 444433322  25689999999999999999999


Q ss_pred             HhhcccCcEE---EEEEcCcchHHHH----HHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhc------
Q 015158          129 ALGDYLGVKV---HACVGGTSVREDQ----RILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLS------  195 (412)
Q Consensus       129 ~~~~~~~~~~---~~~~~~~~~~~~~----~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~------  195 (412)
                      .+....++..   ..++|+.+.....    ....++++|+|+||+.|...+....  . +++++|+||||++++      
T Consensus       143 ~l~~~~~i~~~~i~~~~Gg~~~~e~~~~~~~l~~~~~dIlV~Tp~rL~~~~~~l~--~-~~~~iVvDEaD~~L~~~k~vd  219 (1171)
T TIGR01054       143 SLAEKAGVGTVNIGAYHSRLPTKEKKEFMERIENGDFDILITTTMFLSKNYDELG--P-KFDFIFVDDVDALLKASKNVD  219 (1171)
T ss_pred             HHHHhcCCceeeeeeecCCCCHHHHHHHHHHHhcCCCCEEEECHHHHHHHHHHhc--C-CCCEEEEeChHhhhhccccHH
Confidence            9887666543   3467776654432    2233568999999999988776422  2 799999999999987      


Q ss_pred             -----cCcHHH-HHHH----------------------HHhCCCCce--EEEEeecC-ChHHHHHHHHhcCCCeEEEecC
Q 015158          196 -----RGFKDQ-IYDI----------------------FQLLPPKIQ--VGVFSATM-PPEALEITRKFMNKPVRILVKR  244 (412)
Q Consensus       196 -----~~~~~~-~~~i----------------------~~~~~~~~~--~i~~SAT~-~~~~~~~~~~~~~~~~~~~~~~  244 (412)
                           .+|... +..+                      +..++...+  ++++|||. +....   ..++.....+....
T Consensus       220 ~il~llGF~~e~i~~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~li~~SAT~~p~~~~---~~l~r~ll~~~v~~  296 (1171)
T TIGR01054       220 KLLKLLGFSEELIEKAWKLIRLRLKLYRALHAKKRLELLEAIPGKKRGCLIVSSATGRPRGKR---AKLFRELLGFEVGG  296 (1171)
T ss_pred             HHHHHcCCCHHHHHHHHHHhhhccccchHHHHHHHHHHHHhhhhccCcEEEEEeCCCCccccH---HHHcccccceEecC
Confidence                 345442 3332                      223333433  56789994 33222   12344444455555


Q ss_pred             CccccCCceEEEEEeccchhhHHHHHHHHHhcCCCcEEEEEcch---hHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHH
Q 015158          245 DELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTR---RKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIM  321 (412)
Q Consensus       245 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lif~~~~---~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~  321 (412)
                      ......++.+.+.....   +...+.++++... .++||||+++   +.|+.+++.|++.|+.+..+||+++    ...+
T Consensus       297 ~~~~~r~I~~~~~~~~~---~~~~L~~ll~~l~-~~~IVFv~t~~~~~~a~~l~~~L~~~g~~a~~lhg~~~----~~~l  368 (1171)
T TIGR01054       297 GSDTLRNVVDVYVEDED---LKETLLEIVKKLG-TGGIVYVSIDYGKEKAEEIAEFLENHGVKAVAYHATKP----KEDY  368 (1171)
T ss_pred             ccccccceEEEEEeccc---HHHHHHHHHHHcC-CCEEEEEeccccHHHHHHHHHHHHhCCceEEEEeCCCC----HHHH
Confidence            44455666666654332   2345666766653 6899999999   9999999999999999999999986    3689


Q ss_pred             HHHhcCCCcEEEEc----CCCcCCCCCCC-CCEEEEccCC
Q 015158          322 REFRSGSSRVLITT----DLLARGIDVQQ-VSLVINYDLP  356 (412)
Q Consensus       322 ~~f~~g~~~vlv~t----~~~~~G~d~~~-~~~vi~~~~~  356 (412)
                      +.|++|+++|||+|    +.+++|+|+|+ +++||+++.|
T Consensus       369 ~~Fr~G~~~vLVata~~tdv~aRGIDip~~V~~vI~~~~P  408 (1171)
T TIGR01054       369 EKFAEGEIDVLIGVASYYGTLVRGLDLPERVRYAVFLGVP  408 (1171)
T ss_pred             HHHHcCCCCEEEEeccccCcccccCCCCccccEEEEECCC
Confidence            99999999999995    89999999999 8999986655

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.

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

Probab=100.00  E-value=6e-35  Score=277.08  Aligned_cols=329  Identities=21%  Similarity=0.280  Sum_probs=240.2

Q ss_pred             HCCCCCChHHHHhhhhhhhc-CccEEEECCCCCCchhHhHHHHHHhhcc-------CCCceeEEEEcCCHHHHHHHHHHH
Q 015158           56 AYGFEKPSAIQQRGIVPFCK-GLDVIQQAQSGTGKTATFCSGILQQLDY-------GLVECQALVLAPTRELAQQIEKVM  127 (412)
Q Consensus        56 ~~~~~~l~~~Q~~a~~~~~~-~~~~lv~~~tGsGKT~~~~~~~~~~~~~-------~~~~~~~lil~P~~~L~~q~~~~~  127 (412)
                      -++|..++..|.++++...+ +.|.+|+||||+|||..++++++..+.+       .+.+-+++||+|.++|+.++.+.|
T Consensus       105 ~f~f~~fN~iQS~vFp~aY~SneNMLIcAPTGsGKT~la~L~ILr~ik~~~~~~~i~k~~fKiVYIaPmKALa~Em~~~~  184 (1230)
T KOG0952|consen  105 FFSFEEFNRIQSEVFPVAYKSNENMLICAPTGSGKTVLAELCILRTIKEHEEQGDIAKDDFKIVYIAPMKALAAEMVDKF  184 (1230)
T ss_pred             cccHHHHHHHHHHhhhhhhcCCCCEEEECCCCCCchHHHHHHHHHHHHhhccccccccCCceEEEEechHHHHHHHHHHH
Confidence            45888899999999999886 4799999999999999999999998874       123468999999999999999999


Q ss_pred             HHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCC---CCCCCceEEEEeCCchhhccCcHHHHHH
Q 015158          128 RALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQS---LRPDNIRIFVLDEADEMLSRGFKDQIYD  204 (412)
Q Consensus       128 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~---~~~~~~~~iiiDE~h~~~~~~~~~~~~~  204 (412)
                      .+-....|+.+..++|+.......   ...++|+|+|||+|--.-+++.   -.+..+++||+||+|.+-+ ..+..++.
T Consensus       185 ~kkl~~~gi~v~ELTGD~ql~~te---i~~tqiiVTTPEKwDvvTRk~~~d~~l~~~V~LviIDEVHlLhd-~RGpvlEt  260 (1230)
T KOG0952|consen  185 SKKLAPLGISVRELTGDTQLTKTE---IADTQIIVTTPEKWDVVTRKSVGDSALFSLVRLVIIDEVHLLHD-DRGPVLET  260 (1230)
T ss_pred             hhhcccccceEEEecCcchhhHHH---HHhcCEEEecccceeeeeeeeccchhhhhheeeEEeeeehhhcC-cccchHHH
Confidence            988888899999999998754443   3457999999999954433322   2246789999999996544 34555555


Q ss_pred             HHHh-------CCCCceEEEEeecCChHHHHHHHHhcCCC--eEEEecCCccccCCceEEEEEeccc----------hhh
Q 015158          205 IFQL-------LPPKIQVGVFSATMPPEALEITRKFMNKP--VRILVKRDELTLEGIKQFHVNVEKE----------EWK  265 (412)
Q Consensus       205 i~~~-------~~~~~~~i~~SAT~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~----------~~~  265 (412)
                      +...       .....+++++|||+|+  ......+++-+  .-+........+......+.-....          ...
T Consensus       261 iVaRtlr~vessqs~IRivgLSATlPN--~eDvA~fL~vn~~~glfsFd~~yRPvpL~~~~iG~k~~~~~~~~~~~d~~~  338 (1230)
T KOG0952|consen  261 IVARTLRLVESSQSMIRIVGLSATLPN--YEDVARFLRVNPYAGLFSFDQRYRPVPLTQGFIGIKGKKNRQQKKNIDEVC  338 (1230)
T ss_pred             HHHHHHHHHHhhhhheEEEEeeccCCC--HHHHHHHhcCCCccceeeecccccccceeeeEEeeecccchhhhhhHHHHH
Confidence            5443       3467899999999976  33344444432  1122222222233333333322221          112


Q ss_pred             HHHHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcC-----------------------CCeeEEecCCCCHHHHHHHHH
Q 015158          266 LETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSR-----------------------DHTVSATHGDMDQNTRDIIMR  322 (412)
Q Consensus       266 ~~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~-----------------------~~~~~~~~~~~~~~~r~~~~~  322 (412)
                      .+.+.++++.  +..++|||.++..+.+.++.|.++                       .....++|+++...+|..+.+
T Consensus       339 ~~kv~e~~~~--g~qVlvFvhsR~~Ti~tA~~l~~~a~~~g~~~~f~~~~~~k~l~elf~~g~~iHhAGm~r~DR~l~E~  416 (1230)
T KOG0952|consen  339 YDKVVEFLQE--GHQVLVFVHSRNETIRTAKKLRERAETNGEKDLFLPSPRNKQLKELFQQGMGIHHAGMLRSDRQLVEK  416 (1230)
T ss_pred             HHHHHHHHHc--CCeEEEEEecChHHHHHHHHHHHHHHhcCcccccCCChhhHHHHHHHHhhhhhcccccchhhHHHHHH
Confidence            2333344443  458999999999999888888654                       134778999999999999999


Q ss_pred             HHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccCC-----------CChhhHHHhhhhcccCC--CCceEEEEeccCcHHH
Q 015158          323 EFRSGSSRVLITTDLLARGIDVQQVSLVINYDLP-----------TQPENYLHRIGRSGRFG--RKGVAINFVTRDDERM  389 (412)
Q Consensus       323 ~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~~-----------~s~~~~~Q~~GR~~R~g--~~g~~~~~~~~~~~~~  389 (412)
                      .|..|.++|++||..+..|+|+| +.+||+-+.+           .+.-+.+|..|||||..  ..|.++++.+.+...+
T Consensus       417 ~F~~G~i~vL~cTaTLAwGVNLP-A~aViIKGT~~ydsskg~f~dlgilDVlQifGRAGRPqFd~~G~giIiTt~dkl~~  495 (1230)
T KOG0952|consen  417 EFKEGHIKVLCCTATLAWGVNLP-AYAVIIKGTQVYDSSKGSFVDLGILDVLQIFGRAGRPQFDSSGEGIIITTRDKLDH  495 (1230)
T ss_pred             HHhcCCceEEEecceeeeccCCc-ceEEEecCCcccccccCceeeehHHHHHHHHhccCCCCCCCCceEEEEecccHHHH
Confidence            99999999999999999999999 5555554433           24567899999999964  5688888888776665


Q ss_pred             HHHH
Q 015158          390 LFDI  393 (412)
Q Consensus       390 ~~~~  393 (412)
                      +..+
T Consensus       496 Y~sL  499 (1230)
T KOG0952|consen  496 YESL  499 (1230)
T ss_pred             HHHH
Confidence            4433

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

Probab=100.00  E-value=6.9e-35  Score=271.46  Aligned_cols=292  Identities=18%  Similarity=0.229  Sum_probs=207.7

Q ss_pred             CChHHHHhhhhhhhc----CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCc
Q 015158           61 KPSAIQQRGIVPFCK----GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGV  136 (412)
Q Consensus        61 ~l~~~Q~~a~~~~~~----~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~  136 (412)
                      .|+++|++|+..+.+    ++++++++|||+|||.+++..+....      .++|||||+..|+.||.+.+....... .
T Consensus        36 ~lr~yQ~~al~a~~~~~~~~~~gvivlpTGaGKT~va~~~~~~~~------~~~Lvlv~~~~L~~Qw~~~~~~~~~~~-~  108 (442)
T COG1061          36 ELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAEAIAELK------RSTLVLVPTKELLDQWAEALKKFLLLN-D  108 (442)
T ss_pred             CCcHHHHHHHHHHHhhcccCCceEEEeCCCCCHHHHHHHHHHHhc------CCEEEEECcHHHHHHHHHHHHHhcCCc-c
Confidence            399999999999998    89999999999999999876665432      149999999999999998777754321 2


Q ss_pred             EEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEE
Q 015158          137 KVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVG  216 (412)
Q Consensus       137 ~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i  216 (412)
                      .+..+.|+... ..     . ..|.|+|++++.+......+..+.+++||+||||++.+..+......+....    .++
T Consensus       109 ~~g~~~~~~~~-~~-----~-~~i~vat~qtl~~~~~l~~~~~~~~~liI~DE~Hh~~a~~~~~~~~~~~~~~----~~L  177 (442)
T COG1061         109 EIGIYGGGEKE-LE-----P-AKVTVATVQTLARRQLLDEFLGNEFGLIIFDEVHHLPAPSYRRILELLSAAY----PRL  177 (442)
T ss_pred             ccceecCceec-cC-----C-CcEEEEEhHHHhhhhhhhhhcccccCEEEEEccccCCcHHHHHHHHhhhccc----cee
Confidence            34444443331 11     1 3699999999987521123333479999999999987765443333333322    289


Q ss_pred             EEeecCChHHHH---HHHHhcCCCeEEEecCC------ccccCCceEEEEEec---------------------------
Q 015158          217 VFSATMPPEALE---ITRKFMNKPVRILVKRD------ELTLEGIKQFHVNVE---------------------------  260 (412)
Q Consensus       217 ~~SAT~~~~~~~---~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~---------------------------  260 (412)
                      ++||||......   .+...++ +..+.....      ...+..+........                           
T Consensus       178 GLTATp~R~D~~~~~~l~~~~g-~~vy~~~~~~li~~g~Lap~~~~~i~~~~t~~~~~~~~~~~~~~~~~~~~~~~~~~~  256 (442)
T COG1061         178 GLTATPEREDGGRIGDLFDLIG-PIVYEVSLKELIDEGYLAPYKYVEIKVTLTEDEEREYAKESARFRELLRARGTLRAE  256 (442)
T ss_pred             eeccCceeecCCchhHHHHhcC-CeEeecCHHHHHhCCCccceEEEEEEeccchHHHHHhhhhhhhhhhhhhhhhhhhHH
Confidence            999998643211   1222222 222222211      111111111111000                           


Q ss_pred             --------cchhhHHHHHHHHHhc-CCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcE
Q 015158          261 --------KEEWKLETLCDLYETL-AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRV  331 (412)
Q Consensus       261 --------~~~~~~~~l~~~~~~~-~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~v  331 (412)
                              ....+...+...+..+ ...+++||+.+..+++.++..+...+. +..+++..+..+|..+++.|+.|++++
T Consensus       257 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lif~~~~~~a~~i~~~~~~~~~-~~~it~~t~~~eR~~il~~fr~g~~~~  335 (442)
T COG1061         257 NEARRIAIASERKIAAVRGLLLKHARGDKTLIFASDVEHAYEIAKLFLAPGI-VEAITGETPKEEREAILERFRTGGIKV  335 (442)
T ss_pred             HHHHHHhhccHHHHHHHHHHHHHhcCCCcEEEEeccHHHHHHHHHHhcCCCc-eEEEECCCCHHHHHHHHHHHHcCCCCE
Confidence                    0112233444445544 467999999999999999999998877 889999999999999999999999999


Q ss_pred             EEEcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccC
Q 015158          332 LITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRF  372 (412)
Q Consensus       332 lv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~  372 (412)
                      |+++.++.+|+|+|+++++|+.++..|...|.||+||+.|.
T Consensus       336 lv~~~vl~EGvDiP~~~~~i~~~~t~S~~~~~Q~lGR~LR~  376 (442)
T COG1061         336 LVTVKVLDEGVDIPDADVLIILRPTGSRRLFIQRLGRGLRP  376 (442)
T ss_pred             EEEeeeccceecCCCCcEEEEeCCCCcHHHHHHHhhhhccC
Confidence            99999999999999999999999999999999999999993

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=100.00  E-value=4.3e-34  Score=273.03  Aligned_cols=316  Identities=17%  Similarity=0.178  Sum_probs=222.0

Q ss_pred             ChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEE
Q 015158           62 PSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHAC  141 (412)
Q Consensus        62 l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~  141 (412)
                      |++.|......+..|  .++.++||+|||++++++++.....+   ..++|++|+..|+.|+++.+..++..+|+.+...
T Consensus        71 pydVQlig~l~l~~G--~Iaem~TGeGKTLta~Lpa~l~aL~g---~~V~VVTpn~yLA~Rdae~m~~l~~~LGLsv~~~  145 (762)
T TIGR03714        71 PYDVQVLGAIVLHQG--NIAEMKTGEGKTLTATMPLYLNALTG---KGAMLVTTNDYLAKRDAEEMGPVYEWLGLTVSLG  145 (762)
T ss_pred             ccHHHHHHHHHhcCC--ceeEecCCcchHHHHHHHHHHHhhcC---CceEEeCCCHHHHHHHHHHHHHHHhhcCCcEEEE
Confidence            455555544444444  69999999999999999987655443   4699999999999999999999998899999887


Q ss_pred             EcCcc---hHHHHHHhcCCCcEEEeChHHH-HHHHHc------CCCCCCCceEEEEeCCchhh-ccC-------------
Q 015158          142 VGGTS---VREDQRILSSGVHVVVGTPGRV-FDMLRR------QSLRPDNIRIFVLDEADEML-SRG-------------  197 (412)
Q Consensus       142 ~~~~~---~~~~~~~~~~~~~iii~T~~~l-~~~~~~------~~~~~~~~~~iiiDE~h~~~-~~~-------------  197 (412)
                      .++..   ...........++|+++||..| ...+..      +...++++.++|+||||.++ +..             
T Consensus       146 ~~~s~~~~~~~~~rr~~y~~dIvygTp~~LgfDyLrD~l~~~~~~~~~r~l~~~IVDEaDsILiDeartpliisg~~~~~  225 (762)
T TIGR03714       146 VVDDPDEEYDANEKRKIYNSDIVYTTNSALGFDYLIDNLASNKEGKFLRPFNYVIVDEVDSVLLDSAQTPLVISGAPRVQ  225 (762)
T ss_pred             ECCCCccccCHHHHHHhCCCCEEEECchhhhhhHHHHHhhcchhhcccccCcEEEEecHhhHhhccCcCCeeeeCCCccc
Confidence            76521   1222333445789999999999 444422      23345788999999999864 110             


Q ss_pred             --cHHHHHHHHHhCC-----------------------------------------------------------------
Q 015158          198 --FKDQIYDIFQLLP-----------------------------------------------------------------  210 (412)
Q Consensus       198 --~~~~~~~i~~~~~-----------------------------------------------------------------  210 (412)
                        .......+...+.                                                                 
T Consensus       226 ~~~y~~~~~~v~~l~~~~dy~~d~~~~~v~lt~~G~~~~e~~~~~~~l~~~~~~~~~~~i~~al~A~~~~~~d~dYiV~~  305 (762)
T TIGR03714       226 SNLYHIADTFVRTLKEDVDYIFKKDKKEVWLTDKGIEKAEQYFKIDNLYSEEYFELVRHINLALRAHYLFKRNKDYVVTN  305 (762)
T ss_pred             hHHHHHHHHHHHhcCCCCCeEEEcCCCeeeecHhHHHHHHHHcCCCccCChhhHHHHHHHHHHHHHHHHHhcCCceEEEC
Confidence              0011111111110                                                                 


Q ss_pred             ----------------------------------------------------CCceEEEEeecCChHHHHHHHHhcCCCe
Q 015158          211 ----------------------------------------------------PKIQVGVFSATMPPEALEITRKFMNKPV  238 (412)
Q Consensus       211 ----------------------------------------------------~~~~~i~~SAT~~~~~~~~~~~~~~~~~  238 (412)
                                                                          --.++.|||+|......++ ...++-.+
T Consensus       306 ~~v~ivD~~TGr~~~gr~~~~GLhQaieaKE~v~i~~e~~t~a~It~qn~Fr~Y~kl~GmTGTa~~~~~Ef-~~iY~l~v  384 (762)
T TIGR03714       306 GEVVLLDRITGRLLEGTKLQSGIHQAIEAKEHVELSKETRAMASITYQNLFKMFNKLSGMTGTGKVAEKEF-IETYSLSV  384 (762)
T ss_pred             CEEEEEECCCCcCCCCCCcchHHHHHHHhhcCCCCCCCceeeeeeeHHHHHhhCchhcccCCCChhHHHHH-HHHhCCCE
Confidence                                                                0136788888875544443 34544433


Q ss_pred             EEEecCCccccCCceEEEEEeccchhhHHHHHHHHHh--cCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHH
Q 015158          239 RILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYET--LAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNT  316 (412)
Q Consensus       239 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~--~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~  316 (412)
                      ............  ...-........+...+.+.+..  ....++||||++++.++.+++.|.+.|+.+..+||.+...+
T Consensus       385 ~~IPt~kp~~r~--d~~d~i~~~~~~K~~ai~~~i~~~~~~~~pvLIft~s~~~se~ls~~L~~~gi~~~~L~a~~~~~E  462 (762)
T TIGR03714       385 VKIPTNKPIIRI--DYPDKIYATLPEKLMATLEDVKEYHETGQPVLLITGSVEMSEIYSELLLREGIPHNLLNAQNAAKE  462 (762)
T ss_pred             EEcCCCCCeeee--eCCCeEEECHHHHHHHHHHHHHHHhhCCCCEEEEECcHHHHHHHHHHHHHCCCCEEEecCCChHHH
Confidence            222111111111  11111222334566767666655  35679999999999999999999999999999999999888


Q ss_pred             HHHHHHHHhcCCCcEEEEcCCCcCCCCCC---------CCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcH
Q 015158          317 RDIIMREFRSGSSRVLITTDLLARGIDVQ---------QVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDE  387 (412)
Q Consensus       317 r~~~~~~f~~g~~~vlv~t~~~~~G~d~~---------~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~  387 (412)
                      +..+.+.++.|  .|+|+|+++++|+|++         ++++|+.+++|....+ .|++||+||.|.+|.++.|++..|.
T Consensus       463 ~~ii~~ag~~g--~VlIATdmAgRGtDI~l~~~v~~~GGL~vIit~~~ps~rid-~qr~GRtGRqG~~G~s~~~is~eD~  539 (762)
T TIGR03714       463 AQIIAEAGQKG--AVTVATSMAGRGTDIKLGKGVAELGGLAVIGTERMENSRVD-LQLRGRSGRQGDPGSSQFFVSLEDD  539 (762)
T ss_pred             HHHHHHcCCCC--eEEEEccccccccCCCCCccccccCCeEEEEecCCCCcHHH-HHhhhcccCCCCceeEEEEEccchh
Confidence            87777666555  7999999999999999         8899999988877666 9999999999999999999988655


Q ss_pred             H
Q 015158          388 R  388 (412)
Q Consensus       388 ~  388 (412)
                      -
T Consensus       540 l  540 (762)
T TIGR03714       540 L  540 (762)
T ss_pred             h
Confidence            3

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.

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

Probab=100.00  E-value=3.4e-34  Score=278.89  Aligned_cols=321  Identities=20%  Similarity=0.264  Sum_probs=258.0

Q ss_pred             HCCCCCChHHHHhhhhhhhcC------ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHH
Q 015158           56 AYGFEKPSAIQQRGIVPFCKG------LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRA  129 (412)
Q Consensus        56 ~~~~~~l~~~Q~~a~~~~~~~------~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~  129 (412)
                      .++|. -++-|..|++.+.+.      .+-+|||..|.|||.+++-+++..+..+   ++|.++|||.-|++|.++.|++
T Consensus       590 ~FPye-ET~DQl~AI~eVk~DM~~~kpMDRLiCGDVGFGKTEVAmRAAFkAV~~G---KQVAvLVPTTlLA~QHy~tFke  665 (1139)
T COG1197         590 SFPYE-ETPDQLKAIEEVKRDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVMDG---KQVAVLVPTTLLAQQHYETFKE  665 (1139)
T ss_pred             cCCCc-CCHHHHHHHHHHHHHhccCCcchheeecCcCCcHHHHHHHHHHHHhcCC---CeEEEEcccHHhHHHHHHHHHH
Confidence            67888 699999999998863      4779999999999999999999888766   5999999999999999999999


Q ss_pred             hhcccCcEEEEEEcCcchHHHH----HHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHH
Q 015158          130 LGDYLGVKVHACVGGTSVREDQ----RILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDI  205 (412)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i  205 (412)
                      ....+++++..+..-.+.+...    ....+..||+|+|     +.+......+.+++++||||=|++     +-.-++-
T Consensus       666 RF~~fPV~I~~LSRF~s~kE~~~il~~la~G~vDIvIGT-----HrLL~kdv~FkdLGLlIIDEEqRF-----GVk~KEk  735 (1139)
T COG1197         666 RFAGFPVRIEVLSRFRSAKEQKEILKGLAEGKVDIVIGT-----HRLLSKDVKFKDLGLLIIDEEQRF-----GVKHKEK  735 (1139)
T ss_pred             HhcCCCeeEEEecccCCHHHHHHHHHHHhcCCccEEEec-----hHhhCCCcEEecCCeEEEechhhc-----CccHHHH
Confidence            8888899998888766655543    3356789999999     445566677889999999999984     3344555


Q ss_pred             HHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhHHHHHHHHHhcCCCcEEEEE
Q 015158          206 FQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFV  285 (412)
Q Consensus       206 ~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lif~  285 (412)
                      ++.++.++-++-|||||-|....+......+...+...+....  .+..++...+...-+...+.++.   ++|.+...+
T Consensus       736 LK~Lr~~VDvLTLSATPIPRTL~Msm~GiRdlSvI~TPP~~R~--pV~T~V~~~d~~~ireAI~REl~---RgGQvfYv~  810 (1139)
T COG1197         736 LKELRANVDVLTLSATPIPRTLNMSLSGIRDLSVIATPPEDRL--PVKTFVSEYDDLLIREAILRELL---RGGQVFYVH  810 (1139)
T ss_pred             HHHHhccCcEEEeeCCCCcchHHHHHhcchhhhhccCCCCCCc--ceEEEEecCChHHHHHHHHHHHh---cCCEEEEEe
Confidence            5556678889999999999887777777776666655554433  35555555554333333333333   458899999


Q ss_pred             cchhHHHHHHHHHhcC--CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEcc-CCCChhhH
Q 015158          286 NTRRKVDWLTDKMRSR--DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYD-LPTQPENY  362 (412)
Q Consensus       286 ~~~~~~~~~~~~L~~~--~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~-~~~s~~~~  362 (412)
                      |.++..+.+++.|++.  ...+.+.||.|+..+-+.++..|.+|+++|||||.++++|+|+|+++++|+-. -.+..+++
T Consensus       811 NrV~~Ie~~~~~L~~LVPEarI~vaHGQM~e~eLE~vM~~F~~g~~dVLv~TTIIEtGIDIPnANTiIIe~AD~fGLsQL  890 (1139)
T COG1197         811 NRVESIEKKAERLRELVPEARIAVAHGQMRERELEEVMLDFYNGEYDVLVCTTIIETGIDIPNANTIIIERADKFGLAQL  890 (1139)
T ss_pred             cchhhHHHHHHHHHHhCCceEEEEeecCCCHHHHHHHHHHHHcCCCCEEEEeeeeecCcCCCCCceEEEeccccccHHHH
Confidence            9999999999999986  55799999999999999999999999999999999999999999999998643 34567999


Q ss_pred             HHhhhhcccCCCCceEEEEeccC------cHHHHHHHHH
Q 015158          363 LHRIGRSGRFGRKGVAINFVTRD------DERMLFDIQK  395 (412)
Q Consensus       363 ~Q~~GR~~R~g~~g~~~~~~~~~------~~~~~~~~~~  395 (412)
                      -|.-||+||.+..+.||.++.+.      ..+.++.+..
T Consensus       891 yQLRGRVGRS~~~AYAYfl~p~~k~lT~~A~kRL~aI~~  929 (1139)
T COG1197         891 YQLRGRVGRSNKQAYAYFLYPPQKALTEDAEKRLEAIAS  929 (1139)
T ss_pred             HHhccccCCccceEEEEEeecCccccCHHHHHHHHHHHh
Confidence            99999999999999999999863      4444444444

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=100.00  E-value=1.1e-33  Score=272.80  Aligned_cols=319  Identities=18%  Similarity=0.199  Sum_probs=234.6

Q ss_pred             CCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCc
Q 015158           57 YGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGV  136 (412)
Q Consensus        57 ~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~  136 (412)
                      .|.. |++.|..+...+.+|+  +..+.||+|||++++++++.....+   ..+.|++||..|+.|.++.+..+....|+
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 LGMR-PYDVQLIGALVLHEGN--IAEMQTGEGKTLTATMPLYLNALEG---KGVHLITVNDYLAKRDAEEMGQVYEFLGL  148 (790)
T ss_pred             hCCC-CchHHHHhHHHHcCCc--eeeecCCCcchHHHHHHHHHHHHcC---CCeEEEeCCHHHHHHHHHHHHHHHhhcCC
Confidence            3665 9999999998888876  9999999999999999988555444   48999999999999999999999999999


Q ss_pred             EEEEEEcCcc-hHHHHHHhcCCCcEEEeChHHH-HHHHHcC------CCCCCCceEEEEeCCchhh-ccC----------
Q 015158          137 KVHACVGGTS-VREDQRILSSGVHVVVGTPGRV-FDMLRRQ------SLRPDNIRIFVLDEADEML-SRG----------  197 (412)
Q Consensus       137 ~~~~~~~~~~-~~~~~~~~~~~~~iii~T~~~l-~~~~~~~------~~~~~~~~~iiiDE~h~~~-~~~----------  197 (412)
                      .+..+.|+.+ .....  ....++|+++|+..| +.++...      ....+.+.++|+||+|.++ +..          
T Consensus       149 ~v~~i~g~~~~~~~r~--~~y~~dIvygT~~~l~fDyLrd~~~~~~~~~~~r~~~~~IvDEaDsiLiDea~tpliisg~~  226 (790)
T PRK09200        149 TVGLNFSDIDDASEKK--AIYEADIIYTTNSELGFDYLRDNLADSKEDKVQRPLNYAIIDEIDSILLDEAQTPLIISGKP  226 (790)
T ss_pred             eEEEEeCCCCcHHHHH--HhcCCCEEEECCccccchhHHhccccchhhhcccccceEEEeccccceeccCCCceeeeCCC
Confidence            9999999887 33332  234589999999888 3333321      1245778999999999754 100          


Q ss_pred             -----cHHHHHHHHHhCC--------------------------------------------------------------
Q 015158          198 -----FKDQIYDIFQLLP--------------------------------------------------------------  210 (412)
Q Consensus       198 -----~~~~~~~i~~~~~--------------------------------------------------------------  210 (412)
                           +......+...+.                                                              
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                 0111111111110                                                              


Q ss_pred             -------------------------------------------------------CCceEEEEeecCChHHHHHHHHhcC
Q 015158          211 -------------------------------------------------------PKIQVGVFSATMPPEALEITRKFMN  235 (412)
Q Consensus       211 -------------------------------------------------------~~~~~i~~SAT~~~~~~~~~~~~~~  235 (412)
                                                                             --.++.|||+|...... .+...++
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 VYDGEIVLVDRFTGRVLPGRKLQDGLHQAIEAKEGVEITEENRTMASITIQNLFRMFPKLSGMTGTAKTEEK-EFFEVYN  385 (790)
T ss_pred             EECCEEEEEECCCCcCCCCCccChHHHHHHHHhcCCCcCCCceehhhhhHHHHHHHhHHHhccCCCChHHHH-HHHHHhC
Confidence                                                                   01367888888755443 3444554


Q ss_pred             CCeEEEecCCccccCCceEEEEEeccchhhHHHHHHHHHhc--CCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCC
Q 015158          236 KPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETL--AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMD  313 (412)
Q Consensus       236 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~--~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~  313 (412)
                      -.+.................  .......+...+.+.+...  ...++||||++++.++.++..|.+.|+.+..+||.+.
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 MEVVQIPTNRPIIRIDYPDK--VFVTLDEKYKAVIEEVKERHETGRPVLIGTGSIEQSETFSKLLDEAGIPHNLLNAKNA  463 (790)
T ss_pred             CcEEECCCCCCcccccCCCe--EEcCHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHCCCCEEEecCCcc
Confidence            44332211111111111111  1123345777777766552  5679999999999999999999999999999999998


Q ss_pred             HHHHHHHHHHHhcCCCcEEEEcCCCcCCCCC---CCCC-----EEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccC
Q 015158          314 QNTRDIIMREFRSGSSRVLITTDLLARGIDV---QQVS-----LVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRD  385 (412)
Q Consensus       314 ~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~---~~~~-----~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~  385 (412)
                      ..++..+...+..|  .|+|||+++++|+|+   +.+.     +||.++.|.|...|.|++||+||.|.+|.++.|++..
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            88877777766554  799999999999999   5888     9999999999999999999999999999999999886


Q ss_pred             cHH
Q 015158          386 DER  388 (412)
Q Consensus       386 ~~~  388 (412)
                      |.-
T Consensus       542 D~l  544 (790)
T PRK09200        542 DDL  544 (790)
T ss_pred             HHH
Confidence            553

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=100.00  E-value=2.7e-33  Score=265.95  Aligned_cols=319  Identities=22%  Similarity=0.245  Sum_probs=236.6

Q ss_pred             CCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCc
Q 015158           57 YGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGV  136 (412)
Q Consensus        57 ~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~  136 (412)
                      .|.. |++.|..+...+.+|+  +..++||+|||+++.++++.....+   ..+.|++||..|+.|.++.+..+....|+
T Consensus        53 lg~~-p~~vQlig~~~l~~G~--Iaem~TGeGKTLva~lpa~l~aL~G---~~V~VvTpt~~LA~qdae~~~~l~~~LGL  126 (745)
T TIGR00963        53 LGMR-PFDVQLIGGIALHKGK--IAEMKTGEGKTLTATLPAYLNALTG---KGVHVVTVNDYLAQRDAEWMGQVYRFLGL  126 (745)
T ss_pred             hCCC-ccchHHhhhhhhcCCc--eeeecCCCccHHHHHHHHHHHHHhC---CCEEEEcCCHHHHHHHHHHHHHHhccCCC
Confidence            3666 8999999998888776  9999999999999999885433333   36999999999999999999999999999


Q ss_pred             EEEEEEcCcchHHHHHHhcCCCcEEEeChHHH-HHHHHcC------CCCCCCceEEEEeCCchhhc-cC-----------
Q 015158          137 KVHACVGGTSVREDQRILSSGVHVVVGTPGRV-FDMLRRQ------SLRPDNIRIFVLDEADEMLS-RG-----------  197 (412)
Q Consensus       137 ~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l-~~~~~~~------~~~~~~~~~iiiDE~h~~~~-~~-----------  197 (412)
                      ++..+.|+.+.......  -.++|+++|+..| +.++...      ...++.+.++|+||+|.++- ..           
T Consensus       127 sv~~i~g~~~~~~r~~~--y~~dIvyGT~~rlgfDyLrd~~~~~~~~~~~r~l~~aIIDEaDs~LIDeaRtpLiisg~~~  204 (745)
T TIGR00963       127 SVGLILSGMSPEERREA--YACDITYGTNNELGFDYLRDNMAHSKEEKVQRPFHFAIIDEVDSILIDEARTPLIISGPAE  204 (745)
T ss_pred             eEEEEeCCCCHHHHHHh--cCCCEEEECCCchhhHHHhcccccchhhhhccccceeEeecHHHHhHHhhhhHHhhcCCCC
Confidence            99999998775443333  3479999999999 6666554      23567899999999998542 10           


Q ss_pred             ----cHHHHHHHHHhCC---------------------------------------------------------------
Q 015158          198 ----FKDQIYDIFQLLP---------------------------------------------------------------  210 (412)
Q Consensus       198 ----~~~~~~~i~~~~~---------------------------------------------------------------  210 (412)
                          .......+...+.                                                               
T Consensus       205 ~~~~ly~~a~~i~r~L~~~~dy~~de~~k~v~Lt~~G~~~~e~~~~~~~ly~~~~~~~~~~i~~Al~A~~l~~~d~dYiV  284 (745)
T TIGR00963       205 KSTELYLQANRFAKALEKEVHYEVDEKNRAVLLTEKGIKKAEDLLGVDNLYDLENSPLIHYINNALKAKELFEKDVDYIV  284 (745)
T ss_pred             CchHHHHHHHHHHHhhccCCCeEEecCCCceeECHHHHHHHHHHcCCccccChhhhHHHHHHHHHHHHHHHHhcCCcEEE
Confidence                0000000000000                                                               


Q ss_pred             ------------------------------------------------------CCceEEEEeecCChHHHHHHHHhcCC
Q 015158          211 ------------------------------------------------------PKIQVGVFSATMPPEALEITRKFMNK  236 (412)
Q Consensus       211 ------------------------------------------------------~~~~~i~~SAT~~~~~~~~~~~~~~~  236 (412)
                                                                            --.++.|||+|...... .+...++-
T Consensus       285 ~d~~V~ivD~~TGR~~~gr~ws~GLhQaiEaKE~v~i~~e~~t~a~It~qn~Fr~Y~kl~GmTGTa~te~~-E~~~iY~l  363 (745)
T TIGR00963       285 RDGEVVIVDEFTGRIMEGRRWSDGLHQAIEAKEGVEIQNENQTLATITYQNFFRLYEKLSGMTGTAKTEEE-EFEKIYNL  363 (745)
T ss_pred             ECCEEEEEECCCCcCCCCCccchHHHHHHHHhcCCCcCCCceeeeeeeHHHHHhhCchhhccCCCcHHHHH-HHHHHhCC
Confidence                                                                  01367888888765443 34444444


Q ss_pred             CeEE-EecCCccccCCceEEEEEeccchhhHHHHHHHH-Hhc-CCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCC
Q 015158          237 PVRI-LVKRDELTLEGIKQFHVNVEKEEWKLETLCDLY-ETL-AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMD  313 (412)
Q Consensus       237 ~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~-~~~-~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~  313 (412)
                      .+.. ......... ....  ........+...+.+.+ ..+ .+.++||||++++.++.+++.|.+.|+....+|+.  
T Consensus       364 ~vv~IPtnkp~~R~-d~~d--~i~~t~~~k~~ai~~~i~~~~~~grpvLV~t~si~~se~ls~~L~~~gi~~~~Lna~--  438 (745)
T TIGR00963       364 EVVVVPTNRPVIRK-DLSD--LVYKTEEEKWKAVVDEIKERHAKGQPVLVGTTSVEKSELLSNLLKERGIPHNVLNAK--  438 (745)
T ss_pred             CEEEeCCCCCeeee-eCCC--eEEcCHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHcCCCeEEeeCC--
Confidence            4332 222211111 1111  11222234555554444 222 56799999999999999999999999999999998  


Q ss_pred             HHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCC-------CCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCc
Q 015158          314 QNTRDIIMREFRSGSSRVLITTDLLARGIDVQQ-------VSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDD  386 (412)
Q Consensus       314 ~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~-------~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~  386 (412)
                      ..+|+..+..|..+...|+|||+++++|+|++.       ..+||.++.|.|...+.|+.||+||.|.+|.+..|++..|
T Consensus       439 q~~rEa~ii~~ag~~g~VtIATnmAgRGtDI~l~~V~~~GGl~VI~t~~p~s~ri~~q~~GRtGRqG~~G~s~~~ls~eD  518 (745)
T TIGR00963       439 NHEREAEIIAQAGRKGAVTIATNMAGRGTDIKLEEVKELGGLYVIGTERHESRRIDNQLRGRSGRQGDPGSSRFFLSLED  518 (745)
T ss_pred             hHHHHHHHHHhcCCCceEEEEeccccCCcCCCccchhhcCCcEEEecCCCCcHHHHHHHhccccCCCCCcceEEEEeccH
Confidence            778899999999999999999999999999998       5699999999999999999999999999999999999886


Q ss_pred             HHH
Q 015158          387 ERM  389 (412)
Q Consensus       387 ~~~  389 (412)
                      .-.
T Consensus       519 ~l~  521 (745)
T TIGR00963       519 NLM  521 (745)
T ss_pred             HHH
Confidence            644

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.

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=100.00  E-value=4.2e-33  Score=275.36  Aligned_cols=336  Identities=17%  Similarity=0.132  Sum_probs=226.6

Q ss_pred             CChHHHHhhhhhhhcC--ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEE
Q 015158           61 KPSAIQQRGIVPFCKG--LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKV  138 (412)
Q Consensus        61 ~l~~~Q~~a~~~~~~~--~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~  138 (412)
                      .|.|||..++..+...  .++++..++|.|||..+.+.+...+..+ ...++|||||. .|..||..++.+..   ++..
T Consensus       152 ~l~pHQl~~~~~vl~~~~~R~LLADEvGLGKTIeAglil~~l~~~g-~~~rvLIVvP~-sL~~QW~~El~~kF---~l~~  226 (956)
T PRK04914        152 SLIPHQLYIAHEVGRRHAPRVLLADEVGLGKTIEAGMIIHQQLLTG-RAERVLILVPE-TLQHQWLVEMLRRF---NLRF  226 (956)
T ss_pred             CCCHHHHHHHHHHhhccCCCEEEEeCCcCcHHHHHHHHHHHHHHcC-CCCcEEEEcCH-HHHHHHHHHHHHHh---CCCe
Confidence            4999999999887653  5789999999999988866665544443 34589999996 89999999986643   4444


Q ss_pred             EEEEcCcchHHHH--HHhcCCCcEEEeChHHHHHHH-HcCCCCCCCceEEEEeCCchhhccC--cHHHHHHHHHhCCCCc
Q 015158          139 HACVGGTSVREDQ--RILSSGVHVVVGTPGRVFDML-RRQSLRPDNIRIFVLDEADEMLSRG--FKDQIYDIFQLLPPKI  213 (412)
Q Consensus       139 ~~~~~~~~~~~~~--~~~~~~~~iii~T~~~l~~~~-~~~~~~~~~~~~iiiDE~h~~~~~~--~~~~~~~i~~~~~~~~  213 (412)
                      ..+.+........  .......+++|+|++.+...- ....+....|++||+||||++.+..  -......+........
T Consensus       227 ~i~~~~~~~~~~~~~~~pf~~~~~vI~S~~~l~~~~~~~~~l~~~~wdlvIvDEAH~lk~~~~~~s~~y~~v~~La~~~~  306 (956)
T PRK04914        227 SLFDEERYAEAQHDADNPFETEQLVICSLDFLRRNKQRLEQALAAEWDLLVVDEAHHLVWSEEAPSREYQVVEQLAEVIP  306 (956)
T ss_pred             EEEcCcchhhhcccccCccccCcEEEEEHHHhhhCHHHHHHHhhcCCCEEEEechhhhccCCCCcCHHHHHHHHHhhccC
Confidence            4444332111000  001124689999999886421 1112223478999999999986321  1122333322223345


Q ss_pred             eEEEEeecCChH-HHH------------------H------------------------------HHHhcCC--------
Q 015158          214 QVGVFSATMPPE-ALE------------------I------------------------------TRKFMNK--------  236 (412)
Q Consensus       214 ~~i~~SAT~~~~-~~~------------------~------------------------------~~~~~~~--------  236 (412)
                      .++++||||... ..+                  +                              +..+++.        
T Consensus       307 ~~LLLTATP~q~~~~e~falL~lLdP~~f~~~~~F~~e~~~~~~~a~~v~~l~~~~~~~~~~~~~l~~ll~~~~~~~l~~  386 (956)
T PRK04914        307 GVLLLTATPEQLGQESHFARLRLLDPDRFHDYEAFVEEQQQYRPVADAVQALLAGEKLSDDALNALGELLGEQDIEPLLQ  386 (956)
T ss_pred             CEEEEEcCcccCCcHHHHHhhhhhCCCcCCCHHHHHHHHHhhHHHHHHHHHHhcCCcCCHHHHHHHHHHhcccchhHHHh
Confidence            689999999510 000                  0                              0000000        


Q ss_pred             ---------------------------CeEEEecCCc---cccCCceEEEEEec--------------------------
Q 015158          237 ---------------------------PVRILVKRDE---LTLEGIKQFHVNVE--------------------------  260 (412)
Q Consensus       237 ---------------------------~~~~~~~~~~---~~~~~~~~~~~~~~--------------------------  260 (412)
                                                 .+.+...+..   .............+                          
T Consensus       387 ~~~~~~~~~~~~~~~~i~~L~d~hg~~rvm~RntR~~v~~fp~R~~~~~~l~~~~~y~~~~~~~~~~~~~~~l~pe~~~~  466 (956)
T PRK04914        387 AANSDSEEAQAARQELISELLDRHGTGRVLFRNTRAAVKGFPKRELHPIPLPLPEQYQTAIKVSLEARARDMLYPEQIYQ  466 (956)
T ss_pred             hhcccccccHHHHHHHHHHHHhhcCcceEEEeccHHhhcCCCcCceeEeecCCCHHHHHHHHHhHHHHHHhhcCHHHHHH
Confidence                                       0000000000   00000011101000                          


Q ss_pred             ---------cchhhHHHHHHHHHhcCCCcEEEEEcchhHHHHHHHHH-hcCCCeeEEecCCCCHHHHHHHHHHHhcC--C
Q 015158          261 ---------KEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKM-RSRDHTVSATHGDMDQNTRDIIMREFRSG--S  328 (412)
Q Consensus       261 ---------~~~~~~~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L-~~~~~~~~~~~~~~~~~~r~~~~~~f~~g--~  328 (412)
                               ..+.+...+.++++....+|+||||++++.+..+.+.| ...|+.+..+||+++..+|.++++.|+++  .
T Consensus       467 ~~~~~~~~~~~d~Ki~~L~~~L~~~~~~KvLVF~~~~~t~~~L~~~L~~~~Gi~~~~ihG~~s~~eR~~~~~~F~~~~~~  546 (956)
T PRK04914        467 EFEDNATWWNFDPRVEWLIDFLKSHRSEKVLVICAKAATALQLEQALREREGIRAAVFHEGMSIIERDRAAAYFADEEDG  546 (956)
T ss_pred             HHhhhhhccccCHHHHHHHHHHHhcCCCeEEEEeCcHHHHHHHHHHHhhccCeeEEEEECCCCHHHHHHHHHHHhcCCCC
Confidence                     01234556777777777789999999999999999999 46799999999999999999999999984  5


Q ss_pred             CcEEEEcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHHhcccc
Q 015158          329 SRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVI  401 (412)
Q Consensus       329 ~~vlv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~  401 (412)
                      ..|||||+++++|+|++.+++||+++.|+++..|.||+||++|.|+.+.+.++...........+.++|...+
T Consensus       547 ~~VLIsTdvgseGlNlq~a~~VInfDlP~nP~~~eQRIGR~~RiGQ~~~V~i~~~~~~~t~~e~i~~~~~~~l  619 (956)
T PRK04914        547 AQVLLCSEIGSEGRNFQFASHLVLFDLPFNPDLLEQRIGRLDRIGQKHDIQIHVPYLEGTAQERLFRWYHEGL  619 (956)
T ss_pred             ccEEEechhhccCCCcccccEEEEecCCCCHHHHHHHhcccccCCCCceEEEEEccCCCCHHHHHHHHHhhhc
Confidence            8999999999999999999999999999999999999999999999998888877766555666777666544

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

Probab=100.00  E-value=2.2e-33  Score=263.74  Aligned_cols=310  Identities=19%  Similarity=0.266  Sum_probs=234.4

Q ss_pred             HHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccc
Q 015158           55 YAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYL  134 (412)
Q Consensus        55 ~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~  134 (412)
                      ..++|. |-.+|++|+.++..|.+++|.|+|.+|||.++..++.-...+.   .+.+|..|-++|.+|-++.|+.-... 
T Consensus       292 ~~~pFe-lD~FQk~Ai~~lerg~SVFVAAHTSAGKTvVAEYAialaq~h~---TR~iYTSPIKALSNQKfRDFk~tF~D-  366 (1248)
T KOG0947|consen  292 LIYPFE-LDTFQKEAIYHLERGDSVFVAAHTSAGKTVVAEYAIALAQKHM---TRTIYTSPIKALSNQKFRDFKETFGD-  366 (1248)
T ss_pred             hhCCCC-ccHHHHHHHHHHHcCCeEEEEecCCCCcchHHHHHHHHHHhhc---cceEecchhhhhccchHHHHHHhccc-
Confidence            345777 9999999999999999999999999999999988887766554   48999999999999999999885543 


Q ss_pred             CcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCCCCce
Q 015158          135 GVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQ  214 (412)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~  214 (412)
                         +..++|+....       +.+.++|+|.+.|.+++.+..--.+++..||+||+|.+.+...+..|.+++-.+|.+++
T Consensus       367 ---vgLlTGDvqin-------PeAsCLIMTTEILRsMLYrgadliRDvE~VIFDEVHYiND~eRGvVWEEViIMlP~HV~  436 (1248)
T KOG0947|consen  367 ---VGLLTGDVQIN-------PEASCLIMTTEILRSMLYRGADLIRDVEFVIFDEVHYINDVERGVVWEEVIIMLPRHVN  436 (1248)
T ss_pred             ---cceeecceeeC-------CCcceEeehHHHHHHHHhcccchhhccceEEEeeeeecccccccccceeeeeeccccce
Confidence               33888887644       45789999999999999887766788999999999999988888999999999999999


Q ss_pred             EEEEeecCChHHHHHHHHhc---CCCeEEEecCCccccCCceEEEEEecc------------------------------
Q 015158          215 VGVFSATMPPEALEITRKFM---NKPVRILVKRDELTLEGIKQFHVNVEK------------------------------  261 (412)
Q Consensus       215 ~i~~SAT~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~------------------------------  261 (412)
                      +|++|||.++. .++..+..   ++.+.+...  ...+....++.+.-..                              
T Consensus       437 ~IlLSATVPN~-~EFA~WIGRtK~K~IyViST--~kRPVPLEh~l~t~~~l~kiidq~g~fl~~~~~~a~~~~~~~ak~~  513 (1248)
T KOG0947|consen  437 FILLSATVPNT-LEFADWIGRTKQKTIYVIST--SKRPVPLEHYLYTKKSLFKIIDQNGIFLLKGIKDAKDSLKKEAKFV  513 (1248)
T ss_pred             EEEEeccCCCh-HHHHHHhhhccCceEEEEec--CCCccceEEEEEeccceehhhcccchhhhhcchhhhhhhccccccc
Confidence            99999999754 34333332   222222211  1111111111100000                              


Q ss_pred             ------------------------c----------hh---hHHHHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcCC--
Q 015158          262 ------------------------E----------EW---KLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRD--  302 (412)
Q Consensus       262 ------------------------~----------~~---~~~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~--  302 (412)
                                              .          ..   ..-.+...+.+...-+++|||-|++.|++.+++|...+  
T Consensus       514 ~~~~~~~~~~rgs~~~ggk~~~~~g~~r~~~~~~nrr~~~~~l~lin~L~k~~lLP~VvFvFSkkrCde~a~~L~~~nL~  593 (1248)
T KOG0947|consen  514 DVEKSDARGGRGSQKRGGKTNYHNGGSRGSGIGKNRRKQPTWLDLINHLRKKNLLPVVVFVFSKKRCDEYADYLTNLNLT  593 (1248)
T ss_pred             ccccccccccccccccCCcCCCCCCCcccccccccccccchHHHHHHHHhhcccCceEEEEEccccHHHHHHHHhccCcc
Confidence                                    0          00   12223333444444689999999999999999997641  


Q ss_pred             -------------------------------------CeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCC
Q 015158          303 -------------------------------------HTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQ  345 (412)
Q Consensus       303 -------------------------------------~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~  345 (412)
                                                           ..+.++||++-+--++-++..|..|-++||++|.++.+|+|.|
T Consensus       594 ~~~EKseV~lfl~k~~~rLk~~DR~LPQvl~m~~ll~RGiaVHH~GlLPivKE~VE~LFqrGlVKVLFATETFAMGVNMP  673 (1248)
T KOG0947|consen  594 DSKEKSEVHLFLSKAVARLKGEDRNLPQVLSMRSLLLRGIAVHHGGLLPIVKEVVELLFQRGLVKVLFATETFAMGVNMP  673 (1248)
T ss_pred             cchhHHHHHHHHHHHHHhcChhhccchHHHHHHHHHhhcchhhcccchHHHHHHHHHHHhcCceEEEeehhhhhhhcCCC
Confidence                                                 3488999999999999999999999999999999999999999


Q ss_pred             CCCEEEEccC---------CCChhhHHHhhhhcccCCCC--ceEEEEec
Q 015158          346 QVSLVINYDL---------PTQPENYLHRIGRSGRFGRK--GVAINFVT  383 (412)
Q Consensus       346 ~~~~vi~~~~---------~~s~~~~~Q~~GR~~R~g~~--g~~~~~~~  383 (412)
                       +++|++.+.         ...+.+|.||.|||||+|-+  |.++++..
T Consensus       674 -ARtvVF~Sl~KhDG~efR~L~PGEytQMAGRAGRRGlD~tGTVii~~~  721 (1248)
T KOG0947|consen  674 -ARTVVFSSLRKHDGNEFRELLPGEYTQMAGRAGRRGLDETGTVIIMCK  721 (1248)
T ss_pred             -ceeEEeeehhhccCcceeecCChhHHhhhccccccccCcCceEEEEec
Confidence             455554433         24688999999999999966  44444443

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=100.00  E-value=6.7e-32  Score=270.50  Aligned_cols=303  Identities=22%  Similarity=0.315  Sum_probs=208.0

Q ss_pred             hHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCH----HHHHHHHHHHHH-hhcccCcE
Q 015158           63 SAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTR----ELAQQIEKVMRA-LGDYLGVK  137 (412)
Q Consensus        63 ~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~----~L~~q~~~~~~~-~~~~~~~~  137 (412)
                      +.+-.+++..+.+++.++|+|+||||||+..-. ++.....+ ..+.+++..|++    +++.++++++.. ++...|+.
T Consensus        76 ~~~r~~Il~ai~~~~VviI~GeTGSGKTTqlPq-~lle~g~g-~~g~I~~TQPRRlAArsLA~RVA~El~~~lG~~VGY~  153 (1294)
T PRK11131         76 SQKKQDILEAIRDHQVVIVAGETGSGKTTQLPK-ICLELGRG-VKGLIGHTQPRRLAARTVANRIAEELETELGGCVGYK  153 (1294)
T ss_pred             HHHHHHHHHHHHhCCeEEEECCCCCCHHHHHHH-HHHHcCCC-CCCceeeCCCcHHHHHHHHHHHHHHHhhhhcceecee
Confidence            556667788888888899999999999986432 22222222 123455666865    566666666654 32222322


Q ss_pred             EEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCch-hhccCcHHH-HHHHHHhCCCCceE
Q 015158          138 VHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADE-MLSRGFKDQ-IYDIFQLLPPKIQV  215 (412)
Q Consensus       138 ~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~-~~~~~~~~~-~~~i~~~~~~~~~~  215 (412)
                      +    ...      .....+..|+++|++.|++.+..... ++++++||+||||+ ..+.++... +..++.. .++.++
T Consensus       154 v----rf~------~~~s~~t~I~v~TpG~LL~~l~~d~~-Ls~~~~IIIDEAHERsLn~DfLLg~Lk~lL~~-rpdlKv  221 (1294)
T PRK11131        154 V----RFN------DQVSDNTMVKLMTDGILLAEIQQDRL-LMQYDTIIIDEAHERSLNIDFILGYLKELLPR-RPDLKV  221 (1294)
T ss_pred             e----cCc------cccCCCCCEEEEChHHHHHHHhcCCc-cccCcEEEecCccccccccchHHHHHHHhhhc-CCCceE
Confidence            2    111      11234579999999999998876543 78999999999995 667665543 3333322 246899


Q ss_pred             EEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccc-----hhhHHHHHHHHH---hcCCCcEEEEEcc
Q 015158          216 GVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKE-----EWKLETLCDLYE---TLAITQSVIFVNT  287 (412)
Q Consensus       216 i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~l~~~~~---~~~~~k~lif~~~  287 (412)
                      |++|||++.+  .+...+.+.+ .+.+....   ..+...+......     ......+...+.   ....+.+|||+++
T Consensus       222 ILmSATid~e--~fs~~F~~ap-vI~V~Gr~---~pVei~y~p~~~~~~~~~~d~l~~ll~~V~~l~~~~~GdILVFLpg  295 (1294)
T PRK11131        222 IITSATIDPE--RFSRHFNNAP-IIEVSGRT---YPVEVRYRPIVEEADDTERDQLQAIFDAVDELGREGPGDILIFMSG  295 (1294)
T ss_pred             EEeeCCCCHH--HHHHHcCCCC-EEEEcCcc---ccceEEEeecccccchhhHHHHHHHHHHHHHHhcCCCCCEEEEcCC
Confidence            9999999753  3444343344 34443322   2244444443221     112222222222   2345789999999


Q ss_pred             hhHHHHHHHHHhcCCCe---eEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccC---------
Q 015158          288 RRKVDWLTDKMRSRDHT---VSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDL---------  355 (412)
Q Consensus       288 ~~~~~~~~~~L~~~~~~---~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~---------  355 (412)
                      .++++.+++.|++.+..   +..+||+++..+|..+++.  .|..+|||+|+++++|+|+|++++||+++.         
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   6789999999999999885  578899999999999999999999999863         


Q ss_pred             ---------CCChhhHHHhhhhcccCCCCceEEEEeccCcHH
Q 015158          356 ---------PTQPENYLHRIGRSGRFGRKGVAINFVTRDDER  388 (412)
Q Consensus       356 ---------~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~  388 (412)
                               +.|.+++.||+||+||. .+|.||.++++.+..
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                     34668999999999999 689999999987654

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

Probab=100.00  E-value=3.3e-33  Score=256.49  Aligned_cols=310  Identities=18%  Similarity=0.256  Sum_probs=237.5

Q ss_pred             CCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcE
Q 015158           58 GFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVK  137 (412)
Q Consensus        58 ~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~  137 (412)
                      +|. |-|+|..|+..+-.+.+++|.|.|.+|||.++-.+++..+....   ++||..|-++|.+|-++++..-..    .
T Consensus       127 PF~-LDpFQ~~aI~Cidr~eSVLVSAHTSAGKTVVAeYAIA~sLr~kQ---RVIYTSPIKALSNQKYREl~~EF~----D  198 (1041)
T KOG0948|consen  127 PFT-LDPFQSTAIKCIDRGESVLVSAHTSAGKTVVAEYAIAMSLREKQ---RVIYTSPIKALSNQKYRELLEEFK----D  198 (1041)
T ss_pred             Ccc-cCchHhhhhhhhcCCceEEEEeecCCCcchHHHHHHHHHHHhcC---eEEeeChhhhhcchhHHHHHHHhc----c
Confidence            455 89999999999999999999999999999999999999887664   999999999999999998877433    3


Q ss_pred             EEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEE
Q 015158          138 VHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGV  217 (412)
Q Consensus       138 ~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~  217 (412)
                      |.+.+|+.+..       +.+..+|+|.+.|.+++.++..-.+.+..||+||+|.+-+...+-.|.+-+-.+|.+.+.++
T Consensus       199 VGLMTGDVTIn-------P~ASCLVMTTEILRsMLYRGSEvmrEVaWVIFDEIHYMRDkERGVVWEETIIllP~~vr~VF  271 (1041)
T KOG0948|consen  199 VGLMTGDVTIN-------PDASCLVMTTEILRSMLYRGSEVMREVAWVIFDEIHYMRDKERGVVWEETIILLPDNVRFVF  271 (1041)
T ss_pred             cceeecceeeC-------CCCceeeeHHHHHHHHHhccchHhheeeeEEeeeehhccccccceeeeeeEEeccccceEEE
Confidence            66778877743       45789999999999999988877888999999999999998888888888889999999999


Q ss_pred             EeecCChHHH--HHHHHhcCCCeEEEecCCccccCCceEE---------EEEeccc----hh------------------
Q 015158          218 FSATMPPEAL--EITRKFMNKPVRILVKRDELTLEGIKQF---------HVNVEKE----EW------------------  264 (412)
Q Consensus       218 ~SAT~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------~~~~~~~----~~------------------  264 (412)
                      +|||+++..+  +++..+-.+|..+-.  .+..+....++         +..++..    ++                  
T Consensus       272 LSATiPNA~qFAeWI~~ihkQPcHVVY--TdyRPTPLQHyifP~ggdGlylvVDek~~FrednF~~am~~l~~~~~~~~~  349 (1041)
T KOG0948|consen  272 LSATIPNARQFAEWICHIHKQPCHVVY--TDYRPTPLQHYIFPAGGDGLYLVVDEKGKFREDNFQKAMSVLRKAGESDGK  349 (1041)
T ss_pred             EeccCCCHHHHHHHHHHHhcCCceEEe--ecCCCCcceeeeecCCCCeeEEEEecccccchHHHHHHHHHhhccCCCccc
Confidence            9999976432  233334444443221  11222222222         2222211    00                  


Q ss_pred             --------------------hHHHHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcC-----------------------
Q 015158          265 --------------------KLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSR-----------------------  301 (412)
Q Consensus       265 --------------------~~~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~-----------------------  301 (412)
                                          ..-.+...+-.....++|||+-|+++|+.++-.+.+.                       
T Consensus       350 ~~~~~k~~kG~~~~~~~~~s~i~kiVkmi~~~~~~PVIvFSFSkkeCE~~Alqm~kldfN~deEk~~V~~iF~nAi~~Ls  429 (1041)
T KOG0948|consen  350 KKANKKGRKGGTGGKGPGDSDIYKIVKMIMERNYLPVIVFSFSKKECEAYALQMSKLDFNTDEEKELVETIFNNAIDQLS  429 (1041)
T ss_pred             cccccccccCCcCCCCCCcccHHHHHHHHHhhcCCceEEEEecHhHHHHHHHhhccCcCCChhHHHHHHHHHHHHHHhcC
Confidence                                1112233333334468999999999999998777654                       


Q ss_pred             ----------------CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccC---------C
Q 015158          302 ----------------DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDL---------P  356 (412)
Q Consensus       302 ----------------~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~---------~  356 (412)
                                      ...++++|+++-+--++-+.-.|..|-+++|++|.+++.|+|.|.-++|+ ...         .
T Consensus       430 eeDr~LPqie~iLPLL~RGIGIHHsGLLPIlKE~IEILFqEGLvKvLFATETFsiGLNMPAkTVvF-T~~rKfDG~~fRw  508 (1041)
T KOG0948|consen  430 EEDRELPQIENILPLLRRGIGIHHSGLLPILKEVIEILFQEGLVKVLFATETFSIGLNMPAKTVVF-TAVRKFDGKKFRW  508 (1041)
T ss_pred             hhhccchHHHHHHHHHHhccccccccchHHHHHHHHHHHhccHHHHHHhhhhhhhccCCcceeEEE-eeccccCCcceee
Confidence                            23488999999999999999999999999999999999999999544444 322         2


Q ss_pred             CChhhHHHhhhhcccCCCC--ceEEEEeccC
Q 015158          357 TQPENYLHRIGRSGRFGRK--GVAINFVTRD  385 (412)
Q Consensus       357 ~s~~~~~Q~~GR~~R~g~~--g~~~~~~~~~  385 (412)
                      .|..+|+||.|||||+|.+  |.|++.++..
T Consensus       509 issGEYIQMSGRAGRRG~DdrGivIlmiDek  539 (1041)
T KOG0948|consen  509 ISSGEYIQMSGRAGRRGIDDRGIVILMIDEK  539 (1041)
T ss_pred             ecccceEEecccccccCCCCCceEEEEecCc
Confidence            4678999999999999976  5666666654

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

Probab=100.00  E-value=1.3e-31  Score=270.50  Aligned_cols=303  Identities=18%  Similarity=0.223  Sum_probs=198.6

Q ss_pred             CChHHHHhhhhhhhc-----CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccC
Q 015158           61 KPSAIQQRGIVPFCK-----GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLG  135 (412)
Q Consensus        61 ~l~~~Q~~a~~~~~~-----~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~  135 (412)
                      .+|++|.+|+..+.+     .+++++++|||||||.+++..+...+.. ....++||++|+.+|+.|+.+.|..+.....
T Consensus       413 ~lR~YQ~~AI~ai~~a~~~g~r~~Ll~maTGSGKT~tai~li~~L~~~-~~~~rVLfLvDR~~L~~Qa~~~F~~~~~~~~  491 (1123)
T PRK11448        413 GLRYYQEDAIQAVEKAIVEGQREILLAMATGTGKTRTAIALMYRLLKA-KRFRRILFLVDRSALGEQAEDAFKDTKIEGD  491 (1123)
T ss_pred             CCCHHHHHHHHHHHHHHHhccCCeEEEeCCCCCHHHHHHHHHHHHHhc-CccCeEEEEecHHHHHHHHHHHHHhcccccc
Confidence            489999999988763     3678999999999998876555443333 2346899999999999999999988632212


Q ss_pred             cEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcC-----CCCCCCceEEEEeCCchhhcc--------------
Q 015158          136 VKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQ-----SLRPDNIRIFVLDEADEMLSR--------------  196 (412)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~-----~~~~~~~~~iiiDE~h~~~~~--------------  196 (412)
                      ..+....+....  ..........|+|+|++++.+.+...     ......+++||+||||+....              
T Consensus       492 ~~~~~i~~i~~L--~~~~~~~~~~I~iaTiQtl~~~~~~~~~~~~~~~~~~fdlIIiDEaHRs~~~d~~~~~~~~~~~~~  569 (1123)
T PRK11448        492 QTFASIYDIKGL--EDKFPEDETKVHVATVQGMVKRILYSDDPMDKPPVDQYDCIIVDEAHRGYTLDKEMSEGELQFRDQ  569 (1123)
T ss_pred             cchhhhhchhhh--hhhcccCCCCEEEEEHHHHHHhhhccccccccCCCCcccEEEEECCCCCCccccccccchhccchh
Confidence            111111111100  11112345689999999997765321     134578899999999985321              


Q ss_pred             -CcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCc-----cc---cC-Cce-------------
Q 015158          197 -GFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDE-----LT---LE-GIK-------------  253 (412)
Q Consensus       197 -~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~-----~~---~~-~~~-------------  253 (412)
                       .+...+..++..+  +...||+||||..+..    .+++.++..+.....     ..   ++ .+.             
T Consensus       570 ~~~~~~yr~iL~yF--dA~~IGLTATP~r~t~----~~FG~pv~~Ysl~eAI~DG~Lv~~~~p~~i~t~~~~~gi~~~~~  643 (1123)
T PRK11448        570 LDYVSKYRRVLDYF--DAVKIGLTATPALHTT----EIFGEPVYTYSYREAVIDGYLIDHEPPIRIETRLSQEGIHFEKG  643 (1123)
T ss_pred             hhHHHHHHHHHhhc--CccEEEEecCCccchh----HHhCCeeEEeeHHHHHhcCCcccCcCCEEEEEEecccccccccc
Confidence             1235666777655  3568999999975432    333433322111000     00   00 000             


Q ss_pred             -----------EEE-EEecc----c----------hhhH----HHHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcC--
Q 015158          254 -----------QFH-VNVEK----E----------EWKL----ETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSR--  301 (412)
Q Consensus       254 -----------~~~-~~~~~----~----------~~~~----~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~--  301 (412)
                                 ... ...+.    .          ....    ..+.+.+.....+|+||||.++++|+.+++.|.+.  
T Consensus       644 e~~~~~~~~~~~i~~~~l~d~~~~~~~~~~~~vi~~~~~~~i~~~l~~~l~~~~~~KtiIF~~s~~HA~~i~~~L~~~f~  723 (1123)
T PRK11448        644 EEVEVINTQTGEIDLATLEDEVDFEVEDFNRRVITESFNRVVCEELAKYLDPTGEGKTLIFAATDAHADMVVRLLKEAFK  723 (1123)
T ss_pred             chhhhcchhhhhhhhccCcHHHhhhHHHHHHHHhhHHHHHHHHHHHHHHHhccCCCcEEEEEcCHHHHHHHHHHHHHHHH
Confidence                       000 00000    0          0000    11112222223479999999999999999888653  


Q ss_pred             ----C---CeeEEecCCCCHHHHHHHHHHHhcCCC-cEEEEcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccCC
Q 015158          302 ----D---HTVSATHGDMDQNTRDIIMREFRSGSS-RVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFG  373 (412)
Q Consensus       302 ----~---~~~~~~~~~~~~~~r~~~~~~f~~g~~-~vlv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g  373 (412)
                          +   ..+..++|+.+  ++..++++|++++. .|+|+++++.+|+|+|.+++|+++.++.|...|.||+||+.|..
T Consensus       724 ~~~~~~~~~~v~~itg~~~--~~~~li~~Fk~~~~p~IlVsvdmL~TG~DvP~v~~vVf~rpvkS~~lf~QmIGRgtR~~  801 (1123)
T PRK11448        724 KKYGQVEDDAVIKITGSID--KPDQLIRRFKNERLPNIVVTVDLLTTGIDVPSICNLVFLRRVRSRILYEQMLGRATRLC  801 (1123)
T ss_pred             hhcCCcCccceEEEeCCcc--chHHHHHHHhCCCCCeEEEEecccccCCCcccccEEEEecCCCCHHHHHHHHhhhccCC
Confidence                1   24566888764  46789999999876 58999999999999999999999999999999999999999975


Q ss_pred             C
Q 015158          374 R  374 (412)
Q Consensus       374 ~  374 (412)
                      .
T Consensus       802 ~  802 (1123)
T PRK11448        802 P  802 (1123)
T ss_pred             c
Confidence            4

>PRK05580 primosome assembly protein PriA; Validated

Probab=100.00  E-value=7.3e-31  Score=256.22  Aligned_cols=312  Identities=21%  Similarity=0.276  Sum_probs=217.0

Q ss_pred             CChHHHHhhhhhhhcC---ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcE
Q 015158           61 KPSAIQQRGIVPFCKG---LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVK  137 (412)
Q Consensus        61 ~l~~~Q~~a~~~~~~~---~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~  137 (412)
                      .|++.|+++++.+..+   +++++.++||||||.+|+.++...+..+   .++||++|+++|+.|+.+.+++..   +..
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 TLNPEQAAAVEAIRAAAGFSPFLLDGVTGSGKTEVYLQAIAEVLAQG---KQALVLVPEIALTPQMLARFRARF---GAP  217 (679)
T ss_pred             CCCHHHHHHHHHHHhccCCCcEEEECCCCChHHHHHHHHHHHHHHcC---CeEEEEeCcHHHHHHHHHHHHHHh---CCC
Confidence            4899999999999874   7899999999999999988877776544   589999999999999999998754   567


Q ss_pred             EEEEEcCcchHHH----HHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCc------HHHHHHHHH
Q 015158          138 VHACVGGTSVRED----QRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGF------KDQIYDIFQ  207 (412)
Q Consensus       138 ~~~~~~~~~~~~~----~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~------~~~~~~i~~  207 (412)
                      +..++|+.+....    .....+..+|+|+|+..+.       ..+.++++||+||+|....+..      ...+. +..
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            8888988765433    2334567899999987764       2356899999999998653321      12222 223


Q ss_pred             hCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCc--cccCCceEEEEEecc------chhhHHHHHHHHHhc--C
Q 015158          208 LLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDE--LTLEGIKQFHVNVEK------EEWKLETLCDLYETL--A  277 (412)
Q Consensus       208 ~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~------~~~~~~~l~~~~~~~--~  277 (412)
                      ....+.+++++||||+.+.......  +....+......  ...+.+.  ......      .......+.+.+++.  .
T Consensus       290 a~~~~~~~il~SATps~~s~~~~~~--g~~~~~~l~~r~~~~~~p~v~--~id~~~~~~~~~~~~ls~~l~~~i~~~l~~  365 (679)
T PRK05580        290 AKLENIPVVLGSATPSLESLANAQQ--GRYRLLRLTKRAGGARLPEVE--IIDMRELLRGENGSFLSPPLLEAIKQRLER  365 (679)
T ss_pred             hhccCCCEEEEcCCCCHHHHHHHhc--cceeEEEeccccccCCCCeEE--EEechhhhhhcccCCCCHHHHHHHHHHHHc
Confidence            3446788999999998665544432  222222222111  1112111  111111      001112333333332  3


Q ss_pred             CCcEEEEEcchh------------------------------------------------------------HHHHHHHH
Q 015158          278 ITQSVIFVNTRR------------------------------------------------------------KVDWLTDK  297 (412)
Q Consensus       278 ~~k~lif~~~~~------------------------------------------------------------~~~~~~~~  297 (412)
                      ++++|||+|.+.                                                            .++.+.+.
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            357888877531                                                            44566777


Q ss_pred             HhcC--CCeeEEecCCCC--HHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccCC--CC----------hhh
Q 015158          298 MRSR--DHTVSATHGDMD--QNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLP--TQ----------PEN  361 (412)
Q Consensus       298 L~~~--~~~~~~~~~~~~--~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~~--~s----------~~~  361 (412)
                      |++.  +..+..+|+++.  ..+++++++.|.+|+.+|||+|+++..|+|+|+++.|++++..  .+          ...
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            7665  567889999885  4678999999999999999999999999999999999765443  22          256


Q ss_pred             HHHhhhhcccCCCCceEEEEeccCcHHHH
Q 015158          362 YLHRIGRSGRFGRKGVAINFVTRDDERML  390 (412)
Q Consensus       362 ~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~  390 (412)
                      +.|++||+||.+..|.+++.....+...+
T Consensus       526 l~q~~GRagR~~~~g~viiqT~~p~~~~~  554 (679)
T PRK05580        526 LTQVAGRAGRAEKPGEVLIQTYHPEHPVI  554 (679)
T ss_pred             HHHHHhhccCCCCCCEEEEEeCCCCCHHH
Confidence            89999999999999999987766654444

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

Probab=100.00  E-value=2.8e-32  Score=236.19  Aligned_cols=278  Identities=31%  Similarity=0.493  Sum_probs=221.4

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhhccc---CcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCce
Q 015158          107 ECQALVLAPTRELAQQIEKVMRALGDYL---GVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIR  183 (412)
Q Consensus       107 ~~~~lil~P~~~L~~q~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~  183 (412)
                      .+..+|+-|+++|++|....++++-...   .+.-..+.|+.....++....++.+|+|+||.++...+......+.+..
T Consensus       286 ap~avivepsrelaEqt~N~i~~Fk~h~~np~~r~lLmiggv~~r~Q~~ql~~g~~ivvGtpgRl~~~is~g~~~lt~cr  365 (725)
T KOG0349|consen  286 APEAVIVEPSRELAEQTHNQIEEFKMHTSNPEVRSLLMIGGVLKRTQCKQLKDGTHIVVGTPGRLLQPISKGLVTLTHCR  365 (725)
T ss_pred             CcceeEecCcHHHHHHHHhhHHHHHhhcCChhhhhhhhhhhHHhHHHHHHhhcCceeeecCchhhhhhhhccceeeeeeE
Confidence            3569999999999999999766653222   3344467777777788888889999999999999999998888888999


Q ss_pred             EEEEeCCchhhccCcHHHHHHHHHhCCC------CceEEEEeecCCh-HHHHHHHHhcCCCeEEEecCCccccCCceEEE
Q 015158          184 IFVLDEADEMLSRGFKDQIYDIFQLLPP------KIQVGVFSATMPP-EALEITRKFMNKPVRILVKRDELTLEGIKQFH  256 (412)
Q Consensus       184 ~iiiDE~h~~~~~~~~~~~~~i~~~~~~------~~~~i~~SAT~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  256 (412)
                      ++++||++.++..++...+.++...+|.      ..+.++.|||+.. +.......++..|.-+....++..++.+.++.
T Consensus       366 FlvlDead~lL~qgy~d~I~r~h~qip~~tsdg~rlq~~vCsatlh~feVkk~~ervmhfptwVdLkgeD~vpetvHhvv  445 (725)
T KOG0349|consen  366 FLVLDEADLLLGQGYDDKIYRFHGQIPHMTSDGFRLQSPVCSATLHIFEVKKVGERVMHFPTWVDLKGEDLVPETVHHVV  445 (725)
T ss_pred             EEEecchhhhhhcccHHHHHHHhccchhhhcCCcccccceeeeEEeEEEeeehhhhhccCceeEecccccccchhhccce
Confidence            9999999999998888888888877763      5678999999863 33344555666666666666665555554444


Q ss_pred             EEeccc-----------------------------hhh----H-----HHHHHHHHhcCCCcEEEEEcchhHHHHHHHHH
Q 015158          257 VNVEKE-----------------------------EWK----L-----ETLCDLYETLAITQSVIFVNTRRKVDWLTDKM  298 (412)
Q Consensus       257 ~~~~~~-----------------------------~~~----~-----~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L  298 (412)
                      ..+...                             ...    .     +.-...++.+..++.||||.++..|+.+.+++
T Consensus       446 ~lv~p~~d~sw~~lr~~i~td~vh~kdn~~pg~~Spe~~s~a~kilkgEy~v~ai~~h~mdkaiifcrtk~dcDnLer~~  525 (725)
T KOG0349|consen  446 KLVCPSVDGSWCDLRQFIETDKVHTKDNLLPGQVSPENPSSATKILKGEYGVVAIRRHAMDKAIIFCRTKQDCDNLERMM  525 (725)
T ss_pred             eecCCccCccHHHHhhhhccCCcccccccccccCCCCChhhhhHHhcCchhhhhhhhhccCceEEEEeccccchHHHHHH
Confidence            333221                             001    1     11123356667789999999999999999999


Q ss_pred             hcCC---CeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccCCCC
Q 015158          299 RSRD---HTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRK  375 (412)
Q Consensus       299 ~~~~---~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~  375 (412)
                      ++.|   +.++.+||+..+.+|++.++.|+.+..++||||+...+|+|+..+-.+|.+.+|.....|++||||+||+..-
T Consensus       526 ~qkgg~~~scvclhgDrkP~Erk~nle~Fkk~dvkflictdvaargldi~g~p~~invtlpd~k~nyvhrigrvgraerm  605 (725)
T KOG0349|consen  526 NQKGGKHYSCVCLHGDRKPDERKANLESFKKFDVKFLICTDVAARGLDITGLPFMINVTLPDDKTNYVHRIGRVGRAERM  605 (725)
T ss_pred             HHcCCccceeEEEecCCChhHHHHHHHhhhhcCeEEEEEehhhhccccccCCceEEEEecCcccchhhhhhhccchhhhc
Confidence            9874   5789999999999999999999999999999999999999999999999999999999999999999998777


Q ss_pred             ceEEEEecc
Q 015158          376 GVAINFVTR  384 (412)
Q Consensus       376 g~~~~~~~~  384 (412)
                      |.++.++..
T Consensus       606 glaislvat  614 (725)
T KOG0349|consen  606 GLAISLVAT  614 (725)
T ss_pred             ceeEEEeec
Confidence            777776643

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

Probab=100.00  E-value=1.5e-31  Score=260.42  Aligned_cols=318  Identities=20%  Similarity=0.274  Sum_probs=239.4

Q ss_pred             HHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhc
Q 015158           53 GIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGD  132 (412)
Q Consensus        53 ~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~  132 (412)
                      .....+|. |-++|++++..+..+.+++|++|||+|||+++.+++...+..+.   +++|++|.++|.+|.++++.....
T Consensus       112 ~~~~~~F~-LD~fQ~~a~~~Ler~esVlV~ApTssGKTvVaeyAi~~al~~~q---rviYTsPIKALsNQKyrdl~~~fg  187 (1041)
T COG4581         112 PAREYPFE-LDPFQQEAIAILERGESVLVCAPTSSGKTVVAEYAIALALRDGQ---RVIYTSPIKALSNQKYRDLLAKFG  187 (1041)
T ss_pred             HHHhCCCC-cCHHHHHHHHHHhCCCcEEEEccCCCCcchHHHHHHHHHHHcCC---ceEeccchhhhhhhHHHHHHHHhh
Confidence            34456888 99999999999999999999999999999999999998887764   799999999999999998877543


Q ss_pred             ccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCCCC
Q 015158          133 YLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPK  212 (412)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~  212 (412)
                      ...-.+.+++|+..+.       +++.++|+|.|.|.+++.+.......+..||+||+|.+.+...+..|+.++-.+|..
T Consensus       188 dv~~~vGL~TGDv~IN-------~~A~clvMTTEILRnMlyrg~~~~~~i~~ViFDEvHyi~D~eRG~VWEE~Ii~lP~~  260 (1041)
T COG4581         188 DVADMVGLMTGDVSIN-------PDAPCLVMTTEILRNMLYRGSESLRDIEWVVFDEVHYIGDRERGVVWEEVIILLPDH  260 (1041)
T ss_pred             hhhhhccceecceeeC-------CCCceEEeeHHHHHHHhccCcccccccceEEEEeeeeccccccchhHHHHHHhcCCC
Confidence            2223467888887744       457899999999999999888888899999999999999998899999999999999


Q ss_pred             ceEEEEeecCChHHH--HHHHHhcCCCeEEEecCCccccCCceEEEEEe-------ccch--------------------
Q 015158          213 IQVGVFSATMPPEAL--EITRKFMNKPVRILVKRDELTLEGIKQFHVNV-------EKEE--------------------  263 (412)
Q Consensus       213 ~~~i~~SAT~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~--------------------  263 (412)
                      .+++++|||.++..+  ..++..-..+..+.......  ....++++.-       +...                    
T Consensus       261 v~~v~LSATv~N~~EF~~Wi~~~~~~~~~vv~t~~Rp--vPL~~~~~~~~~l~~lvde~~~~~~~~~~~a~~~l~~~~~~  338 (1041)
T COG4581         261 VRFVFLSATVPNAEEFAEWIQRVHSQPIHVVSTEHRP--VPLEHFVYVGKGLFDLVDEKKKFNAENFPSANRSLSCFSEK  338 (1041)
T ss_pred             CcEEEEeCCCCCHHHHHHHHHhccCCCeEEEeecCCC--CCeEEEEecCCceeeeecccccchhhcchhhhhhhhccchh
Confidence            999999999976422  23333333333332222111  1112211111       0000                    


Q ss_pred             --------------------------hhHHHHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcC----------------
Q 015158          264 --------------------------WKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSR----------------  301 (412)
Q Consensus       264 --------------------------~~~~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~----------------  301 (412)
                                                .....+...+.....-++++|+-++..|+..+..+...                
T Consensus       339 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~iv~~l~~~~~lP~I~F~FSr~~Ce~~a~~~~~ldl~~~~~~e~~i~~ii  418 (1041)
T COG4581         339 VRETDDGDVGRYARRTKALRGSAKGPAGRPEIVNKLDKDNLLPAIVFSFSRRGCEEAAQILSTLDLVLTEEKERAIREII  418 (1041)
T ss_pred             ccccCccccccccccccccCCcccccccchHHHhhhhhhcCCceEEEEEchhhHHHHHHHhcccccccCCcHHHHHHHHH
Confidence                                      00011233333334458999999999999887777522                


Q ss_pred             ------------CC-------------eeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccC-
Q 015158          302 ------------DH-------------TVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDL-  355 (412)
Q Consensus       302 ------------~~-------------~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~-  355 (412)
                                  +.             .+.++|+++-+..+..+.+.|..|-.+|+++|.+++.|+|.|.-++|+ .+. 
T Consensus       419 ~~~i~~L~~ed~~lp~~~~~~~~~L~RGiavHH~GlLP~~K~~vE~Lfq~GLvkvvFaTeT~s~GiNmPartvv~-~~l~  497 (1041)
T COG4581         419 DHAIGDLAEEDRELPLQILEISALLLRGIAVHHAGLLPAIKELVEELFQEGLVKVVFATETFAIGINMPARTVVF-TSLS  497 (1041)
T ss_pred             HHHHhhcChhhhcCcccHHHHHHHHhhhhhhhccccchHHHHHHHHHHhccceeEEeehhhhhhhcCCcccceee-eeeE
Confidence                        11             256889999999999999999999999999999999999999544443 332 


Q ss_pred             --------CCChhhHHHhhhhcccCCCC--ceEEEEecc
Q 015158          356 --------PTQPENYLHRIGRSGRFGRK--GVAINFVTR  384 (412)
Q Consensus       356 --------~~s~~~~~Q~~GR~~R~g~~--g~~~~~~~~  384 (412)
                              .-++.+|.|+.||+||+|.+  |.++++..+
T Consensus       498 K~dG~~~r~L~~gEy~QmsGRAGRRGlD~~G~vI~~~~~  536 (1041)
T COG4581         498 KFDGNGHRWLSPGEYTQMSGRAGRRGLDVLGTVIVIEPP  536 (1041)
T ss_pred             EecCCceeecChhHHHHhhhhhccccccccceEEEecCC
Confidence                    35789999999999999976  566665433

>PRK09694 helicase Cas3; Provisional

Probab=100.00  E-value=1.3e-29  Score=249.30  Aligned_cols=310  Identities=17%  Similarity=0.168  Sum_probs=202.0

Q ss_pred             CCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccc--CcE
Q 015158           60 EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYL--GVK  137 (412)
Q Consensus        60 ~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~--~~~  137 (412)
                      ..|+|+|+.+......+..+++.+|||+|||.+++.++......+ ...+++|..||.++++++++++.++....  ..+
T Consensus       285 ~~p~p~Q~~~~~~~~~pgl~ileApTGsGKTEAAL~~A~~l~~~~-~~~gi~~aLPT~Atan~m~~Rl~~~~~~~f~~~~  363 (878)
T PRK09694        285 YQPRQLQTLVDALPLQPGLTIIEAPTGSGKTEAALAYAWRLIDQG-LADSIIFALPTQATANAMLSRLEALASKLFPSPN  363 (878)
T ss_pred             CCChHHHHHHHhhccCCCeEEEEeCCCCCHHHHHHHHHHHHHHhC-CCCeEEEECcHHHHHHHHHHHHHHHHHHhcCCCc
Confidence            359999998865544567789999999999999987766544333 34589999999999999999987643211  345


Q ss_pred             EEEEEcCcchHHHH---------------------HHhc------CCCcEEEeChHHHHHHHHcCC-CCCCC----ceEE
Q 015158          138 VHACVGGTSVREDQ---------------------RILS------SGVHVVVGTPGRVFDMLRRQS-LRPDN----IRIF  185 (412)
Q Consensus       138 ~~~~~~~~~~~~~~---------------------~~~~------~~~~iii~T~~~l~~~~~~~~-~~~~~----~~~i  185 (412)
                      +...+|........                     ..+.      --..|+|+|.++++..+...+ ...+.    -++|
T Consensus       364 v~L~Hg~a~l~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~kr~llapi~V~TiDQlL~a~l~~kh~~lR~~~La~svv  443 (878)
T PRK09694        364 LILAHGNSRFNHLFQSLKSRAATEQGQEEAWVQCCEWLSQSNKRVFLGQIGVCTIDQVLISVLPVKHRFIRGFGLGRSVL  443 (878)
T ss_pred             eEeecCcchhhhhhhhhhcccccccccchhhhHHHHHHhhhhhhhhcCCEEEcCHHHHHHHHHccchHHHHHHhhccCeE
Confidence            66666654321110                     0011      115899999999875544321 11122    2489


Q ss_pred             EEeCCchhhccCcHHHHHHHHHhC-CCCceEEEEeecCChHHHHHHHHhcCCCeEE----------EecCCc-----ccc
Q 015158          186 VLDEADEMLSRGFKDQIYDIFQLL-PPKIQVGVFSATMPPEALEITRKFMNKPVRI----------LVKRDE-----LTL  249 (412)
Q Consensus       186 iiDE~h~~~~~~~~~~~~~i~~~~-~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~----------~~~~~~-----~~~  249 (412)
                      |+||+|.+-.. ....+..++..+ ....++|+||||++....+.+...++.....          ......     ...
T Consensus       444 IiDEVHAyD~y-m~~lL~~~L~~l~~~g~~vIllSATLP~~~r~~L~~a~~~~~~~~~~~~YPlvt~~~~~~~~~~~~~~  522 (878)
T PRK09694        444 IVDEVHAYDAY-MYGLLEAVLKAQAQAGGSVILLSATLPATLKQKLLDTYGGHDPVELSSAYPLITWRGVNGAQRFDLSA  522 (878)
T ss_pred             EEechhhCCHH-HHHHHHHHHHHHHhcCCcEEEEeCCCCHHHHHHHHHHhccccccccccccccccccccccceeeeccc
Confidence            99999976432 334444444433 3467799999999987766554433211000          000000     000


Q ss_pred             -----CCceEEEE-Ee--ccchhhHHHHHHHHHhc-CCCcEEEEEcchhHHHHHHHHHhcCC---CeeEEecCCCCHHHH
Q 015158          250 -----EGIKQFHV-NV--EKEEWKLETLCDLYETL-AITQSVIFVNTRRKVDWLTDKMRSRD---HTVSATHGDMDQNTR  317 (412)
Q Consensus       250 -----~~~~~~~~-~~--~~~~~~~~~l~~~~~~~-~~~k~lif~~~~~~~~~~~~~L~~~~---~~~~~~~~~~~~~~r  317 (412)
                           +.-..... ..  .........+..+++.. .+++++||||+++.++.+++.|++.+   ..+..+||.++..+|
T Consensus       523 ~~~~~~~~~~v~v~~~~~~~~~~~~~~l~~i~~~~~~g~~vLVf~NTV~~Aq~ly~~L~~~~~~~~~v~llHsrf~~~dR  602 (878)
T PRK09694        523 HPEQLPARFTIQLEPICLADMLPDLTLLQRMIAAANAGAQVCLICNLVDDAQKLYQRLKELNNTQVDIDLFHARFTLNDR  602 (878)
T ss_pred             cccccCcceEEEEEeeccccccCHHHHHHHHHHHHhcCCEEEEEECCHHHHHHHHHHHHhhCCCCceEEEEeCCCCHHHH
Confidence                 00011111 11  11111223344444432 45789999999999999999999764   579999999999998


Q ss_pred             H----HHHHHH-hcCC---CcEEEEcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccCCC
Q 015158          318 D----IIMREF-RSGS---SRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGR  374 (412)
Q Consensus       318 ~----~~~~~f-~~g~---~~vlv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~  374 (412)
                      .    ++++.| ++|+   ..|||+|++++.|+|+ +++++|....|  ...++||+||++|.+.
T Consensus       603 ~~~E~~vl~~fgk~g~r~~~~ILVaTQViE~GLDI-d~DvlItdlaP--idsLiQRaGR~~R~~~  664 (878)
T PRK09694        603 REKEQRVIENFGKNGKRNQGRILVATQVVEQSLDL-DFDWLITQLCP--VDLLFQRLGRLHRHHR  664 (878)
T ss_pred             HHHHHHHHHHHHhcCCcCCCeEEEECcchhheeec-CCCeEEECCCC--HHHHHHHHhccCCCCC
Confidence            4    567777 5565   4799999999999999 57888865555  6899999999999864

>cd00268 DEADc DEAD-box helicases

Probab=100.00  E-value=1.1e-30  Score=221.02  Aligned_cols=200  Identities=53%  Similarity=0.809  Sum_probs=179.6

Q ss_pred             cccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccC--CCceeEEEEcCCHH
Q 015158           41 FDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYG--LVECQALVLAPTRE  118 (412)
Q Consensus        41 f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~--~~~~~~lil~P~~~  118 (412)
                      |+++++++.+.+.+...++..|+++|.+++..+.+++++++.+|||+|||.+++++++..+...  ..+++++|++|+++
T Consensus         1 ~~~~~~~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~TG~GKT~~~~~~~l~~~~~~~~~~~~~viii~p~~~   80 (203)
T cd00268           1 FEELGLSPELLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEKLDPSPKKDGPQALILAPTRE   80 (203)
T ss_pred             CCcCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHHHHHHHHHHhhcccCCceEEEEcCCHH
Confidence            6788999999999999999999999999999999999999999999999999999999888765  45678999999999


Q ss_pred             HHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCc
Q 015158          119 LAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGF  198 (412)
Q Consensus       119 L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~  198 (412)
                      |+.|+.+.+..+....+..+..++|+............+++|+|+|++.+...+.+......+++++|+||+|.+.+.++
T Consensus        81 L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~l~~~~~~~~~l~~lIvDE~h~~~~~~~  160 (203)
T cd00268          81 LALQIAEVARKLGKHTNLKVVVIYGGTSIDKQIRKLKRGPHIVVATPGRLLDLLERGKLDLSKVKYLVLDEADRMLDMGF  160 (203)
T ss_pred             HHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHhcCCCCEEEEChHHHHHHHHcCCCChhhCCEEEEeChHHhhccCh
Confidence            99999999999887778888899998877666656666789999999999999888777788899999999999888888


Q ss_pred             HHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEE
Q 015158          199 KDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRI  240 (412)
Q Consensus       199 ~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~  240 (412)
                      ...+..+...++...+++++|||+++.....+..+...++.+
T Consensus       161 ~~~~~~~~~~l~~~~~~~~~SAT~~~~~~~~~~~~~~~~~~~  202 (203)
T cd00268         161 EDQIREILKLLPKDRQTLLFSATMPKEVRDLARKFLRNPVRI  202 (203)
T ss_pred             HHHHHHHHHhCCcccEEEEEeccCCHHHHHHHHHHCCCCEEe
Confidence            899999999998899999999999998888888888877654

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=99.98  E-value=6.4e-30  Score=215.49  Aligned_cols=306  Identities=18%  Similarity=0.209  Sum_probs=220.1

Q ss_pred             CChHHHHhhhhhhhc----CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCc
Q 015158           61 KPSAIQQRGIVPFCK----GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGV  136 (412)
Q Consensus        61 ~l~~~Q~~a~~~~~~----~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~  136 (412)
                      +|++.|+.+-+.+.+    ..+.+|+|-||+|||......+...+..+   .++.+..|+...+-+.+.++++...  +.
T Consensus        97 ~Ls~~Q~~as~~l~q~i~~k~~~lv~AV~GaGKTEMif~~i~~al~~G---~~vciASPRvDVclEl~~Rlk~aF~--~~  171 (441)
T COG4098          97 TLSPGQKKASNQLVQYIKQKEDTLVWAVTGAGKTEMIFQGIEQALNQG---GRVCIASPRVDVCLELYPRLKQAFS--NC  171 (441)
T ss_pred             ccChhHHHHHHHHHHHHHhcCcEEEEEecCCCchhhhHHHHHHHHhcC---CeEEEecCcccchHHHHHHHHHhhc--cC
Confidence            489999998888664    57899999999999988877777777665   5899999999999999999888543  56


Q ss_pred             EEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEE
Q 015158          137 KVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVG  216 (412)
Q Consensus       137 ~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i  216 (412)
                      .+..++|+.....       ...++|+|.++|++...       .+|++|+||++.+.-..-...-..+..........|
T Consensus       172 ~I~~Lyg~S~~~f-------r~plvVaTtHQLlrFk~-------aFD~liIDEVDAFP~~~d~~L~~Av~~ark~~g~~I  237 (441)
T COG4098         172 DIDLLYGDSDSYF-------RAPLVVATTHQLLRFKQ-------AFDLLIIDEVDAFPFSDDQSLQYAVKKARKKEGATI  237 (441)
T ss_pred             CeeeEecCCchhc-------cccEEEEehHHHHHHHh-------hccEEEEeccccccccCCHHHHHHHHHhhcccCceE
Confidence            7788888765322       25799999999987654       789999999998654433344445556666777899


Q ss_pred             EEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccch-----hhH-HHHHHHHHhc--CCCcEEEEEcch
Q 015158          217 VFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEE-----WKL-ETLCDLYETL--AITQSVIFVNTR  288 (412)
Q Consensus       217 ~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~-~~l~~~~~~~--~~~k~lif~~~~  288 (412)
                      .+|||++..+...+...-.....+.........+ + ..+.+...-.     .++ ..+..++++.  .+.+++||++++
T Consensus       238 ylTATp~k~l~r~~~~g~~~~~klp~RfH~~pLp-v-Pkf~w~~~~~k~l~r~kl~~kl~~~lekq~~~~~P~liF~p~I  315 (441)
T COG4098         238 YLTATPTKKLERKILKGNLRILKLPARFHGKPLP-V-PKFVWIGNWNKKLQRNKLPLKLKRWLEKQRKTGRPVLIFFPEI  315 (441)
T ss_pred             EEecCChHHHHHHhhhCCeeEeecchhhcCCCCC-C-CceEEeccHHHHhhhccCCHHHHHHHHHHHhcCCcEEEEecch
Confidence            9999998765554443222112111111111111 1 1122222211     111 2556666665  347999999999


Q ss_pred             hHHHHHHHHHhcC--CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccCC--CChhhHHH
Q 015158          289 RKVDWLTDKMRSR--DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLP--TQPENYLH  364 (412)
Q Consensus       289 ~~~~~~~~~L~~~--~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~~--~s~~~~~Q  364 (412)
                      +..+.++..|++.  ...+..+|+.  ...|.+..+.|++|++++|++|.++++|+.+|++++.++-...  ++.+.++|
T Consensus       316 ~~~eq~a~~lk~~~~~~~i~~Vhs~--d~~R~EkV~~fR~G~~~lLiTTTILERGVTfp~vdV~Vlgaeh~vfTesaLVQ  393 (441)
T COG4098         316 ETMEQVAAALKKKLPKETIASVHSE--DQHRKEKVEAFRDGKITLLITTTILERGVTFPNVDVFVLGAEHRVFTESALVQ  393 (441)
T ss_pred             HHHHHHHHHHHhhCCccceeeeecc--CccHHHHHHHHHcCceEEEEEeehhhcccccccceEEEecCCcccccHHHHHH
Confidence            9999999999553  3355677774  4578999999999999999999999999999999998866544  78999999


Q ss_pred             hhhhcccCC--CCceEEEEeccCcHHH
Q 015158          365 RIGRSGRFG--RKGVAINFVTRDDERM  389 (412)
Q Consensus       365 ~~GR~~R~g--~~g~~~~~~~~~~~~~  389 (412)
                      ..||+||.-  +.|.++.|-.-....+
T Consensus       394 IaGRvGRs~~~PtGdv~FFH~G~skaM  420 (441)
T COG4098         394 IAGRVGRSLERPTGDVLFFHYGKSKAM  420 (441)
T ss_pred             HhhhccCCCcCCCCcEEEEeccchHHH
Confidence            999999973  4566665554444433

>TIGR00595 priA primosomal protein N'

Probab=99.98  E-value=3.6e-30  Score=242.64  Aligned_cols=304  Identities=21%  Similarity=0.296  Sum_probs=202.8

Q ss_pred             EEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHH----HHHhc
Q 015158           80 IQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVRED----QRILS  155 (412)
Q Consensus        80 lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~  155 (412)
                      ++.++||||||.+|+.++...+..+   .++||++|+.+|+.|+.+.+++..   +..+..++++.+....    .....
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 LLFGVTGSGKTEVYLQAIEKVLALG---KSVLVLVPEIALTPQMIQRFKYRF---GSQVAVLHSGLSDSEKLQAWRKVKN   74 (505)
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHcC---CeEEEEeCcHHHHHHHHHHHHHHh---CCcEEEEECCCCHHHHHHHHHHHHc
Confidence            4789999999999987776665543   489999999999999999998754   5667788887654432    33445


Q ss_pred             CCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccC-----c-HHHHHHHHHhCCCCceEEEEeecCChHHHHH
Q 015158          156 SGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRG-----F-KDQIYDIFQLLPPKIQVGVFSATMPPEALEI  229 (412)
Q Consensus       156 ~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~-----~-~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~  229 (412)
                      +..+|+|+|+..++       ..+.++++||+||.|....+.     | ...+..+.. ...+.+++++||||+.+....
T Consensus        75 g~~~IVVGTrsalf-------~p~~~l~lIIVDEeh~~sykq~~~p~y~ar~~a~~ra-~~~~~~vil~SATPsles~~~  146 (505)
T TIGR00595        75 GEILVVIGTRSALF-------LPFKNLGLIIVDEEHDSSYKQEEGPRYHARDVAVYRA-KKFNCPVVLGSATPSLESYHN  146 (505)
T ss_pred             CCCCEEECChHHHc-------CcccCCCEEEEECCCccccccccCCCCcHHHHHHHHH-HhcCCCEEEEeCCCCHHHHHH
Confidence            67899999988764       235689999999999865332     1 122333333 335788999999998654444


Q ss_pred             HHHhcCCCeEEEecC--CccccCCceEEEEEeccch---hhHHHHHHHHHhc--CCCcEEEEEcchhH------------
Q 015158          230 TRKFMNKPVRILVKR--DELTLEGIKQFHVNVEKEE---WKLETLCDLYETL--AITQSVIFVNTRRK------------  290 (412)
Q Consensus       230 ~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~---~~~~~l~~~~~~~--~~~k~lif~~~~~~------------  290 (412)
                      ...  +.........  .....+.+.  ........   .....+.+.+++.  .++++|||+|++..            
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            321  2211111111  111111111  11221111   1122333333332  34589999776543            


Q ss_pred             ------------------------------------------------HHHHHHHHhcC--CCeeEEecCCCCHHHH--H
Q 015158          291 ------------------------------------------------VDWLTDKMRSR--DHTVSATHGDMDQNTR--D  318 (412)
Q Consensus       291 ------------------------------------------------~~~~~~~L~~~--~~~~~~~~~~~~~~~r--~  318 (412)
                                                                      .+.+.+.|++.  +..+..+|++++...+  +
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                                                            46777777766  5688899999876655  8


Q ss_pred             HHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccCCC------------ChhhHHHhhhhcccCCCCceEEEEeccCc
Q 015158          319 IIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPT------------QPENYLHRIGRSGRFGRKGVAINFVTRDD  386 (412)
Q Consensus       319 ~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~~~------------s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~  386 (412)
                      .+++.|.+|+.+|||+|++++.|+|+|+++.|++++...            ....+.|++||+||.++.|.+++.....+
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            999999999999999999999999999999987554431            13568999999999999999987665544


Q ss_pred             HHHH-----HHHHHHhcccc
Q 015158          387 ERML-----FDIQKFYNVVI  401 (412)
Q Consensus       387 ~~~~-----~~~~~~~~~~~  401 (412)
                      ...+     ..++.|+..++
T Consensus       383 ~~~~~~~~~~d~~~f~~~el  402 (505)
T TIGR00595       383 HPAIQAALTGDYEAFYEQEL  402 (505)
T ss_pred             CHHHHHHHhCCHHHHHHHHH
Confidence            3322     23445555544

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).

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=99.98  E-value=2.7e-30  Score=259.97  Aligned_cols=308  Identities=19%  Similarity=0.222  Sum_probs=211.9

Q ss_pred             hHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhh-cccCcEEEEE
Q 015158           63 SAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALG-DYLGVKVHAC  141 (412)
Q Consensus        63 ~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~-~~~~~~~~~~  141 (412)
                      +.+..+.+..+..++.++|+|+||||||+..-..++.. ..+ ..++|++.-|++.-+...++.+.+.. ...|..+...
T Consensus        69 ~~~~~~Il~~l~~~~vvii~g~TGSGKTTqlPq~lle~-~~~-~~~~I~~tQPRRlAA~svA~RvA~elg~~lG~~VGY~  146 (1283)
T TIGR01967        69 SAKREDIAEAIAENQVVIIAGETGSGKTTQLPKICLEL-GRG-SHGLIGHTQPRRLAARTVAQRIAEELGTPLGEKVGYK  146 (1283)
T ss_pred             HHHHHHHHHHHHhCceEEEeCCCCCCcHHHHHHHHHHc-CCC-CCceEecCCccHHHHHHHHHHHHHHhCCCcceEEeeE
Confidence            44446777778788889999999999998654444332 112 23467778898887777776665532 2223334332


Q ss_pred             EcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCch-hhccCcHHH-HHHHHHhCCCCceEEEEe
Q 015158          142 VGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADE-MLSRGFKDQ-IYDIFQLLPPKIQVGVFS  219 (412)
Q Consensus       142 ~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~-~~~~~~~~~-~~~i~~~~~~~~~~i~~S  219 (412)
                      .....      ....+..|.++|++.|++.+.... .+.++++||+||+|+ ..+.++... +..++.. .++.++|+||
T Consensus       147 vR~~~------~~s~~T~I~~~TdGiLLr~l~~d~-~L~~~~~IIIDEaHERsL~~D~LL~lLk~il~~-rpdLKlIlmS  218 (1283)
T TIGR01967       147 VRFHD------QVSSNTLVKLMTDGILLAETQQDR-FLSRYDTIIIDEAHERSLNIDFLLGYLKQLLPR-RPDLKIIITS  218 (1283)
T ss_pred             EcCCc------ccCCCceeeeccccHHHHHhhhCc-ccccCcEEEEcCcchhhccchhHHHHHHHHHhh-CCCCeEEEEe
Confidence            22111      123456899999999999887654 368899999999995 667665544 4555443 3578999999


Q ss_pred             ecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccc-----hhhHHHHHHHHHh---cCCCcEEEEEcchhHH
Q 015158          220 ATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKE-----EWKLETLCDLYET---LAITQSVIFVNTRRKV  291 (412)
Q Consensus       220 AT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~l~~~~~~---~~~~k~lif~~~~~~~  291 (412)
                      ||++.  .. +..+++....+.+....   ..+...+......     ......+...+..   ...+.+|||+++.+++
T Consensus       219 ATld~--~~-fa~~F~~apvI~V~Gr~---~PVev~Y~~~~~~~~~~~~~~~~~i~~~I~~l~~~~~GdILVFLpg~~EI  292 (1283)
T TIGR01967       219 ATIDP--ER-FSRHFNNAPIIEVSGRT---YPVEVRYRPLVEEQEDDDLDQLEAILDAVDELFAEGPGDILIFLPGEREI  292 (1283)
T ss_pred             CCcCH--HH-HHHHhcCCCEEEECCCc---ccceeEEecccccccchhhhHHHHHHHHHHHHHhhCCCCEEEeCCCHHHH
Confidence            99964  33 44444433334333221   1233333322211     1122222222222   2447899999999999


Q ss_pred             HHHHHHHhcCC---CeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccCC------------
Q 015158          292 DWLTDKMRSRD---HTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLP------------  356 (412)
Q Consensus       292 ~~~~~~L~~~~---~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~~------------  356 (412)
                      +.+++.|++.+   ..+..+||+++.++|..+++.+  +..+|||+|+++++|+|+|++++||+.+.+            
T Consensus       293 ~~l~~~L~~~~~~~~~VlpLhg~Ls~~eQ~~vf~~~--~~rkIVLATNIAEtSLTIpgV~yVIDsGl~r~~~yd~~~~~~  370 (1283)
T TIGR01967       293 RDAAEILRKRNLRHTEILPLYARLSNKEQQRVFQPH--SGRRIVLATNVAETSLTVPGIHYVIDTGTARISRYSYRTKVQ  370 (1283)
T ss_pred             HHHHHHHHhcCCCCcEEEeccCCCCHHHHHHHhCCC--CCceEEEeccHHHhccccCCeeEEEeCCCccccccccccCcc
Confidence            99999998764   4588999999999999886643  347899999999999999999999998843            


Q ss_pred             ------CChhhHHHhhhhcccCCCCceEEEEeccCcHHH
Q 015158          357 ------TQPENYLHRIGRSGRFGRKGVAINFVTRDDERM  389 (412)
Q Consensus       357 ------~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~  389 (412)
                            .|.+++.||.||+||.+ +|.||.++++.+...
T Consensus       371 ~L~~~~ISkasa~QRaGRAGR~~-~G~cyRLyte~~~~~  408 (1283)
T TIGR01967       371 RLPIEPISQASANQRKGRCGRVA-PGICIRLYSEEDFNS  408 (1283)
T ss_pred             ccCCccCCHHHHHHHhhhhCCCC-CceEEEecCHHHHHh
Confidence                  46789999999999997 999999999876653

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.

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

Probab=99.97  E-value=4.1e-30  Score=247.62  Aligned_cols=334  Identities=20%  Similarity=0.271  Sum_probs=239.0

Q ss_pred             CHHHHHHHHHCCCCCChHHHHhhhhhhhcC-ccEEEECCCCCCchhHhHHHHHHhhccCCC--------ceeEEEEcCCH
Q 015158           47 QENLLRGIYAYGFEKPSAIQQRGIVPFCKG-LDVIQQAQSGTGKTATFCSGILQQLDYGLV--------ECQALVLAPTR  117 (412)
Q Consensus        47 ~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~-~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~--------~~~~lil~P~~  117 (412)
                      +.+-..++.  |...+++.|-......+.+ .+.+++||||+|||..+++.+++.+..+..        ..+++|++|.+
T Consensus       297 P~Wnq~aF~--g~~sLNrIQS~v~daAl~~~EnmLlCAPTGaGKTNVAvLtiLqel~~h~r~dgs~nl~~fKIVYIAPmK  374 (1674)
T KOG0951|consen  297 PKWNQPAFF--GKQSLNRIQSKVYDAALRGDENMLLCAPTGAGKTNVAVLTILQELGNHLREDGSVNLAPFKIVYIAPMK  374 (1674)
T ss_pred             cchhhhhcc--cchhhhHHHHHHHHHHhcCcCcEEEeccCCCCchHHHHHHHHHHHhcccccccceecccceEEEEeeHH
Confidence            333344443  6667999999999998876 689999999999999999999998865432        34799999999


Q ss_pred             HHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCC--CCCCCceEEEEeCCchhhc
Q 015158          118 ELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQS--LRPDNIRIFVLDEADEMLS  195 (412)
Q Consensus       118 ~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~--~~~~~~~~iiiDE~h~~~~  195 (412)
                      +|++.|...+.+....+|+.|..++|+......   -....+|+++|||++--.-++..  ...+-++++|+||+|.+-+
T Consensus       375 aLvqE~VgsfSkRla~~GI~V~ElTgD~~l~~~---qieeTqVIV~TPEK~DiITRk~gdraY~qlvrLlIIDEIHLLhD  451 (1674)
T KOG0951|consen  375 ALVQEMVGSFSKRLAPLGITVLELTGDSQLGKE---QIEETQVIVTTPEKWDIITRKSGDRAYEQLVRLLIIDEIHLLHD  451 (1674)
T ss_pred             HHHHHHHHHHHhhccccCcEEEEecccccchhh---hhhcceeEEeccchhhhhhcccCchhHHHHHHHHhhhhhhhccc
Confidence            999999999999888899999999998764322   11346899999999855444322  1124578999999996533


Q ss_pred             cCcHHHHHHHHHhC-------CCCceEEEEeecCChHHHHHHHHhcC-CCeEEEecCCccccCCceEEEEEeccchh-h-
Q 015158          196 RGFKDQIYDIFQLL-------PPKIQVGVFSATMPPEALEITRKFMN-KPVRILVKRDELTLEGIKQFHVNVEKEEW-K-  265 (412)
Q Consensus       196 ~~~~~~~~~i~~~~-------~~~~~~i~~SAT~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~-  265 (412)
                      . .+..+..+....       ..+++.+++|||+|+-  .....+++ ++.-.........+-.+.+.+.-+..... + 
T Consensus       452 d-RGpvLESIVaRt~r~ses~~e~~RlVGLSATLPNy--~DV~~Fl~v~~~glf~fd~syRpvPL~qq~Igi~ek~~~~~  528 (1674)
T KOG0951|consen  452 D-RGPVLESIVARTFRRSESTEEGSRLVGLSATLPNY--EDVASFLRVDPEGLFYFDSSYRPVPLKQQYIGITEKKPLKR  528 (1674)
T ss_pred             c-cchHHHHHHHHHHHHhhhcccCceeeeecccCCch--hhhHHHhccCcccccccCcccCcCCccceEeccccCCchHH
Confidence            2 345554443332       3478999999999863  33333332 22222222233334445555554443221 1 


Q ss_pred             ----H-HHHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcC-------------------------------------CC
Q 015158          266 ----L-ETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSR-------------------------------------DH  303 (412)
Q Consensus       266 ----~-~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~-------------------------------------~~  303 (412)
                          . ..+..+++.....++|||+.|++++-+.++.+++.                                     .+
T Consensus       529 ~qamNe~~yeKVm~~agk~qVLVFVHsRkET~ktA~aIRd~~le~dtls~fmre~s~s~eilrtea~~~kn~dLkdLLpy  608 (1674)
T KOG0951|consen  529 FQAMNEACYEKVLEHAGKNQVLVFVHSRKETAKTARAIRDKALEEDTLSRFMREDSASREILRTEAGQAKNPDLKDLLPY  608 (1674)
T ss_pred             HHHHHHHHHHHHHHhCCCCcEEEEEEechHHHHHHHHHHHHHhhhhHHHHHHhcccchhhhhhhhhhcccChhHHHHhhc
Confidence                1 23344555556689999999999888888877632                                     35


Q ss_pred             eeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEcc-----------CCCChhhHHHhhhhcccC
Q 015158          304 TVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYD-----------LPTQPENYLHRIGRSGRF  372 (412)
Q Consensus       304 ~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~-----------~~~s~~~~~Q~~GR~~R~  372 (412)
                      .+..+|++|++.+|..+++.|.+|+++|+++|..++.|+|+|.-. ||+=+           .+.++.+..||.||+||.
T Consensus       609 gfaIHhAGl~R~dR~~~EdLf~~g~iqvlvstatlawgvnlpaht-Viikgtqvy~pekg~w~elsp~dv~qmlgragrp  687 (1674)
T KOG0951|consen  609 GFAIHHAGLNRKDRELVEDLFADGHIQVLVSTATLAWGVNLPAHT-VIIKGTQVYDPEKGRWTELSPLDVMQMLGRAGRP  687 (1674)
T ss_pred             cceeeccCCCcchHHHHHHHHhcCceeEEEeehhhhhhcCCCcce-EEecCccccCcccCccccCCHHHHHHHHhhcCCC
Confidence            688999999999999999999999999999999999999999544 44332           245789999999999997


Q ss_pred             CC--CceEEEEeccCcHHH
Q 015158          373 GR--KGVAINFVTRDDERM  389 (412)
Q Consensus       373 g~--~g~~~~~~~~~~~~~  389 (412)
                      +.  .|.++++....+...
T Consensus       688 ~~D~~gegiiit~~se~qy  706 (1674)
T KOG0951|consen  688 QYDTCGEGIIITDHSELQY  706 (1674)
T ss_pred             ccCcCCceeeccCchHhhh
Confidence            64  466776666655443

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=99.97  E-value=3.8e-29  Score=248.25  Aligned_cols=314  Identities=20%  Similarity=0.211  Sum_probs=215.1

Q ss_pred             CChHHHHhhhhhhh----cCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCc
Q 015158           61 KPSAIQQRGIVPFC----KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGV  136 (412)
Q Consensus        61 ~l~~~Q~~a~~~~~----~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~  136 (412)
                      .|++||.+++..+.    .|.++|+...+|.|||+.++..+..........+++|||||. ++..+|.+++.++++  ..
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            58999999999875    467899999999999988755444322222234579999996 667889999999875  45


Q ss_pred             EEEEEEcCcchHHHH---HHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCCCCc
Q 015158          137 KVHACVGGTSVREDQ---RILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKI  213 (412)
Q Consensus       137 ~~~~~~~~~~~~~~~---~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~  213 (412)
                      .+..++|........   ......++|+|+||+.+.+...  .+...+|++||+||||.+.+..  ......+..+. ..
T Consensus       246 ~v~~~~G~~~eR~~~~~~~~~~~~~dVvITSYe~l~~e~~--~L~k~~W~~VIvDEAHrIKN~~--Sklskalr~L~-a~  320 (1033)
T PLN03142        246 RAVKFHGNPEERAHQREELLVAGKFDVCVTSFEMAIKEKT--ALKRFSWRYIIIDEAHRIKNEN--SLLSKTMRLFS-TN  320 (1033)
T ss_pred             ceEEEeCCHHHHHHHHHHHhcccCCCcceecHHHHHHHHH--HhccCCCCEEEEcCccccCCHH--HHHHHHHHHhh-cC
Confidence            666777765432221   1223568999999999876432  2333468999999999987654  34445555554 34


Q ss_pred             eEEEEeecCChHHHHHHHHhcCC--C----------------------------------eEEEecC--CccccCCceEE
Q 015158          214 QVGVFSATMPPEALEITRKFMNK--P----------------------------------VRILVKR--DELTLEGIKQF  255 (412)
Q Consensus       214 ~~i~~SAT~~~~~~~~~~~~~~~--~----------------------------------~~~~~~~--~~~~~~~~~~~  255 (412)
                      ..+++||||-.+....+..++..  |                                  ..+....  .....+.....
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            46899999853222211111100  0                                  0000000  00000001111


Q ss_pred             EEEecc--------------------------------------------------------------chhhHHHHHHHH
Q 015158          256 HVNVEK--------------------------------------------------------------EEWKLETLCDLY  273 (412)
Q Consensus       256 ~~~~~~--------------------------------------------------------------~~~~~~~l~~~~  273 (412)
                      .+.+..                                                              ...+...+..++
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            111110                                                              012333344444


Q ss_pred             Hhc--CCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcC---CCcEEEEcCCCcCCCCCCCCC
Q 015158          274 ETL--AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSG---SSRVLITTDLLARGIDVQQVS  348 (412)
Q Consensus       274 ~~~--~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g---~~~vlv~t~~~~~G~d~~~~~  348 (412)
                      ...  .+.++|||++.......+.++|...++.+..++|+++..+|..+++.|++.   ...+|++|.+++.|+|+..++
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            433  346999999999999999999999999999999999999999999999863   235788999999999999999


Q ss_pred             EEEEccCCCChhhHHHhhhhcccCCCCceEEEEe
Q 015158          349 LVINYDLPTQPENYLHRIGRSGRFGRKGVAINFV  382 (412)
Q Consensus       349 ~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~  382 (412)
                      +||+++++|++....|++||+.|.|+...+.++.
T Consensus       561 ~VIiyD~dWNP~~d~QAidRaHRIGQkk~V~VyR  594 (1033)
T PLN03142        561 IVILYDSDWNPQVDLQAQDRAHRIGQKKEVQVFR  594 (1033)
T ss_pred             EEEEeCCCCChHHHHHHHHHhhhcCCCceEEEEE
Confidence            9999999999999999999999999887654443

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=99.97  E-value=2e-28  Score=236.15  Aligned_cols=318  Identities=19%  Similarity=0.248  Sum_probs=228.1

Q ss_pred             CCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcE
Q 015158           58 GFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVK  137 (412)
Q Consensus        58 ~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~  137 (412)
                      |.. |++.|...--.+..|+  +..++||+|||+++.++++.....+   ..+.|++|+..|+.|.++.+..+....|+.
T Consensus        80 g~~-~ydvQliGg~~Lh~G~--Iaem~TGeGKTL~a~Lpa~~~al~G---~~V~VvTpn~yLA~qd~e~m~~l~~~lGLt  153 (896)
T PRK13104         80 GLR-HFDVQLIGGMVLHEGN--IAEMRTGEGKTLVATLPAYLNAISG---RGVHIVTVNDYLAKRDSQWMKPIYEFLGLT  153 (896)
T ss_pred             CCC-cchHHHhhhhhhccCc--cccccCCCCchHHHHHHHHHHHhcC---CCEEEEcCCHHHHHHHHHHHHHHhcccCce
Confidence            555 7888888777776665  8899999999999999999766544   369999999999999999999999999999


Q ss_pred             EEEEEcCcchHHHHHHhcCCCcEEEeChHHH-HHHHHcC-CCCC-----CCceEEEEeCCchhh-ccC------------
Q 015158          138 VHACVGGTSVREDQRILSSGVHVVVGTPGRV-FDMLRRQ-SLRP-----DNIRIFVLDEADEML-SRG------------  197 (412)
Q Consensus       138 ~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l-~~~~~~~-~~~~-----~~~~~iiiDE~h~~~-~~~------------  197 (412)
                      +..+.|+.+.......  -.++|+++||..| +.++... .+..     +.+.++|+||+|.++ +..            
T Consensus       154 v~~i~gg~~~~~r~~~--y~~dIvygT~grlgfDyLrd~~~~~~~~~v~r~l~~~IvDEaDsiLIDeArtPLIISg~~~~  231 (896)
T PRK13104        154 VGVIYPDMSHKEKQEA--YKADIVYGTNNEYGFDYLRDNMAFSLTDKVQRELNFAIVDEVDSILIDEARTPLIISGAAED  231 (896)
T ss_pred             EEEEeCCCCHHHHHHH--hCCCEEEECChhhhHHHHhcCCccchHhhhccccceEEeccHhhhhhhccCCceeeeCCCcc
Confidence            9999998776554333  3579999999999 7777654 2322     578999999999854 110            


Q ss_pred             ---cHHHHHHHHHhCCC---------------------------------------------------------------
Q 015158          198 ---FKDQIYDIFQLLPP---------------------------------------------------------------  211 (412)
Q Consensus       198 ---~~~~~~~i~~~~~~---------------------------------------------------------------  211 (412)
                         .......+...+..                                                               
T Consensus       232 ~~~~y~~~~~~v~~l~~~~~~~~~~dy~idek~~~v~Lte~G~~~~e~~~~~~~il~~~~~l~~~~~~~~~~~i~~aL~A  311 (896)
T PRK13104        232 SSELYIKINSLIPQLKKQEEEGDEGDYTIDEKQKQAHLTDAGHLHIEELLTKAKLLDPGESLYHASNIMLMHHVNAALKA  311 (896)
T ss_pred             chHHHHHHHHHHHHHHhccccCCCCCEEEEcCCCceEEchHHHHHHHHHHHhCCccCCcccccCchhhhHHHHHHHHHHH
Confidence               01111111111100                                                               


Q ss_pred             -------------------------------------------------------------------CceEEEEeecCCh
Q 015158          212 -------------------------------------------------------------------KIQVGVFSATMPP  224 (412)
Q Consensus       212 -------------------------------------------------------------------~~~~i~~SAT~~~  224 (412)
                                                                                         -.++-|||+|...
T Consensus       312 ~~lf~~d~dYiV~dg~V~iVDe~TGR~m~grr~s~GLHQaiEaKE~v~i~~e~~t~AsIT~Qn~Fr~Y~kLsGMTGTa~t  391 (896)
T PRK13104        312 HAMFHRDIDYIVKDNQVVIVDEHTGRTMPGRRWSEGLHQAVEAKEGVPIQNENQTLASITFQNFFRMYNKLSGMTGTADT  391 (896)
T ss_pred             HHHhcCCCceEEECCEEEEEECCCCCcCCCCCcChHHHHHHHHHcCCCCCCCceeeeeehHHHHHHhcchhccCCCCChh
Confidence                                                                               1244555555543


Q ss_pred             HHHHHHHHhcCCCeE-EEecCCccccCCceEEEEEeccchhhHHHHHHHHHh-c-CCCcEEEEEcchhHHHHHHHHHhcC
Q 015158          225 EALEITRKFMNKPVR-ILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYET-L-AITQSVIFVNTRRKVDWLTDKMRSR  301 (412)
Q Consensus       225 ~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~-~~~k~lif~~~~~~~~~~~~~L~~~  301 (412)
                      ...+ +...++-.+. +...........-.   ........+...+.+.+.. + .+.++||||+|++.++.+++.|.+.
T Consensus       392 e~~E-f~~iY~l~Vv~IPtnkp~~R~d~~d---~v~~t~~~k~~av~~~i~~~~~~g~PVLVgt~Sie~sE~ls~~L~~~  467 (896)
T PRK13104        392 EAYE-FQQIYNLEVVVIPTNRSMIRKDEAD---LVYLTQADKFQAIIEDVRECGVRKQPVLVGTVSIEASEFLSQLLKKE  467 (896)
T ss_pred             HHHH-HHHHhCCCEEECCCCCCcceecCCC---eEEcCHHHHHHHHHHHHHHHHhCCCCEEEEeCcHHHHHHHHHHHHHc
Confidence            3222 2223322221 11111111110011   1122233455555444433 3 5579999999999999999999999


Q ss_pred             CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCC------------------------------------
Q 015158          302 DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQ------------------------------------  345 (412)
Q Consensus       302 ~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~------------------------------------  345 (412)
                      |+...++|+.+...++..+.+.|+.|.  |+|||+++++|+|+.                                    
T Consensus       468 gi~h~vLnak~~q~Ea~iia~Ag~~G~--VtIATNmAGRGtDI~Lggn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~  545 (896)
T PRK13104        468 NIKHQVLNAKFHEKEAQIIAEAGRPGA--VTIATNMAGRGTDIVLGGSLAADLANLPADASEQEKEAVKKEWQKRHDEVI  545 (896)
T ss_pred             CCCeEeecCCCChHHHHHHHhCCCCCc--EEEeccCccCCcceecCCchhhhhhccccchhhHHHHHHHHHhhhhhhHHH
Confidence            999999999999999999999999985  999999999999976                                    


Q ss_pred             --CCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHHH
Q 015158          346 --QVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERM  389 (412)
Q Consensus       346 --~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~  389 (412)
                        +--+||....+.|...-.|..||+||-|.+|.+-.|++-.|.-.
T Consensus       546 ~~GGL~VIgTerhesrRID~QLrGRaGRQGDPGss~f~lSleD~l~  591 (896)
T PRK13104        546 AAGGLRIIGSERHESRRIDNQLRGRAGRQGDPGSSRFYLSLEDNLM  591 (896)
T ss_pred             HcCCCEEEeeccCchHHHHHHhccccccCCCCCceEEEEEcCcHHH
Confidence              23478888999999999999999999999999999998876643

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=99.97  E-value=4.2e-28  Score=233.63  Aligned_cols=320  Identities=19%  Similarity=0.221  Sum_probs=236.7

Q ss_pred             CCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCc
Q 015158           57 YGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGV  136 (412)
Q Consensus        57 ~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~  136 (412)
                      .|.. |++.|.-..-.+.+|+  +..+.||+|||+++.++++-....+.   .+-|++|+..|+.|.++.+..+...+|+
T Consensus        78 lg~~-~~dvQlig~l~L~~G~--Iaem~TGeGKTLva~lpa~l~aL~G~---~V~IvTpn~yLA~rd~e~~~~l~~~LGl  151 (830)
T PRK12904         78 LGMR-HFDVQLIGGMVLHEGK--IAEMKTGEGKTLVATLPAYLNALTGK---GVHVVTVNDYLAKRDAEWMGPLYEFLGL  151 (830)
T ss_pred             hCCC-CCccHHHhhHHhcCCc--hhhhhcCCCcHHHHHHHHHHHHHcCC---CEEEEecCHHHHHHHHHHHHHHHhhcCC
Confidence            3666 8999998887777775  88999999999999998863333332   5779999999999999999999999999


Q ss_pred             EEEEEEcCcchHHHHHHhcCCCcEEEeChHHH-HHHHHcCC------CCCCCceEEEEeCCchhh-ccC-----------
Q 015158          137 KVHACVGGTSVREDQRILSSGVHVVVGTPGRV-FDMLRRQS------LRPDNIRIFVLDEADEML-SRG-----------  197 (412)
Q Consensus       137 ~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l-~~~~~~~~------~~~~~~~~iiiDE~h~~~-~~~-----------  197 (412)
                      ++..+.|+.+........  .++|+++|+..| +.++....      ...+.+.++|+||++.++ +..           
T Consensus       152 sv~~i~~~~~~~er~~~y--~~dI~ygT~~elgfDyLrd~~~~~~~~~~~r~~~~aIvDEaDsiLIDeArtpLiiSg~~~  229 (830)
T PRK12904        152 SVGVILSGMSPEERREAY--AADITYGTNNEFGFDYLRDNMVFSLEERVQRGLNYAIVDEVDSILIDEARTPLIISGPAE  229 (830)
T ss_pred             eEEEEcCCCCHHHHHHhc--CCCeEEECCcchhhhhhhcccccchhhhcccccceEEEechhhheeccCCCceeeECCCC
Confidence            999999988766554443  479999999999 76765443      235678899999999854 110           


Q ss_pred             ----cHHHHHHHHHhCC---------------------------------------------------------------
Q 015158          198 ----FKDQIYDIFQLLP---------------------------------------------------------------  210 (412)
Q Consensus       198 ----~~~~~~~i~~~~~---------------------------------------------------------------  210 (412)
                          ....+..+...+.                                                               
T Consensus       230 ~~~~~y~~~~~~v~~l~~~~dy~vde~~~~v~lte~G~~~~e~~~~~~~ly~~~~~~~~~~i~~AL~A~~l~~~d~dYiV  309 (830)
T PRK12904        230 DSSELYKRANKIVPTLEKEGDYTVDEKSRTVGLTEEGIEKAEKLLGIENLYDPENIALVHHLNQALRAHELFKRDVDYIV  309 (830)
T ss_pred             cccHHHHHHHHHHHhcCCCCCeEEEcCCCeeeECHHHHHHHHHHhCCccccChhhhHHHHHHHHHHHHHHHHhcCCcEEE
Confidence                1111111111110                                                               


Q ss_pred             ------------------------------------------------------CCceEEEEeecCChHHHHHHHHhcCC
Q 015158          211 ------------------------------------------------------PKIQVGVFSATMPPEALEITRKFMNK  236 (412)
Q Consensus       211 ------------------------------------------------------~~~~~i~~SAT~~~~~~~~~~~~~~~  236 (412)
                                                                            --.++.|||+|...... .+...++-
T Consensus       310 ~dg~V~ivDe~TGR~~~gr~ws~GLHQaiEaKE~v~i~~e~~t~a~It~qn~Fr~Y~kl~GmTGTa~te~~-E~~~iY~l  388 (830)
T PRK12904        310 KDGEVVIVDEFTGRLMPGRRYSDGLHQAIEAKEGVKIQNENQTLASITFQNYFRMYEKLAGMTGTADTEAE-EFREIYNL  388 (830)
T ss_pred             ECCEEEEEECCCCccCCCCccchHHHHHHHHhcCCCCCCCceeeeeeeHHHHHHhcchhcccCCCcHHHHH-HHHHHhCC
Confidence                                                                  01367888888865443 34444444


Q ss_pred             CeEEEecCCccccCCceEEEEEeccchhhHHHHHHHHHh--cCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCH
Q 015158          237 PVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYET--LAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQ  314 (412)
Q Consensus       237 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~--~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~  314 (412)
                      .+............  ...-........+...+.+.+..  ..+.++||||+|++.++.+++.|.+.++.+..+|+.  .
T Consensus       389 ~vv~IPtnkp~~r~--d~~d~i~~t~~~K~~aI~~~I~~~~~~grpVLIft~Si~~se~Ls~~L~~~gi~~~vLnak--q  464 (830)
T PRK12904        389 DVVVIPTNRPMIRI--DHPDLIYKTEKEKFDAVVEDIKERHKKGQPVLVGTVSIEKSELLSKLLKKAGIPHNVLNAK--N  464 (830)
T ss_pred             CEEEcCCCCCeeee--eCCCeEEECHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHCCCceEeccCc--h
Confidence            33322111111111  11111222334567777777755  456799999999999999999999999999999995  6


Q ss_pred             HHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCC--------------------------------------CCEEEEccCC
Q 015158          315 NTRDIIMREFRSGSSRVLITTDLLARGIDVQQ--------------------------------------VSLVINYDLP  356 (412)
Q Consensus       315 ~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~--------------------------------------~~~vi~~~~~  356 (412)
                      .+|+..+..|..+...|+|||+++++|+|++-                                      --|||....+
T Consensus       465 ~eREa~Iia~Ag~~g~VtIATNmAGRGtDI~LgGn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~GGLhVigTerh  544 (830)
T PRK12904        465 HEREAEIIAQAGRPGAVTIATNMAGRGTDIKLGGNPEMLAAALLEEETEEQIAKIKAEWQEEHEEVLEAGGLHVIGTERH  544 (830)
T ss_pred             HHHHHHHHHhcCCCceEEEecccccCCcCccCCCchhhhhhhhhhhhhhHHHHHHHHHHhhhhhhHHHcCCCEEEecccC
Confidence            78999999999999999999999999999873                                      3478888999


Q ss_pred             CChhhHHHhhhhcccCCCCceEEEEeccCcHHH
Q 015158          357 TQPENYLHRIGRSGRFGRKGVAINFVTRDDERM  389 (412)
Q Consensus       357 ~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~  389 (412)
                      .|...-.|..||+||-|.+|.+-.|++-.|.-.
T Consensus       545 esrRid~QlrGRagRQGdpGss~f~lSleD~l~  577 (830)
T PRK12904        545 ESRRIDNQLRGRSGRQGDPGSSRFYLSLEDDLM  577 (830)
T ss_pred             chHHHHHHhhcccccCCCCCceeEEEEcCcHHH
Confidence            999999999999999999999999998876643

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=99.97  E-value=2.5e-28  Score=234.31  Aligned_cols=319  Identities=17%  Similarity=0.180  Sum_probs=228.8

Q ss_pred             CCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCc
Q 015158           57 YGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGV  136 (412)
Q Consensus        57 ~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~  136 (412)
                      .|.. |++.|.-+.-.+..|+  +..+.||+|||+++.++++.....+   ..+-+++|+.-|+.|-++.+..+...+|+
T Consensus        77 ~g~~-~~dvQlig~l~l~~G~--iaEm~TGEGKTLvA~l~a~l~al~G---~~v~vvT~neyLA~Rd~e~~~~~~~~LGl  150 (796)
T PRK12906         77 LGLR-PFDVQIIGGIVLHEGN--IAEMKTGEGKTLTATLPVYLNALTG---KGVHVVTVNEYLSSRDATEMGELYRWLGL  150 (796)
T ss_pred             hCCC-CchhHHHHHHHHhcCC--cccccCCCCCcHHHHHHHHHHHHcC---CCeEEEeccHHHHHhhHHHHHHHHHhcCC
Confidence            3666 8999998887777776  8999999999999988888776655   48999999999999999999999999999


Q ss_pred             EEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCC-------CCCCceEEEEeCCchhh-ccC-----------
Q 015158          137 KVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSL-------RPDNIRIFVLDEADEML-SRG-----------  197 (412)
Q Consensus       137 ~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~-------~~~~~~~iiiDE~h~~~-~~~-----------  197 (412)
                      .+..+.++.+.......  -.++|+++|...|.--+.+...       ..+.+.+.|+||++.++ +..           
T Consensus       151 ~vg~i~~~~~~~~r~~~--y~~dI~Y~t~~e~gfDyLRD~m~~~~~~~v~r~~~~aIvDEvDSiLiDeartPLiisg~~~  228 (796)
T PRK12906        151 TVGLNLNSMSPDEKRAA--YNCDITYSTNSELGFDYLRDNMVVYKEQMVQRPLNYAIVDEVDSILIDEARTPLIISGQAE  228 (796)
T ss_pred             eEEEeCCCCCHHHHHHH--hcCCCeecCCccccccchhhccccchhhhhccCcceeeeccchheeeccCCCceecCCCCC
Confidence            99999987665544333  4578999998877432222221       23567889999999743 100           


Q ss_pred             ----cHHHHHHHHHh----------------------------------------CC-----------------------
Q 015158          198 ----FKDQIYDIFQL----------------------------------------LP-----------------------  210 (412)
Q Consensus       198 ----~~~~~~~i~~~----------------------------------------~~-----------------------  210 (412)
                          ....+..+...                                        +.                       
T Consensus       229 ~~~~~y~~~~~~v~~l~~~~~~~~~~~~~~~dy~id~~~k~v~lte~G~~~~e~~~~i~~l~~~~~~~~~~~i~~Al~A~  308 (796)
T PRK12906        229 KATDLYIRADRFVKTLIKDEAEDGDDDEDTGDYKIDEKTKTISLTEQGIRKAEKLFGLDNLYDSENTALAHHIDQALRAN  308 (796)
T ss_pred             cchHHHHHHHHHHHHHHhhhhccccccCCCCceEEEcccCceeecHHHHHHHHHHcCCccccCchhhhHHHHHHHHHHHH
Confidence                00011111100                                        00                       


Q ss_pred             -----------------------------------------------------------------CCceEEEEeecCChH
Q 015158          211 -----------------------------------------------------------------PKIQVGVFSATMPPE  225 (412)
Q Consensus       211 -----------------------------------------------------------------~~~~~i~~SAT~~~~  225 (412)
                                                                                       --.++.|||+|...+
T Consensus       309 ~l~~~d~dYiV~d~~V~ivD~~TGR~~~gr~ws~GLHQaieaKe~v~i~~e~~t~a~It~qnfFr~Y~kl~GmTGTa~~e  388 (796)
T PRK12906        309 YIMLKDIDYVVQDGEVLIVDEFTGRVMEGRRYSDGLHQAIEAKEGVKIQEENQTLATITYQNFFRMYKKLSGMTGTAKTE  388 (796)
T ss_pred             HHHhcCCcEEEECCEEEEEeCCCCCcCCCCccChHHHHHHHHhcCCCcCCCceeeeeehHHHHHHhcchhhccCCCCHHH
Confidence                                                                             013567777777544


Q ss_pred             HHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhHHHHHHHHHhc--CCCcEEEEEcchhHHHHHHHHHhcCCC
Q 015158          226 ALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETL--AITQSVIFVNTRRKVDWLTDKMRSRDH  303 (412)
Q Consensus       226 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~--~~~k~lif~~~~~~~~~~~~~L~~~~~  303 (412)
                      .. .+...++-.+............  ...-........+...+.+.+...  .+.++||||+|++.++.+++.|.+.++
T Consensus       389 ~~-Ef~~iY~l~vv~IPtnkp~~r~--d~~d~i~~t~~~K~~al~~~i~~~~~~g~pvLI~t~si~~se~ls~~L~~~gi  465 (796)
T PRK12906        389 EE-EFREIYNMEVITIPTNRPVIRK--DSPDLLYPTLDSKFNAVVKEIKERHAKGQPVLVGTVAIESSERLSHLLDEAGI  465 (796)
T ss_pred             HH-HHHHHhCCCEEEcCCCCCeeee--eCCCeEEcCHHHHHHHHHHHHHHHHhCCCCEEEEeCcHHHHHHHHHHHHHCCC
Confidence            33 3344444333221111110000  111111223345666777666443  568999999999999999999999999


Q ss_pred             eeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCC---CCC-----EEEEccCCCChhhHHHhhhhcccCCCC
Q 015158          304 TVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQ---QVS-----LVINYDLPTQPENYLHRIGRSGRFGRK  375 (412)
Q Consensus       304 ~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~---~~~-----~vi~~~~~~s~~~~~Q~~GR~~R~g~~  375 (412)
                      .+..+|+.+...++..+.+.++.|.  |+|+|+++++|+|++   .+.     |||.+..|.|...+.|+.||+||.|.+
T Consensus       466 ~~~~Lna~~~~~Ea~ii~~ag~~g~--VtIATnmAGRGtDI~l~~~V~~~GGLhVI~te~pes~ri~~Ql~GRtGRqG~~  543 (796)
T PRK12906        466 PHAVLNAKNHAKEAEIIMNAGQRGA--VTIATNMAGRGTDIKLGPGVKELGGLAVIGTERHESRRIDNQLRGRSGRQGDP  543 (796)
T ss_pred             CeeEecCCcHHHHHHHHHhcCCCce--EEEEeccccCCCCCCCCcchhhhCCcEEEeeecCCcHHHHHHHhhhhccCCCC
Confidence            9999999988777777777666555  999999999999995   788     999999999999999999999999999


Q ss_pred             ceEEEEeccCcHH
Q 015158          376 GVAINFVTRDDER  388 (412)
Q Consensus       376 g~~~~~~~~~~~~  388 (412)
                      |.+..|++..|.-
T Consensus       544 G~s~~~~sleD~l  556 (796)
T PRK12906        544 GSSRFYLSLEDDL  556 (796)
T ss_pred             cceEEEEeccchH
Confidence            9999999887653

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

Probab=99.96  E-value=3.8e-28  Score=227.65  Aligned_cols=294  Identities=18%  Similarity=0.247  Sum_probs=200.8

Q ss_pred             CChHHHHhhhhhhhc----C-ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccC
Q 015158           61 KPSAIQQRGIVPFCK----G-LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLG  135 (412)
Q Consensus        61 ~l~~~Q~~a~~~~~~----~-~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~  135 (412)
                      .+|++|..|+..+.+    | +.++++|+||+|||.+++. ++..+......+++|+++.+++|+.|....+..+.+. +
T Consensus       165 ~~RyyQ~~AI~rv~Eaf~~g~~raLlvMATGTGKTrTAia-ii~rL~r~~~~KRVLFLaDR~~Lv~QA~~af~~~~P~-~  242 (875)
T COG4096         165 GPRYYQIIAIRRVIEAFSKGQNRALLVMATGTGKTRTAIA-IIDRLIKSGWVKRVLFLADRNALVDQAYGAFEDFLPF-G  242 (875)
T ss_pred             cchHHHHHHHHHHHHHHhcCCceEEEEEecCCCcceeHHH-HHHHHHhcchhheeeEEechHHHHHHHHHHHHHhCCC-c
Confidence            499999999988764    3 5699999999999998754 4445554456679999999999999999998887653 3


Q ss_pred             cEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcC-----CCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCC
Q 015158          136 VKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQ-----SLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLP  210 (412)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~-----~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~  210 (412)
                      -....+.+...        ..++.|+++|++++.......     .+...+||+||+||||+-.-..+.    .++..+.
T Consensus       243 ~~~n~i~~~~~--------~~s~~i~lsTyqt~~~~~~~~~~~~~~f~~g~FDlIvIDEaHRgi~~~~~----~I~dYFd  310 (875)
T COG4096         243 TKMNKIEDKKG--------DTSSEIYLSTYQTMTGRIEQKEDEYRRFGPGFFDLIVIDEAHRGIYSEWS----SILDYFD  310 (875)
T ss_pred             cceeeeecccC--------CcceeEEEeehHHHHhhhhccccccccCCCCceeEEEechhhhhHHhhhH----HHHHHHH
Confidence            33333332221        124789999999998877654     345677999999999985433333    4444432


Q ss_pred             CCceEEEEeecCChHHHHHHHHhc-CCCeEEEecCCc-----cccCCceEEE----------------------------
Q 015158          211 PKIQVGVFSATMPPEALEITRKFM-NKPVRILVKRDE-----LTLEGIKQFH----------------------------  256 (412)
Q Consensus       211 ~~~~~i~~SAT~~~~~~~~~~~~~-~~~~~~~~~~~~-----~~~~~~~~~~----------------------------  256 (412)
                        ...+++||||..........++ +.|...+...+.     ..++.+....                            
T Consensus       311 --A~~~gLTATP~~~~d~~T~~~F~g~Pt~~YsleeAV~DGfLvpy~vi~i~~~~~~~G~~~~~~serek~~g~~i~~dd  388 (875)
T COG4096         311 --AATQGLTATPKETIDRSTYGFFNGEPTYAYSLEEAVEDGFLVPYKVIRIDTDFDLDGWKPDAGSEREKLQGEAIDEDD  388 (875)
T ss_pred             --HHHHhhccCcccccccccccccCCCcceeecHHHHhhccccCCCCceEEeeeccccCcCcCccchhhhhhccccCccc
Confidence              2246779999876555555666 555544322111     0011111100                            


Q ss_pred             ------------EEeccchhhHHHHHHHHHhc--C--CCcEEEEEcchhHHHHHHHHHhcC-----CCeeEEecCCCCHH
Q 015158          257 ------------VNVEKEEWKLETLCDLYETL--A--ITQSVIFVNTRRKVDWLTDKMRSR-----DHTVSATHGDMDQN  315 (412)
Q Consensus       257 ------------~~~~~~~~~~~~l~~~~~~~--~--~~k~lif~~~~~~~~~~~~~L~~~-----~~~~~~~~~~~~~~  315 (412)
                                  ......+.....+.+.++..  .  .+|+||||.+..||+.+...|.+.     +.-+..+.++- ..
T Consensus       389 ~~~~~~d~dr~~v~~~~~~~V~r~~~~~l~~~~~g~~~~KTIvFa~n~dHAe~i~~~~~~~ype~~~~~a~~IT~d~-~~  467 (875)
T COG4096         389 QNFEARDFDRTLVIPFRTETVARELTEYLKRGATGDEIGKTIVFAKNHDHAERIREALVNEYPEYNGRYAMKITGDA-EQ  467 (875)
T ss_pred             ccccccccchhccccchHHHHHHHHHHHhccccCCCccCceEEEeeCcHHHHHHHHHHHHhCccccCceEEEEeccc-hh
Confidence                        11111122344555666652  1  479999999999999999999875     23456666653 22


Q ss_pred             HHHHHHHHHhc-CC-CcEEEEcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccC
Q 015158          316 TRDIIMREFRS-GS-SRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRF  372 (412)
Q Consensus       316 ~r~~~~~~f~~-g~-~~vlv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~  372 (412)
                       -...+..|.. .+ ..|.++++++.+|+|+|.|.+++++....|...|.||+||+-|.
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             3344555554 44 35778889999999999999999999999999999999999995

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

Probab=99.96  E-value=1.3e-27  Score=226.37  Aligned_cols=334  Identities=17%  Similarity=0.217  Sum_probs=234.6

Q ss_pred             HHHHHCCCCCChHHHHhhhhh--hhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHH
Q 015158           52 RGIYAYGFEKPSAIQQRGIVP--FCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRA  129 (412)
Q Consensus        52 ~~l~~~~~~~l~~~Q~~a~~~--~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~  129 (412)
                      -.....|...++.||.+.+..  ++++++.+...||+.|||+++.+.++..+...+  ..++++.|..+.+.+-...+..
T Consensus       214 ~~~~~kgi~~~fewq~ecls~~~~~e~~nliys~Pts~gktlvaeilml~~~l~~r--r~~llilp~vsiv~Ek~~~l~~  291 (1008)
T KOG0950|consen  214 LYAKDKGILKLFEWQAECLSLPRLLERKNLIYSLPTSAGKTLVAEILMLREVLCRR--RNVLLILPYVSIVQEKISALSP  291 (1008)
T ss_pred             HHHHhhhHHHHHHHHHHHhcchhhhcccceEEeCCCccchHHHHHHHHHHHHHHHh--hceeEecceeehhHHHHhhhhh
Confidence            344456888899999988765  778899999999999999999888887765432  4699999999999988888999


Q ss_pred             hhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHc--CCCCCCCceEEEEeCCchhhccCcHHHHHHHHH
Q 015158          130 LGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRR--QSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQ  207 (412)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~--~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~  207 (412)
                      +....|+.+..+.|........    ....+.|+|.|+-..+...  ..-....+++||+||.|.+.+.+....+..++.
T Consensus       292 ~~~~~G~~ve~y~g~~~p~~~~----k~~sv~i~tiEkanslin~lie~g~~~~~g~vvVdElhmi~d~~rg~~lE~~l~  367 (1008)
T KOG0950|consen  292 FSIDLGFPVEEYAGRFPPEKRR----KRESVAIATIEKANSLINSLIEQGRLDFLGMVVVDELHMIGDKGRGAILELLLA  367 (1008)
T ss_pred             hccccCCcchhhcccCCCCCcc----cceeeeeeehHhhHhHHHHHHhcCCccccCcEEEeeeeeeeccccchHHHHHHH
Confidence            9888899999888776654432    2357999999986544322  122346789999999999998886666655544


Q ss_pred             h-----CCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCC--ceEEEEEeccch---------------hh
Q 015158          208 L-----LPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEG--IKQFHVNVEKEE---------------WK  265 (412)
Q Consensus       208 ~-----~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~---------------~~  265 (412)
                      .     .....++|+||||+++.  ..++.++...++....+...-.+.  +....+......               ..
T Consensus       368 k~~y~~~~~~~~iIGMSATi~N~--~lL~~~L~A~~y~t~fRPv~L~E~ik~G~~i~~~~r~~~lr~ia~l~~~~~g~~d  445 (1008)
T KOG0950|consen  368 KILYENLETSVQIIGMSATIPNN--SLLQDWLDAFVYTTRFRPVPLKEYIKPGSLIYESSRNKVLREIANLYSSNLGDED  445 (1008)
T ss_pred             HHHHhccccceeEeeeecccCCh--HHHHHHhhhhheecccCcccchhccCCCcccccchhhHHHHHhhhhhhhhcccCC
Confidence            3     23456799999999763  444444443222221111110000  111111110000               00


Q ss_pred             HHHHHHHHHhc-CC-CcEEEEEcchhHHHHHHHHHhcC--------------------------------------CCee
Q 015158          266 LETLCDLYETL-AI-TQSVIFVNTRRKVDWLTDKMRSR--------------------------------------DHTV  305 (412)
Q Consensus       266 ~~~l~~~~~~~-~~-~k~lif~~~~~~~~~~~~~L~~~--------------------------------------~~~~  305 (412)
                      .+.+..+..+. .. .++||||+++..|+.++..+...                                      ...+
T Consensus       446 pD~~v~L~tet~~e~~~~lvfc~sk~~ce~~a~~~~~~vpk~~~~e~~~~~~~~~s~s~~lr~~~~~ld~Vl~~ti~~Gv  525 (1008)
T KOG0950|consen  446 PDHLVGLCTETAPEGSSVLVFCPSKKNCENVASLIAKKVPKHIKSEKRLGLWELLSISNLLRRIPGILDPVLAKTIPYGV  525 (1008)
T ss_pred             CcceeeehhhhhhcCCeEEEEcCcccchHHHHHHHHHHhhHhhhhhhhhhHHHHHHHHhHhhcCCcccchHHheeccccc
Confidence            01111121111 11 35999999999999887555321                                      2458


Q ss_pred             EEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEcc----CCCChhhHHHhhhhcccCCCC--ceEE
Q 015158          306 SATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYD----LPTQPENYLHRIGRSGRFGRK--GVAI  379 (412)
Q Consensus       306 ~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~----~~~s~~~~~Q~~GR~~R~g~~--g~~~  379 (412)
                      .++|++++.++|+.+...|++|...|+++|+++..|+|+|..++++-..    ...+..+|.||+||+||+|.+  |.++
T Consensus       526 AyHhaGLT~eER~~iE~afr~g~i~vl~aTSTlaaGVNLPArRVIiraP~~g~~~l~~~~YkQM~GRAGR~gidT~Gdsi  605 (1008)
T KOG0950|consen  526 AYHHAGLTSEEREIIEAAFREGNIFVLVATSTLAAGVNLPARRVIIRAPYVGREFLTRLEYKQMVGRAGRTGIDTLGDSI  605 (1008)
T ss_pred             eecccccccchHHHHHHHHHhcCeEEEEecchhhccCcCCcceeEEeCCccccchhhhhhHHhhhhhhhhcccccCcceE
Confidence            8999999999999999999999999999999999999999777776332    345788999999999999854  8899


Q ss_pred             EEeccCcHHHHHHH
Q 015158          380 NFVTRDDERMLFDI  393 (412)
Q Consensus       380 ~~~~~~~~~~~~~~  393 (412)
                      +++.+.+.+....+
T Consensus       606 LI~k~~e~~~~~~l  619 (1008)
T KOG0950|consen  606 LIIKSSEKKRVREL  619 (1008)
T ss_pred             EEeeccchhHHHHH
Confidence            99999988765533

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

Probab=99.96  E-value=6.7e-27  Score=226.72  Aligned_cols=311  Identities=17%  Similarity=0.257  Sum_probs=226.8

Q ss_pred             ChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHH-hhcccCcEEEE
Q 015158           62 PSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRA-LGDYLGVKVHA  140 (412)
Q Consensus        62 l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~-~~~~~~~~~~~  140 (412)
                      -+....+.+..+.+++.++|.++||||||+..-..++..-.  ..++++.+.-|++--+...++.+.+ +....|-.|.+
T Consensus        51 v~~~~~~i~~ai~~~~vvii~getGsGKTTqlP~~lle~g~--~~~g~I~~tQPRRlAArsvA~RvAeel~~~~G~~VGY  128 (845)
T COG1643          51 VTAVRDEILKAIEQNQVVIIVGETGSGKTTQLPQFLLEEGL--GIAGKIGCTQPRRLAARSVAERVAEELGEKLGETVGY  128 (845)
T ss_pred             cHHHHHHHHHHHHhCCEEEEeCCCCCChHHHHHHHHHhhhc--ccCCeEEecCchHHHHHHHHHHHHHHhCCCcCceeeE
Confidence            46677788888889999999999999999887666665543  2345788899999777777766655 33333444444


Q ss_pred             EEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchh-hccCcH-HHHHHHHHhCCCCceEEEE
Q 015158          141 CVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEM-LSRGFK-DQIYDIFQLLPPKIQVGVF  218 (412)
Q Consensus       141 ~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~-~~~~~~-~~~~~i~~~~~~~~~~i~~  218 (412)
                      ..-..+      .......|-++|.+.|++.+....+ ++.+++||+||+|+= ++.++. ..+..+....++..++|.|
T Consensus       129 ~iRfe~------~~s~~Trik~mTdGiLlrei~~D~~-Ls~ys~vIiDEaHERSl~tDilLgllk~~~~~rr~DLKiIim  201 (845)
T COG1643         129 SIRFES------KVSPRTRIKVMTDGILLREIQNDPL-LSGYSVVIIDEAHERSLNTDILLGLLKDLLARRRDDLKLIIM  201 (845)
T ss_pred             EEEeec------cCCCCceeEEeccHHHHHHHhhCcc-cccCCEEEEcchhhhhHHHHHHHHHHHHHHhhcCCCceEEEE
Confidence            332221      1234568999999999999887654 678999999999982 233333 3445556667778999999


Q ss_pred             eecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchh-hHHHHHHHHHh---cCCCcEEEEEcchhHHHHH
Q 015158          219 SATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEW-KLETLCDLYET---LAITQSVIFVNTRRKVDWL  294 (412)
Q Consensus       219 SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~l~~~~~~---~~~~k~lif~~~~~~~~~~  294 (412)
                      |||+..   +.+..++++...+.+....   ..++..|......+. ....+...+..   ...|.+|||.+..++.+..
T Consensus       202 SATld~---~rfs~~f~~apvi~i~GR~---fPVei~Y~~~~~~d~~l~~ai~~~v~~~~~~~~GdILvFLpG~~EI~~~  275 (845)
T COG1643         202 SATLDA---ERFSAYFGNAPVIEIEGRT---YPVEIRYLPEAEADYILLDAIVAAVDIHLREGSGSILVFLPGQREIERT  275 (845)
T ss_pred             ecccCH---HHHHHHcCCCCEEEecCCc---cceEEEecCCCCcchhHHHHHHHHHHHhccCCCCCEEEECCcHHHHHHH
Confidence            999975   4555666644434433322   123333323322222 33334333333   3458999999999999999


Q ss_pred             HHHHhc----CCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccC---------------
Q 015158          295 TDKMRS----RDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDL---------------  355 (412)
Q Consensus       295 ~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~---------------  355 (412)
                      ++.|.+    ....+..+||.++.+++.++++--..|+.+|+++|++.++++.+++++.||.-+.               
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    3578999999999999999888777777889999999999999999999997654               


Q ss_pred             ---CCChhhHHHhhhhcccCCCCceEEEEeccCcHH
Q 015158          356 ---PTQPENYLHRIGRSGRFGRKGVAINFVTRDDER  388 (412)
Q Consensus       356 ---~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~  388 (412)
                         |.|.++..||.||+||. .+|.||-+++..+..
T Consensus       356 ~~~~ISqAsA~QRaGRAGR~-~pGicyRLyse~~~~  390 (845)
T COG1643         356 ETEPISKASADQRAGRAGRT-GPGICYRLYSEEDFL  390 (845)
T ss_pred             eEEEechhhhhhhccccccC-CCceEEEecCHHHHH
Confidence               46888999999999999 589999999985554

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=99.95  E-value=5.9e-26  Score=218.79  Aligned_cols=147  Identities=23%  Similarity=0.327  Sum_probs=123.8

Q ss_pred             cCCCCHHHHHHHH-----HCCCCCC---hHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEc
Q 015158           43 AMGLQENLLRGIY-----AYGFEKP---SAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLA  114 (412)
Q Consensus        43 ~~~l~~~~~~~l~-----~~~~~~l---~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~  114 (412)
                      .+++.....+.+.     ..||..|   +|+|.++++.+..+++.+..++||+|||++|+++++..+..+.   .++||+
T Consensus        66 afal~re~~~r~lg~~~~~~G~~~p~~~tp~qvQ~I~~i~l~~gvIAeaqTGeGKTLAf~LP~l~~aL~g~---~v~IVT  142 (970)
T PRK12899         66 AYGVVKNVCRRLAGTPVEVSGYHQQWDMVPYDVQILGAIAMHKGFITEMQTGEGKTLTAVMPLYLNALTGK---PVHLVT  142 (970)
T ss_pred             HhCCCHHHHHHHhccccccccccCCCCCChHHHHHhhhhhcCCCeEEEeCCCCChHHHHHHHHHHHHhhcC---CeEEEe
Confidence            4566677766665     4688877   9999999999999999999999999999999999997765442   488999


Q ss_pred             CCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHH-HHHHHcCCCCCC-------CceEEE
Q 015158          115 PTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRV-FDMLRRQSLRPD-------NIRIFV  186 (412)
Q Consensus       115 P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l-~~~~~~~~~~~~-------~~~~ii  186 (412)
                      |++.|+.|..+.+..+....++++..+.|+..........  .++|+|+||..| +.++....+..+       .+.++|
T Consensus       143 pTrELA~Qdae~m~~L~k~lGLsV~~i~GG~~~~eq~~~y--~~DIVygTPgRLgfDyLrd~~~~~~~~~~vqr~~~~~I  220 (970)
T PRK12899        143 VNDYLAQRDCEWVGSVLRWLGLTTGVLVSGSPLEKRKEIY--QCDVVYGTASEFGFDYLRDNSIATRKEEQVGRGFYFAI  220 (970)
T ss_pred             CCHHHHHHHHHHHHHHHhhcCCeEEEEeCCCCHHHHHHHc--CCCEEEECCChhHHHHhhCCCCCcCHHHhhcccccEEE
Confidence            9999999999999999988899999999998877665443  589999999999 888877655443       568999


Q ss_pred             EeCCchhh
Q 015158          187 LDEADEML  194 (412)
Q Consensus       187 iDE~h~~~  194 (412)
                      +|||+.++
T Consensus       221 IDEADsmL  228 (970)
T PRK12899        221 IDEVDSIL  228 (970)
T ss_pred             Eechhhhh
Confidence            99999864

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

Probab=99.95  E-value=2.8e-26  Score=210.37  Aligned_cols=310  Identities=15%  Similarity=0.234  Sum_probs=222.2

Q ss_pred             ChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHH-hhcccCcEEEE
Q 015158           62 PSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRA-LGDYLGVKVHA  140 (412)
Q Consensus        62 l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~-~~~~~~~~~~~  140 (412)
                      .+.+-.+.+..+.+++.++|.|+||||||+..-..++..-...  .+++.+.-|++.-+...+++... .....|-.|..
T Consensus        52 I~~~r~~il~~ve~nqvlIviGeTGsGKSTQipQyL~eaG~~~--~g~I~~TQPRRVAavslA~RVAeE~~~~lG~~VGY  129 (674)
T KOG0922|consen   52 IYKYRDQILYAVEDNQVLIVIGETGSGKSTQIPQYLAEAGFAS--SGKIACTQPRRVAAVSLAKRVAEEMGCQLGEEVGY  129 (674)
T ss_pred             HHHHHHHHHHHHHHCCEEEEEcCCCCCccccHhHHHHhccccc--CCcEEeecCchHHHHHHHHHHHHHhCCCcCceeee
Confidence            5667778888899999999999999999988766665553322  23488889998766666655443 33333444443


Q ss_pred             EEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhh-ccC-cHHHHHHHHHhCCCCceEEEE
Q 015158          141 CVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEML-SRG-FKDQIYDIFQLLPPKIQVGVF  218 (412)
Q Consensus       141 ~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~-~~~-~~~~~~~i~~~~~~~~~~i~~  218 (412)
                      ...-.      +.......|.++|.+.|++....... ++.+++||+||||+=. ..+ ....+++++.. ++..++|.+
T Consensus       130 ~IRFe------d~ts~~TrikymTDG~LLRE~l~Dp~-LskYsvIIlDEAHERsl~TDiLlGlLKki~~~-R~~LklIim  201 (674)
T KOG0922|consen  130 TIRFE------DSTSKDTRIKYMTDGMLLREILKDPL-LSKYSVIILDEAHERSLHTDILLGLLKKILKK-RPDLKLIIM  201 (674)
T ss_pred             EEEec------ccCCCceeEEEecchHHHHHHhcCCc-cccccEEEEechhhhhhHHHHHHHHHHHHHhc-CCCceEEEE
Confidence            33211      11223468999999999998876554 5789999999999722 111 22333344333 346889999


Q ss_pred             eecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhHHHHHHHHH---hcCCCcEEEEEcchhHHHHHH
Q 015158          219 SATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYE---TLAITQSVIFVNTRRKVDWLT  295 (412)
Q Consensus       219 SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~---~~~~~k~lif~~~~~~~~~~~  295 (412)
                      |||+..   +.+..+++....+.+....   ..++..+...+..++....+...++   ..+.+-+|||...+++++.++
T Consensus       202 SATlda---~kfS~yF~~a~i~~i~GR~---fPVei~y~~~p~~dYv~a~~~tv~~Ih~~E~~GDILvFLtGqeEIe~~~  275 (674)
T KOG0922|consen  202 SATLDA---EKFSEYFNNAPILTIPGRT---FPVEILYLKEPTADYVDAALITVIQIHLTEPPGDILVFLTGQEEIEAAC  275 (674)
T ss_pred             eeeecH---HHHHHHhcCCceEeecCCC---CceeEEeccCCchhhHHHHHHHHHHHHccCCCCCEEEEeCCHHHHHHHH
Confidence            999964   4455566654444433322   2345555555554544444444443   345588999999999999999


Q ss_pred             HHHhcC----CC----eeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccC------------
Q 015158          296 DKMRSR----DH----TVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDL------------  355 (412)
Q Consensus       296 ~~L~~~----~~----~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~------------  355 (412)
                      +.|.+.    +.    -+..+||.++.+++.++++.-..|..+|+++|++.++.+.++++..||.-|.            
T Consensus       276 ~~l~e~~~~~~~~~~~~~lply~aL~~e~Q~rvF~p~p~g~RKvIlsTNIAETSlTI~GI~YVVDsG~vK~~~y~p~~g~  355 (674)
T KOG0922|consen  276 ELLRERAKSLPEDCPELILPLYGALPSEEQSRVFDPAPPGKRKVILSTNIAETSLTIDGIRYVVDSGFVKQKKYNPRTGL  355 (674)
T ss_pred             HHHHHHhhhccccCcceeeeecccCCHHHhhccccCCCCCcceEEEEcceeeeeEEecceEEEEcCCceEEEeeccccCc
Confidence            999875    11    2567899999999999999888899999999999999999999999996553            


Q ss_pred             ------CCChhhHHHhhhhcccCCCCceEEEEeccCcHH
Q 015158          356 ------PTQPENYLHRIGRSGRFGRKGVAINFVTRDDER  388 (412)
Q Consensus       356 ------~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~  388 (412)
                            |.|.++..||.||+||.| +|.||-++++.+..
T Consensus       356 ~~L~v~~ISkasA~QRaGRAGRt~-pGkcyRLYte~~~~  393 (674)
T KOG0922|consen  356 DSLIVVPISKASANQRAGRAGRTG-PGKCYRLYTESAYD  393 (674)
T ss_pred             cceeEEechHHHHhhhcccCCCCC-CceEEEeeeHHHHh
Confidence                  468899999999999995 79999999988764

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

Probab=99.95  E-value=6.8e-26  Score=221.35  Aligned_cols=321  Identities=16%  Similarity=0.156  Sum_probs=192.2

Q ss_pred             ChHHHHhhhhhhhc----------CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhh
Q 015158           62 PSAIQQRGIVPFCK----------GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALG  131 (412)
Q Consensus        62 l~~~Q~~a~~~~~~----------~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~  131 (412)
                      ++++|.+|+..+..          .+.++++++||||||.+++..+...+ .....+++|+++|+..|..|+.+.+..+.
T Consensus       239 ~r~~Q~~av~~~~~~~~~~~~~~~~~~gli~~~TGsGKT~t~~~la~~l~-~~~~~~~vl~lvdR~~L~~Q~~~~f~~~~  317 (667)
T TIGR00348       239 QRYMQYRAVKKIVESITRKTWGKDERGGLIWHTQGSGKTLTMLFAARKAL-ELLKNPKVFFVVDRRELDYQLMKEFQSLQ  317 (667)
T ss_pred             hHHHHHHHHHHHHHHHHhcccCCCCceeEEEEecCCCccHHHHHHHHHHH-hhcCCCeEEEEECcHHHHHHHHHHHHhhC
Confidence            79999999988642          25799999999999998876665444 33345789999999999999999999875


Q ss_pred             cccCcEEEEEEcCcchHHHHHHh-cCCCcEEEeChHHHHHHHHcC--CCCCC-CceEEEEeCCchhhccCcHHHHHHHH-
Q 015158          132 DYLGVKVHACVGGTSVREDQRIL-SSGVHVVVGTPGRVFDMLRRQ--SLRPD-NIRIFVLDEADEMLSRGFKDQIYDIF-  206 (412)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~~-~~~~~iii~T~~~l~~~~~~~--~~~~~-~~~~iiiDE~h~~~~~~~~~~~~~i~-  206 (412)
                      ...   +   .+..+........ .....|+|+|.++|.+.+...  ..... .-.+||+||||+.....    +...+ 
T Consensus       318 ~~~---~---~~~~s~~~L~~~l~~~~~~iivtTiQk~~~~~~~~~~~~~~~~~~~lvIvDEaHrs~~~~----~~~~l~  387 (667)
T TIGR00348       318 KDC---A---ERIESIAELKRLLEKDDGGIIITTIQKFDKKLKEEEEKFPVDRKEVVVIFDEAHRSQYGE----LAKNLK  387 (667)
T ss_pred             CCC---C---cccCCHHHHHHHHhCCCCCEEEEEhHHhhhhHhhhhhccCCCCCCEEEEEEcCccccchH----HHHHHH
Confidence            310   1   1111122222222 234689999999998644321  11111 11389999999854332    33333 


Q ss_pred             HhCCCCceEEEEeecCChHHHHHHHHhc----CCCeEEEecCCccccCCceEEEEE-------ecc--------------
Q 015158          207 QLLPPKIQVGVFSATMPPEALEITRKFM----NKPVRILVKRDELTLEGIKQFHVN-------VEK--------------  261 (412)
Q Consensus       207 ~~~~~~~~~i~~SAT~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~-------~~~--------------  261 (412)
                      ..++ +...+|+||||...........+    +.+...+.........-...+.+.       ++.              
T Consensus       388 ~~~p-~a~~lGfTaTP~~~~d~~t~~~f~~~fg~~i~~Y~~~~AI~dG~~~~i~Y~~~~~~~~~~~~~l~~~~~~~~~~~  466 (667)
T TIGR00348       388 KALK-NASFFGFTGTPIFKKDRDTSLTFAYVFGRYLHRYFITDAIRDGLTVKIDYEDRLPEDHLDRKKLDAFFDEIFELL  466 (667)
T ss_pred             hhCC-CCcEEEEeCCCcccccccccccccCCCCCeEEEeeHHHHhhcCCeeeEEEEecchhhccChHHHHHHHHHHHHhh
Confidence            3444 57799999999632111111111    222222111111110000000000       000              


Q ss_pred             ----ch--------------------hhHHHHH-----HHHHhc--CCCcEEEEEcchhHHHHHHHHHhcC-----CCee
Q 015158          262 ----EE--------------------WKLETLC-----DLYETL--AITQSVIFVNTRRKVDWLTDKMRSR-----DHTV  305 (412)
Q Consensus       262 ----~~--------------------~~~~~l~-----~~~~~~--~~~k~lif~~~~~~~~~~~~~L~~~-----~~~~  305 (412)
                          .+                    .....+.     .+.+..  ..+|++|||.++.+|..+++.|.+.     +...
T Consensus       467 ~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~ia~~i~~h~~~~~~~~~~kamvv~~sr~~a~~~~~~l~~~~~~~~~~~~  546 (667)
T TIGR00348       467 PERIREITKESLKEKLQKTKKILFNEDRLESIAKDIAEHYAKFKELFKFKAMVVAISRYACVEEKNALDEELNEKFEASA  546 (667)
T ss_pred             hccccHHHHHHHHHHHHHHHhhhcChHHHHHHHHHHHHHHHHhhhcccCceeEEEecHHHHHHHHHHHHhhcccccCCee
Confidence                00                    0000111     111111  2379999999999999999888654     2345


Q ss_pred             EEecCCCCHH---------------------HHHHHHHHHhc-CCCcEEEEcCCCcCCCCCCCCCEEEEccCCCChhhHH
Q 015158          306 SATHGDMDQN---------------------TRDIIMREFRS-GSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYL  363 (412)
Q Consensus       306 ~~~~~~~~~~---------------------~r~~~~~~f~~-g~~~vlv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~  363 (412)
                      .++++..+..                     ....++++|++ ++++++|+++++.+|+|.|.++++++..+..+ ..++
T Consensus       547 vv~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Fk~~~~~~ilIVvdmllTGFDaP~l~tLyldKplk~-h~Ll  625 (667)
T TIGR00348       547 IVMTGKESDDAEIRDYNKHIRTKFDKSDGFEIYYKDLERFKKEENPKLLIVVDMLLTGFDAPILNTLYLDKPLKY-HGLL  625 (667)
T ss_pred             EEecCCccchhHHHHHHHHhccccccchhhhHHHHHHHHhcCCCCceEEEEEcccccccCCCccceEEEeccccc-cHHH
Confidence            5565543322                     22468888976 68899999999999999999999997766554 5689


Q ss_pred             HhhhhcccC-CCC-ceEEEEeccCcHHHHHHHHH
Q 015158          364 HRIGRSGRF-GRK-GVAINFVTRDDERMLFDIQK  395 (412)
Q Consensus       364 Q~~GR~~R~-g~~-g~~~~~~~~~~~~~~~~~~~  395 (412)
                      |++||+.|. ++. ..++++......+.+..-.+
T Consensus       626 Qai~R~nR~~~~~K~~g~IvDy~g~~~~l~~Al~  659 (667)
T TIGR00348       626 QAIARTNRIDGKDKTFGLIVDYRGLEKSLIDALS  659 (667)
T ss_pred             HHHHHhccccCCCCCCEEEEECcChHHHHHHHHH
Confidence            999999994 332 23455555555554444333

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

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=99.95  E-value=5.1e-26  Score=218.88  Aligned_cols=317  Identities=18%  Similarity=0.205  Sum_probs=226.1

Q ss_pred             CCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcE
Q 015158           58 GFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVK  137 (412)
Q Consensus        58 ~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~  137 (412)
                      |.. |++.|.-.--.+.+|+  +..++||.|||+++.++++.....+   ..+.||+|+..|+.+-++.+..++...|++
T Consensus        80 gm~-~ydVQliGgl~L~~G~--IaEm~TGEGKTL~a~lp~~l~al~g---~~VhIvT~ndyLA~RD~e~m~~l~~~lGls  153 (908)
T PRK13107         80 EMR-HFDVQLLGGMVLDSNR--IAEMRTGEGKTLTATLPAYLNALTG---KGVHVITVNDYLARRDAENNRPLFEFLGLT  153 (908)
T ss_pred             CCC-cCchHHhcchHhcCCc--cccccCCCCchHHHHHHHHHHHhcC---CCEEEEeCCHHHHHHHHHHHHHHHHhcCCe
Confidence            555 7888887776666665  8899999999999999988666554   359999999999999999999999999999


Q ss_pred             EEEEEcCcchHHHHHHhcCCCcEEEeChHHH-HHHHHcC-CCC-----CCCceEEEEeCCchhhccC-------------
Q 015158          138 VHACVGGTSVREDQRILSSGVHVVVGTPGRV-FDMLRRQ-SLR-----PDNIRIFVLDEADEMLSRG-------------  197 (412)
Q Consensus       138 ~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l-~~~~~~~-~~~-----~~~~~~iiiDE~h~~~~~~-------------  197 (412)
                      +.++.++.+...  ....-.++|+++|+..| +.++... ...     .+.+.++|+||++.++-..             
T Consensus       154 v~~i~~~~~~~~--r~~~Y~~dI~YgT~~e~gfDyLrdnm~~~~~~~vqr~~~~aIvDEvDsiLiDEArtPLIISg~~~~  231 (908)
T PRK13107        154 VGINVAGLGQQE--KKAAYNADITYGTNNEFGFDYLRDNMAFSPQERVQRPLHYALIDEVDSILIDEARTPLIISGAAED  231 (908)
T ss_pred             EEEecCCCCHHH--HHhcCCCCeEEeCCCcccchhhhccCccchhhhhccccceeeecchhhhccccCCCceeecCCCcc
Confidence            999988876533  33334679999999999 6666554 222     2678899999999754210             


Q ss_pred             ---cHHHHHHHHHhCC----------------------------------------------------------------
Q 015158          198 ---FKDQIYDIFQLLP----------------------------------------------------------------  210 (412)
Q Consensus       198 ---~~~~~~~i~~~~~----------------------------------------------------------------  210 (412)
                         ....+..+...+.                                                                
T Consensus       232 ~~~~y~~~~~~v~~L~~~~~~~~~~~~~~~dy~idek~~~v~LTe~G~~~~e~~l~~~~~~~~~~~l~~~~~~~~~~~i~  311 (908)
T PRK13107        232 SSELYIKINTLIPNLIRQDKEDTEEYVGEGDYSIDEKAKQVHFTERGQEKVENLLIERGMLAEGDSLYSAANISLLHHVN  311 (908)
T ss_pred             chHHHHHHHHHHHHHHhhhhccccccCCCCCEEEecCCCeeeechHHHHHHHHHHHhCCcccCcccccCchhhHHHHHHH
Confidence               0000110000000                                                                


Q ss_pred             -----------------------------------------------------------------------CCceEEEEe
Q 015158          211 -----------------------------------------------------------------------PKIQVGVFS  219 (412)
Q Consensus       211 -----------------------------------------------------------------------~~~~~i~~S  219 (412)
                                                                                             --.++.|||
T Consensus       312 ~aL~A~~lf~~d~dYiV~dg~V~IVDe~TGRim~grrwsdGLHQaIEaKE~v~I~~e~~t~AsIT~QnfFr~Y~kL~GMT  391 (908)
T PRK13107        312 AALRAHTLFEKDVDYIVQDNEVIIVDEHTGRTMPGRRWSEGLHQAVEAKEGVHIQNENQTLASITFQNYFRQYEKLAGMT  391 (908)
T ss_pred             HHHHHHHHHhcCCceEEECCEEEEEECCCCCCCCCCccchHHHHHHHHhcCCCCCCCceeeeeehHHHHHHhhhHhhccc
Confidence                                                                                   012455666


Q ss_pred             ecCChHHHHHHHHhcCCCeE-EEecCCccccCCceEEEEEeccchhhHHHHHHHHHh-c-CCCcEEEEEcchhHHHHHHH
Q 015158          220 ATMPPEALEITRKFMNKPVR-ILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYET-L-AITQSVIFVNTRRKVDWLTD  296 (412)
Q Consensus       220 AT~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~-~~~k~lif~~~~~~~~~~~~  296 (412)
                      +|......+ +...++-.+. +......... .....+  ......+...+.+-+.. + .+.++||||.|++.++.+++
T Consensus       392 GTa~te~~E-f~~iY~l~Vv~IPTnkp~~R~-d~~d~i--y~t~~~K~~Aii~ei~~~~~~GrpVLV~t~sv~~se~ls~  467 (908)
T PRK13107        392 GTADTEAFE-FQHIYGLDTVVVPTNRPMVRK-DMADLV--YLTADEKYQAIIKDIKDCRERGQPVLVGTVSIEQSELLAR  467 (908)
T ss_pred             CCChHHHHH-HHHHhCCCEEECCCCCCccce-eCCCcE--EeCHHHHHHHHHHHHHHHHHcCCCEEEEeCcHHHHHHHHH
Confidence            665443333 2223332222 2211111111 111111  12223344444443333 2 45799999999999999999


Q ss_pred             HHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCC-------------------------------
Q 015158          297 KMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQ-------------------------------  345 (412)
Q Consensus       297 ~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~-------------------------------  345 (412)
                      .|.+.++.+..+|+.....++..+.+.|+.|.  |+|||+++++|+|+.                               
T Consensus       468 ~L~~~gi~~~vLnak~~~~Ea~ii~~Ag~~G~--VtIATnmAGRGTDIkLggn~~~~~~~~~~~~~~~~~~~~~~~~~~~  545 (908)
T PRK13107        468 LMVKEKIPHEVLNAKFHEREAEIVAQAGRTGA--VTIATNMAGRGTDIVLGGNWNMEIEALENPTAEQKAKIKADWQIRH  545 (908)
T ss_pred             HHHHCCCCeEeccCcccHHHHHHHHhCCCCCc--EEEecCCcCCCcceecCCchHHhhhhhcchhhHHHHHHHHHHHhhH
Confidence            99999999999999999999999999999988  999999999999987                               


Q ss_pred             ------CCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHH
Q 015158          346 ------QVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDER  388 (412)
Q Consensus       346 ------~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~  388 (412)
                            +--+||....+.|...-.|..||+||-|.+|.+..|++-.|.-
T Consensus       546 ~~V~~~GGL~VIgTerheSrRID~QLrGRaGRQGDPGss~f~lSlED~L  594 (908)
T PRK13107        546 DEVVAAGGLHILGTERHESRRIDNQLRGRAGRQGDAGSSRFYLSMEDSL  594 (908)
T ss_pred             HHHHHcCCCEEEecccCchHHHHhhhhcccccCCCCCceeEEEEeCcHH
Confidence                  2347888999999999999999999999999999999887763

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

Probab=99.95  E-value=2.4e-26  Score=188.84  Aligned_cols=163  Identities=28%  Similarity=0.485  Sum_probs=139.0

Q ss_pred             hHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEE
Q 015158           63 SAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACV  142 (412)
Q Consensus        63 ~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~  142 (412)
                      +|+|.++++.+.+++++++.+|||+|||.+++.+++..+... ...++++++|+++|++|..+.+..+....+..+..++
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            589999999999999999999999999999999999888766 4458999999999999999999999877778888888


Q ss_pred             cCcchH-HHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCC--CCceEEEEe
Q 015158          143 GGTSVR-EDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLP--PKIQVGVFS  219 (412)
Q Consensus       143 ~~~~~~-~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~--~~~~~i~~S  219 (412)
                      ++.... ........+++|+|+||++|...+.....+..++++||+||+|.+..+.+...+..+...+.  .+.+++++|
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            887755 33444456789999999999999987655666799999999999998877888888887763  368999999


Q ss_pred             ecCChHH
Q 015158          220 ATMPPEA  226 (412)
Q Consensus       220 AT~~~~~  226 (412)
                      ||++.+.
T Consensus       160 AT~~~~~  166 (169)
T PF00270_consen  160 ATLPSNV  166 (169)
T ss_dssp             SSSTHHH
T ss_pred             eCCChhH
Confidence            9998544

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 ....

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

Probab=99.94  E-value=1.4e-24  Score=207.10  Aligned_cols=279  Identities=22%  Similarity=0.323  Sum_probs=200.3

Q ss_pred             CCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccC-c
Q 015158           58 GFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLG-V  136 (412)
Q Consensus        58 ~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~-~  136 (412)
                      |+ +|+..|+-....+..|+++-+.||||.|||.-.++..+....   .++++++++||..|+.|..+.+.++....+ .
T Consensus        80 G~-~~ws~QR~WakR~~rg~SFaiiAPTGvGKTTfg~~~sl~~a~---kgkr~yii~PT~~Lv~Q~~~kl~~~~e~~~~~  155 (1187)
T COG1110          80 GF-RPWSAQRVWAKRLVRGKSFAIIAPTGVGKTTFGLLMSLYLAK---KGKRVYIIVPTTTLVRQVYERLKKFAEDAGSL  155 (1187)
T ss_pred             CC-CchHHHHHHHHHHHcCCceEEEcCCCCchhHHHHHHHHHHHh---cCCeEEEEecCHHHHHHHHHHHHHHHhhcCCc
Confidence            66 599999999999999999999999999999655443333322   336999999999999999999999876554 3


Q ss_pred             EEEE-EEcCcchHH----HHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccC-----------cHH
Q 015158          137 KVHA-CVGGTSVRE----DQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRG-----------FKD  200 (412)
Q Consensus       137 ~~~~-~~~~~~~~~----~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~-----------~~~  200 (412)
                      .+.. +|+.-+...    ..++..++++|+|+|.+.|...+..  +..-+|++|++|+++.++-.+           |..
T Consensus       156 ~~~~~yh~~l~~~ekee~le~i~~gdfdIlitTs~FL~k~~e~--L~~~kFdfifVDDVDA~LkaskNvDriL~LlGf~e  233 (1187)
T COG1110         156 DVLVVYHSALPTKEKEEALERIESGDFDILITTSQFLSKRFEE--LSKLKFDFIFVDDVDAILKASKNVDRLLRLLGFSE  233 (1187)
T ss_pred             ceeeeeccccchHHHHHHHHHHhcCCccEEEEeHHHHHhhHHH--hcccCCCEEEEccHHHHHhccccHHHHHHHcCCCH
Confidence            3333 555533332    2444567899999999888776653  222478999999999865322           110


Q ss_pred             -----------------------HHHHHHHh--------CCCCceEEEEeecCChH--HHHHHHHhcCCCeEEEecCCcc
Q 015158          201 -----------------------QIYDIFQL--------LPPKIQVGVFSATMPPE--ALEITRKFMNKPVRILVKRDEL  247 (412)
Q Consensus       201 -----------------------~~~~i~~~--------~~~~~~~i~~SAT~~~~--~~~~~~~~~~~~~~~~~~~~~~  247 (412)
                                             .+.++...        -.+...+++.|||..+.  -...+..+++..+    .....
T Consensus       234 E~i~~a~~~~~lr~~~~~~~~~~~~~e~~~~~e~~~~~~r~k~g~LvvsSATg~~rg~R~~LfReLlgFev----G~~~~  309 (1187)
T COG1110         234 EVIESAYELIKLRRKLYGEKRAERVREELREVEREREKKRRKLGILVVSSATGKPRGSRLKLFRELLGFEV----GSGGE  309 (1187)
T ss_pred             HHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHhccCCceEEEeeccCCCCCchHHHHHHHhCCcc----Cccch
Confidence                                   11111110        11346789999997542  3345555655332    33333


Q ss_pred             ccCCceEEEEEeccchhhHHHHHHHHHhcCCCcEEEEEcc---hhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHH
Q 015158          248 TLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNT---RRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREF  324 (412)
Q Consensus       248 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lif~~~---~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f  324 (412)
                      ...++...+...    .....+.++++.... .+|||++.   ++.+++++++|+.+|+++..+|+.     ..+.++.|
T Consensus       310 ~LRNIvD~y~~~----~~~e~~~elvk~lG~-GgLIfV~~d~G~e~aeel~e~Lr~~Gi~a~~~~a~-----~~~~le~F  379 (1187)
T COG1110         310 GLRNIVDIYVES----ESLEKVVELVKKLGD-GGLIFVPIDYGREKAEELAEYLRSHGINAELIHAE-----KEEALEDF  379 (1187)
T ss_pred             hhhheeeeeccC----ccHHHHHHHHHHhCC-CeEEEEEcHHhHHHHHHHHHHHHhcCceEEEeecc-----chhhhhhh
Confidence            344555555444    455666777777654 68999999   999999999999999999999984     37789999


Q ss_pred             hcCCCcEEEEcC----CCcCCCCCCC-CCEEEEccCC
Q 015158          325 RSGSSRVLITTD----LLARGIDVQQ-VSLVINYDLP  356 (412)
Q Consensus       325 ~~g~~~vlv~t~----~~~~G~d~~~-~~~vi~~~~~  356 (412)
                      ..|++++||++.    .+.+|+|+|. ++.+|+++.|
T Consensus       380 ~~GeidvLVGvAsyYG~lVRGlDLP~rirYaIF~GvP  416 (1187)
T COG1110         380 EEGEVDVLVGVASYYGVLVRGLDLPHRIRYAVFYGVP  416 (1187)
T ss_pred             ccCceeEEEEecccccceeecCCchhheeEEEEecCC
Confidence            999999999865    7889999994 8888888876

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

Probab=99.94  E-value=5.2e-25  Score=203.65  Aligned_cols=316  Identities=20%  Similarity=0.205  Sum_probs=221.4

Q ss_pred             CChHHHHhhhhhhhc----CccEEEECCCCCCchhHhHHHHHHhhcc-CCCceeEEEEcCCHHHHHHHHHHHHHhhcccC
Q 015158           61 KPSAIQQRGIVPFCK----GLDVIQQAQSGTGKTATFCSGILQQLDY-GLVECQALVLAPTRELAQQIEKVMRALGDYLG  135 (412)
Q Consensus        61 ~l~~~Q~~a~~~~~~----~~~~lv~~~tGsGKT~~~~~~~~~~~~~-~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~  135 (412)
                      .+++||.+.++++.+    |-++|+...+|-|||+..+..+. .+.. ....+..||+||...|.. |.+++.+|++  +
T Consensus       167 ~lr~YQveGlnWLi~l~engingILaDEMGLGKTlQtIs~l~-yl~~~~~~~GPfLVi~P~StL~N-W~~Ef~rf~P--~  242 (971)
T KOG0385|consen  167 ELRDYQLEGLNWLISLYENGINGILADEMGLGKTLQTISLLG-YLKGRKGIPGPFLVIAPKSTLDN-WMNEFKRFTP--S  242 (971)
T ss_pred             ccchhhhccHHHHHHHHhcCcccEeehhcccchHHHHHHHHH-HHHHhcCCCCCeEEEeeHhhHHH-HHHHHHHhCC--C
Confidence            499999999999774    56899999999999977543333 3322 223456999999877655 8899999987  7


Q ss_pred             cEEEEEEcCcchHHH--HH-HhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCCCC
Q 015158          136 VKVHACVGGTSVRED--QR-ILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPK  212 (412)
Q Consensus       136 ~~~~~~~~~~~~~~~--~~-~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~  212 (412)
                      +++..++|+......  .+ ...+..+|+|+||++..+.-  .-+..-+|.++||||+|++.+..  ..+.+++..+.. 
T Consensus       243 l~~~~~~Gdk~eR~~~~r~~~~~~~fdV~iTsYEi~i~dk--~~lk~~~W~ylvIDEaHRiKN~~--s~L~~~lr~f~~-  317 (971)
T KOG0385|consen  243 LNVVVYHGDKEERAALRRDIMLPGRFDVCITSYEIAIKDK--SFLKKFNWRYLVIDEAHRIKNEK--SKLSKILREFKT-  317 (971)
T ss_pred             cceEEEeCCHHHHHHHHHHhhccCCCceEeehHHHHHhhH--HHHhcCCceEEEechhhhhcchh--hHHHHHHHHhcc-
Confidence            889999998754332  12 23457899999999987642  22333478999999999998775  555566666653 


Q ss_pred             ceEEEEeecCChHHHHHHHHhcC------------------------------------------------------CC-
Q 015158          213 IQVGVFSATMPPEALEITRKFMN------------------------------------------------------KP-  237 (412)
Q Consensus       213 ~~~i~~SAT~~~~~~~~~~~~~~------------------------------------------------------~~-  237 (412)
                      ...+++|+||-.+-...+..+++                                                      +. 
T Consensus       318 ~nrLLlTGTPLQNNL~ELWaLLnFllPdiF~~~e~F~swF~~~~~~~~~e~v~~Lh~vL~pFlLRR~K~dVe~sLppKkE  397 (971)
T KOG0385|consen  318 DNRLLLTGTPLQNNLHELWALLNFLLPDIFNSAEDFDSWFDFTNCEGDQELVSRLHKVLRPFLLRRIKSDVEKSLPPKKE  397 (971)
T ss_pred             cceeEeeCCcccccHHHHHHHHHhhchhhccCHHHHHHHHcccccccCHHHHHHHHhhhhHHHHHHHHHhHhhcCCCcce
Confidence            34689999985211111111100                                                      00 


Q ss_pred             eEEEecCCc--------------------c-------------ccCCceEEEEEe--------------ccchhhHHHHH
Q 015158          238 VRILVKRDE--------------------L-------------TLEGIKQFHVNV--------------EKEEWKLETLC  270 (412)
Q Consensus       238 ~~~~~~~~~--------------------~-------------~~~~~~~~~~~~--------------~~~~~~~~~l~  270 (412)
                      +.+......                    .             -+....+.+...              .....+...|.
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            000000000                    0             000001111000              00123556666


Q ss_pred             HHHHhc--CCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCC---CcEEEEcCCCcCCCCCC
Q 015158          271 DLYETL--AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGS---SRVLITTDLLARGIDVQ  345 (412)
Q Consensus       271 ~~~~~~--~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~---~~vlv~t~~~~~G~d~~  345 (412)
                      .++...  .+.++|||.+-....+-+.++.--+++....+.|.++.++|...++.|....   .-++++|.+.+.|+|+.
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            666654  4579999999999999999999889999999999999999999999998853   34678999999999999


Q ss_pred             CCCEEEEccCCCChhhHHHhhhhcccCCCCceEE--EEeccC
Q 015158          346 QVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAI--NFVTRD  385 (412)
Q Consensus       346 ~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~--~~~~~~  385 (412)
                      .+++||+++..|++..=.|+..|++|.|+...+.  -+++..
T Consensus       558 aADtVIlyDSDWNPQ~DLQAmDRaHRIGQ~K~V~V~RLiten  599 (971)
T KOG0385|consen  558 AADTVILYDSDWNPQVDLQAMDRAHRIGQKKPVVVYRLITEN  599 (971)
T ss_pred             cccEEEEecCCCCchhhhHHHHHHHhhCCcCceEEEEEeccc
Confidence            9999999999999999999999999999876544  455554

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=99.94  E-value=2e-25  Score=220.34  Aligned_cols=322  Identities=17%  Similarity=0.210  Sum_probs=211.1

Q ss_pred             CChHHHHhhhhhhhcC---c-cEEEECCCCCCchhHhHHHHHHhhcc-CCCceeEEEEcCCHHHHHHHHHHHHHhhcccC
Q 015158           61 KPSAIQQRGIVPFCKG---L-DVIQQAQSGTGKTATFCSGILQQLDY-GLVECQALVLAPTRELAQQIEKVMRALGDYLG  135 (412)
Q Consensus        61 ~l~~~Q~~a~~~~~~~---~-~~lv~~~tGsGKT~~~~~~~~~~~~~-~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~  135 (412)
                      ..+++|..++..+...   . .+++.+|||+|||.+.+.++...+.. .....+++++.|++++.+++.+.++.+....+
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~vl~aPTG~GKT~asl~~a~~~~~~~~~~~~r~i~vlP~~t~ie~~~~r~~~~~~~~~  274 (733)
T COG1203         195 EGYELQEKALELILRLEKRSLLVVLEAPTGYGKTEASLILALALLDEKIKLKSRVIYVLPFRTIIEDMYRRAKEIFGLFS  274 (733)
T ss_pred             hhhHHHHHHHHHHHhcccccccEEEEeCCCCChHHHHHHHHHHHhhccccccceEEEEccHHHHHHHHHHHHHhhhcccc
Confidence            3589999999998864   4 67899999999999998888877766 34567999999999999999999988654433


Q ss_pred             cEEEEEEcCcchHHHHHH--------------hcCCCcEEEeChHHHHHHHHc-CCCC-C--CCceEEEEeCCchhhccC
Q 015158          136 VKVHACVGGTSVREDQRI--------------LSSGVHVVVGTPGRVFDMLRR-QSLR-P--DNIRIFVLDEADEMLSRG  197 (412)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~--------------~~~~~~iii~T~~~l~~~~~~-~~~~-~--~~~~~iiiDE~h~~~~~~  197 (412)
                      ......++..........              ...-..+.++|+......... .... .  -..+.+|+||+|.+....
T Consensus       275 ~~~~~~h~~~~~~~~~~~~~~~~~~~~~~ds~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~S~vIlDE~h~~~~~~  354 (733)
T COG1203         275 VIGKSLHSSSKEPLLLEPDQDILLTLTTNDSYKKLLLALIVVTPIQILIFSVKGFKFEFLALLLTSLVILDEVHLYADET  354 (733)
T ss_pred             cccccccccccchhhhccccccceeEEecccccceeccccccCHhHhhhhhccccchHHHHHHHhhchhhccHHhhcccc
Confidence            322212333221111000              000122334444443332111 1111 0  123689999999877663


Q ss_pred             cHHHHHHHHH-hCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCc---cccCCceEE-EEEeccchhhHHHHHHH
Q 015158          198 FKDQIYDIFQ-LLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDE---LTLEGIKQF-HVNVEKEEWKLETLCDL  272 (412)
Q Consensus       198 ~~~~~~~i~~-~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~-~~~~~~~~~~~~~l~~~  272 (412)
                      ....+..++. ....+.++++||||+|+...+.+...+.....+......   .....+... ...... ..........
T Consensus       355 ~~~~l~~~i~~l~~~g~~ill~SATlP~~~~~~l~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~-~~~~~~~~~~  433 (733)
T COG1203         355 MLAALLALLEALAEAGVPVLLMSATLPPFLKEKLKKALGKGREVVENAKFCPKEDEPGLKRKERVDVED-GPQEELIELI  433 (733)
T ss_pred             hHHHHHHHHHHHHhCCCCEEEEecCCCHHHHHHHHHHHhcccceeccccccccccccccccccchhhhh-hhhHhhhhcc
Confidence            2333333333 333478899999999998888888777665544433220   000111110 000000 0000111111


Q ss_pred             HHh-cCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHh----cCCCcEEEEcCCCcCCCCCCCC
Q 015158          273 YET-LAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFR----SGSSRVLITTDLLARGIDVQQV  347 (412)
Q Consensus       273 ~~~-~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~----~g~~~vlv~t~~~~~G~d~~~~  347 (412)
                      ... ..+++++|.||++..|.++++.|+..+..+..+||.+...+|.+.++.+.    .++..|+|+|++++.|+|+. .
T Consensus       434 ~~~~~~~~kvlvI~NTV~~Aie~Y~~Lk~~~~~v~LlHSRf~~~dR~~ke~~l~~~~~~~~~~IvVaTQVIEagvDid-f  512 (733)
T COG1203         434 SEEVKEGKKVLVIVNTVDRAIELYEKLKEKGPKVLLLHSRFTLKDREEKERELKKLFKQNEGFIVVATQVIEAGVDID-F  512 (733)
T ss_pred             hhhhccCCcEEEEEecHHHHHHHHHHHHhcCCCEEEEecccchhhHHHHHHHHHHHHhccCCeEEEEeeEEEEEeccc-c
Confidence            122 24479999999999999999999998878999999999999998888655    46788999999999999985 6


Q ss_pred             CEEEEccCCCChhhHHHhhhhcccCC--CCceEEEEeccCc
Q 015158          348 SLVINYDLPTQPENYLHRIGRSGRFG--RKGVAINFVTRDD  386 (412)
Q Consensus       348 ~~vi~~~~~~s~~~~~Q~~GR~~R~g--~~g~~~~~~~~~~  386 (412)
                      +.+|  .-+.....++||+||++|.|  ..|.++++.....
T Consensus       513 d~mI--Te~aPidSLIQR~GRv~R~g~~~~~~~~v~~~~~~  551 (733)
T COG1203         513 DVLI--TELAPIDSLIQRAGRVNRHGKKENGKIYVYNDEER  551 (733)
T ss_pred             Ceee--ecCCCHHHHHHHHHHHhhcccccCCceeEeecccC
Confidence            7665  34466899999999999999  5677777776543

>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=1.1e-25  Score=198.89  Aligned_cols=312  Identities=16%  Similarity=0.160  Sum_probs=215.9

Q ss_pred             CCCCChHHHHhhhhhhhcC---ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccc
Q 015158           58 GFEKPSAIQQRGIVPFCKG---LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYL  134 (412)
Q Consensus        58 ~~~~l~~~Q~~a~~~~~~~---~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~  134 (412)
                      +-..++|||++++.....+   ++.+|+.|||+|||++.+-+++.      ..+++|++|.+...++||..++..|+..-
T Consensus       299 Pst~iRpYQEksL~KMFGNgRARSGiIVLPCGAGKtLVGvTAa~t------ikK~clvLcts~VSVeQWkqQfk~wsti~  372 (776)
T KOG1123|consen  299 PSTQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKTLVGVTAACT------IKKSCLVLCTSAVSVEQWKQQFKQWSTIQ  372 (776)
T ss_pred             cccccCchHHHHHHHHhCCCcccCceEEEecCCCCceeeeeeeee------ecccEEEEecCccCHHHHHHHHHhhcccC
Confidence            5557999999999998875   68899999999999887544432      23479999999999999999999998777


Q ss_pred             CcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcC--------CCCCCCceEEEEeCCchhhccCcHHHHHHHH
Q 015158          135 GVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQ--------SLRPDNIRIFVLDEADEMLSRGFKDQIYDIF  206 (412)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~--------~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~  206 (412)
                      +..+..++.+.+.     .+..++.|+|+||.++.+--.+.        .+..+.|+++++||+|-+....|++.+.-+.
T Consensus       373 d~~i~rFTsd~Ke-----~~~~~~gvvvsTYsMva~t~kRS~eaek~m~~l~~~EWGllllDEVHvvPA~MFRRVlsiv~  447 (776)
T KOG1123|consen  373 DDQICRFTSDAKE-----RFPSGAGVVVTTYSMVAYTGKRSHEAEKIMDFLRGREWGLLLLDEVHVVPAKMFRRVLSIVQ  447 (776)
T ss_pred             ccceEEeeccccc-----cCCCCCcEEEEeeehhhhcccccHHHHHHHHHHhcCeeeeEEeehhccchHHHHHHHHHHHH
Confidence            7788888876552     24467899999998875432211        1234679999999999988887887777777


Q ss_pred             HhCCCCceEEEEeecCChHHHHH--HHHhcCCCeEEEecCCccc----cCCceEEEEEecc-------------------
Q 015158          207 QLLPPKIQVGVFSATMPPEALEI--TRKFMNKPVRILVKRDELT----LEGIKQFHVNVEK-------------------  261 (412)
Q Consensus       207 ~~~~~~~~~i~~SAT~~~~~~~~--~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~-------------------  261 (412)
                      .++     .+++|||+-.+....  +..+.+ |..+.....+..    ...+....++++.                   
T Consensus       448 aHc-----KLGLTATLvREDdKI~DLNFLIG-PKlYEAnWmdL~~kGhIA~VqCaEVWCpMt~eFy~eYL~~~t~kr~lL  521 (776)
T KOG1123|consen  448 AHC-----KLGLTATLVREDDKITDLNFLIG-PKLYEANWMDLQKKGHIAKVQCAEVWCPMTPEFYREYLRENTRKRMLL  521 (776)
T ss_pred             HHh-----hccceeEEeeccccccccceeec-chhhhccHHHHHhCCceeEEeeeeeecCCCHHHHHHHHhhhhhhhhee
Confidence            766     599999985432211  111111 100000000000    0011111111111                   


Q ss_pred             ---chhhHHHHHHHHHhc--CCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhc-CCCcEEEEc
Q 015158          262 ---EEWKLETLCDLYETL--AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRS-GSSRVLITT  335 (412)
Q Consensus       262 ---~~~~~~~l~~~~~~~--~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~-g~~~vlv~t  335 (412)
                         ...+...-.-+++.+  +++|+|||..+.-....++-.|.     -.+++|.+++.+|.+|++.|+. ..++.++.+
T Consensus       522 yvMNP~KFraCqfLI~~HE~RgDKiIVFsDnvfALk~YAikl~-----KpfIYG~Tsq~ERm~ILqnFq~n~~vNTIFlS  596 (776)
T KOG1123|consen  522 YVMNPNKFRACQFLIKFHERRGDKIIVFSDNVFALKEYAIKLG-----KPFIYGPTSQNERMKILQNFQTNPKVNTIFLS  596 (776)
T ss_pred             eecCcchhHHHHHHHHHHHhcCCeEEEEeccHHHHHHHHHHcC-----CceEECCCchhHHHHHHHhcccCCccceEEEe
Confidence               122333333333333  56899999998877777776664     3478999999999999999986 478899999


Q ss_pred             CCCcCCCCCCCCCEEEEccC-CCChhhHHHhhhhcccCCC---C---ceEEEEeccCcHHHHH
Q 015158          336 DLLARGIDVQQVSLVINYDL-PTQPENYLHRIGRSGRFGR---K---GVAINFVTRDDERMLF  391 (412)
Q Consensus       336 ~~~~~G~d~~~~~~vi~~~~-~~s~~~~~Q~~GR~~R~g~---~---g~~~~~~~~~~~~~~~  391 (412)
                      .+..+.+|+|.++++|..+. .-|..+-.||.||..|+.+   +   .--|.+++.+..++.+
T Consensus       597 KVgDtSiDLPEAnvLIQISSH~GSRRQEAQRLGRILRAKk~~de~fnafFYSLVS~DTqEM~Y  659 (776)
T KOG1123|consen  597 KVGDTSIDLPEANVLIQISSHGGSRRQEAQRLGRILRAKKRNDEEFNAFFYSLVSKDTQEMYY  659 (776)
T ss_pred             eccCccccCCcccEEEEEcccccchHHHHHHHHHHHHHhhcCccccceeeeeeeecchHHHHh
Confidence            99999999999999998765 4578899999999999632   2   2345555666555543

>KOG0923 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.93  E-value=1.6e-24  Score=197.38  Aligned_cols=326  Identities=15%  Similarity=0.206  Sum_probs=226.1

Q ss_pred             CCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHH-HHhhcccCcE
Q 015158           59 FEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVM-RALGDYLGVK  137 (412)
Q Consensus        59 ~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~-~~~~~~~~~~  137 (412)
                      ....+++-.+.+.++..++-++|.+.||||||......+...=.. ..+.++-+..|++.-+...+... .+++..+|-.
T Consensus       263 sLPVy~ykdell~av~e~QVLiI~GeTGSGKTTQiPQyL~EaGyt-k~gk~IgcTQPRRVAAmSVAaRVA~EMgvkLG~e  341 (902)
T KOG0923|consen  263 SLPVYPYKDELLKAVKEHQVLIIVGETGSGKTTQIPQYLYEAGYT-KGGKKIGCTQPRRVAAMSVAARVAEEMGVKLGHE  341 (902)
T ss_pred             cCCchhhHHHHHHHHHhCcEEEEEcCCCCCccccccHHHHhcccc-cCCceEeecCcchHHHHHHHHHHHHHhCcccccc
Confidence            334678888889999999999999999999998876655544222 23445778889887666554433 3343333333


Q ss_pred             EEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhh-ccC-cHHHHHHHHHhCCCCceE
Q 015158          138 VHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEML-SRG-FKDQIYDIFQLLPPKIQV  215 (412)
Q Consensus       138 ~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~-~~~-~~~~~~~i~~~~~~~~~~  215 (412)
                      |.....      ..++.....-+-++|.++|++.+.... ++..+++||+||||+=. ..+ ....+..| ...++..++
T Consensus       342 VGYsIR------FEdcTSekTvlKYMTDGmLlREfL~ep-dLasYSViiiDEAHERTL~TDILfgLvKDI-ar~RpdLKl  413 (902)
T KOG0923|consen  342 VGYSIR------FEDCTSEKTVLKYMTDGMLLREFLSEP-DLASYSVIIVDEAHERTLHTDILFGLVKDI-ARFRPDLKL  413 (902)
T ss_pred             cceEEE------eccccCcceeeeeecchhHHHHHhccc-cccceeEEEeehhhhhhhhhhHHHHHHHHH-HhhCCcceE
Confidence            322211      111223445788999999999887543 46789999999999722 111 12222333 334578899


Q ss_pred             EEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhHHHHHHHHHhc---CCCcEEEEEcchhHHH
Q 015158          216 GVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETL---AITQSVIFVNTRRKVD  292 (412)
Q Consensus       216 i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~---~~~k~lif~~~~~~~~  292 (412)
                      +..|||+..   +-+..++.....+.+....   ..+..++...+..++....+..+++-+   +.+.+|||....++.+
T Consensus       414 lIsSAT~DA---ekFS~fFDdapIF~iPGRR---yPVdi~Yt~~PEAdYldAai~tVlqIH~tqp~GDILVFltGQeEIE  487 (902)
T KOG0923|consen  414 LISSATMDA---EKFSAFFDDAPIFRIPGRR---YPVDIFYTKAPEADYLDAAIVTVLQIHLTQPLGDILVFLTGQEEIE  487 (902)
T ss_pred             EeeccccCH---HHHHHhccCCcEEeccCcc---cceeeecccCCchhHHHHHHhhheeeEeccCCccEEEEeccHHHHH
Confidence            999999964   4455566555444443322   234555555555454445555555544   4478999999999988


Q ss_pred             HHHHHHhcC---------CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccC--------
Q 015158          293 WLTDKMRSR---------DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDL--------  355 (412)
Q Consensus       293 ~~~~~L~~~---------~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~--------  355 (412)
                      .+.+.|.++         .+-+..+|+.++...+.+|++---.|-.+|+++|+++++.+.++++..||.-+.        
T Consensus       488 t~~e~l~~~~~~LGski~eliv~PiYaNLPselQakIFePtP~gaRKVVLATNIAETSlTIdgI~yViDpGf~K~nsynp  567 (902)
T KOG0923|consen  488 TVKENLKERCRRLGSKIRELIVLPIYANLPSELQAKIFEPTPPGARKVVLATNIAETSLTIDGIKYVIDPGFVKQNSYNP  567 (902)
T ss_pred             HHHHHHHHHHHHhccccceEEEeeccccCChHHHHhhcCCCCCCceeEEEeecchhhceeecCeEEEecCccccccCcCC
Confidence            888777653         356788999999999999999888889999999999999999999999995442        


Q ss_pred             ----------CCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHHhccccc
Q 015158          356 ----------PTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIE  402 (412)
Q Consensus       356 ----------~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~  402 (412)
                                |.|.+...||.||+||.| +|+|+-+++.....+  .++.....+++
T Consensus       568 rtGmesL~v~piSKAsA~QRaGRAGRtg-PGKCfRLYt~~aY~~--eLE~~t~PEIq  621 (902)
T KOG0923|consen  568 RTGMESLLVTPISKASANQRAGRAGRTG-PGKCFRLYTAWAYEH--ELEEMTVPEIQ  621 (902)
T ss_pred             CcCceeEEEeeechhhhhhhccccCCCC-CCceEEeechhhhhh--hhccCCCccee
Confidence                      568889999999999997 799999999776543  34433333333

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

Probab=99.93  E-value=1.3e-23  Score=195.40  Aligned_cols=320  Identities=18%  Similarity=0.171  Sum_probs=218.9

Q ss_pred             CChHHHHhhhhhhhc----CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCc
Q 015158           61 KPSAIQQRGIVPFCK----GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGV  136 (412)
Q Consensus        61 ~l~~~Q~~a~~~~~~----~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~  136 (412)
                      .|.+||++.+..+.+    +...|+...+|-|||...+..+......++-.+++|||||. .+..||.++|..|+.  ..
T Consensus       205 ~Lf~yQreGV~WL~~L~~q~~GGILgDeMGLGKTIQiisFLaaL~~S~k~~~paLIVCP~-Tii~qW~~E~~~w~p--~~  281 (923)
T KOG0387|consen  205 KLFPYQREGVQWLWELYCQRAGGILGDEMGLGKTIQIISFLAALHHSGKLTKPALIVCPA-TIIHQWMKEFQTWWP--PF  281 (923)
T ss_pred             HhhHHHHHHHHHHHHHHhccCCCeecccccCccchhHHHHHHHHhhcccccCceEEEccH-HHHHHHHHHHHHhCc--ce
Confidence            478999999998764    56689999999999965543333322222334689999995 788999999999876  45


Q ss_pred             EEEEEEcCcchH---------H----HHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHH
Q 015158          137 KVHACVGGTSVR---------E----DQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIY  203 (412)
Q Consensus       137 ~~~~~~~~~~~~---------~----~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~  203 (412)
                      .+..+++.....         .    ..........|+++|++.|.-.  ...+....|+++|+||.|.+-+.+  ..+.
T Consensus       282 rv~ilh~t~s~~r~~~~~~~~~~~~~L~r~~~~~~~ilitty~~~r~~--~d~l~~~~W~y~ILDEGH~IrNpn--s~is  357 (923)
T KOG0387|consen  282 RVFILHGTGSGARYDASHSSHKKDKLLIRKVATDGGILITTYDGFRIQ--GDDLLGILWDYVILDEGHRIRNPN--SKIS  357 (923)
T ss_pred             EEEEEecCCcccccccchhhhhhhhhheeeecccCcEEEEehhhhccc--CcccccccccEEEecCcccccCCc--cHHH
Confidence            677777655421         1    1112234457999999987532  234445678999999999998876  5555


Q ss_pred             HHHHhCCCCceEEEEeecCChHHHHHHHHhc------------------CCCeEEEecCC--------------------
Q 015158          204 DIFQLLPPKIQVGVFSATMPPEALEITRKFM------------------NKPVRILVKRD--------------------  245 (412)
Q Consensus       204 ~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~------------------~~~~~~~~~~~--------------------  245 (412)
                      ..+..++ ..+.|.+|+||-.+-...+..++                  ..|+..-....                    
T Consensus       358 lackki~-T~~RiILSGTPiQNnL~ELwsLfDFv~PG~Lgt~~~F~~~f~~pI~~GgyaNAs~~qv~~aykca~~Lr~lI  436 (923)
T KOG0387|consen  358 LACKKIR-TVHRIILSGTPIQNNLTELWSLFDFVFPGKLGTLPVFQQNFEHPINRGGYANASPRQVQTAYKCAVALRDLI  436 (923)
T ss_pred             HHHHhcc-ccceEEeeCccccchHHHHHHHhhhccCCcccchHHHHhhhhhheeccccCCCCHHHHHHHHHHHHHHHHHh
Confidence            5555565 44578899998532111111111                  00000000000                    


Q ss_pred             -------------ccccCCceEEEE-------------------------------------------------------
Q 015158          246 -------------ELTLEGIKQFHV-------------------------------------------------------  257 (412)
Q Consensus       246 -------------~~~~~~~~~~~~-------------------------------------------------------  257 (412)
                                   ....+.-...++                                                       
T Consensus       437 ~PylLRR~K~dv~~~~Lp~K~E~VlfC~LT~~QR~~Y~~fl~s~~v~~i~ng~~~~l~Gi~iLrkICnHPdll~~~~~~~  516 (923)
T KOG0387|consen  437 SPYLLRRMKSDVKGLKLPKKEEIVLFCRLTKLQRRLYQRFLNSSEVNKILNGKRNCLSGIDILRKICNHPDLLDRRDEDE  516 (923)
T ss_pred             HHHHHHHHHHHhhhccCCCccceEEEEeccHHHHHHHHHHhhhHHHHHHHcCCccceechHHHHhhcCCcccccCccccc
Confidence                         000000000000                                                       


Q ss_pred             -------EeccchhhHHHHHHHHHhc--CCCcEEEEEcchhHHHHHHHHHh-cCCCeeEEecCCCCHHHHHHHHHHHhcC
Q 015158          258 -------NVEKEEWKLETLCDLYETL--AITQSVIFVNTRRKVDWLTDKMR-SRDHTVSATHGDMDQNTRDIIMREFRSG  327 (412)
Q Consensus       258 -------~~~~~~~~~~~l~~~~~~~--~~~k~lif~~~~~~~~~~~~~L~-~~~~~~~~~~~~~~~~~r~~~~~~f~~g  327 (412)
                             -......+...+..+++..  .+.++|+|.+++.-...+-..|. ..++.+..+.|.++...|..++++|+++
T Consensus       517 ~~~~D~~g~~k~sGKm~vl~~ll~~W~kqg~rvllFsqs~~mLdilE~fL~~~~~ysylRmDGtT~~~~R~~lVd~Fne~  596 (923)
T KOG0387|consen  517 KQGPDYEGDPKRSGKMKVLAKLLKDWKKQGDRVLLFSQSRQMLDILESFLRRAKGYSYLRMDGTTPAALRQKLVDRFNED  596 (923)
T ss_pred             ccCCCcCCChhhcchHHHHHHHHHHHhhCCCEEEEehhHHHHHHHHHHHHHhcCCceEEEecCCCccchhhHHHHhhcCC
Confidence                   0001123566677776664  44699999999999999999998 5899999999999999999999999987


Q ss_pred             CC-c-EEEEcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccCCCCce--EEEEeccCcHH
Q 015158          328 SS-R-VLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGV--AINFVTRDDER  388 (412)
Q Consensus       328 ~~-~-vlv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~--~~~~~~~~~~~  388 (412)
                      +. . +|++|.+.+-|+|+.+++.||++++.|+|..=.|+.-|+-|.|+...  +|-+++...-+
T Consensus       597 ~s~~VFLLTTrvGGLGlNLTgAnRVIIfDPdWNPStD~QAreRawRiGQkkdV~VYRL~t~gTIE  661 (923)
T KOG0387|consen  597 ESIFVFLLTTRVGGLGLNLTGANRVIIFDPDWNPSTDNQARERAWRIGQKKDVVVYRLMTAGTIE  661 (923)
T ss_pred             CceEEEEEEecccccccccccCceEEEECCCCCCccchHHHHHHHhhcCccceEEEEEecCCcHH
Confidence            54 3 56688899999999999999999999999999999999999998754  55566665433

>KOG0924 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.93  E-value=4.8e-24  Score=194.81  Aligned_cols=310  Identities=16%  Similarity=0.207  Sum_probs=213.9

Q ss_pred             ChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHH-hhcccCcEEEE
Q 015158           62 PSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRA-LGDYLGVKVHA  140 (412)
Q Consensus        62 l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~-~~~~~~~~~~~  140 (412)
                      .-.++.+.+..+..++-++|+++||||||......++..=..  .++-+-+..|++.-+...++.+.. +....|..|..
T Consensus       357 vf~~R~~ll~~ir~n~vvvivgETGSGKTTQl~QyL~edGY~--~~GmIGcTQPRRvAAiSVAkrVa~EM~~~lG~~VGY  434 (1042)
T KOG0924|consen  357 VFACRDQLLSVIRENQVVVIVGETGSGKTTQLAQYLYEDGYA--DNGMIGCTQPRRVAAISVAKRVAEEMGVTLGDTVGY  434 (1042)
T ss_pred             hHHHHHHHHHHHhhCcEEEEEecCCCCchhhhHHHHHhcccc--cCCeeeecCchHHHHHHHHHHHHHHhCCccccccce
Confidence            456777788888889999999999999998876655544222  123466667888877777666554 33333333332


Q ss_pred             EEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhh-ccCcHHHHHHHHHhCCCCceEEEEe
Q 015158          141 CVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEML-SRGFKDQIYDIFQLLPPKIQVGVFS  219 (412)
Q Consensus       141 ~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~-~~~~~~~~~~i~~~~~~~~~~i~~S  219 (412)
                      ...-      .........|-++|.+.|++...... .+.++++||+||||+=. +.+..-.+.+....-+.+.++|.+|
T Consensus       435 sIRF------EdvT~~~T~IkymTDGiLLrEsL~d~-~L~kYSviImDEAHERslNtDilfGllk~~larRrdlKliVtS  507 (1042)
T KOG0924|consen  435 SIRF------EDVTSEDTKIKYMTDGILLRESLKDR-DLDKYSVIIMDEAHERSLNTDILFGLLKKVLARRRDLKLIVTS  507 (1042)
T ss_pred             EEEe------eecCCCceeEEEeccchHHHHHhhhh-hhhheeEEEechhhhcccchHHHHHHHHHHHHhhccceEEEee
Confidence            2211      11122345788999999987665433 35689999999999833 2221222222222334588999999


Q ss_pred             ecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhHHHHHHHHHhc---CCCcEEEEEcchhHHHHHHH
Q 015158          220 ATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETL---AITQSVIFVNTRRKVDWLTD  296 (412)
Q Consensus       220 AT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~---~~~k~lif~~~~~~~~~~~~  296 (412)
                      ||+..   +.+..+++....+.+....   ..+...+...+..++....+...+.-+   ..+.+|||....+.++..+.
T Consensus       508 ATm~a---~kf~nfFgn~p~f~IpGRT---yPV~~~~~k~p~eDYVeaavkq~v~Ihl~~~~GdilIfmtGqediE~t~~  581 (1042)
T KOG0924|consen  508 ATMDA---QKFSNFFGNCPQFTIPGRT---YPVEIMYTKTPVEDYVEAAVKQAVQIHLSGPPGDILIFMTGQEDIECTCD  581 (1042)
T ss_pred             ccccH---HHHHHHhCCCceeeecCCc---cceEEEeccCchHHHHHHHHhhheEeeccCCCCCEEEecCCCcchhHHHH
Confidence            99964   3444555544334433322   123444444444444444555554444   34789999999988877766


Q ss_pred             HHhcC----------CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccC-----------
Q 015158          297 KMRSR----------DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDL-----------  355 (412)
Q Consensus       297 ~L~~~----------~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~-----------  355 (412)
                      .++++          ++.+..+++.++..-+.++++....|..++||+|+++++.+.+|++..||..+.           
T Consensus       582 ~i~~~l~ql~~~~~~~L~vlpiYSQLp~dlQ~kiFq~a~~~vRK~IvATNIAETSLTi~gI~yVID~Gy~K~kvyn~~~G  661 (1042)
T KOG0924|consen  582 IIKEKLEQLDSAPTTDLAVLPIYSQLPADLQAKIFQKAEGGVRKCIVATNIAETSLTIPGIRYVIDTGYCKLKVYNPRIG  661 (1042)
T ss_pred             HHHHHHHhhhcCCCCceEEEeehhhCchhhhhhhcccCCCCceeEEEeccchhhceeecceEEEEecCceeeeecccccc
Confidence            66542          678999999999999999999888899999999999999999999999996553           


Q ss_pred             -------CCChhhHHHhhhhcccCCCCceEEEEeccCcH
Q 015158          356 -------PTQPENYLHRIGRSGRFGRKGVAINFVTRDDE  387 (412)
Q Consensus       356 -------~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~  387 (412)
                             |.|.+..-||.||+||.| +|.||-+++...+
T Consensus       662 ~D~L~~~pIS~AnA~QRaGRAGRt~-pG~cYRlYTe~ay  699 (1042)
T KOG0924|consen  662 MDALQIVPISQANADQRAGRAGRTG-PGTCYRLYTEDAY  699 (1042)
T ss_pred             cceeEEEechhccchhhccccCCCC-CcceeeehhhhHH
Confidence                   678899999999999996 7999999998654

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

Probab=99.92  E-value=1.7e-23  Score=200.28  Aligned_cols=325  Identities=21%  Similarity=0.289  Sum_probs=218.1

Q ss_pred             CChHHHHhhhhhhhcC----ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCc
Q 015158           61 KPSAIQQRGIVPFCKG----LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGV  136 (412)
Q Consensus        61 ~l~~~Q~~a~~~~~~~----~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~  136 (412)
                      .+++-|..|++.+.+.    ...++.+.||||||.+|+-++...+..++   .+|+++|-.+|..|+.+.|+...   +.
T Consensus       198 ~Ln~~Q~~a~~~i~~~~~~~~~~Ll~GvTGSGKTEvYl~~i~~~L~~Gk---qvLvLVPEI~Ltpq~~~rf~~rF---g~  271 (730)
T COG1198         198 ALNQEQQAAVEAILSSLGGFAPFLLDGVTGSGKTEVYLEAIAKVLAQGK---QVLVLVPEIALTPQLLARFKARF---GA  271 (730)
T ss_pred             ccCHHHHHHHHHHHHhcccccceeEeCCCCCcHHHHHHHHHHHHHHcCC---EEEEEeccccchHHHHHHHHHHh---CC
Confidence            5788999999998766    67899999999999999999999888774   89999999999999999998865   46


Q ss_pred             EEEEEEcCcch----HHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhc--c---CcHHHHHHHHH
Q 015158          137 KVHACVGGTSV----REDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLS--R---GFKDQIYDIFQ  207 (412)
Q Consensus       137 ~~~~~~~~~~~----~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~--~---~~~~~~~~i~~  207 (412)
                      ++..++++-+.    ..|.+...++..|+|+|-..++-       .+.++++||+||=|.-.-  .   .|...--.++.
T Consensus       272 ~v~vlHS~Ls~~er~~~W~~~~~G~~~vVIGtRSAlF~-------Pf~~LGLIIvDEEHD~sYKq~~~prYhARdvA~~R  344 (730)
T COG1198         272 KVAVLHSGLSPGERYRVWRRARRGEARVVIGTRSALFL-------PFKNLGLIIVDEEHDSSYKQEDGPRYHARDVAVLR  344 (730)
T ss_pred             ChhhhcccCChHHHHHHHHHHhcCCceEEEEechhhcC-------chhhccEEEEeccccccccCCcCCCcCHHHHHHHH
Confidence            67777766554    34566667889999999544432       346899999999997431  1   12222223333


Q ss_pred             hCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecC--CccccCCceEEEEEeccchhh-----HHHHHHHHHhc--CC
Q 015158          208 LLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKR--DELTLEGIKQFHVNVEKEEWK-----LETLCDLYETL--AI  278 (412)
Q Consensus       208 ~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~-----~~~l~~~~~~~--~~  278 (412)
                      .-..++++|+-||||+-+.......  +.........  .....+.+.  ...+......     ...+.+.+++.  .+
T Consensus       345 a~~~~~pvvLgSATPSLES~~~~~~--g~y~~~~L~~R~~~a~~p~v~--iiDmr~e~~~~~~~lS~~Ll~~i~~~l~~g  420 (730)
T COG1198         345 AKKENAPVVLGSATPSLESYANAES--GKYKLLRLTNRAGRARLPRVE--IIDMRKEPLETGRSLSPALLEAIRKTLERG  420 (730)
T ss_pred             HHHhCCCEEEecCCCCHHHHHhhhc--CceEEEEccccccccCCCcce--EEeccccccccCccCCHHHHHHHHHHHhcC
Confidence            3345788999999997654444422  2111222211  112222222  2222221111     13344444332  44


Q ss_pred             CcEEEEEcchhHH------------------------------------------------------------HHHHHHH
Q 015158          279 TQSVIFVNTRRKV------------------------------------------------------------DWLTDKM  298 (412)
Q Consensus       279 ~k~lif~~~~~~~------------------------------------------------------------~~~~~~L  298 (412)
                      +.+|+|.|.+..+                                                            +++.+.|
T Consensus       421 eQ~llflnRRGys~~l~C~~Cg~v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~~L~~~G~GterieeeL  500 (730)
T COG1198         421 EQVLLFLNRRGYAPLLLCRDCGYIAECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSEHLRAVGPGTERIEEEL  500 (730)
T ss_pred             CeEEEEEccCCccceeecccCCCcccCCCCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCCCeeEEecccHHHHHHHH
Confidence            6788888776433                                                            2222222


Q ss_pred             hcC--CCeeEEecCCCCH--HHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccCCC------------ChhhH
Q 015158          299 RSR--DHTVSATHGDMDQ--NTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPT------------QPENY  362 (412)
Q Consensus       299 ~~~--~~~~~~~~~~~~~--~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~~~------------s~~~~  362 (412)
                      ++.  +..+..+.++...  ..-+..+..|.+|+.+|||+|+++..|.|+|++..|..++...            ...-+
T Consensus       501 ~~~FP~~rv~r~d~Dtt~~k~~~~~~l~~~~~ge~dILiGTQmiaKG~~fp~vtLVgvl~aD~~L~~~DfRA~Er~fqll  580 (730)
T COG1198         501 KRLFPGARIIRIDSDTTRRKGALEDLLDQFANGEADILIGTQMIAKGHDFPNVTLVGVLDADTGLGSPDFRASERTFQLL  580 (730)
T ss_pred             HHHCCCCcEEEEccccccchhhHHHHHHHHhCCCCCeeecchhhhcCCCcccceEEEEEechhhhcCCCcchHHHHHHHH
Confidence            222  3446666666533  3457889999999999999999999999999999987654321            23457


Q ss_pred             HHhhhhcccCCCCceEEEEeccCcHHHHHH-----HHHHhccccc
Q 015158          363 LHRIGRSGRFGRKGVAINFVTRDDERMLFD-----IQKFYNVVIE  402 (412)
Q Consensus       363 ~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~-----~~~~~~~~~~  402 (412)
                      .|-.||+||.+.+|.+++-....+...++.     +..|++.+++
T Consensus       581 ~QvaGRAgR~~~~G~VvIQT~~P~hp~i~~~~~~dy~~F~~~El~  625 (730)
T COG1198         581 MQVAGRAGRAGKPGEVVIQTYNPDHPAIQALKRGDYEAFYEQELA  625 (730)
T ss_pred             HHHHhhhccCCCCCeEEEEeCCCCcHHHHHHHhcCHHHHHHHHHH
Confidence            899999999999999999988887665544     3455555443

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

Probab=99.92  E-value=1.7e-22  Score=203.76  Aligned_cols=332  Identities=15%  Similarity=0.152  Sum_probs=205.7

Q ss_pred             CHHHHHHHHHCCCCCChHHHHhhhh----hhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHH
Q 015158           47 QENLLRGIYAYGFEKPSAIQQRGIV----PFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQ  122 (412)
Q Consensus        47 ~~~~~~~l~~~~~~~l~~~Q~~a~~----~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q  122 (412)
                      .+.+.+.+...||. +|+.|.+.+.    .+.+++++++.||||+|||++|+++++....   .+.+++|.+||++|.+|
T Consensus       232 ~~~~~~~~~~~~~~-~r~~Q~~~~~~i~~~~~~~~~~~~eA~TG~GKT~ayLlp~~~~~~---~~~~vvi~t~t~~Lq~Q  307 (850)
T TIGR01407       232 SSLFSKNIDRLGLE-YRPEQLKLAELVLDQLTHSEKSLIEAPTGTGKTLGYLLPALYYAI---TEKPVVISTNTKVLQSQ  307 (850)
T ss_pred             cHHHHHhhhhcCCc-cCHHHHHHHHHHHHHhccCCcEEEECCCCCchhHHHHHHHHHHhc---CCCeEEEEeCcHHHHHH
Confidence            34667777778888 8999998665    5556889999999999999999999887654   23589999999999999


Q ss_pred             HHH-HHHHhhcccC--cEEEEEEcCcchH---H---------------------------------------------HH
Q 015158          123 IEK-VMRALGDYLG--VKVHACVGGTSVR---E---------------------------------------------DQ  151 (412)
Q Consensus       123 ~~~-~~~~~~~~~~--~~~~~~~~~~~~~---~---------------------------------------------~~  151 (412)
                      +.. ++..+....+  +++..+.|..+.-   .                                             +.
T Consensus       308 l~~~~~~~l~~~~~~~~~~~~~kG~~~ylcl~k~~~~l~~~~~~~~~~~~~~~~~~wl~~T~tGD~~el~~~~~~~~~~~  387 (850)
T TIGR01407       308 LLEKDIPLLNEILNFKINAALIKGKSNYLSLGKFSQILKDNTDNYEFNIFKMQVLVWLTETETGDLDELNLKGGNKMFFA  387 (850)
T ss_pred             HHHHHHHHHHHHcCCCceEEEEEcchhhccHHHHHHHHhcCCCcHHHHHHHHHHHHHhccCCccCHhhccCCCcchhhHH
Confidence            865 4544433322  4444444333210   0                                             00


Q ss_pred             -----------------------HHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccC-------c---
Q 015158          152 -----------------------RILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRG-------F---  198 (412)
Q Consensus       152 -----------------------~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~-------~---  198 (412)
                                             ......++|+|+++..|+..+.....-+...+.+|+||||++.+..       +   
T Consensus       388 ~i~~~~~l~~~c~~~~~Cf~~~ar~~a~~AdivItNHa~L~~~~~~~~~ilp~~~~lIiDEAH~L~d~a~~~~~~~ls~~  467 (850)
T TIGR01407       388 QVRHDGNLSKKDLFYEVDFYNRAQKNAEQAQILITNHAYLITRLVDNPELFPSFRDLIIDEAHHLPDIAENQLQEELDYA  467 (850)
T ss_pred             HhhcCCCCCCCCCCccccHHHHHHHHHhcCCEEEecHHHHHHHhhcccccCCCCCEEEEECcchHHHHHHHHhcceeCHH
Confidence                                   0012345899999999888765433223456899999999865310       0   


Q ss_pred             --HHH----------------------------------------------------------------HHHHHHh----
Q 015158          199 --KDQ----------------------------------------------------------------IYDIFQL----  208 (412)
Q Consensus       199 --~~~----------------------------------------------------------------~~~i~~~----  208 (412)
                        ...                                                                +......    
T Consensus       468 ~~~~~l~~l~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~l~~~~~~~~~~~~~l~~~~~~~~~~  547 (850)
T TIGR01407       468 DIKYQIDLIGKGENEQLLKRIQQLEKQEILEKLFDFETKDILKDLQAILDKLNKLLQIFSELSHKTVDQLRKFDLALKDD  547 (850)
T ss_pred             HHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHH
Confidence              000                                                                0000000    


Q ss_pred             -------C-------------------------------------CCCceEEEEeecCChH-HHHHHHHhcCCCeE--EE
Q 015158          209 -------L-------------------------------------PPKIQVGVFSATMPPE-ALEITRKFMNKPVR--IL  241 (412)
Q Consensus       209 -------~-------------------------------------~~~~~~i~~SAT~~~~-~~~~~~~~~~~~~~--~~  241 (412)
                             +                                     +....+|++|||+... ..+.....++-...  ..
T Consensus       548 ~~~l~~~~~~~~~~wi~~~~~~~~~~~~l~~~pl~~~~~l~~~~~~~~~~~il~SATL~~~~~~~~~~~~lGl~~~~~~~  627 (850)
T TIGR01407       548 FKNIEQSLKEGHTSWISIENLQQKSTIRLYIKDYEVGDVLTKRLLPKFKSLIFTSATLKFSHSFESFPQLLGLTDVHFNT  627 (850)
T ss_pred             HHHHHHHhccCCeEEEEecCCCCCceEEEEeeeCcHHHHHHHHHhccCCeEEEEecccccCCChHHHHHhcCCCccccce
Confidence                   0                                     0134689999999742 23445444443211  11


Q ss_pred             ecCCccc-cCCceEEEEE--ec-----cchhhHH----HHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcCC--CeeEE
Q 015158          242 VKRDELT-LEGIKQFHVN--VE-----KEEWKLE----TLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRD--HTVSA  307 (412)
Q Consensus       242 ~~~~~~~-~~~~~~~~~~--~~-----~~~~~~~----~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~--~~~~~  307 (412)
                      ....... ..+ ...+..  .+     .......    .+.+++.. ..+++|||++|.+..+.++..|....  .....
T Consensus       628 ~~~spf~~~~~-~~l~v~~d~~~~~~~~~~~~~~~ia~~i~~l~~~-~~g~~LVlftS~~~l~~v~~~L~~~~~~~~~~~  705 (850)
T TIGR01407       628 IEPTPLNYAEN-QRVLIPTDAPAIQNKSLEEYAQEIASYIIEITAI-TSPKILVLFTSYEMLHMVYDMLNELPEFEGYEV  705 (850)
T ss_pred             ecCCCCCHHHc-CEEEecCCCCCCCCCChHHHHHHHHHHHHHHHHh-cCCCEEEEeCCHHHHHHHHHHHhhhccccCceE
Confidence            1100001 111 112211  11     0111122    22333333 44799999999999999999997521  12222


Q ss_pred             ecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCC--EEEEccCCCC---------------------------
Q 015158          308 THGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVS--LVINYDLPTQ---------------------------  358 (412)
Q Consensus       308 ~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~--~vi~~~~~~s---------------------------  358 (412)
                      +..+.. ..|.+++++|++++..||++|+.+.+|+|+|+..  .||+.+.|+.                           
T Consensus       706 l~q~~~-~~r~~ll~~F~~~~~~iLlgt~sf~EGVD~~g~~l~~viI~~LPf~~p~dp~~~a~~~~~~~~g~~~f~~~~l  784 (850)
T TIGR01407       706 LAQGIN-GSRAKIKKRFNNGEKAILLGTSSFWEGVDFPGNGLVCLVIPRLPFANPKHPLTKKYWQKLEQEGKNPFYDYVL  784 (850)
T ss_pred             EecCCC-ccHHHHHHHHHhCCCeEEEEcceeecccccCCCceEEEEEeCCCCCCCCCHHHHHHHHHHHHhcCCchHHhhH
Confidence            333322 4788999999999999999999999999999754  5677776642                           


Q ss_pred             ---hhhHHHhhhhcccCCCCceEEEEeccC
Q 015158          359 ---PENYLHRIGRSGRFGRKGVAINFVTRD  385 (412)
Q Consensus       359 ---~~~~~Q~~GR~~R~g~~g~~~~~~~~~  385 (412)
                         ...+.|.+||+.|...+..++++++..
T Consensus       785 P~A~~~l~Qa~GRlIRs~~D~G~v~ilD~R  814 (850)
T TIGR01407       785 PMAIIRLRQALGRLIRRENDRGSIVILDRR  814 (850)
T ss_pred             HHHHHHHHHhhccccccCCceEEEEEEccc
Confidence               134689999999997766666666664

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.

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

Probab=99.91  E-value=9.9e-23  Score=197.15  Aligned_cols=331  Identities=18%  Similarity=0.226  Sum_probs=233.3

Q ss_pred             CHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHH
Q 015158           47 QENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKV  126 (412)
Q Consensus        47 ~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~  126 (412)
                      ++.....+....-...+..++.++..+.+++.+++.+.||+|||+.....+++........+++++.-|++--+...+++
T Consensus       159 s~~~~~~~~~R~~LPa~~~r~~Il~~i~~~qVvvIsGeTGcGKTTQvpQfiLd~~~~~~~~~~IicTQPRRIsAIsvAeR  238 (924)
T KOG0920|consen  159 SESYKEMLRFRESLPAYKMRDTILDAIEENQVVVISGETGCGKTTQVPQFILDEAIESGAACNIICTQPRRISAISVAER  238 (924)
T ss_pred             hhHHHHHHHHHHhCccHHHHHHHHHHHHhCceEEEeCCCCCCchhhhhHHHHHHHHhcCCCCeEEecCCchHHHHHHHHH
Confidence            34444444433333468889999999999999999999999999998888888764444677899999998777666666


Q ss_pred             HHH-hhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhh-ccCcHHHHHH
Q 015158          127 MRA-LGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEML-SRGFKDQIYD  204 (412)
Q Consensus       127 ~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~-~~~~~~~~~~  204 (412)
                      +.. .+...|..|....+..+..      .....+.+||.+.|++.+.. .-...++..||+||+|+=. +.+|...+.+
T Consensus       239 Va~ER~~~~g~~VGYqvrl~~~~------s~~t~L~fcTtGvLLr~L~~-~~~l~~vthiivDEVHER~i~~DflLi~lk  311 (924)
T KOG0920|consen  239 VAKERGESLGEEVGYQVRLESKR------SRETRLLFCTTGVLLRRLQS-DPTLSGVTHIIVDEVHERSINTDFLLILLK  311 (924)
T ss_pred             HHHHhccccCCeeeEEEeeeccc------CCceeEEEecHHHHHHHhcc-CcccccCceeeeeeEEEccCCcccHHHHHH
Confidence            544 3333454554444333221      22368999999999998877 3446789999999999833 4445555555


Q ss_pred             HHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccc----------------cCCceEEE-----------E
Q 015158          205 IFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELT----------------LEGIKQFH-----------V  257 (412)
Q Consensus       205 i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~----------------~~~~~~~~-----------~  257 (412)
                      .+...+++.++|+||||...   +.+..+++....+.+......                ........           .
T Consensus       312 ~lL~~~p~LkvILMSAT~da---e~fs~YF~~~pvi~i~grtfpV~~~fLEDil~~~~~~~~~~~~~~~~~~~~~~~~~~  388 (924)
T KOG0920|consen  312 DLLPRNPDLKVILMSATLDA---ELFSDYFGGCPVITIPGRTFPVKEYFLEDILSKTGYVSEDDSARSGPERSQLRLARL  388 (924)
T ss_pred             HHhhhCCCceEEEeeeecch---HHHHHHhCCCceEeecCCCcchHHHHHHHHHHHhcccccccccccccccCccccccc
Confidence            55556689999999999973   445555554443333221110                00000000           0


Q ss_pred             EeccchhhHHHHHHHH----HhcCCCcEEEEEcchhHHHHHHHHHhcC-------CCeeEEecCCCCHHHHHHHHHHHhc
Q 015158          258 NVEKEEWKLETLCDLY----ETLAITQSVIFVNTRRKVDWLTDKMRSR-------DHTVSATHGDMDQNTRDIIMREFRS  326 (412)
Q Consensus       258 ~~~~~~~~~~~l~~~~----~~~~~~k~lif~~~~~~~~~~~~~L~~~-------~~~~~~~~~~~~~~~r~~~~~~f~~  326 (412)
                      .....+.....+..++    .....+.+|||.+...++..+++.|...       ..-+..+|+.++..++..+...--.
T Consensus       389 ~~~~~~id~~Li~~li~~I~~~~~~GaILVFLPG~~eI~~~~~~L~~~~~f~~~~~~~ilplHs~~~s~eQ~~VF~~pp~  468 (924)
T KOG0920|consen  389 KLWEPEIDYDLIEDLIEYIDEREFEGAILVFLPGWEEILQLKELLEVNLPFADSLKFAILPLHSSIPSEEQQAVFKRPPK  468 (924)
T ss_pred             hhccccccHHHHHHHHHhcccCCCCceEEEEcCCHHHHHHHHHHhhhccccccccceEEEeccccCChHHHHHhcCCCCC
Confidence            0000112233333333    2234588999999999999999999653       3567888999999999999998888


Q ss_pred             CCCcEEEEcCCCcCCCCCCCCCEEEEccCC------------------CChhhHHHhhhhcccCCCCceEEEEeccCcHH
Q 015158          327 GSSRVLITTDLLARGIDVQQVSLVINYDLP------------------TQPENYLHRIGRSGRFGRKGVAINFVTRDDER  388 (412)
Q Consensus       327 g~~~vlv~t~~~~~G~d~~~~~~vi~~~~~------------------~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~  388 (412)
                      |..+||++|++++++|.++++-.||..+..                  -|.+...||.||+||. .+|.||.+++.....
T Consensus       469 g~RKIIlaTNIAETSITIdDVvyVIDsG~~Ke~~yD~~~~~s~l~~~wvSkAna~QR~GRAGRv-~~G~cy~L~~~~~~~  547 (924)
T KOG0920|consen  469 GTRKIILATNIAETSITIDDVVYVIDSGLVKEKSYDPERKVSCLLLSWVSKANAKQRRGRAGRV-RPGICYHLYTRSRYE  547 (924)
T ss_pred             CcchhhhhhhhHhhcccccCeEEEEecCeeeeeeecccCCcchhheeeccccchHHhcccccCc-cCCeeEEeechhhhh
Confidence            999999999999999999999999976642                  4678899999999999 789999999886544

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=99.91  E-value=2.3e-22  Score=189.44  Aligned_cols=317  Identities=19%  Similarity=0.216  Sum_probs=220.1

Q ss_pred             CCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCc
Q 015158           57 YGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGV  136 (412)
Q Consensus        57 ~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~  136 (412)
                      .|.. |++.|.-+...++.|+  +..+.||.|||+++.++++.....+   ..+-+++|+.-|+.+-++.+..+...+|+
T Consensus        75 lg~r-~ydvQlig~l~Ll~G~--VaEM~TGEGKTLvA~l~a~l~AL~G---~~VhvvT~NdyLA~RDae~m~~ly~~LGL  148 (764)
T PRK12326         75 LGLR-PFDVQLLGALRLLAGD--VIEMATGEGKTLAGAIAAAGYALQG---RRVHVITVNDYLARRDAEWMGPLYEALGL  148 (764)
T ss_pred             cCCC-cchHHHHHHHHHhCCC--cccccCCCCHHHHHHHHHHHHHHcC---CCeEEEcCCHHHHHHHHHHHHHHHHhcCC
Confidence            3666 8999999999998885  7799999999999988887666554   48999999999999999999999999999


Q ss_pred             EEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCC-------CCCCCceEEEEeCCchhh-ccC-----------
Q 015158          137 KVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQS-------LRPDNIRIFVLDEADEML-SRG-----------  197 (412)
Q Consensus       137 ~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~-------~~~~~~~~iiiDE~h~~~-~~~-----------  197 (412)
                      .+..+.++.+.......  -.++|+++|...|---+.+..       ...+.+.+.|+||++.++ +..           
T Consensus       149 svg~i~~~~~~~err~a--Y~~DItYgTn~e~gFDyLRDnm~~~~~~~v~R~~~faIVDEvDSiLIDeArtPLiISg~~~  226 (764)
T PRK12326        149 TVGWITEESTPEERRAA--YACDVTYASVNEIGFDVLRDQLVTDVADLVSPNPDVAIIDEADSVLVDEALVPLVLAGSTP  226 (764)
T ss_pred             EEEEECCCCCHHHHHHH--HcCCCEEcCCcccccccchhhhccChHhhcCCccceeeecchhhheeccccCceeeeCCCc
Confidence            99999887765544333  357999999877633222211       123567899999999753 100           


Q ss_pred             ---cHHHHHHHHHhCC----------------------------------------------------------------
Q 015158          198 ---FKDQIYDIFQLLP----------------------------------------------------------------  210 (412)
Q Consensus       198 ---~~~~~~~i~~~~~----------------------------------------------------------------  210 (412)
                         .......+...+.                                                                
T Consensus       227 ~~~~y~~~~~~v~~L~~~~dy~ide~~k~v~LTe~G~~~~e~~l~~~~ly~~~~~~~~~~~i~~AL~A~~l~~~d~dYiV  306 (764)
T PRK12326        227 GEAPRGEIAELVRRLREGKDYEIDDDGRNVHLTDKGARKVEKALGGIDLYSEEHVGTTLTQVNVALHAHALLQRDVHYIV  306 (764)
T ss_pred             chhHHHHHHHHHHhcCcCCcEEEEcCCCeeEecHHHHHHHHHHcCCccccCcchhHHHHHHHHHHHHHHHHHhcCCcEEE
Confidence               0001111111110                                                                


Q ss_pred             ------------------------------------------------------CCceEEEEeecCChHHHHHHHHhcCC
Q 015158          211 ------------------------------------------------------PKIQVGVFSATMPPEALEITRKFMNK  236 (412)
Q Consensus       211 ------------------------------------------------------~~~~~i~~SAT~~~~~~~~~~~~~~~  236 (412)
                                                                            --.++.|||+|..... +.+...++-
T Consensus       307 ~dgeV~iVDe~TGRvm~grrwsdGLHQaIEaKE~v~i~~e~~t~AsIT~QnfFr~Y~kLsGMTGTa~t~~-~Ef~~iY~l  385 (764)
T PRK12326        307 RDGKVHLINASRGRIAQLQRWPDGLQAAVEAKEGLETTETGEVLDTITVQALIGRYPTVCGMTGTAVAAG-EQLRQFYDL  385 (764)
T ss_pred             ECCEEEEEECCCCCcCCCCccChHHHHHHHHHcCCCCCCCceeeehhhHHHHHHhcchheeecCCChhHH-HHHHHHhCC
Confidence                                                                  0136788888876544 344444444


Q ss_pred             CeEEE-ecCCccccCCceEEEEEeccchhhHHHHHHHH-Hhc-CCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCC
Q 015158          237 PVRIL-VKRDELTLEGIKQFHVNVEKEEWKLETLCDLY-ETL-AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMD  313 (412)
Q Consensus       237 ~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~-~~~-~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~  313 (412)
                      .+... ............   ........+...+.+-+ +.+ .+.++||.+.|++..+.+++.|.+.+++..++++...
T Consensus       386 ~Vv~IPtnkp~~R~d~~d---~iy~t~~~k~~Aii~ei~~~~~~GrPVLVgt~sI~~SE~ls~~L~~~gI~h~vLNAk~~  462 (764)
T PRK12326        386 GVSVIPPNKPNIREDEAD---RVYATAAEKNDAIVEHIAEVHETGQPVLVGTHDVAESEELAERLRAAGVPAVVLNAKND  462 (764)
T ss_pred             cEEECCCCCCceeecCCC---ceEeCHHHHHHHHHHHHHHHHHcCCCEEEEeCCHHHHHHHHHHHHhCCCcceeeccCch
Confidence            43221 111111111111   11222334554444433 333 5579999999999999999999999999999998744


Q ss_pred             HHHHHHHHHHHhcC-CCcEEEEcCCCcCCCCCC---------------CCCEEEEccCCCChhhHHHhhhhcccCCCCce
Q 015158          314 QNTRDIIMREFRSG-SSRVLITTDLLARGIDVQ---------------QVSLVINYDLPTQPENYLHRIGRSGRFGRKGV  377 (412)
Q Consensus       314 ~~~r~~~~~~f~~g-~~~vlv~t~~~~~G~d~~---------------~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~  377 (412)
                      ..+ ..++.  +.| ...|.|+|+++++|.|+.               +--|||....+.|...-.|..||+||-|.+|.
T Consensus       463 ~~E-A~IIa--~AG~~gaVTIATNMAGRGTDIkLg~~~~~~~~~V~~~GGLhVIgTerheSrRID~QLrGRaGRQGDpGs  539 (764)
T PRK12326        463 AEE-ARIIA--EAGKYGAVTVSTQMAGRGTDIRLGGSDEADRDRVAELGGLHVIGTGRHRSERLDNQLRGRAGRQGDPGS  539 (764)
T ss_pred             HhH-HHHHH--hcCCCCcEEEEecCCCCccCeecCCCcccchHHHHHcCCcEEEeccCCchHHHHHHHhcccccCCCCCc
Confidence            333 33333  355 445999999999999987               33478989999999999999999999999999


Q ss_pred             EEEEeccCcHH
Q 015158          378 AINFVTRDDER  388 (412)
Q Consensus       378 ~~~~~~~~~~~  388 (412)
                      +..|++-.|.-
T Consensus       540 s~f~lSleDdl  550 (764)
T PRK12326        540 SVFFVSLEDDV  550 (764)
T ss_pred             eeEEEEcchhH
Confidence            99999887663

>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]

Probab=99.91  E-value=6.4e-24  Score=205.50  Aligned_cols=345  Identities=19%  Similarity=0.181  Sum_probs=232.6

Q ss_pred             CCCCCChhhhccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhh----cCccEEEECCCCCCchhHhHHHHHHhhcc
Q 015158           28 QDFFTSYDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFC----KGLDVIQQAQSGTGKTATFCSGILQQLDY  103 (412)
Q Consensus        28 ~~~~~~~~~~~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~----~~~~~lv~~~tGsGKT~~~~~~~~~~~~~  103 (412)
                      +..-..+.+....|..+..++.+...      .+||.||.+.++.++    .++++|+...+|-|||...+-.+......
T Consensus       343 p~~~~~~~~~rp~~~Kle~qp~~~~g------~~LRdyQLeGlNWl~~~W~~~~n~ILADEmgLgktvqti~fl~~l~~~  416 (1373)
T KOG0384|consen  343 PNKGCKYRPQRPRFRKLEKQPEYKGG------NELRDYQLEGLNWLLYSWYKRNNCILADEMGLGKTVQTITFLSYLFHS  416 (1373)
T ss_pred             CCCccccCccchhHHHhhcCcccccc------chhhhhhcccchhHHHHHHhcccceehhhcCCCcchHHHHHHHHHHHh
Confidence            33444444555677777666666555      459999999999876    47899999999999995543323222222


Q ss_pred             CCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHh----cC-----CCcEEEeChHHHHHHHHc
Q 015158          104 GLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL----SS-----GVHVVVGTPGRVFDMLRR  174 (412)
Q Consensus       104 ~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~-----~~~iii~T~~~l~~~~~~  174 (412)
                      ....+..|+|+|...+. .|.++|..+.   ..++.+++|+..........    ..     ..+++++|++.++.--. 
T Consensus       417 ~~~~gpflvvvplst~~-~W~~ef~~w~---~mn~i~y~g~~~sr~~i~~ye~~~~~~~~~lkf~~lltTye~~LkDk~-  491 (1373)
T KOG0384|consen  417 LQIHGPFLVVVPLSTIT-AWEREFETWT---DMNVIVYHGNLESRQLIRQYEFYHSSNTKKLKFNALLTTYEIVLKDKA-  491 (1373)
T ss_pred             hhccCCeEEEeehhhhH-HHHHHHHHHh---hhceeeeecchhHHHHHHHHHheecCCccccccceeehhhHHHhccHh-
Confidence            32345799999987754 4888888876   67888899887755543221    12     47899999999864322 


Q ss_pred             CCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcC--CCeEEEe----------
Q 015158          175 QSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMN--KPVRILV----------  242 (412)
Q Consensus       175 ~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~--~~~~~~~----------  242 (412)
                       -+..-.+.++++||||++-+..  ..+...+..+.. ...+++|+||..+....+..++.  .|..+..          
T Consensus       492 -~L~~i~w~~~~vDeahrLkN~~--~~l~~~l~~f~~-~~rllitgTPlQNsikEL~sLl~Fl~P~kf~~~~~f~~~~~~  567 (1373)
T KOG0384|consen  492 -ELSKIPWRYLLVDEAHRLKNDE--SKLYESLNQFKM-NHRLLITGTPLQNSLKELWSLLHFLMPGKFDSWDEFLEEFDE  567 (1373)
T ss_pred             -hhccCCcceeeecHHhhcCchH--HHHHHHHHHhcc-cceeeecCCCccccHHHHHHHhcccCCCCCCcHHHHHHhhcc
Confidence             2223367899999999987654  344444555543 34688999986432222222211  0000000          


Q ss_pred             -----------------------cCCccccCCceE---------------------------------------------
Q 015158          243 -----------------------KRDELTLEGIKQ---------------------------------------------  254 (412)
Q Consensus       243 -----------------------~~~~~~~~~~~~---------------------------------------------  254 (412)
                                             ..+...++....                                             
T Consensus       568 ~~e~~~~~L~~~L~P~~lRr~kkdvekslp~k~E~IlrVels~lQk~yYk~ILtkN~~~LtKG~~g~~~~lLNimmELkK  647 (1373)
T KOG0384|consen  568 ETEEQVRKLQQILKPFLLRRLKKDVEKSLPPKEETILRVELSDLQKQYYKAILTKNFSALTKGAKGSTPSLLNIMMELKK  647 (1373)
T ss_pred             hhHHHHHHHHHHhhHHHHHHHHhhhccCCCCCcceEEEeehhHHHHHHHHHHHHhhHHHHhccCCCCCchHHHHHHHHHH
Confidence                                   000000111111                                             


Q ss_pred             ----EEEEeccchhh---------HHHHHHHH-------------Hhc--CCCcEEEEEcchhHHHHHHHHHhcCCCeeE
Q 015158          255 ----FHVNVEKEEWK---------LETLCDLY-------------ETL--AITQSVIFVNTRRKVDWLTDKMRSRDHTVS  306 (412)
Q Consensus       255 ----~~~~~~~~~~~---------~~~l~~~~-------------~~~--~~~k~lif~~~~~~~~~~~~~L~~~~~~~~  306 (412)
                          .++.-...+..         ...+..++             ...  .+.++|||.+-+.-.+-++++|..+++...
T Consensus       648 ccNHpyLi~gaee~~~~~~~~~~~d~~L~~lI~sSGKlVLLDKLL~rLk~~GHrVLIFSQMVRmLDIL~eYL~~r~ypfQ  727 (1373)
T KOG0384|consen  648 CCNHPYLIKGAEEKILGDFRDKMRDEALQALIQSSGKLVLLDKLLPRLKEGGHRVLIFSQMVRMLDILAEYLSLRGYPFQ  727 (1373)
T ss_pred             hcCCccccCcHHHHHHHhhhhcchHHHHHHHHHhcCcEEeHHHHHHHHhcCCceEEEhHHHHHHHHHHHHHHHHcCCcce
Confidence                11111000000         11223222             222  236899999999999999999999999999


Q ss_pred             EecCCCCHHHHHHHHHHHhcC---CCcEEEEcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccCCCCc--eEEEE
Q 015158          307 ATHGDMDQNTRDIIMREFRSG---SSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKG--VAINF  381 (412)
Q Consensus       307 ~~~~~~~~~~r~~~~~~f~~g---~~~vlv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g--~~~~~  381 (412)
                      .+.|...-+.|.+.++.|...   ...+|+||.+.+-|||+..+++||+|+..|++..=+|+..|++|.|+..  .+|-+
T Consensus       728 RLDGsvrgelRq~AIDhFnap~SddFvFLLSTRAGGLGINLatADTVIIFDSDWNPQNDLQAqARaHRIGQkk~VnVYRL  807 (1373)
T KOG0384|consen  728 RLDGSVRGELRQQAIDHFNAPDSDDFVFLLSTRAGGLGINLATADTVIIFDSDWNPQNDLQAQARAHRIGQKKHVNVYRL  807 (1373)
T ss_pred             eccCCcchHHHHHHHHhccCCCCCceEEEEecccCcccccccccceEEEeCCCCCcchHHHHHHHHHhhcccceEEEEEE
Confidence            999999999999999999973   5678999999999999999999999999999999999999999999875  47777


Q ss_pred             eccCcH
Q 015158          382 VTRDDE  387 (412)
Q Consensus       382 ~~~~~~  387 (412)
                      ++.+..
T Consensus       808 VTk~Tv  813 (1373)
T KOG0384|consen  808 VTKNTV  813 (1373)
T ss_pred             ecCCch
Confidence            877633

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

Probab=99.91  E-value=1.8e-21  Score=185.39  Aligned_cols=315  Identities=18%  Similarity=0.136  Sum_probs=201.8

Q ss_pred             CChHHHHhhhhhhhcC----------ccEEEECCCCCCchhHhHHHHHHhhccCCCc-----eeEEEEcCCHHHHHHHHH
Q 015158           61 KPSAIQQRGIVPFCKG----------LDVIQQAQSGTGKTATFCSGILQQLDYGLVE-----CQALVLAPTRELAQQIEK  125 (412)
Q Consensus        61 ~l~~~Q~~a~~~~~~~----------~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~-----~~~lil~P~~~L~~q~~~  125 (412)
                      .++|||++.+.-+.++          ..+++...+|+|||+..+..+...+... +.     .+.|||+| ..|+..|.+
T Consensus       238 ~LrPHQ~EG~~FL~knl~g~~~~~~~~GCImAd~~GlGKTlq~IsflwtlLrq~-P~~~~~~~k~lVV~P-~sLv~nWkk  315 (776)
T KOG0390|consen  238 ILRPHQREGFEFLYKNLAGLIRPKNSGGCIMADEPGLGKTLQCISFIWTLLRQF-PQAKPLINKPLVVAP-SSLVNNWKK  315 (776)
T ss_pred             hcCchHHHHHHHHHhhhhcccccCCCCceEeeCCCCcchHHHHHHHHHHHHHhC-cCccccccccEEEcc-HHHHHHHHH
Confidence            4899999999887752          3468889999999988766666555543 44     68999999 588999999


Q ss_pred             HHHHhhcccCcEEEEEEcCcchHH--HHHH-----hcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCc
Q 015158          126 VMRALGDYLGVKVHACVGGTSVRE--DQRI-----LSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGF  198 (412)
Q Consensus       126 ~~~~~~~~~~~~~~~~~~~~~~~~--~~~~-----~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~  198 (412)
                      +|.+|.....+....+.+......  ...+     ..-...|.+.+++.+......  +....++++|+||.|..-+.. 
T Consensus       316 EF~KWl~~~~i~~l~~~~~~~~~w~~~~sil~~~~~~~~~~vli~sye~~~~~~~~--il~~~~glLVcDEGHrlkN~~-  392 (776)
T KOG0390|consen  316 EFGKWLGNHRINPLDFYSTKKSSWIKLKSILFLGYKQFTTPVLIISYETASDYCRK--ILLIRPGLLVCDEGHRLKNSD-  392 (776)
T ss_pred             HHHHhccccccceeeeecccchhhhhhHHHHHhhhhheeEEEEeccHHHHHHHHHH--HhcCCCCeEEECCCCCccchh-
Confidence            999997765677777777665300  0111     112346889999999765543  334578999999999977665 


Q ss_pred             HHHHHHHHHhCCCCceEEEEeecCChH-HHHHHHHh-----------------cCCCe----------------------
Q 015158          199 KDQIYDIFQLLPPKIQVGVFSATMPPE-ALEITRKF-----------------MNKPV----------------------  238 (412)
Q Consensus       199 ~~~~~~i~~~~~~~~~~i~~SAT~~~~-~~~~~~~~-----------------~~~~~----------------------  238 (412)
                       ..+...+..+. -.+.|++|+||-.+ ..+.+.-+                 +..+.                      
T Consensus       393 -s~~~kaL~~l~-t~rRVLLSGTp~QNdl~EyFnlL~fvrP~~Lgs~~sf~k~~~~~i~~~~~~~~s~e~~~~~~rl~eL  470 (776)
T KOG0390|consen  393 -SLTLKALSSLK-TPRRVLLTGTPIQNDLKEYFNLLDFVRPGFLGSISSFKKKFEIPILRGRDADASEEDREREERLQEL  470 (776)
T ss_pred             -hHHHHHHHhcC-CCceEEeeCCcccccHHHHHHHHhhcChhhccchHHHHHHhhcccccccCCCcchhhhhhHHHHHHH
Confidence             44555555554 44579999998421 11111100                 00000                      


Q ss_pred             --------EEEec-CCccccCCceEEEEEeccchh---------------------------------------------
Q 015158          239 --------RILVK-RDELTLEGIKQFHVNVEKEEW---------------------------------------------  264 (412)
Q Consensus       239 --------~~~~~-~~~~~~~~~~~~~~~~~~~~~---------------------------------------------  264 (412)
                              ..+.. ......|....+.+.+....-                                             
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 000011112222222221110                                             


Q ss_pred             ----------------------------hHHHHHHHHHhc---CCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCC
Q 015158          265 ----------------------------KLETLCDLYETL---AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMD  313 (412)
Q Consensus       265 ----------------------------~~~~l~~~~~~~---~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~  313 (412)
                                                  +...|..++...   ...++.+..|-....+.+....+-+|..+..++|.++
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                                        111111221111   1112233333334444444444445999999999999


Q ss_pred             HHHHHHHHHHHhcCCC--c-EEEEcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEe
Q 015158          314 QNTRDIIMREFRSGSS--R-VLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFV  382 (412)
Q Consensus       314 ~~~r~~~~~~f~~g~~--~-vlv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~  382 (412)
                      ..+|..+++.|++...  . +|.++.+.+.|+++-+++.||++++.|+++.-.|+++|+-|.|+...|++|-
T Consensus       631 ~~qRq~~vd~FN~p~~~~~vfLlSsKAgg~GinLiGAsRlil~D~dWNPa~d~QAmaR~~RdGQKk~v~iYr  702 (776)
T KOG0390|consen  631 IKQRQKLVDTFNDPESPSFVFLLSSKAGGEGLNLIGASRLILFDPDWNPAVDQQAMARAWRDGQKKPVYIYR  702 (776)
T ss_pred             hHHHHHHHHhccCCCCCceEEEEecccccCceeecccceEEEeCCCCCchhHHHHHHHhccCCCcceEEEEE
Confidence            9999999999998432  3 5556789999999999999999999999999999999999999988777654

>KOG0925 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.90  E-value=1.9e-22  Score=177.93  Aligned_cols=327  Identities=15%  Similarity=0.196  Sum_probs=221.7

Q ss_pred             ccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCH
Q 015158           38 YDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTR  117 (412)
Q Consensus        38 ~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~  117 (412)
                      ..+|.+.+.++.+.+.|+.+.-...+..+.+.+..+..++-+++++.||||||...-.+.+.......  ..+....|.+
T Consensus        24 ~Npf~~~p~s~rY~~ilk~R~~LPvw~~k~~F~~~l~~nQ~~v~vGetgsGKttQiPq~~~~~~~~~~--~~v~CTQprr  101 (699)
T KOG0925|consen   24 INPFNGKPYSQRYYDILKKRRELPVWEQKEEFLKLLLNNQIIVLVGETGSGKTTQIPQFVLEYELSHL--TGVACTQPRR  101 (699)
T ss_pred             cCCCCCCcCcHHHHHHHHHHhcCchHHhHHHHHHHHhcCceEEEEecCCCCccccCcHHHHHHHHhhc--cceeecCchH
Confidence            78999999999999999987666567777788888888999999999999999887766666544332  3466677888


Q ss_pred             HHHHHHHHHHHH-hhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhh--
Q 015158          118 ELAQQIEKVMRA-LGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEML--  194 (412)
Q Consensus       118 ~L~~q~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~--  194 (412)
                      .-+.+.+.+... +-...|-+|.....      ..++...+.-.-+||.++|++..-...+ +..+++||+||||+=.  
T Consensus       102 vaamsva~RVadEMDv~lG~EVGysIr------fEdC~~~~T~Lky~tDgmLlrEams~p~-l~~y~viiLDeahERtlA  174 (699)
T KOG0925|consen  102 VAAMSVAQRVADEMDVTLGEEVGYSIR------FEDCTSPNTLLKYCTDGMLLREAMSDPL-LGRYGVIILDEAHERTLA  174 (699)
T ss_pred             HHHHHHHHHHHHHhccccchhcccccc------ccccCChhHHHHHhcchHHHHHHhhCcc-cccccEEEechhhhhhHH
Confidence            777766655443 21112222221111      1111112223446888888776655443 4679999999999722  


Q ss_pred             ccCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhHHHHHHHHH
Q 015158          195 SRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYE  274 (412)
Q Consensus       195 ~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  274 (412)
                      .......++.+.... +..++|.||||+..   .-++.++++...+.+..    ...++.++......+.-...+..+++
T Consensus       175 TDiLmGllk~v~~~r-pdLk~vvmSatl~a---~Kfq~yf~n~Pll~vpg----~~PvEi~Yt~e~erDylEaairtV~q  246 (699)
T KOG0925|consen  175 TDILMGLLKEVVRNR-PDLKLVVMSATLDA---EKFQRYFGNAPLLAVPG----THPVEIFYTPEPERDYLEAAIRTVLQ  246 (699)
T ss_pred             HHHHHHHHHHHHhhC-CCceEEEeecccch---HHHHHHhCCCCeeecCC----CCceEEEecCCCChhHHHHHHHHHHH
Confidence            222334455555555 58999999999864   45666777766666554    12344455544443433334444444


Q ss_pred             hc---CCCcEEEEEcchhHHHHHHHHHhcC---------CCeeEEecCCCCHHHHHHHHHHHh---cC--CCcEEEEcCC
Q 015158          275 TL---AITQSVIFVNTRRKVDWLTDKMRSR---------DHTVSATHGDMDQNTRDIIMREFR---SG--SSRVLITTDL  337 (412)
Q Consensus       275 ~~---~~~k~lif~~~~~~~~~~~~~L~~~---------~~~~~~~~~~~~~~~r~~~~~~f~---~g--~~~vlv~t~~  337 (412)
                      -+   ..|.++||..+.++.+..++.+...         ...+..+|    +.++..+++-..   +|  ..+|+|+|++
T Consensus       247 ih~~ee~GDilvFLtgeeeIe~aC~~i~re~~~L~~~~g~l~v~PLy----P~~qq~iFep~p~~~~~~~~RkvVvstni  322 (699)
T KOG0925|consen  247 IHMCEEPGDILVFLTGEEEIEDACRKISREVDNLGPQVGPLKVVPLY----PAQQQRIFEPAPEKRNGAYGRKVVVSTNI  322 (699)
T ss_pred             HHhccCCCCEEEEecCHHHHHHHHHHHHHHHHhhccccCCceEEecC----chhhccccCCCCcccCCCccceEEEEecc
Confidence            33   4588999999999999999988743         23566666    223333332221   22  3579999999


Q ss_pred             CcCCCCCCCCCEEEEcc------------------CCCChhhHHHhhhhcccCCCCceEEEEeccCc
Q 015158          338 LARGIDVQQVSLVINYD------------------LPTQPENYLHRIGRSGRFGRKGVAINFVTRDD  386 (412)
Q Consensus       338 ~~~G~d~~~~~~vi~~~------------------~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~  386 (412)
                      .++.+.++++.+||.-+                  .|.|.++..||.||+||. .+|+|+.++++..
T Consensus       323 aetsltidgiv~VIDpGf~kqkVYNPRIRvesllv~PISkasA~qR~gragrt-~pGkcfrLYte~~  388 (699)
T KOG0925|consen  323 AETSLTIDGIVFVIDPGFSKQKVYNPRIRVESLLVSPISKASAQQRAGRAGRT-RPGKCFRLYTEEA  388 (699)
T ss_pred             hheeeeeccEEEEecCchhhhcccCcceeeeeeeeccchHhHHHHHhhhccCC-CCCceEEeecHHh
Confidence            99999999999999644                  367899999999999999 7999999998753

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=99.90  E-value=2.8e-22  Score=194.16  Aligned_cols=124  Identities=19%  Similarity=0.241  Sum_probs=109.5

Q ss_pred             hhhHHHHHHHHHhc--CCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcC
Q 015158          263 EWKLETLCDLYETL--AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLAR  340 (412)
Q Consensus       263 ~~~~~~l~~~~~~~--~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~  340 (412)
                      ..+...+.+.+...  .+.++||||+|++.++.+++.|.+.++.+.++|+  .+.+|+..+..|..+...|+|+|+++++
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            45677777777554  5689999999999999999999999999999997  5778999999999999999999999999


Q ss_pred             CCCCC---CCC-----EEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHH
Q 015158          341 GIDVQ---QVS-----LVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDER  388 (412)
Q Consensus       341 G~d~~---~~~-----~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~  388 (412)
                      |+|++   .+.     +||.+..|.|...+.|++||+||.|.+|.+..|++..|.-
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   343     4488889999999999999999999999999999887664

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=99.90  E-value=5.9e-22  Score=191.22  Aligned_cols=316  Identities=17%  Similarity=0.197  Sum_probs=215.7

Q ss_pred             CCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcE
Q 015158           58 GFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVK  137 (412)
Q Consensus        58 ~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~  137 (412)
                      |.. |++.|.-.--.+.+|+  +..+.||+|||+++.++++.....+   ..+-+++|+..|+.+-++.+..+....|+.
T Consensus        80 Gm~-~ydVQliGg~~Lh~G~--iaEM~TGEGKTLvA~l~a~l~al~G---~~VhvvT~ndyLA~RD~e~m~~l~~~lGl~  153 (913)
T PRK13103         80 GMR-HFDVQLIGGMTLHEGK--IAEMRTGEGKTLVGTLAVYLNALSG---KGVHVVTVNDYLARRDANWMRPLYEFLGLS  153 (913)
T ss_pred             CCC-cchhHHHhhhHhccCc--cccccCCCCChHHHHHHHHHHHHcC---CCEEEEeCCHHHHHHHHHHHHHHhcccCCE
Confidence            555 8888888777776665  8899999999999988887665554   479999999999999999999999999999


Q ss_pred             EEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCC-------CCCceEEEEeCCchhh-ccC------------
Q 015158          138 VHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLR-------PDNIRIFVLDEADEML-SRG------------  197 (412)
Q Consensus       138 ~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~-------~~~~~~iiiDE~h~~~-~~~------------  197 (412)
                      +.++.++.+........  .++|+++|...|---+.+....       .+.+.++|+||+|.++ +..            
T Consensus       154 v~~i~~~~~~~err~~Y--~~dI~YGT~~e~gFDYLrD~~~~~~~~~vqr~l~~aIVDEvDsiLIDEArtPLIISg~~~~  231 (913)
T PRK13103        154 VGIVTPFQPPEEKRAAY--AADITYGTNNEFGFDYLRDNMAFSLDDKFQRELNFAVIDEVDSILIDEARTPLIISGQAED  231 (913)
T ss_pred             EEEECCCCCHHHHHHHh--cCCEEEEcccccccchhhccceechhhhcccccceeEechhhheeccccCCceeecCCCcc
Confidence            99998877655444333  3799999988862222222222       3678899999999753 110            


Q ss_pred             ---cHHHHHHHHHhC-----------------------------------------------------------------
Q 015158          198 ---FKDQIYDIFQLL-----------------------------------------------------------------  209 (412)
Q Consensus       198 ---~~~~~~~i~~~~-----------------------------------------------------------------  209 (412)
                         ....+..+...+                                                                 
T Consensus       232 ~~~~y~~~~~~v~~L~~~~~~~~~~~~~~~~y~idek~~~v~LTe~G~~~~e~~~~~~~i~~~~~~ly~~~~~~~~~~i~  311 (913)
T PRK13103        232 SSKLYIEINRLIPRLKQHIEEVEGQVTQEGHFTIDEKTRQVELNEAGHQFIEEMLTQAGLLAEGESLYSAHNLGLLTHVY  311 (913)
T ss_pred             chHHHHHHHHHHHHHHhhhhccccccCCCCCeEEEcCCCeeeechHHHHHHHHHhhhCCCcccchhccChhhhHHHHHHH
Confidence               000011111000                                                                 


Q ss_pred             ---C-------------------------------------------------------------------CCceEEEEe
Q 015158          210 ---P-------------------------------------------------------------------PKIQVGVFS  219 (412)
Q Consensus       210 ---~-------------------------------------------------------------------~~~~~i~~S  219 (412)
                         .                                                                   --.++.|||
T Consensus       312 ~AL~A~~lf~~d~dYiV~dg~V~IVDe~TGR~m~grrwsdGLHQaIEaKE~v~I~~e~~t~AsIT~QnfFr~Y~kLsGMT  391 (913)
T PRK13103        312 AGLRAHKLFHRNVEYIVQDGQVLLIDEHTGRTMPGRRLSEGLHQAIEAKENLNIQAESQTLASTTFQNYFRLYNKLSGMT  391 (913)
T ss_pred             HHHHHHHHHhcCCcEEEECCEEEEEECCCCCcCCCCccchHHHHHHHHHcCCCcCCCceeEEeehHHHHHHhcchhccCC
Confidence               0                                                                   012566677


Q ss_pred             ecCChHHHHHHHHhcCCCeEE-EecCCccccCCceEEEEEeccchhhHHHHHHHHHh-c-CCCcEEEEEcchhHHHHHHH
Q 015158          220 ATMPPEALEITRKFMNKPVRI-LVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYET-L-AITQSVIFVNTRRKVDWLTD  296 (412)
Q Consensus       220 AT~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~-~~~k~lif~~~~~~~~~~~~  296 (412)
                      +|......+ +...++-.+.. ....... .......  .......+...+.+-+.. + .+.++||-+.|++..+.+++
T Consensus       392 GTa~te~~E-f~~iY~l~Vv~IPTnkP~~-R~D~~d~--vy~t~~eK~~Ai~~ei~~~~~~GrPVLVGT~SVe~SE~ls~  467 (913)
T PRK13103        392 GTADTEAFE-FRQIYGLDVVVIPPNKPLA-RKDFNDL--VYLTAEEKYAAIITDIKECMALGRPVLVGTATIETSEHMSN  467 (913)
T ss_pred             CCCHHHHHH-HHHHhCCCEEECCCCCCcc-cccCCCe--EEcCHHHHHHHHHHHHHHHHhCCCCEEEEeCCHHHHHHHHH
Confidence            776544333 33333333322 2222111 1111111  122223455554444433 3 45799999999999999999


Q ss_pred             HHhcCCCeeEEecCCCCHHHHHHHHHHHhcC-CCcEEEEcCCCcCCCCCC------------------------------
Q 015158          297 KMRSRDHTVSATHGDMDQNTRDIIMREFRSG-SSRVLITTDLLARGIDVQ------------------------------  345 (412)
Q Consensus       297 ~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g-~~~vlv~t~~~~~G~d~~------------------------------  345 (412)
                      .|.+.++...+++......+ ..|+.  ..| ...|.|+|+++++|.|+.                              
T Consensus       468 ~L~~~gi~h~VLNAk~~~~E-A~IIa--~AG~~GaVTIATNMAGRGTDIkLg~n~~~~~~~~~~~~~~~~~~~~~~~~~~  544 (913)
T PRK13103        468 LLKKEGIEHKVLNAKYHEKE-AEIIA--QAGRPGALTIATNMAGRGTDILLGGNWEVEVAALENPTPEQIAQIKADWQKR  544 (913)
T ss_pred             HHHHcCCcHHHhccccchhH-HHHHH--cCCCCCcEEEeccCCCCCCCEecCCchHHHHHhhhhhhHHHHHHHHHHHHhH
Confidence            99999999888887644333 23333  456 456999999999999985                              


Q ss_pred             -------CCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHH
Q 015158          346 -------QVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDER  388 (412)
Q Consensus       346 -------~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~  388 (412)
                             +--+||....+.|...-.|..||+||-|.+|.+-.|++-.|.-
T Consensus       545 ~e~V~e~GGLhVIgTerheSrRID~QLrGRaGRQGDPGsS~f~lSlED~L  594 (913)
T PRK13103        545 HQQVIEAGGLHVIASERHESRRIDNQLRGRAGRQGDPGSSRFYLSLEDSL  594 (913)
T ss_pred             HHHHHHcCCCEEEeeccCchHHHHHHhccccccCCCCCceEEEEEcCcHH
Confidence                   3457888999999999999999999999999999999886653

>COG4889 Predicted helicase [General function prediction only]

Probab=99.90  E-value=7e-24  Score=198.55  Aligned_cols=358  Identities=18%  Similarity=0.190  Sum_probs=210.4

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcC----ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEc
Q 015158           39 DTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKG----LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLA  114 (412)
Q Consensus        39 ~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~----~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~  114 (412)
                      -+|+.+.. .++...+.-..-.+|||||+.|+....++    .+.-+.++||+|||++.+- +...+..    .++|+++
T Consensus       140 IDW~~f~p-~e~~~nl~l~~~kk~R~hQq~Aid~a~~~F~~n~RGkLIMAcGTGKTfTsLk-isEala~----~~iL~Lv  213 (1518)
T COG4889         140 IDWDIFDP-TELQDNLPLKKPKKPRPHQQTAIDAAKEGFSDNDRGKLIMACGTGKTFTSLK-ISEALAA----ARILFLV  213 (1518)
T ss_pred             CChhhcCc-cccccccccCCCCCCChhHHHHHHHHHhhcccccCCcEEEecCCCccchHHH-HHHHHhh----hheEeec
Confidence            44555433 34455555556667999999999998875    4567889999999998753 3344433    4899999


Q ss_pred             CCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHH-------------------------HHHhcCCCcEEEeChHHHH
Q 015158          115 PTRELAQQIEKVMRALGDYLGVKVHACVGGTSVRED-------------------------QRILSSGVHVVVGTPGRVF  169 (412)
Q Consensus       115 P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------------------------~~~~~~~~~iii~T~~~l~  169 (412)
                      |+.+|..|+.+++..-.. ..+.....+++......                         ......+--|+++||+++.
T Consensus       214 PSIsLLsQTlrew~~~~~-l~~~a~aVcSD~kvsrs~eDik~sdl~~p~sT~~~~il~~~~~~~k~~~~~vvFsTYQSl~  292 (1518)
T COG4889         214 PSISLLSQTLREWTAQKE-LDFRASAVCSDDKVSRSAEDIKASDLPIPVSTDLEDILSEMEHRQKANGLTVVFSTYQSLP  292 (1518)
T ss_pred             chHHHHHHHHHHHhhccC-ccceeEEEecCccccccccccccccCCCCCcccHHHHHHHHHHhhccCCcEEEEEcccchH
Confidence            999999999988876422 23333333333321110                         0112234469999999998


Q ss_pred             HHHHcCCCCCCCceEEEEeCCchhhccCcH----HHHHHHHHhC-CCCceEEEEeecCChHHHHHHHHhcCC-CeEEEec
Q 015158          170 DMLRRQSLRPDNIRIFVLDEADEMLSRGFK----DQIYDIFQLL-PPKIQVGVFSATMPPEALEITRKFMNK-PVRILVK  243 (412)
Q Consensus       170 ~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~----~~~~~i~~~~-~~~~~~i~~SAT~~~~~~~~~~~~~~~-~~~~~~~  243 (412)
                      ..-+....-+..+++||+||||+...-.+.    ..+.++-+.- -+..+.+.|||||.--.+..-..--.. .....+.
T Consensus       293 ~i~eAQe~G~~~fDliicDEAHRTtGa~~a~dd~saFt~vHs~~niKa~kRlYmTATPkiy~eS~K~kAkd~s~~l~SMD  372 (1518)
T COG4889         293 RIKEAQEAGLDEFDLIICDEAHRTTGATLAGDDKSAFTRVHSDQNIKAAKRLYMTATPKIYSESSKAKAKDHSAELSSMD  372 (1518)
T ss_pred             HHHHHHHcCCCCccEEEecchhccccceecccCcccceeecCcchhHHHHhhhcccCchhhchhhhhhhhhccceeeccc
Confidence            877666666788999999999985432111    1111111000 013457899999842110000000000 0000000


Q ss_pred             CCc-------------cc----cCCceEEEEEeccc---------------hhhHHHHHHH-------HHhc--------
Q 015158          244 RDE-------------LT----LEGIKQFHVNVEKE---------------EWKLETLCDL-------YETL--------  276 (412)
Q Consensus       244 ~~~-------------~~----~~~~~~~~~~~~~~---------------~~~~~~l~~~-------~~~~--------  276 (412)
                      .+.             ..    ....+.++..++..               .-..+....+       .+..        
T Consensus       373 De~~fGeef~rl~FgeAv~rdlLTDYKVmvlaVd~~~i~~~~~~~~~~~~~~L~~dd~~kIvG~wnGlakr~g~~n~~~~  452 (1518)
T COG4889         373 DELTFGEEFHRLGFGEAVERDLLTDYKVMVLAVDKEVIAGVLQSVLSGPSKGLALDDVSKIVGCWNGLAKRNGEDNDLKN  452 (1518)
T ss_pred             hhhhhchhhhcccHHHHHHhhhhccceEEEEEechhhhhhhhhhhccCcccccchhhhhhhhhhhhhhhhhccccccccC
Confidence            000             00    00111112221110               1111111111       1111        


Q ss_pred             ------CCCcEEEEEcchhHHHHHHHHHhc---------------CCCeeEEecCCCCHHHHHHHHHH---HhcCCCcEE
Q 015158          277 ------AITQSVIFVNTRRKVDWLTDKMRS---------------RDHTVSATHGDMDQNTRDIIMRE---FRSGSSRVL  332 (412)
Q Consensus       277 ------~~~k~lif~~~~~~~~~~~~~L~~---------------~~~~~~~~~~~~~~~~r~~~~~~---f~~g~~~vl  332 (412)
                            +..+.+-||.+++....+++.+..               ..+.+..+.|.|+..+|...+..   |...+.+||
T Consensus       453 ~~~d~ap~~RAIaF~k~I~tSK~i~~sFe~Vve~Y~~Elk~d~~nL~iSi~HvDGtmNal~R~~l~~l~~~~~~neckIl  532 (1518)
T COG4889         453 IKADTAPMQRAIAFAKDIKTSKQIAESFETVVEAYDEELKKDFKNLKISIDHVDGTMNALERLDLLELKNTFEPNECKIL  532 (1518)
T ss_pred             CcCCchHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHhcCCCceEEeecccccccHHHHHHHHhccCCCCcchheee
Confidence                  113568899888777766655532               13456677888998888554442   233467788


Q ss_pred             EEcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccCCC-CceEEEEec---------------cCcHHHHHHHHHH
Q 015158          333 ITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGR-KGVAINFVT---------------RDDERMLFDIQKF  396 (412)
Q Consensus       333 v~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~-~g~~~~~~~---------------~~~~~~~~~~~~~  396 (412)
                      -...++++|+|+|.++.||++++..|+.+.+|.+||+.|..+ ...+|++++               ..+.+.+..+.+.
T Consensus       533 SNaRcLSEGVDVPaLDsViFf~pr~smVDIVQaVGRVMRKa~gK~yGYIILPIalpegi~p~~~l~~n~nFk~VWqVlnA  612 (1518)
T COG4889         533 SNARCLSEGVDVPALDSVIFFDPRSSMVDIVQAVGRVMRKAKGKKYGYIILPIALPEGIKPLDELVNNTNFKNVWQVLKA  612 (1518)
T ss_pred             ccchhhhcCCCccccceEEEecCchhHHHHHHHHHHHHHhCcCCccceEEEEeccCCCCCchHHHhcCccHHHHHHHHHH
Confidence            888899999999999999999999999999999999999743 234555553               2355666667777


Q ss_pred             hcccccc
Q 015158          397 YNVVIEE  403 (412)
Q Consensus       397 ~~~~~~~  403 (412)
                      ++.+.+.
T Consensus       613 LRShD~a  619 (1518)
T COG4889         613 LRSHDEA  619 (1518)
T ss_pred             HHhcCHH
Confidence            7665553

>KOG1000 consensus Chromatin remodeling protein HARP/SMARCAL1, DEAD-box superfamily [Chromatin structure and dynamics]

Probab=99.90  E-value=3.3e-21  Score=170.44  Aligned_cols=327  Identities=14%  Similarity=0.170  Sum_probs=218.9

Q ss_pred             CCChHHHHhhhhhhh-cCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEE
Q 015158           60 EKPSAIQQRGIVPFC-KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKV  138 (412)
Q Consensus        60 ~~l~~~Q~~a~~~~~-~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~  138 (412)
                      ..+-|+|++.+...+ .|.++++...+|-|||..++..+......+    ..|||||. ++...|++.+..|.+...- +
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            457899999998854 578899999999999998865444333333    69999995 6677799999998765432 4


Q ss_pred             EEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEE
Q 015158          139 HACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVF  218 (412)
Q Consensus       139 ~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~  218 (412)
                      ....++.....+   ......|.|.+++.+..+-.  .+....+++||+||+|.+.+.. ....+.+...+..-.++|++
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 FVVDKSSDPLPD---VCTSNTVAIVSYEQLSLLHD--ILKKEKYRVVIFDESHMLKDSK-TKRTKAATDLLKVAKHVILL  344 (689)
T ss_pred             EEEecccCCccc---cccCCeEEEEEHHHHHHHHH--HHhcccceEEEEechhhhhccc-hhhhhhhhhHHHHhhheEEe
Confidence            444433332211   12335799999999865433  2333568999999999876554 34455555555566779999


Q ss_pred             eecCCh-------------------HHHHHHHHhcCC-CeEEEecCC--------------------------ccccCCc
Q 015158          219 SATMPP-------------------EALEITRKFMNK-PVRILVKRD--------------------------ELTLEGI  252 (412)
Q Consensus       219 SAT~~~-------------------~~~~~~~~~~~~-~~~~~~~~~--------------------------~~~~~~~  252 (412)
                      |+||.-                   +..++...+... ...+-.+..                          ...++.-
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            999841                   111111111110 000000000                          0011221


Q ss_pred             eEEEEEeccc------------------------------------hhhHHHHHHHHHh------cCCCcEEEEEcchhH
Q 015158          253 KQFHVNVEKE------------------------------------EWKLETLCDLYET------LAITQSVIFVNTRRK  290 (412)
Q Consensus       253 ~~~~~~~~~~------------------------------------~~~~~~l~~~~~~------~~~~k~lif~~~~~~  290 (412)
                      +...+.....                                    ..+...+.+.+..      ....|.+|||....-
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            2222211110                                    1123333344333      244689999999999


Q ss_pred             HHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcC-CCcE-EEEcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhhh
Q 015158          291 VDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSG-SSRV-LITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGR  368 (412)
Q Consensus       291 ~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g-~~~v-lv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR  368 (412)
                      .+.+...+.++++..+.+.|..++.+|....+.|+.. +..| +++..+.++|+++...+.|++.+++|++.-++|+-.|
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            9999999999999999999999999999999999875 4444 4566789999999999999999999999999999999


Q ss_pred             cccCCCCceEEEEecc----CcHHHHHHHHHHhc
Q 015158          369 SGRFGRKGVAINFVTR----DDERMLFDIQKFYN  398 (412)
Q Consensus       369 ~~R~g~~g~~~~~~~~----~~~~~~~~~~~~~~  398 (412)
                      +.|.|+...+.+++.-    -|+.....+.+.+.
T Consensus       585 aHRiGQkssV~v~ylvAKgT~Ddy~Wp~l~~KL~  618 (689)
T KOG1000|consen  585 AHRIGQKSSVFVQYLVAKGTADDYMWPMLQQKLD  618 (689)
T ss_pred             hhhccccceeeEEEEEecCchHHHHHHHHHHHHH
Confidence            9999998776555532    25555555555443

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

Probab=99.90  E-value=1.1e-21  Score=185.91  Aligned_cols=158  Identities=18%  Similarity=0.147  Sum_probs=115.1

Q ss_pred             ChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCc-EEEE
Q 015158           62 PSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGV-KVHA  140 (412)
Q Consensus        62 l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~-~~~~  140 (412)
                      |..||.+.+..+-.+.+++|++||.+|||.+...++=..+... ...-+++++|+++|+.|....+......... ....
T Consensus       512 Pd~WQ~elLDsvDr~eSavIVAPTSaGKTfisfY~iEKVLRes-D~~VVIyvaPtKaLVnQvsa~VyaRF~~~t~~rg~s  590 (1330)
T KOG0949|consen  512 PDEWQRELLDSVDRNESAVIVAPTSAGKTFISFYAIEKVLRES-DSDVVIYVAPTKALVNQVSANVYARFDTKTFLRGVS  590 (1330)
T ss_pred             CcHHHHHHhhhhhcccceEEEeeccCCceeccHHHHHHHHhhc-CCCEEEEecchHHHhhhhhHHHHHhhccCccccchh
Confidence            8889999999999999999999999999988766666555544 4456999999999999998777665422211 1111


Q ss_pred             EEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHc---CCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEE
Q 015158          141 CVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRR---QSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGV  217 (412)
Q Consensus       141 ~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~---~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~  217 (412)
                      +.|.-+  .+..+..-.++|+|+-|+-+...+..   ......++++||+||+|.+.+..-...+..+....  .++.++
T Consensus       591 l~g~lt--qEYsinp~nCQVLITvPecleslLlspp~~q~~cerIRyiIfDEVH~iG~~ed~l~~Eqll~li--~CP~L~  666 (1330)
T KOG0949|consen  591 LLGDLT--QEYSINPWNCQVLITVPECLESLLLSPPHHQKFCERIRYIIFDEVHLIGNEEDGLLWEQLLLLI--PCPFLV  666 (1330)
T ss_pred             hHhhhh--HHhcCCchhceEEEEchHHHHHHhcCchhhhhhhhcceEEEechhhhccccccchHHHHHHHhc--CCCeeE
Confidence            222221  23333334689999999999888776   33445788999999999988766555555555544  567999


Q ss_pred             EeecCCh
Q 015158          218 FSATMPP  224 (412)
Q Consensus       218 ~SAT~~~  224 (412)
                      +|||..+
T Consensus       667 LSATigN  673 (1330)
T KOG0949|consen  667 LSATIGN  673 (1330)
T ss_pred             EecccCC
Confidence            9999875

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=99.89  E-value=2.1e-20  Score=180.79  Aligned_cols=129  Identities=25%  Similarity=0.362  Sum_probs=112.2

Q ss_pred             hHHHHHHHHHhc--CCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCC
Q 015158          265 KLETLCDLYETL--AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGI  342 (412)
Q Consensus       265 ~~~~l~~~~~~~--~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~  342 (412)
                      ....+.+.+...  .+.+++|||++++.++.+++.|.+.|+.+..+|++++..+|.++++.|++|+++|+|||+.+++|+
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            444444444442  457899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCEEEEcc-----CCCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHH
Q 015158          343 DVQQVSLVINYD-----LPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQ  394 (412)
Q Consensus       343 d~~~~~~vi~~~-----~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~  394 (412)
                      |+|.+++|++++     .|.+...|+|++||+||. ..|.+++|.+..+..+...+.
T Consensus       507 DiP~v~lVvi~DadifG~p~~~~~~iqriGRagR~-~~G~vi~~~~~~~~~~~~ai~  562 (655)
T TIGR00631       507 DLPEVSLVAILDADKEGFLRSERSLIQTIGRAARN-VNGKVIMYADKITDSMQKAIE  562 (655)
T ss_pred             eeCCCcEEEEeCcccccCCCCHHHHHHHhcCCCCC-CCCEEEEEEcCCCHHHHHHHH
Confidence            999999999877     788999999999999998 689999999987654444443

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

>COG0556 UvrB Helicase subunit of the DNA excision repair complex [DNA replication, recombination, and repair]

Probab=99.89  E-value=1.2e-20  Score=168.76  Aligned_cols=169  Identities=24%  Similarity=0.288  Sum_probs=125.8

Q ss_pred             CceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccch-hhHHHHHHHHHhc-CCCcEEEEEcchh
Q 015158          212 KIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEE-WKLETLCDLYETL-AITQSVIFVNTRR  289 (412)
Q Consensus       212 ~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~l~~~~~~~-~~~k~lif~~~~~  289 (412)
                      ..|.|++||||++.-.+   .-.+..+.-.+.+....-+     ...+.+.. ...+.+.++.+.. .+.++||-+-+++
T Consensus       386 ~~q~i~VSATPg~~E~e---~s~~~vveQiIRPTGLlDP-----~ievRp~~~QvdDL~~EI~~r~~~~eRvLVTtLTKk  457 (663)
T COG0556         386 IPQTIYVSATPGDYELE---QSGGNVVEQIIRPTGLLDP-----EIEVRPTKGQVDDLLSEIRKRVAKNERVLVTTLTKK  457 (663)
T ss_pred             cCCEEEEECCCChHHHH---hccCceeEEeecCCCCCCC-----ceeeecCCCcHHHHHHHHHHHHhcCCeEEEEeehHH
Confidence            46899999999763222   1222222222222222111     12222222 2334444444432 4589999999999


Q ss_pred             HHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccC-----CCChhhHHH
Q 015158          290 KVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDL-----PTQPENYLH  364 (412)
Q Consensus       290 ~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~-----~~s~~~~~Q  364 (412)
                      -|+.+.++|.+.|+.+..+|++...-+|.++++..+.|+++|||+.+.+-+|+|+|.+..|.+++.     ..|..+++|
T Consensus       458 mAEdLT~Yl~e~gikv~YlHSdidTlER~eIirdLR~G~~DvLVGINLLREGLDiPEVsLVAIlDADKeGFLRse~SLIQ  537 (663)
T COG0556         458 MAEDLTEYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQ  537 (663)
T ss_pred             HHHHHHHHHHhcCceEEeeeccchHHHHHHHHHHHhcCCccEEEeehhhhccCCCcceeEEEEeecCccccccccchHHH
Confidence            999999999999999999999999999999999999999999999999999999999999988764     578999999


Q ss_pred             hhhhcccCCCCceEEEEeccCcHHH
Q 015158          365 RIGRSGRFGRKGVAINFVTRDDERM  389 (412)
Q Consensus       365 ~~GR~~R~g~~g~~~~~~~~~~~~~  389 (412)
                      .+||+.|- -.|.++++.+.-...+
T Consensus       538 tIGRAARN-~~GkvIlYAD~iT~sM  561 (663)
T COG0556         538 TIGRAARN-VNGKVILYADKITDSM  561 (663)
T ss_pred             HHHHHhhc-cCCeEEEEchhhhHHH
Confidence            99999997 5799998887754433

>KOG0926 consensus DEAH-box RNA helicase [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.88  E-value=1.1e-21  Score=182.33  Aligned_cols=308  Identities=17%  Similarity=0.191  Sum_probs=198.6

Q ss_pred             HhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccC---CCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEc
Q 015158           67 QRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYG---LVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVG  143 (412)
Q Consensus        67 ~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~---~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~  143 (412)
                      .++++.|..+.-++|+|.||||||+..-..++.+=...   ...+-+-|.-|++.-+-.++++...-....+..|.....
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            35677777788899999999999988766565542211   123457788899877777766554422224444444332


Q ss_pred             CcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccC--cHHHHHHHH---HhCC------CC
Q 015158          144 GTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRG--FKDQIYDIF---QLLP------PK  212 (412)
Q Consensus       144 ~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~--~~~~~~~i~---~~~~------~~  212 (412)
                      -..      .......|-++|.+.|++.+.+ .+.+..++.||+||||+=.-..  ....+.++.   ....      ..
T Consensus       342 fd~------ti~e~T~IkFMTDGVLLrEi~~-DflL~kYSvIIlDEAHERSvnTDILiGmLSRiV~LR~k~~ke~~~~kp  414 (1172)
T KOG0926|consen  342 FDG------TIGEDTSIKFMTDGVLLREIEN-DFLLTKYSVIILDEAHERSVNTDILIGMLSRIVPLRQKYYKEQCQIKP  414 (1172)
T ss_pred             ecc------ccCCCceeEEecchHHHHHHHH-hHhhhhceeEEechhhhccchHHHHHHHHHHHHHHHHHHhhhhcccCc
Confidence            111      1223468999999999998865 4556889999999999732111  112222222   2222      26


Q ss_pred             ceEEEEeecCChHHHHHHHHhcCCCe-EEEecCCccccCCceEEEEEeccchhhHHHHHH---HHHhcCCCcEEEEEcch
Q 015158          213 IQVGVFSATMPPEALEITRKFMNKPV-RILVKRDELTLEGIKQFHVNVEKEEWKLETLCD---LYETLAITQSVIFVNTR  288 (412)
Q Consensus       213 ~~~i~~SAT~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~---~~~~~~~~k~lif~~~~  288 (412)
                      .+.|.||||+.-........++..+. .+.+....   ..+...+-.....++..+.+..   +.++.+.|.+|||+..+
T Consensus       415 LKLIIMSATLRVsDFtenk~LFpi~pPlikVdARQ---fPVsIHF~krT~~DYi~eAfrKtc~IH~kLP~G~ILVFvTGQ  491 (1172)
T KOG0926|consen  415 LKLIIMSATLRVSDFTENKRLFPIPPPLIKVDARQ---FPVSIHFNKRTPDDYIAEAFRKTCKIHKKLPPGGILVFVTGQ  491 (1172)
T ss_pred             eeEEEEeeeEEecccccCceecCCCCceeeeeccc---CceEEEeccCCCchHHHHHHHHHHHHhhcCCCCcEEEEEeCh
Confidence            78999999996544443444444322 22222211   1122222222222333344443   44555779999999999


Q ss_pred             hHHHHHHHHHhcCC------------------------------------------------------------------
Q 015158          289 RKVDWLTDKMRSRD------------------------------------------------------------------  302 (412)
Q Consensus       289 ~~~~~~~~~L~~~~------------------------------------------------------------------  302 (412)
                      .++.++++.|+++.                                                                  
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            99999999998751                                                                  


Q ss_pred             ---------------------------------CeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCE
Q 015158          303 ---------------------------------HTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSL  349 (412)
Q Consensus       303 ---------------------------------~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~  349 (412)
                                                       .-+..+++-++.+.+.++++.-..|..-++|+|+.+++.+.+|+++.
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                                             00333344456666666666556677779999999999999999999


Q ss_pred             EEEccCC------------------CChhhHHHhhhhcccCCCCceEEEEeccC
Q 015158          350 VINYDLP------------------TQPENYLHRIGRSGRFGRKGVAINFVTRD  385 (412)
Q Consensus       350 vi~~~~~------------------~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~  385 (412)
                      ||..|..                  .|.+.--||.||+||.| +|.||-+|+..
T Consensus       652 VVD~Gr~K~R~Yd~~TGV~~FeV~wiSkASadQRAGRAGRtg-pGHcYRLYSSA  704 (1172)
T KOG0926|consen  652 VVDCGRVKERLYDSKTGVSSFEVDWISKASADQRAGRAGRTG-PGHCYRLYSSA  704 (1172)
T ss_pred             EEeccchhhhccccccCceeEEEEeeeccccchhccccCCCC-CCceeehhhhH
Confidence            9976642                  46778899999999996 79999999764

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=99.88  E-value=7.6e-21  Score=160.68  Aligned_cols=187  Identities=37%  Similarity=0.567  Sum_probs=146.9

Q ss_pred             HCCCCCChHHHHhhhhhhhcC-ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccc
Q 015158           56 AYGFEKPSAIQQRGIVPFCKG-LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYL  134 (412)
Q Consensus        56 ~~~~~~l~~~Q~~a~~~~~~~-~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~  134 (412)
                      .+++..++++|.+++..+... +++++.++||+|||.++..+++..+.... ..++++++|+..++.|+.+.+.......
T Consensus         3 ~~~~~~~~~~Q~~~~~~~~~~~~~~~i~~~~GsGKT~~~~~~~~~~~~~~~-~~~~l~~~p~~~~~~~~~~~~~~~~~~~   81 (201)
T smart00487        3 KFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGK-GKRVLVLVPTRELAEQWAEELKKLGPSL   81 (201)
T ss_pred             ccCCCCCCHHHHHHHHHHHcCCCcEEEECCCCCchhHHHHHHHHHHhcccC-CCcEEEEeCCHHHHHHHHHHHHHHhccC
Confidence            346677999999999999998 99999999999999998888888776542 3579999999999999999998876544


Q ss_pred             CcEEEEEEcCcc-hHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCCCCc
Q 015158          135 GVKVHACVGGTS-VREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKI  213 (412)
Q Consensus       135 ~~~~~~~~~~~~-~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~  213 (412)
                      ........++.. ............+++++|++.+.............++++|+||+|.+....+...+..+...+++..
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~t~~~l~~~~~~~~~~~~~~~~iIiDE~h~~~~~~~~~~~~~~~~~~~~~~  161 (201)
T smart00487       82 GLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDLLELSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNV  161 (201)
T ss_pred             CeEEEEEeCCcchHHHHHHHhcCCCCEEEeChHHHHHHHHcCCcCHhHCCEEEEECHHHHhcCCcHHHHHHHHHhCCccc
Confidence            423333333333 3333333333349999999999998887666667889999999999887567788888888888889


Q ss_pred             eEEEEeecCChHHHHHHHHhcCCCeEEEec
Q 015158          214 QVGVFSATMPPEALEITRKFMNKPVRILVK  243 (412)
Q Consensus       214 ~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~  243 (412)
                      +++++|||++.+.......++.....+...
T Consensus       162 ~~v~~saT~~~~~~~~~~~~~~~~~~~~~~  191 (201)
T smart00487      162 QLLLLSATPPEEIENLLELFLNDPVFIDVG  191 (201)
T ss_pred             eEEEEecCCchhHHHHHHHhcCCCEEEeCC
Confidence            999999999988888888777755555444

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

Probab=99.88  E-value=5.8e-21  Score=184.81  Aligned_cols=317  Identities=20%  Similarity=0.234  Sum_probs=215.1

Q ss_pred             CChHHHHhhhhhhhc----CccEEEECCCCCCchhHhHHHHHHhhccCC------CceeEEEEcCCHHHHHHHHHHHHHh
Q 015158           61 KPSAIQQRGIVPFCK----GLDVIQQAQSGTGKTATFCSGILQQLDYGL------VECQALVLAPTRELAQQIEKVMRAL  130 (412)
Q Consensus        61 ~l~~~Q~~a~~~~~~----~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~------~~~~~lil~P~~~L~~q~~~~~~~~  130 (412)
                      .+|.||.+.++++..    +-++|++..+|-|||+..+-.++......+      .....|||||. .|+.-|..++.++
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            489999999998763    457899999999999876544443333221      12348999996 8899999999999


Q ss_pred             hcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCC
Q 015158          131 GDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLP  210 (412)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~  210 (412)
                      ++.  +++..+.|........+..-++++|+|++|+.+.+-+..  +....|-++|+||-|-+.+..  ..+.+..+.+.
T Consensus      1054 ~pf--L~v~~yvg~p~~r~~lR~q~~~~~iiVtSYDv~RnD~d~--l~~~~wNYcVLDEGHVikN~k--tkl~kavkqL~ 1127 (1549)
T KOG0392|consen 1054 FPF--LKVLQYVGPPAERRELRDQYKNANIIVTSYDVVRNDVDY--LIKIDWNYCVLDEGHVIKNSK--TKLTKAVKQLR 1127 (1549)
T ss_pred             cch--hhhhhhcCChHHHHHHHhhccccceEEeeHHHHHHHHHH--HHhcccceEEecCcceecchH--HHHHHHHHHHh
Confidence            875  677777777665555444455679999999998765542  222467799999999766543  44555555554


Q ss_pred             CCceEEEEeecCChH-HHHH-----------------HHHhcCCCeEEEecCC---------------------------
Q 015158          211 PKIQVGVFSATMPPE-ALEI-----------------TRKFMNKPVRILVKRD---------------------------  245 (412)
Q Consensus       211 ~~~~~i~~SAT~~~~-~~~~-----------------~~~~~~~~~~~~~~~~---------------------------  245 (412)
                      .+ +.+.+|+||-.+ ..+.                 ++.-+++|+.......                           
T Consensus      1128 a~-hRLILSGTPIQNnvleLWSLFdFLMPGfLGtEKqFqsrf~kpI~asRd~K~Sske~EaG~lAleaLHKqVLPF~LRR 1206 (1549)
T KOG0392|consen 1128 AN-HRLILSGTPIQNNVLELWSLFDFLMPGFLGTEKQFQSRFGKPILASRDPKSSSKEQEAGVLALEALHKQVLPFLLRR 1206 (1549)
T ss_pred             hc-ceEEeeCCCcccCHHHHHHHHHHhcccccCcHHHHHHHhcchhhhhcCcccchhHHHhhHHHHHHHHHHHHHHHHHH
Confidence            33 468899998421 1110                 0010111110000000                           


Q ss_pred             -------ccccCCceEEE-------------------------------------------------------EEecc--
Q 015158          246 -------ELTLEGIKQFH-------------------------------------------------------VNVEK--  261 (412)
Q Consensus       246 -------~~~~~~~~~~~-------------------------------------------------------~~~~~--  261 (412)
                             +..+..+..++                                                       .....  
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                   00000011111                                                       11110  


Q ss_pred             ---------------------chhhHHHHHHHHHhcC----------------CCcEEEEEcchhHHHHHHHHHhcC---
Q 015158          262 ---------------------EEWKLETLCDLYETLA----------------ITQSVIFVNTRRKVDWLTDKMRSR---  301 (412)
Q Consensus       262 ---------------------~~~~~~~l~~~~~~~~----------------~~k~lif~~~~~~~~~~~~~L~~~---  301 (412)
                                           +..|..++.+++....                ..++||||+-+..++-+.+-|-+.   
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                                 1235566666664431                247999999999999888777554   


Q ss_pred             CCeeEEecCCCCHHHHHHHHHHHhcC-CCcEEE-EcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccCCCCce--
Q 015158          302 DHTVSATHGDMDQNTRDIIMREFRSG-SSRVLI-TTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGV--  377 (412)
Q Consensus       302 ~~~~~~~~~~~~~~~r~~~~~~f~~g-~~~vlv-~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~--  377 (412)
                      ......+.|..++.+|.++.++|+++ .++||+ +|...+.|+|+.++++||+++..|++..=.|++.||+|.|++..  
T Consensus      1367 sVtymRLDGSVpp~~R~kiV~~FN~DptIDvLlLTThVGGLGLNLTGADTVVFvEHDWNPMrDLQAMDRAHRIGQKrvVN 1446 (1549)
T KOG0392|consen 1367 SVTYMRLDGSVPPGDRQKIVERFNEDPTIDVLLLTTHVGGLGLNLTGADTVVFVEHDWNPMRDLQAMDRAHRIGQKRVVN 1446 (1549)
T ss_pred             ceeEEEecCCCCcHHHHHHHHHhcCCCceeEEEEeeeccccccccCCCceEEEEecCCCchhhHHHHHHHHhhcCceeee
Confidence            23455889999999999999999998 788775 56799999999999999999999999999999999999998765  


Q ss_pred             EEEEeccC
Q 015158          378 AINFVTRD  385 (412)
Q Consensus       378 ~~~~~~~~  385 (412)
                      +|-+++..
T Consensus      1447 VyRlItrG 1454 (1549)
T KOG0392|consen 1447 VYRLITRG 1454 (1549)
T ss_pred             eeeehhcc
Confidence            56666665

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

Probab=99.87  E-value=1.7e-19  Score=179.56  Aligned_cols=320  Identities=17%  Similarity=0.195  Sum_probs=194.7

Q ss_pred             HHCCCCCChHHHHhhhhhhh----cCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHH-HHHHHH
Q 015158           55 YAYGFEKPSAIQQRGIVPFC----KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQI-EKVMRA  129 (412)
Q Consensus        55 ~~~~~~~l~~~Q~~a~~~~~----~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~-~~~~~~  129 (412)
                      ...+|. .|+-|.+....+.    +++.+++.++||+|||++|+++++...    .+.+++|.+||++|.+|. .+.+..
T Consensus       240 ~~~~~e-~R~~Q~~ma~~V~~~l~~~~~~~~eA~tGtGKT~ayllp~l~~~----~~~~vvI~t~T~~Lq~Ql~~~~i~~  314 (820)
T PRK07246        240 ALLGLE-ERPKQESFAKLVGEDFHDGPASFIEAQTGIGKTYGYLLPLLAQS----DQRQIIVSVPTKILQDQIMAEEVKA  314 (820)
T ss_pred             ccCCCc-cCHHHHHHHHHHHHHHhCCCcEEEECCCCCcHHHHHHHHHHHhc----CCCcEEEEeCcHHHHHHHHHHHHHH
Confidence            334666 8999998554433    467889999999999999999988654    235899999999999999 466666


Q ss_pred             hhcccCcEEEEEEcCcchHHH------------------------------------------------H----------
Q 015158          130 LGDYLGVKVHACVGGTSVRED------------------------------------------------Q----------  151 (412)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~~~~------------------------------------------------~----------  151 (412)
                      +....++++..+.|+.+.--.                                                .          
T Consensus       315 l~~~~~~~~~~~kg~~~ylcl~k~~~~l~~~~~~~~~~~~~~~il~Wl~~T~tGD~~El~~~~~~~~~w~~i~~~~~~~~  394 (820)
T PRK07246        315 IQEVFHIDCHSLKGPQNYLKLDAFYDSLQQNDDNRLVNRYKMQLLVWLTETETGDLDEIKQKQRYAAYFDQLKHDGNLSQ  394 (820)
T ss_pred             HHHhcCCcEEEEECCcccccHHHHHHHhhccCcchHHHHHHHHHHHHHhcCCCCCHhhccCCccccHHHHHhhccCCCCC
Confidence            665556666555544321000                                                0          


Q ss_pred             -------------HHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccC-----c-------HH------
Q 015158          152 -------------RILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRG-----F-------KD------  200 (412)
Q Consensus       152 -------------~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~-----~-------~~------  200 (412)
                                   ......++|+|+.+..|...+..... +...+.+|+||||++.+..     .       ..      
T Consensus       395 ~cp~~~~cf~~~ar~~a~~AdivItNHall~~~~~~~~~-~p~~~~lIiDEAH~l~~~~~~~~~~~~~~~~~~~~l~~~~  473 (820)
T PRK07246        395 SSLFYDYDFWKRSYEKAKTARLLITNHAYFLTRVQDDKD-FARNKVLVFDEAQKLMLQLEQLSRHQLNITSFLQTIQKAL  473 (820)
T ss_pred             CCCcchhhHHHHHHHHHHhCCEEEEchHHHHHHHhhccC-CCCCCEEEEECcchhHHHHHHHhcceecHHHHHHHHHHHH
Confidence                         00023357999999988876644332 4568999999999865211     0       00      


Q ss_pred             --------------------------------------------HH-----------HHHHHh-----------------
Q 015158          201 --------------------------------------------QI-----------YDIFQL-----------------  208 (412)
Q Consensus       201 --------------------------------------------~~-----------~~i~~~-----------------  208 (412)
                                                                  .+           ..++..                 
T Consensus       474 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~l~~l~~~~~~~~~~~~~~~~~~~W~e~~~~~~~~~  553 (820)
T PRK07246        474 SGPLPLLQKRLLESISFELLQLSEQFYQGKERQLIHDSLSRLHQYFSELEVAGFQELQAFFATAEGDYWLESEKQSEKRV  553 (820)
T ss_pred             HHHHHHHhhhhHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCeEEEEecCCCCcce
Confidence                                                        00           000000                 


Q ss_pred             ----------------CCCCceEEEEeecCCh-HHHHHHHHhcCCCeEEEecCCccccCCceEEEEE--ecc-----chh
Q 015158          209 ----------------LPPKIQVGVFSATMPP-EALEITRKFMNKPVRILVKRDELTLEGIKQFHVN--VEK-----EEW  264 (412)
Q Consensus       209 ----------------~~~~~~~i~~SAT~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~-----~~~  264 (412)
                                      ++....+|++|||+.. .... +...++-......... .....-...+..  ++.     ...
T Consensus       554 ~~l~~~pl~v~~~~~~~~~~~~~i~tSATL~v~~~f~-~~~~lGl~~~~~~~~~-~~~~~~~~~~i~~~~p~~~~~~~~~  631 (820)
T PRK07246        554 TYLNSASKAFTHFSQLLPETCKTYFVSATLQISPRVS-LADLLGFEEYLFHKIE-KDKKQDQLVVVDQDMPLVTETSDEV  631 (820)
T ss_pred             eEEEeeeCcHHHHHHHHhcCCeEEEEecccccCCCCc-HHHHcCCCccceecCC-CChHHccEEEeCCCCCCCCCCChHH
Confidence                            0012467888888852 1112 3333332111110000 011111111111  111     111


Q ss_pred             hHHHHHHHHHh--cCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCC
Q 015158          265 KLETLCDLYET--LAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGI  342 (412)
Q Consensus       265 ~~~~l~~~~~~--~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~  342 (412)
                      ....+.+.+..  ...++++|+++|.+..+.+++.|......+ ...|...  .+.+++++|++++..||++|..+.+|+
T Consensus       632 ~~~~~~~~i~~~~~~~g~~LVLFtS~~~l~~v~~~l~~~~~~~-l~Qg~~~--~~~~l~~~F~~~~~~vLlG~~sFwEGV  708 (820)
T PRK07246        632 YAEEIAKRLEELKQLQQPILVLFNSKKHLLAVSDLLDQWQVSH-LAQEKNG--TAYNIKKRFDRGEQQILLGLGSFWEGV  708 (820)
T ss_pred             HHHHHHHHHHHHHhcCCCEEEEECcHHHHHHHHHHHhhcCCcE-EEeCCCc--cHHHHHHHHHcCCCeEEEecchhhCCC
Confidence            22222222211  345899999999999999999997664444 4444322  256789999998889999999999999


Q ss_pred             CCCC--CCEEEEccCCCC------------------------------hhhHHHhhhhcccCCCCceEEEEeccC
Q 015158          343 DVQQ--VSLVINYDLPTQ------------------------------PENYLHRIGRSGRFGRKGVAINFVTRD  385 (412)
Q Consensus       343 d~~~--~~~vi~~~~~~s------------------------------~~~~~Q~~GR~~R~g~~g~~~~~~~~~  385 (412)
                      |+|+  ...||+.++|+.                              ...+.|.+||+.|...+..+++++++.
T Consensus       709 D~p~~~~~~viI~kLPF~~P~dP~~~a~~~~~~~~g~~~F~~~~lP~A~iklkQg~GRLIRs~~D~Gvv~ilD~R  783 (820)
T PRK07246        709 DFVQADRMIEVITRLPFDNPEDPFVKKMNQYLLQEGKNPFYDYFLPMTILRLKQAIGRTMRREDQKSAVLILDRR  783 (820)
T ss_pred             CCCCCCeEEEEEecCCCCCCCCHHHHHHHHHHHHhCCCchhheeHHHHHHHHHHHhcccccCCCCcEEEEEECCc
Confidence            9973  555677776632                              224799999999987655566666665

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=99.86  E-value=9.7e-20  Score=177.62  Aligned_cols=143  Identities=27%  Similarity=0.358  Sum_probs=125.2

Q ss_pred             hHHHHHHHHHhc--CCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCC
Q 015158          265 KLETLCDLYETL--AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGI  342 (412)
Q Consensus       265 ~~~~l~~~~~~~--~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~  342 (412)
                      ....+.+.+...  .+.+++|||++++.++.+++.|.+.|+.+..+||+++..+|..++..|+.|+..|+|+|+.+++|+
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            344444444432  456899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCEEEEccC-----CCChhhHHHhhhhcccCCCCceEEEEecc---------CcHHHHHHHHHHhccccccCChhh
Q 015158          343 DVQQVSLVINYDL-----PTQPENYLHRIGRSGRFGRKGVAINFVTR---------DDERMLFDIQKFYNVVIEELPANV  408 (412)
Q Consensus       343 d~~~~~~vi~~~~-----~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~---------~~~~~~~~~~~~~~~~~~~~~~~~  408 (412)
                      |+|.+++|++++.     |.+...|+||+||+||. ..|.+++|.+.         .+....+.++..|+.....+|..+
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            9999999998764     67999999999999996 78999999984         466777888999999998888765

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=99.86  E-value=1.1e-19  Score=174.02  Aligned_cols=316  Identities=16%  Similarity=0.184  Sum_probs=213.4

Q ss_pred             CCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcE
Q 015158           58 GFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVK  137 (412)
Q Consensus        58 ~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~  137 (412)
                      |.. |++.|.-..-.+..|+  +..+.||-|||+++.++++-....+   ..|-|++.+.-|+..-++++..++..+|++
T Consensus        76 G~r-~ydVQliGglvLh~G~--IAEMkTGEGKTLvAtLpayLnAL~G---kgVhVVTvNdYLA~RDae~mg~vy~fLGLs  149 (925)
T PRK12903         76 GKR-PYDVQIIGGIILDLGS--VAEMKTGEGKTITSIAPVYLNALTG---KGVIVSTVNEYLAERDAEEMGKVFNFLGLS  149 (925)
T ss_pred             CCC-cCchHHHHHHHHhcCC--eeeecCCCCccHHHHHHHHHHHhcC---CceEEEecchhhhhhhHHHHHHHHHHhCCc
Confidence            665 8999998887777774  7899999999999988776443333   468888999999999999999999999999


Q ss_pred             EEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCC-------CCCCceEEEEeCCchhh-ccC------------
Q 015158          138 VHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSL-------RPDNIRIFVLDEADEML-SRG------------  197 (412)
Q Consensus       138 ~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~-------~~~~~~~iiiDE~h~~~-~~~------------  197 (412)
                      +.+...+........  .-.++|+++|...|---+.+...       ..+.+.+.|+||++.++ +..            
T Consensus       150 vG~i~~~~~~~~rr~--aY~~DItYgTn~E~gFDYLRDnm~~~~~~~vqR~~~faIVDEVDSILIDEArTPLIISg~~~~  227 (925)
T PRK12903        150 VGINKANMDPNLKRE--AYACDITYSVHSELGFDYLRDNMVSSKEEKVQRGLNFCLIDEVDSILIDEAKTPLIISGGQSN  227 (925)
T ss_pred             eeeeCCCCChHHHHH--hccCCCeeecCcccchhhhhhcccccHHHhcCcccceeeeccchheeecccCCcccccCCCcc
Confidence            998887655443333  34579999998877443322222       23567789999999753 110            


Q ss_pred             ---cHHHHHHHHHhCC----------------------------------------------------------------
Q 015158          198 ---FKDQIYDIFQLLP----------------------------------------------------------------  210 (412)
Q Consensus       198 ---~~~~~~~i~~~~~----------------------------------------------------------------  210 (412)
                         .......+...+.                                                                
T Consensus       228 ~~~~Y~~~~~~v~~L~~~dy~iDek~k~v~LTe~G~~~~E~~l~i~nLy~~~n~~l~h~i~~AL~A~~lf~rd~dYiV~d  307 (925)
T PRK12903        228 DSNLYLAADQFVRTLKEDDYKIDEETKAISLTEKGIKKANKFFKLKNLYDIENSELVHRIQNALRAHKVMKEDVEYIVRD  307 (925)
T ss_pred             chHHHHHHHHHHHhccccceEEecccceEEECHhHHHHHHHHcCCCcccChhhHHHHHHHHHHHHHHHHHhcCCceEEEC
Confidence               1111111111111                                                                


Q ss_pred             ----------------------------------------------------CCceEEEEeecCChHHHHHHHHhcCCCe
Q 015158          211 ----------------------------------------------------PKIQVGVFSATMPPEALEITRKFMNKPV  238 (412)
Q Consensus       211 ----------------------------------------------------~~~~~i~~SAT~~~~~~~~~~~~~~~~~  238 (412)
                                                                          --.++.|||+|......++. ..++-.+
T Consensus       308 g~V~IVDefTGR~m~gRrwsdGLHQaIEAKEgv~I~~e~~TlAsIT~QnfFr~Y~kLsGMTGTA~te~~Ef~-~iY~l~V  386 (925)
T PRK12903        308 GKIELVDQFTGRIMEGRSYSEGLQQAIQAKEMVEIEPETKTLATITYQNFFRLFKKLSGMTGTAKTEEQEFI-DIYNMRV  386 (925)
T ss_pred             CEEEEEECCCCCCCCCCccchHHHHHHHHHcCCCCCCCceeeeeehHHHHHHhcchhhccCCCCHHHHHHHH-HHhCCCE
Confidence                                                                01356777777755444433 3333332


Q ss_pred             E-EEecCCccccCCceEEEEEeccchhhHHHHHHHHH-hc-CCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHH
Q 015158          239 R-ILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYE-TL-AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQN  315 (412)
Q Consensus       239 ~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~-~~-~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~  315 (412)
                      . +...........-..+   +.....+...+.+-+. .+ .+.++||.|.|++..+.+++.|.+.|+...++++.....
T Consensus       387 v~IPTnkP~~R~D~~d~i---y~t~~~K~~Aii~ei~~~~~~gqPVLVgT~SIe~SE~ls~~L~~~gi~h~vLNAk~~e~  463 (925)
T PRK12903        387 NVVPTNKPVIRKDEPDSI---FGTKHAKWKAVVKEVKRVHKKGQPILIGTAQVEDSETLHELLLEANIPHTVLNAKQNAR  463 (925)
T ss_pred             EECCCCCCeeeeeCCCcE---EEcHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHCCCCceeecccchhh
Confidence            2 2222211111111111   1222334444444333 33 557999999999999999999999999999999864432


Q ss_pred             HHHHHHHHHhcC-CCcEEEEcCCCcCCCCCCCC--------CEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCc
Q 015158          316 TRDIIMREFRSG-SSRVLITTDLLARGIDVQQV--------SLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDD  386 (412)
Q Consensus       316 ~r~~~~~~f~~g-~~~vlv~t~~~~~G~d~~~~--------~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~  386 (412)
                      + ..++.  ..| ...|.|+|+++++|.|+.--        -|||....+.|...-.|..||+||-|.+|.+-.|++-.|
T Consensus       464 E-A~IIa--~AG~~GaVTIATNMAGRGTDI~Lg~~V~~~GGLhVIgTerheSrRIDnQLrGRaGRQGDpGss~f~lSLeD  540 (925)
T PRK12903        464 E-AEIIA--KAGQKGAITIATNMAGRGTDIKLSKEVLELGGLYVLGTDKAESRRIDNQLRGRSGRQGDVGESRFFISLDD  540 (925)
T ss_pred             H-HHHHH--hCCCCCeEEEecccccCCcCccCchhHHHcCCcEEEecccCchHHHHHHHhcccccCCCCCcceEEEecch
Confidence            2 22332  556 45699999999999998732        289999999999999999999999999999998888776


Q ss_pred             HH
Q 015158          387 ER  388 (412)
Q Consensus       387 ~~  388 (412)
                      .-
T Consensus       541 ~L  542 (925)
T PRK12903        541 QL  542 (925)
T ss_pred             HH
Confidence            53

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

Probab=99.86  E-value=6.2e-21  Score=177.48  Aligned_cols=320  Identities=18%  Similarity=0.202  Sum_probs=213.2

Q ss_pred             CCCCChHHHHhhhhhhh----cCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcc
Q 015158           58 GFEKPSAIQQRGIVPFC----KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDY  133 (412)
Q Consensus        58 ~~~~l~~~Q~~a~~~~~----~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~  133 (412)
                      ++. |.+||.-.++++.    .+-++|+...+|-|||...+. .+..+......+.-|||||...| +.|.+++.+||+ 
T Consensus       397 ~i~-LkdYQlvGvNWL~Llyk~~l~gILADEMGLGKTiQvIa-FlayLkq~g~~gpHLVVvPsSTl-eNWlrEf~kwCP-  472 (941)
T KOG0389|consen  397 GIQ-LKDYQLVGVNWLLLLYKKKLNGILADEMGLGKTIQVIA-FLAYLKQIGNPGPHLVVVPSSTL-ENWLREFAKWCP-  472 (941)
T ss_pred             CCc-ccchhhhhHHHHHHHHHccccceehhhccCcchhHHHH-HHHHHHHcCCCCCcEEEecchhH-HHHHHHHHHhCC-
Confidence            444 8999999988865    356789999999999976543 33344333335579999999776 458999999997 


Q ss_pred             cCcEEEEEEcCcchHHHH--HHh--cCCCcEEEeChHHHHHHHHcC-CCCCCCceEEEEeCCchhhccCcHHHHHHHHHh
Q 015158          134 LGVKVHACVGGTSVREDQ--RIL--SSGVHVVVGTPGRVFDMLRRQ-SLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQL  208 (412)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~--~~~--~~~~~iii~T~~~l~~~~~~~-~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~  208 (412)
                       .+.+..++|........  ...  ..+++|+++||.....--... -+...+++++|+||.|.+.+.. ...+..+.. 
T Consensus       473 -sl~Ve~YyGSq~ER~~lR~~i~~~~~~ydVllTTY~la~~~kdDRsflk~~~~n~viyDEgHmLKN~~-SeRy~~LM~-  549 (941)
T KOG0389|consen  473 -SLKVEPYYGSQDERRELRERIKKNKDDYDVLLTTYNLAASSKDDRSFLKNQKFNYVIYDEGHMLKNRT-SERYKHLMS-  549 (941)
T ss_pred             -ceEEEeccCcHHHHHHHHHHHhccCCCccEEEEEeecccCChHHHHHHHhccccEEEecchhhhhccc-hHHHHHhcc-
Confidence             57788888877543331  112  247899999997664211111 1123468899999999877665 333333332 


Q ss_pred             CCCCceEEEEeecCCh-HHHHHHHHh------------------c-----------------------------------
Q 015158          209 LPPKIQVGVFSATMPP-EALEITRKF------------------M-----------------------------------  234 (412)
Q Consensus       209 ~~~~~~~i~~SAT~~~-~~~~~~~~~------------------~-----------------------------------  234 (412)
                      ++ ....+++|+||-. ++.+++.-+                  +                                   
T Consensus       550 I~-An~RlLLTGTPLQNNL~ELiSLL~FvlP~vF~~~~~dl~~if~~k~~~d~d~e~~~l~qerIsrAK~im~PFILRR~  628 (941)
T KOG0389|consen  550 IN-ANFRLLLTGTPLQNNLKELISLLAFVLPKVFDSSMEDLDVIFKAKKTSDGDIENALLSQERISRAKTIMKPFILRRL  628 (941)
T ss_pred             cc-ccceEEeeCCcccccHHHHHHHHHHHhhHhhhccchHHHHHHhccCCccchhhHHHHHHHHHHHHHHhhhHHHHHHH
Confidence            22 3346889999741 111111000                  0                                   


Q ss_pred             ---------CCCeEE---EecC-------------------Cccc--cCC----------------ceEEEE--------
Q 015158          235 ---------NKPVRI---LVKR-------------------DELT--LEG----------------IKQFHV--------  257 (412)
Q Consensus       235 ---------~~~~~~---~~~~-------------------~~~~--~~~----------------~~~~~~--------  257 (412)
                               .+...+   ....                   ....  ..+                ++.+|.        
T Consensus       629 K~qVL~~LPpK~~~Ie~c~mse~Q~~~Y~~~~~~~~~~~~~~~~ns~~~~~~vlmqlRK~AnHPLL~R~~Y~de~L~~ma  708 (941)
T KOG0389|consen  629 KSQVLKQLPPKIQRIEYCEMSEKQKQLYDELIELYDVKLNEVSKNSELKSGNVLMQLRKAANHPLLFRSIYTDEKLRKMA  708 (941)
T ss_pred             HHHHHHhcCCccceeEeeecchHHHHHHHHHHHHHhhhccccccccccccchHHHHHHHHhcChhHHHHhccHHHHHHHH
Confidence                     000000   0000                   0000  000                000000        


Q ss_pred             ------------------------------------------Eec----cchhhHHHHHHHHHhc--CCCcEEEEEcchh
Q 015158          258 ------------------------------------------NVE----KEEWKLETLCDLYETL--AITQSVIFVNTRR  289 (412)
Q Consensus       258 ------------------------------------------~~~----~~~~~~~~l~~~~~~~--~~~k~lif~~~~~  289 (412)
                                                                .+.    ....+...|..++.+.  .++++|||.+.-.
T Consensus       709 k~il~e~ay~~~n~qyIfEDm~~msDfelHqLc~~f~~~~~f~L~d~~~mdSgK~r~L~~LLp~~k~~G~RVLiFSQFTq  788 (941)
T KOG0389|consen  709 KRILNEPAYKKANEQYIFEDMEVMSDFELHQLCCQFRHLSKFQLKDDLWMDSGKCRKLKELLPKIKKKGDRVLIFSQFTQ  788 (941)
T ss_pred             HHHhCchhhhhcCHHHHHHHHHhhhHHHHHHHHHhcCCCcccccCCchhhhhhhHhHHHHHHHHHhhcCCEEEEeeHHHH
Confidence                                                      000    0123556666666664  3379999999999


Q ss_pred             HHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCC-Cc-EEEEcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhh
Q 015158          290 KVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGS-SR-VLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIG  367 (412)
Q Consensus       290 ~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~-~~-vlv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~G  367 (412)
                      -.+-+.-.|..+++....+.|.+.-.+|..++..|...+ +. +|++|.+.+.|||+..+++||+++..+++-.=.|+-.
T Consensus       789 mLDILE~~L~~l~~~ylRLDGsTqV~~RQ~lId~Fn~d~difVFLLSTKAGG~GINLt~An~VIihD~dFNP~dD~QAED  868 (941)
T KOG0389|consen  789 MLDILEVVLDTLGYKYLRLDGSTQVNDRQDLIDEFNTDKDIFVFLLSTKAGGFGINLTCANTVIIHDIDFNPYDDKQAED  868 (941)
T ss_pred             HHHHHHHHHHhcCceEEeecCCccchHHHHHHHhhccCCceEEEEEeeccCcceecccccceEEEeecCCCCcccchhHH
Confidence            999999999999999999999999999999999999864 33 5678999999999999999999999999999999999


Q ss_pred             hcccCCCCce--EEEEeccC
Q 015158          368 RSGRFGRKGV--AINFVTRD  385 (412)
Q Consensus       368 R~~R~g~~g~--~~~~~~~~  385 (412)
                      |++|.|+...  ++.+++.+
T Consensus       869 RcHRvGQtkpVtV~rLItk~  888 (941)
T KOG0389|consen  869 RCHRVGQTKPVTVYRLITKS  888 (941)
T ss_pred             HHHhhCCcceeEEEEEEecC
Confidence            9999998665  45555554

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=99.84  E-value=1.3e-18  Score=167.64  Aligned_cols=319  Identities=17%  Similarity=0.153  Sum_probs=211.5

Q ss_pred             CCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCc
Q 015158           57 YGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGV  136 (412)
Q Consensus        57 ~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~  136 (412)
                      .|+. |++.|.-+.-.+.+|  -+..+.||.|||+++.++++-....   +..+-|++++..|+.+-++.+..+...+|+
T Consensus        73 lG~r-~ydvQlig~l~L~~G--~IaEm~TGEGKTL~a~l~ayl~aL~---G~~VhVvT~NdyLA~RD~e~m~pvy~~LGL  146 (870)
T CHL00122         73 LGLR-HFDVQLIGGLVLNDG--KIAEMKTGEGKTLVATLPAYLNALT---GKGVHIVTVNDYLAKRDQEWMGQIYRFLGL  146 (870)
T ss_pred             hCCC-CCchHhhhhHhhcCC--ccccccCCCCchHHHHHHHHHHHhc---CCceEEEeCCHHHHHHHHHHHHHHHHHcCC
Confidence            3666 888998887666655  4899999999999998887543333   347999999999999999999999999999


Q ss_pred             EEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCC-------CCCCceEEEEeCCchhh-ccC-----------
Q 015158          137 KVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSL-------RPDNIRIFVLDEADEML-SRG-----------  197 (412)
Q Consensus       137 ~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~-------~~~~~~~iiiDE~h~~~-~~~-----------  197 (412)
                      .+.+..++.+.....  ..-.++|+++|...|---+.+..+       ..+.+.+.|+||++.++ +..           
T Consensus       147 svg~i~~~~~~~err--~aY~~DItYgTn~e~gFDyLRDnm~~~~~~~v~r~~~faIVDEvDSiLIDeArTPLiISg~~~  224 (870)
T CHL00122        147 TVGLIQEGMSSEERK--KNYLKDITYVTNSELGFDYLRDNMALSLSDVVQRPFNYCIIDEVDSILIDEARTPLIISGQSK  224 (870)
T ss_pred             ceeeeCCCCChHHHH--HhcCCCCEecCCccccccchhhccCcChHHhhccccceeeeecchhheeccCCCceeccCCCc
Confidence            999988776654433  334578999998766322222221       23567899999999753 110           


Q ss_pred             ----cHHHHHHHHHhCC---------------------------------------------------------------
Q 015158          198 ----FKDQIYDIFQLLP---------------------------------------------------------------  210 (412)
Q Consensus       198 ----~~~~~~~i~~~~~---------------------------------------------------------------  210 (412)
                          .......+...+.                                                               
T Consensus       225 ~~~~~y~~~~~~v~~L~~~~dy~vdek~k~v~LTe~G~~~~e~~l~i~~ly~~~~~~~~~i~~AL~A~~lf~~d~dYiV~  304 (870)
T CHL00122        225 TNIDKYIVADELAKYLEKNVHYEVDEKNKNVILTEQGILFIEKILKIEDLYSANDPWIPYILNALKAKELFFKNVHYIVR  304 (870)
T ss_pred             cchHHHHHHHHHHHhcCcCCCeEEEcCCCceEecHHHHHHHHHHcCCccccccccHHHHHHHHHHHHHHHHhcCCcEEEE
Confidence                0000000111000                                                               


Q ss_pred             -----------------------------------------------------CCceEEEEeecCChHHHHHHHHhcCCC
Q 015158          211 -----------------------------------------------------PKIQVGVFSATMPPEALEITRKFMNKP  237 (412)
Q Consensus       211 -----------------------------------------------------~~~~~i~~SAT~~~~~~~~~~~~~~~~  237 (412)
                                                                           --.++.|||+|..... ..+...++-.
T Consensus       305 dgeV~iVDe~TGR~m~grrws~GLHQaiEaKEgv~It~e~~tlAsIT~QnfFr~Y~kL~GMTGTa~te~-~Ef~~iY~l~  383 (870)
T CHL00122        305 NNEIIIVDEFTGRIMPGRRWSDGLHQAIEAKENLPIRQETETLASITYQNFFLLYPKLSGMTGTAKTEE-LEFEKIYNLE  383 (870)
T ss_pred             CCEEEEEECCCCcCCCCCccchHHHHHHHhhcCCCCCCCceeeeeeeHHHHHHhCchhcccCCCCHHHH-HHHHHHhCCC
Confidence                                                                 0136788888886543 3344455444


Q ss_pred             eEEE-ecCCccccCCceEEEEEeccchhhHH-HHHHHHHhc-CCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCH
Q 015158          238 VRIL-VKRDELTLEGIKQFHVNVEKEEWKLE-TLCDLYETL-AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQ  314 (412)
Q Consensus       238 ~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~-~l~~~~~~~-~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~  314 (412)
                      +... ........ ....  ........+.. .+.++...+ .+.|+||-|.|++..+.+++.|.+.|+...++++....
T Consensus       384 vv~IPtnkp~~R~-d~~d--~v~~t~~~K~~AI~~ei~~~~~~grPVLIgT~SIe~SE~ls~~L~~~gi~h~vLNAk~~~  460 (870)
T CHL00122        384 VVCIPTHRPMLRK-DLPD--LIYKDELSKWRAIADECLQMHQTGRPILIGTTTIEKSELLSQLLKEYRLPHQLLNAKPEN  460 (870)
T ss_pred             EEECCCCCCccce-eCCC--eEEeCHHHHHHHHHHHHHHHHhcCCCEEEeeCCHHHHHHHHHHHHHcCCccceeeCCCcc
Confidence            4332 22211111 1111  11222233434 334444444 45799999999999999999999999999999986322


Q ss_pred             -HHHHHHHHHHhcC-CCcEEEEcCCCcCCCCCCCC---------------------------------------------
Q 015158          315 -NTRDIIMREFRSG-SSRVLITTDLLARGIDVQQV---------------------------------------------  347 (412)
Q Consensus       315 -~~r~~~~~~f~~g-~~~vlv~t~~~~~G~d~~~~---------------------------------------------  347 (412)
                       +.-..++.  ..| ...|.|+|+++++|.|+.=-                                             
T Consensus       461 ~~~EA~IIA--~AG~~G~VTIATNMAGRGTDI~Lgg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  538 (870)
T CHL00122        461 VRRESEIVA--QAGRKGSITIATNMAGRGTDIILGGNPEFKLKKELYDLLLSYKSNEKISTISQNFLNILNSLKNDLKFL  538 (870)
T ss_pred             chhHHHHHH--hcCCCCcEEEeccccCCCcCeecCCchhHHHHHHHhhhhcccccccccccccccchhhhhhcccchhhh
Confidence             22233444  355 45699999999999996511                                             


Q ss_pred             -------------------------------------------------------CEEEEccCCCChhhHHHhhhhcccC
Q 015158          348 -------------------------------------------------------SLVINYDLPTQPENYLHRIGRSGRF  372 (412)
Q Consensus       348 -------------------------------------------------------~~vi~~~~~~s~~~~~Q~~GR~~R~  372 (412)
                                                                             -+||-.+...|...=.|..||+||-
T Consensus       539 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~e~V~~~GGL~VIgTErheSrRIDnQLrGRaGRQ  618 (870)
T CHL00122        539 SLSDFENLKILNEASEISIPKNSYQLSLRFLYNELLEKYKKLQEKEKKIVKKLGGLYVIGTERHESRRIDNQLRGRAGRQ  618 (870)
T ss_pred             cccccccccccccccccccccchhhhhhhhHHHHHHHHHHHHhhhhHHHHHHcCCCEEEecCcCchHHHHHHHhccccCC
Confidence                                                                   1455666777888889999999999


Q ss_pred             CCCceEEEEeccCcHHH
Q 015158          373 GRKGVAINFVTRDDERM  389 (412)
Q Consensus       373 g~~g~~~~~~~~~~~~~  389 (412)
                      |.||.+-.|++-.|.-.
T Consensus       619 GDPG~s~f~lSLED~l~  635 (870)
T CHL00122        619 GDPGSSRFFLSLEDNLL  635 (870)
T ss_pred             CCCCcceEEEEeccHHH
Confidence            99999999988776643

>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated

Probab=99.84  E-value=7.7e-18  Score=170.84  Aligned_cols=109  Identities=13%  Similarity=0.196  Sum_probs=83.5

Q ss_pred             CCCcEEEEEcchhHHHHHHHHHhcCCC--eeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCC--CCEEEE
Q 015158          277 AITQSVIFVNTRRKVDWLTDKMRSRDH--TVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQ--VSLVIN  352 (412)
Q Consensus       277 ~~~k~lif~~~~~~~~~~~~~L~~~~~--~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~--~~~vi~  352 (412)
                      ..+++||+++|.+..+.+++.|.....  ....+.-+++...|.+++++|++++-.||++|..+.+|||+|+  +++||+
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            457999999999999999999976422  1222322333345789999999988889999999999999996  588888


Q ss_pred             ccCCCC------------------------------hhhHHHhhhhcccCCCCceEEEEeccC
Q 015158          353 YDLPTQ------------------------------PENYLHRIGRSGRFGRKGVAINFVTRD  385 (412)
Q Consensus       353 ~~~~~s------------------------------~~~~~Q~~GR~~R~g~~g~~~~~~~~~  385 (412)
                      .+.|+.                              ...+.|.+||+.|...+..++++++..
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            887742                              223589999999997765566666665

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

Probab=99.84  E-value=1.5e-19  Score=162.71  Aligned_cols=351  Identities=15%  Similarity=0.099  Sum_probs=237.1

Q ss_pred             HHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhc--
Q 015158           55 YAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGD--  132 (412)
Q Consensus        55 ~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~--  132 (412)
                      ..+.-...+.+|.+++..+.+|++.++.-.+.+||++++..+....+... +....+++.|+.++++...+.+.-...  
T Consensus       280 ~~~~~E~~~~~~~~~~~~~~~G~~~~~~~~~~~GK~~~~~~~s~~~~~~~-~~s~~~~~~~~~~~~~~~~~~~~V~~~~I  358 (1034)
T KOG4150|consen  280 NKNTGESGIAISLELLKFASEGRADGGNEARQAGKGTCPTSGSRKFQTLC-HATNSLLPSEMVEHLRNGSKGQVVHVEVI  358 (1034)
T ss_pred             hcccccchhhhhHHHHhhhhhcccccccchhhcCCccCcccchhhhhhcC-cccceecchhHHHHhhccCCceEEEEEeh
Confidence            33444568899999999999999999999999999999988777655433 344688999999988766543211100  


Q ss_pred             -ccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCC----CCCceEEEEeCCchhhccC---cHHHHHH
Q 015158          133 -YLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLR----PDNIRIFVLDEADEMLSRG---FKDQIYD  204 (412)
Q Consensus       133 -~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~----~~~~~~iiiDE~h~~~~~~---~~~~~~~  204 (412)
                       ...-.+.-...+............+..++++.+...........+.    .-+..+++.||+|.+....   ....++.
T Consensus       359 ~~~K~A~V~~~D~~sE~~~~A~~R~~~~~~~s~~~~~~s~~L~~~~~~~~~~~~~~~~~~~~~~~Y~~~~~~~~~~~~R~  438 (1034)
T KOG4150|consen  359 KARKSAYVEMSDKLSETTKSALKRIGLNTLYSHQAEAISAALAKSLCYNVPVFEELCKDTNSCALYLFPTKALAQDQLRA  438 (1034)
T ss_pred             hhhhcceeecccCCCchhHHHHHhcCcceeecCHHHHHHHHhhhccccccHHHHHHHhcccceeeeecchhhHHHHHHHH
Confidence             0011122223333333444445567789999998876544432222    2234579999999754321   1233444


Q ss_pred             HHHhC-----CCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccc--------hhhHHHHHH
Q 015158          205 IFQLL-----PPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKE--------EWKLETLCD  271 (412)
Q Consensus       205 i~~~~-----~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------~~~~~~l~~  271 (412)
                      +.+.+     ..+.+++-.+||+.... .....+++-.....+.. +-.+.+-++++.+.++.        +.+......
T Consensus       439 L~~L~~~F~~~~~~~~~~~~~~~K~~~-~~~~~~~~~~E~~Li~~-DGSPs~~K~~V~WNP~~~P~~~~~~~~~i~E~s~  516 (1034)
T KOG4150|consen  439 LSDLIKGFEASINMGVYDGDTPYKDRT-RLRSELANLSELELVTI-DGSPSSEKLFVLWNPSAPPTSKSEKSSKVVEVSH  516 (1034)
T ss_pred             HHHHHHHHHhhcCcceEeCCCCcCCHH-HHHHHhcCCcceEEEEe-cCCCCccceEEEeCCCCCCcchhhhhhHHHHHHH
Confidence            44333     24678888899986554 44445555443322222 22334455666655442        112222222


Q ss_pred             HHHhc--CCCcEEEEEcchhHHHHHHHHHhc----CCC----eeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCC
Q 015158          272 LYETL--AITQSVIFVNTRRKVDWLTDKMRS----RDH----TVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARG  341 (412)
Q Consensus       272 ~~~~~--~~~k~lif~~~~~~~~~~~~~L~~----~~~----~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G  341 (412)
                      ++.+.  .+-++|-||++++-|+-+....++    .+.    .+..+.|+...++|.++...+-.|++.-+|+|++++-|
T Consensus       517 ~~~~~i~~~~R~IAFC~~R~~CEL~~~~~R~I~~ET~~~LV~~i~SYRGGY~A~DRRKIE~~~F~G~L~giIaTNALELG  596 (1034)
T KOG4150|consen  517 LFAEMVQHGLRCIAFCPSRKLCELVLCLTREILAETAPHLVEAITSYRGGYIAEDRRKIESDLFGGKLCGIIATNALELG  596 (1034)
T ss_pred             HHHHHHHcCCcEEEeccHHHHHHHHHHHHHHHHHHhhHHHHHHHHhhcCccchhhHHHHHHHhhCCeeeEEEecchhhhc
Confidence            22222  235899999999999876554443    232    35678899999999999999999999999999999999


Q ss_pred             CCCCCCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEe--ccCcHHHHHHHHHHhccccccCChhh
Q 015158          342 IDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFV--TRDDERMLFDIQKFYNVVIEELPANV  408 (412)
Q Consensus       342 ~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~  408 (412)
                      +|+...+.|++.+.|.|.+.+.|..||+||++++..++.+.  .+-|..++.+.+..+...+.++..++
T Consensus       597 IDIG~LDAVl~~GFP~S~aNl~QQ~GRAGRRNk~SLavyva~~~PVDQ~Y~~HP~~l~~~pN~EL~LD~  665 (1034)
T KOG4150|consen  597 IDIGHLDAVLHLGFPGSIANLWQQAGRAGRRNKPSLAVYVAFLGPVDQYYMSHPDKLFGSPNEELHLDS  665 (1034)
T ss_pred             cccccceeEEEccCchhHHHHHHHhccccccCCCceEEEEEeccchhhHhhcCcHHHhCCCcceeEEec
Confidence            99999999999999999999999999999999887655544  45577788888888888777766655

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

Probab=99.83  E-value=2.2e-17  Score=157.43  Aligned_cols=114  Identities=13%  Similarity=0.109  Sum_probs=82.3

Q ss_pred             HHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhc----CCCcEEEEcCCCcCCCCC
Q 015158          269 LCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRS----GSSRVLITTDLLARGIDV  344 (412)
Q Consensus       269 l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~----g~~~vlv~t~~~~~G~d~  344 (412)
                      +..++.. ..|+++|.+.|.+..+.+++.|...-.-...+.|+.+  .+..++++|++    |...||++|..+.+|||+
T Consensus       462 ~~~~~~~-~~G~~lvLfTS~~~~~~~~~~l~~~l~~~~l~qg~~~--~~~~l~~~f~~~~~~~~~~vL~gt~sfweGvDv  538 (636)
T TIGR03117       462 TAAILRK-AQGGTLVLTTAFSHISAIGQLVELGIPAEIVIQSEKN--RLASAEQQFLALYANGIQPVLIAAGGAWTGIDL  538 (636)
T ss_pred             HHHHHHH-cCCCEEEEechHHHHHHHHHHHHhhcCCCEEEeCCCc--cHHHHHHHHHHhhcCCCCcEEEeCCcccccccc
Confidence            3344443 4479999999999999999999764223344445432  34668888887    468899999999999999


Q ss_pred             --------C--CCCEEEEccCCCCh-------------------------hhHHHhhhhcccCCCC--ceEEEEeccC
Q 015158          345 --------Q--QVSLVINYDLPTQP-------------------------ENYLHRIGRSGRFGRK--GVAINFVTRD  385 (412)
Q Consensus       345 --------~--~~~~vi~~~~~~s~-------------------------~~~~Q~~GR~~R~g~~--g~~~~~~~~~  385 (412)
                              |  .+++||+...|+.+                         -.+.|.+||..|...+  ..++.++++.
T Consensus       539 ~~~~~~p~~G~~Ls~ViI~kLPF~~~dp~a~~~~~~~~g~~~f~~~p~a~i~lkQg~GRLIR~~~D~~~G~i~ilD~R  616 (636)
T TIGR03117       539 THKPVSPDKDNLLTDLIITCAPFGLNRSLSMLKRIRKTSVRPWEIINESLMMLRQGLGRLVRHPDMPQNRRIHMLDGR  616 (636)
T ss_pred             CCccCCCCCCCcccEEEEEeCCCCcCChHHHHHHHHhcCCChHhhhHHHHHHHHHhcCceeecCCCcCceEEEEEeCC
Confidence                    3  38889988877432                         2468999999998766  4455555554

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.

>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=99.81  E-value=7.7e-19  Score=137.69  Aligned_cols=118  Identities=44%  Similarity=0.721  Sum_probs=109.5

Q ss_pred             hhHHHHHHHHHhcC--CCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCC
Q 015158          264 WKLETLCDLYETLA--ITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARG  341 (412)
Q Consensus       264 ~~~~~l~~~~~~~~--~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G  341 (412)
                      .+...+..++....  .+++||||++...++.+++.|.+.+..+..+||+++..+|..+.+.|.++...++++|+++++|
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            56677777777664  6899999999999999999999888999999999999999999999999999999999999999


Q ss_pred             CCCCCCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEE
Q 015158          342 IDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINF  381 (412)
Q Consensus       342 ~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~  381 (412)
                      +|+|.+++|++++.+++...+.|++||++|.|+.|.++++
T Consensus        92 ~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~  131 (131)
T cd00079          92 IDLPNVSVVINYDLPWSPSSYLQRIGRAGRAGQKGTAILL  131 (131)
T ss_pred             cChhhCCEEEEeCCCCCHHHheecccccccCCCCceEEeC
Confidence            9999999999999999999999999999999998888764

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=99.80  E-value=3.8e-18  Score=135.78  Aligned_cols=144  Identities=41%  Similarity=0.570  Sum_probs=112.4

Q ss_pred             ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcC
Q 015158           77 LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSS  156 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  156 (412)
                      +++++.+|||+|||.+++..+....... ...+++|++|+..++.|+.+.+...... +..+..+.+.............
T Consensus         1 ~~~~i~~~~G~GKT~~~~~~~~~~~~~~-~~~~~lv~~p~~~l~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~   78 (144)
T cd00046           1 RDVLLAAPTGSGKTLAALLPILELLDSL-KGGQVLVLAPTRELANQVAERLKELFGE-GIKVGYLIGGTSIKQQEKLLSG   78 (144)
T ss_pred             CCEEEECCCCCchhHHHHHHHHHHHhcc-cCCCEEEEcCcHHHHHHHHHHHHHHhhC-CcEEEEEecCcchhHHHHHhcC
Confidence            3679999999999999988888776542 3458999999999999999988887654 5777777776665554444566


Q ss_pred             CCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEeecC
Q 015158          157 GVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATM  222 (412)
Q Consensus       157 ~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~  222 (412)
                      ..+|+++|++.+.............++++|+||+|.+....................+++++||||
T Consensus        79 ~~~i~i~t~~~~~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~~~~~~~~~~~~i~~saTp  144 (144)
T cd00046          79 KTDIVVGTPGRLLDELERLKLSLKKLDLLILDEAHRLLNQGFGLLGLKILLKLPKDRQVLLLSATP  144 (144)
T ss_pred             CCCEEEECcHHHHHHHHcCCcchhcCCEEEEeCHHHHhhcchHHHHHHHHhhCCccceEEEEeccC
Confidence            789999999999888876655566789999999999877654443333445556788899999997

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

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=99.79  E-value=3.6e-17  Score=157.48  Aligned_cols=274  Identities=18%  Similarity=0.173  Sum_probs=176.4

Q ss_pred             CCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcE
Q 015158           58 GFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVK  137 (412)
Q Consensus        58 ~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~  137 (412)
                      |.. |++.|.-.--.+..|+  +..+.||-|||+++.++++-....+   ..+-||+++.-|+..-++++..+....|+.
T Consensus        83 G~r-~ydVQliGgl~Lh~G~--IAEM~TGEGKTL~atlpaylnAL~G---kgVhVVTvNdYLA~RDae~m~~vy~~LGLt  156 (939)
T PRK12902         83 GMR-HFDVQLIGGMVLHEGQ--IAEMKTGEGKTLVATLPSYLNALTG---KGVHVVTVNDYLARRDAEWMGQVHRFLGLS  156 (939)
T ss_pred             CCC-cchhHHHhhhhhcCCc--eeeecCCCChhHHHHHHHHHHhhcC---CCeEEEeCCHHHHHhHHHHHHHHHHHhCCe
Confidence            665 8889988887777665  8899999999999988877654444   479999999999999999999999999999


Q ss_pred             EEEEEcCcchHHHHHHhcCCCcEEEeChHHHH-----HHHH--cCCCCCCCceEEEEeCCchhh-ccC------------
Q 015158          138 VHACVGGTSVREDQRILSSGVHVVVGTPGRVF-----DMLR--RQSLRPDNIRIFVLDEADEML-SRG------------  197 (412)
Q Consensus       138 ~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~-----~~~~--~~~~~~~~~~~iiiDE~h~~~-~~~------------  197 (412)
                      +.+..++.....  +...-.++|+++|...|-     ..+.  ......+.+.+.|+||++.++ +..            
T Consensus       157 vg~i~~~~~~~e--rr~aY~~DItYgTn~e~gFDYLRDnm~~~~~~~vqR~~~faIVDEvDSILIDEArTPLIISg~~~~  234 (939)
T PRK12902        157 VGLIQQDMSPEE--RKKNYACDITYATNSELGFDYLRDNMATDISEVVQRPFNYCVIDEVDSILIDEARTPLIISGQVER  234 (939)
T ss_pred             EEEECCCCChHH--HHHhcCCCeEEecCCcccccchhhhhcccccccccCccceEEEecccceeeccCCCcccccCCCcc
Confidence            999877665433  334456899999998772     2111  112234678899999999753 110            


Q ss_pred             ---cHHHHHHHHHhCC----------------------------------------------------------------
Q 015158          198 ---FKDQIYDIFQLLP----------------------------------------------------------------  210 (412)
Q Consensus       198 ---~~~~~~~i~~~~~----------------------------------------------------------------  210 (412)
                         .......+...+.                                                                
T Consensus       235 ~~~~y~~~~~~~~~L~~~~~~~~~~dy~idek~~~v~LTe~G~~~~e~~~~i~nLy~~~~~~~~~i~~AL~A~~lf~~d~  314 (939)
T PRK12902        235 PQEKYQKAAEVAAALQRKDGIDPEGDYEVDEKQRNVLLTDEGFAKAEQLLGVSDLFDPQDPWAHYIFNALKAKELFIKDV  314 (939)
T ss_pred             chHHHHHHHHHHHHhhhhcccCCCCCeEEecCCCeeeEcHHHHHHHHHHhCchhhcCcccHHHHHHHHHHHHHHHHhcCC
Confidence               0001111111000                                                                


Q ss_pred             ----------------------------------------------------------CCceEEEEeecCChHHHHHHHH
Q 015158          211 ----------------------------------------------------------PKIQVGVFSATMPPEALEITRK  232 (412)
Q Consensus       211 ----------------------------------------------------------~~~~~i~~SAT~~~~~~~~~~~  232 (412)
                                                                                --.++.|||+|......+ +..
T Consensus       315 dYiV~dg~V~IVDe~TGR~m~grrws~GLHQaIEaKE~v~it~e~~tlAsIT~QnfFr~Y~kLsGMTGTa~te~~E-f~~  393 (939)
T PRK12902        315 NYIVRNGEVVIVDEFTGRVMPGRRWSDGLHQAIEAKEGVEIQPETQTLASITYQNFFLLYPKLAGMTGTAKTEEVE-FEK  393 (939)
T ss_pred             eEEEECCEEEEEECCCCCCCCCCccchHHHHHHHhhcCCCCCCCceeeeeeeHHHHHhhCchhcccCCCCHHHHHH-HHH
Confidence                                                                      013567777776544333 333


Q ss_pred             hcCCCeE-EEecCCccccCCceEEEEEeccchhhHHHHH-HHHHhc-CCCcEEEEEcchhHHHHHHHHHhcCCCeeEEec
Q 015158          233 FMNKPVR-ILVKRDELTLEGIKQFHVNVEKEEWKLETLC-DLYETL-AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATH  309 (412)
Q Consensus       233 ~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~-~~~~~~-~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~  309 (412)
                      .++-.+. +...........-...   ......+...+. ++...+ .+.|+||-+.|++..+.+++.|.+.|+...+++
T Consensus       394 iY~l~Vv~IPTnkP~~R~d~~d~v---y~t~~~K~~Ai~~ei~~~~~~GrPVLIgT~SVe~SE~ls~~L~~~gi~h~vLN  470 (939)
T PRK12902        394 TYKLEVTVIPTNRPRRRQDWPDQV---YKTEIAKWRAVANETAEMHKQGRPVLVGTTSVEKSELLSALLQEQGIPHNLLN  470 (939)
T ss_pred             HhCCcEEEcCCCCCeeeecCCCeE---EcCHHHHHHHHHHHHHHHHhCCCCEEEeeCCHHHHHHHHHHHHHcCCchheee
Confidence            3333332 2222211111111111   122233444444 444443 567999999999999999999999999999999


Q ss_pred             CCC-CHHHHHHHHHHHhcCC-CcEEEEcCCCcCCCCCC
Q 015158          310 GDM-DQNTRDIIMREFRSGS-SRVLITTDLLARGIDVQ  345 (412)
Q Consensus       310 ~~~-~~~~r~~~~~~f~~g~-~~vlv~t~~~~~G~d~~  345 (412)
                      ..- ..+.-..|+.  ..|. ..|.|+|+++++|.|+.
T Consensus       471 Ak~~~~~~EA~IIa--~AG~~GaVTIATNMAGRGTDIk  506 (939)
T PRK12902        471 AKPENVEREAEIVA--QAGRKGAVTIATNMAGRGTDII  506 (939)
T ss_pred             CCCcchHhHHHHHH--hcCCCCcEEEeccCCCCCcCEe
Confidence            862 2222233444  3564 45999999999999965

>KOG0953 consensus Mitochondrial RNA helicase SUV3, DEAD-box superfamily [RNA processing and modification]

Probab=99.79  E-value=4.6e-18  Score=152.88  Aligned_cols=280  Identities=17%  Similarity=0.187  Sum_probs=184.4

Q ss_pred             ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcC
Q 015158           77 LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSS  156 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  156 (412)
                      +-++-++||.||||.-++.    ++...   +..++..|.+-|+.+.++.+.+.    |+.+..++|........+  ..
T Consensus       192 kIi~H~GPTNSGKTy~ALq----rl~~a---ksGvycGPLrLLA~EV~~r~na~----gipCdL~TGeE~~~~~~~--~~  258 (700)
T KOG0953|consen  192 KIIMHVGPTNSGKTYRALQ----RLKSA---KSGVYCGPLRLLAHEVYDRLNAL----GIPCDLLTGEERRFVLDN--GN  258 (700)
T ss_pred             eEEEEeCCCCCchhHHHHH----HHhhh---ccceecchHHHHHHHHHHHhhhc----CCCccccccceeeecCCC--CC
Confidence            3356689999999976543    44333   47899999999999999988886    788888887655322211  23


Q ss_pred             CCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCC-CCceEEEEeecCCh-HHHHHHHHhc
Q 015158          157 GVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLP-PKIQVGVFSATMPP-EALEITRKFM  234 (412)
Q Consensus       157 ~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~-~~~~~i~~SAT~~~-~~~~~~~~~~  234 (412)
                      .+..+-||.|+..-        ...+++.|+||++.+.+...+-.|.+.+--+. ....   +-+-+.- ++...+...-
T Consensus       259 ~a~hvScTVEM~sv--------~~~yeVAViDEIQmm~Dp~RGwAWTrALLGl~AdEiH---LCGepsvldlV~~i~k~T  327 (700)
T KOG0953|consen  259 PAQHVSCTVEMVSV--------NTPYEVAVIDEIQMMRDPSRGWAWTRALLGLAADEIH---LCGEPSVLDLVRKILKMT  327 (700)
T ss_pred             cccceEEEEEEeec--------CCceEEEEehhHHhhcCcccchHHHHHHHhhhhhhhh---ccCCchHHHHHHHHHhhc
Confidence            46788888777531        24689999999999987765544444332221 1222   2222211 2222222233


Q ss_pred             CCCeEEEecCCccccCCceEEEEEeccchhhHHHHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcCCCe-eEEecCCCC
Q 015158          235 NKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHT-VSATHGDMD  313 (412)
Q Consensus       235 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~-~~~~~~~~~  313 (412)
                      ++.+.++...             ...+ -...+.+..-++....|. .|+|-|++....+...+.+.+.. +.+++|+++
T Consensus       328 Gd~vev~~Ye-------------Rl~p-L~v~~~~~~sl~nlk~GD-CvV~FSkk~I~~~k~kIE~~g~~k~aVIYGsLP  392 (700)
T KOG0953|consen  328 GDDVEVREYE-------------RLSP-LVVEETALGSLSNLKPGD-CVVAFSKKDIFTVKKKIEKAGNHKCAVIYGSLP  392 (700)
T ss_pred             CCeeEEEeec-------------ccCc-ceehhhhhhhhccCCCCC-eEEEeehhhHHHHHHHHHHhcCcceEEEecCCC
Confidence            3333222111             1111 112223444445544443 56677888999999999988765 999999999


Q ss_pred             HHHHHHHHHHHhc--CCCcEEEEcCCCcCCCCCCCCCEEEEccC---------CCChhhHHHhhhhcccCCC---CceEE
Q 015158          314 QNTRDIIMREFRS--GSSRVLITTDLLARGIDVQQVSLVINYDL---------PTQPENYLHRIGRSGRFGR---KGVAI  379 (412)
Q Consensus       314 ~~~r~~~~~~f~~--g~~~vlv~t~~~~~G~d~~~~~~vi~~~~---------~~s~~~~~Q~~GR~~R~g~---~g~~~  379 (412)
                      ++.|.+.-..|++  ++.+|+|+|+++++|+|+ +++.||+++.         +.+..+..|..||+||.|.   .|.+.
T Consensus       393 PeTr~aQA~~FNd~~~e~dvlVAsDAIGMGLNL-~IrRiiF~sl~Kysg~e~~~it~sqikQIAGRAGRf~s~~~~G~vT  471 (700)
T KOG0953|consen  393 PETRLAQAALFNDPSNECDVLVASDAIGMGLNL-NIRRIIFYSLIKYSGRETEDITVSQIKQIAGRAGRFGSKYPQGEVT  471 (700)
T ss_pred             CchhHHHHHHhCCCCCccceEEeeccccccccc-ceeEEEEeecccCCcccceeccHHHHHHHhhcccccccCCcCceEE
Confidence            9999999999998  799999999999999999 5888887765         3567889999999999863   46665


Q ss_pred             EEeccCcHHHHHHHHHHhccc
Q 015158          380 NFVTRDDERMLFDIQKFYNVV  400 (412)
Q Consensus       380 ~~~~~~~~~~~~~~~~~~~~~  400 (412)
                      .+..++    +..+.+.++..
T Consensus       472 tl~~eD----L~~L~~~l~~p  488 (700)
T KOG0953|consen  472 TLHSED----LKLLKRILKRP  488 (700)
T ss_pred             EeeHhh----HHHHHHHHhCC
Confidence            555433    33444444433

>KOG0386 consensus Chromatin remodeling complex SWI/SNF, component SWI2 and related ATPases (DNA/RNA helicase superfamily) [Chromatin structure and dynamics; Transcription]

Probab=99.79  E-value=1.5e-18  Score=165.71  Aligned_cols=319  Identities=17%  Similarity=0.180  Sum_probs=212.7

Q ss_pred             CChHHHHhhhhhhhc----CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCc
Q 015158           61 KPSAIQQRGIVPFCK----GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGV  136 (412)
Q Consensus        61 ~l~~~Q~~a~~~~~~----~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~  136 (412)
                      .+.+||.+.+.++.+    +-+.++...+|-|||...+..+...+......+..+|++|+..|.. |..++..|..  .+
T Consensus       394 ~Lk~YQl~GLqWmVSLyNNnLNGILADEMGLGKTIQtIsLitYLmE~K~~~GP~LvivPlstL~N-W~~Ef~kWaP--Sv  470 (1157)
T KOG0386|consen  394 ELKEYQLHGLQWMVSLYNNNLNGILADEMGLGKTIQTISLITYLMEHKQMQGPFLIIVPLSTLVN-WSSEFPKWAP--SV  470 (1157)
T ss_pred             CCchhhhhhhHHHhhccCCCcccccchhcccchHHHHHHHHHHHHHHcccCCCeEEeccccccCC-chhhcccccc--ce
Confidence            599999999988664    3578999999999997765555554444444567999999999887 7777888765  34


Q ss_pred             EEEEEEcCcchHH--HHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCCCCce
Q 015158          137 KVHACVGGTSVRE--DQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQ  214 (412)
Q Consensus       137 ~~~~~~~~~~~~~--~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~  214 (412)
                      ....+.|......  ...+..++++|+++|++.+.+  .+..+..-+|.++||||.|++.+..  ..+...+...-....
T Consensus       471 ~~i~YkGtp~~R~~l~~qir~gKFnVLlTtyEyiik--dk~lLsKI~W~yMIIDEGHRmKNa~--~KLt~~L~t~y~~q~  546 (1157)
T KOG0386|consen  471 QKIQYKGTPQQRSGLTKQQRHGKFNVLLTTYEYIIK--DKALLSKISWKYMIIDEGHRMKNAI--CKLTDTLNTHYRAQR  546 (1157)
T ss_pred             eeeeeeCCHHHHhhHHHHHhcccceeeeeeHHHhcC--CHHHHhccCCcceeecccccccchh--hHHHHHhhccccchh
Confidence            4445555433221  134445789999999998754  2222223467899999999987643  333333332222344


Q ss_pred             EEEEeecCChHHHH------------------HHHHhcCCCeEEEec---------------------------------
Q 015158          215 VGVFSATMPPEALE------------------ITRKFMNKPVRILVK---------------------------------  243 (412)
Q Consensus       215 ~i~~SAT~~~~~~~------------------~~~~~~~~~~~~~~~---------------------------------  243 (412)
                      .+++|+||.-+...                  .+..+++.|..-...                                 
T Consensus       547 RLLLTGTPLQN~LpELWaLLNFlLP~IFnS~~~FeqWFN~PFantGek~eLteEEtlLIIrRLHkVLRPFlLRRlKkeVE  626 (1157)
T KOG0386|consen  547 RLLLTGTPLQNNLPELWALLNFLLPNIFNSCKAFEQWFNQPFANTGEKVELTEEETLLIIRRLHKVLRPFLLRRLKKEVE  626 (1157)
T ss_pred             hhhhcCChhhhccHHHHHHHHHhccchhhhHhHHHHHhhhhhhhcCCcccccchHHHHHHHHHHHhhhHHHHHhhhHHHh
Confidence            56677776311000                  011111111000000                                 


Q ss_pred             -----------------------------------C--Ccc--------------------ccCCceEEEE------Eec
Q 015158          244 -----------------------------------R--DEL--------------------TLEGIKQFHV------NVE  260 (412)
Q Consensus       244 -----------------------------------~--~~~--------------------~~~~~~~~~~------~~~  260 (412)
                                                         .  ...                    ...++...+.      .+-
T Consensus       627 ~~LPdKve~viKC~mSalQq~lY~~m~~~g~l~~d~~~g~~g~k~L~N~imqLRKiCNHP~lf~~ve~~~~~~~~~~dL~  706 (1157)
T KOG0386|consen  627 QELPDKVEDVIKCDMSALQQSLYKQMQNKGQLLKDTAKGKKGYKPLFNTIMQLRKLCNHPYLFANVENSYTLHYDIKDLV  706 (1157)
T ss_pred             hhCchhhhHhhheehhhhhHhhhHHHHhCCCCCcCchhccccchhhhhHhHHHHHhcCCchhhhhhccccccccChhHHH
Confidence                                               0  000                    0000000000      000


Q ss_pred             cchhhHHHHHHHHHhc--CCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCC---CcEEEEc
Q 015158          261 KEEWKLETLCDLYETL--AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGS---SRVLITT  335 (412)
Q Consensus       261 ~~~~~~~~l~~~~~~~--~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~---~~vlv~t  335 (412)
                      ....+...+..++.+.  .+++++.||.-..-...+..+|.=+++....+.|.+...+|...++.|+...   ..+|++|
T Consensus       707 R~sGKfELLDRiLPKLkatgHRVLlF~qMTrlmdimEdyL~~~~~kYlRLDG~TK~~eRg~ll~~FN~Pds~yf~Fllst  786 (1157)
T KOG0386|consen  707 RVSGKFELLDRILPKLKATGHRVLLFSQMTRLMDILEDYLQIREYKYLRLDGQTKVEERGDLLEIFNAPDSPYFIFLLST  786 (1157)
T ss_pred             HhccHHHHHHhhhHHHHhcCcchhhHHHHHHHHHHHHHHHhhhhhheeeecCCcchhhHHHHHHHhcCCCCceeeeeeee
Confidence            1123455566666554  4589999999999999999999988999999999999999999999999753   3467789


Q ss_pred             CCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCc
Q 015158          336 DLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDD  386 (412)
Q Consensus       336 ~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~  386 (412)
                      .+.+.|+|+..+++||+++..|++....|+-.|+.|.|+...+-++....-
T Consensus       787 ragglglNlQtadtviifdsdwnp~~d~qaqdrahrigq~~evRv~rl~tv  837 (1157)
T KOG0386|consen  787 RAGGLGLNLQTADTVIIFDSDWNPHQDLQAQDRAHRIGQKKEVRVLRLITV  837 (1157)
T ss_pred             cccccccchhhcceEEEecCCCCchhHHHHHHHHHHhhchhheeeeeeehh
Confidence            999999999999999999999999999999999999998877666665543

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

Probab=99.79  E-value=7.5e-18  Score=155.25  Aligned_cols=105  Identities=19%  Similarity=0.257  Sum_probs=92.8

Q ss_pred             CCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhc--CCCcEE-EEcCCCcCCCCCCCCCEEEEc
Q 015158          277 AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRS--GSSRVL-ITTDLLARGIDVQQVSLVINY  353 (412)
Q Consensus       277 ~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~--g~~~vl-v~t~~~~~G~d~~~~~~vi~~  353 (412)
                      ..+|++|..+-.....-+...|++.|.....++|.....+|..+++.|..  |...|+ ++-.+.+.|+|+-+.+|+|++
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            45788888888888888999999999999999999999999999999986  434554 556788999999999999999


Q ss_pred             cCCCChhhHHHhhhhcccCCCCceEEEE
Q 015158          354 DLPTQPENYLHRIGRSGRFGRKGVAINF  381 (412)
Q Consensus       354 ~~~~s~~~~~Q~~GR~~R~g~~g~~~~~  381 (412)
                      ++.|+++--.|+..|+.|.|+...+++.
T Consensus       825 DlHWNPaLEqQAcDRIYR~GQkK~V~Ih  852 (901)
T KOG4439|consen  825 DLHWNPALEQQACDRIYRMGQKKDVFIH  852 (901)
T ss_pred             ecccCHHHHHHHHHHHHHhcccCceEEE
Confidence            9999999999999999999988776654

>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=99.78  E-value=1.1e-18  Score=145.52  Aligned_cols=150  Identities=17%  Similarity=0.183  Sum_probs=102.0

Q ss_pred             ChHHHHhhhhhhhc-------CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccc
Q 015158           62 PSAIQQRGIVPFCK-------GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYL  134 (412)
Q Consensus        62 l~~~Q~~a~~~~~~-------~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~  134 (412)
                      |+++|.+++..+..       .+++++.+|||+|||.+++..+.....      ++++++|+..|.+|+.+.+..+....
T Consensus         4 lr~~Q~~ai~~i~~~~~~~~~~~~~ll~~~tGsGKT~~~~~~~~~l~~------~~l~~~p~~~l~~Q~~~~~~~~~~~~   77 (184)
T PF04851_consen    4 LRPYQQEAIARIINSLENKKEERRVLLNAPTGSGKTIIALALILELAR------KVLIVAPNISLLEQWYDEFDDFGSEK   77 (184)
T ss_dssp             E-HHHHHHHHHHHHHHHTTSGCSEEEEEESTTSSHHHHHHHHHHHHHC------EEEEEESSHHHHHHHHHHHHHHSTTS
T ss_pred             CCHHHHHHHHHHHHHHHhcCCCCCEEEEECCCCCcChhhhhhhhcccc------ceeEecCHHHHHHHHHHHHHHhhhhh
Confidence            89999999999884       588999999999999998765554433      79999999999999999996654321


Q ss_pred             CcEEEEE-----------E-cCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCC-----------CCCCCceEEEEeCCc
Q 015158          135 GVKVHAC-----------V-GGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQS-----------LRPDNIRIFVLDEAD  191 (412)
Q Consensus       135 ~~~~~~~-----------~-~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~-----------~~~~~~~~iiiDE~h  191 (412)
                       ......           . ................+++++|++.+........           .....+++||+||||
T Consensus        78 -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~vI~DEaH  156 (184)
T PF04851_consen   78 -YNFFEKSIKPAYDSKEFISIQDDISDKSESDNNDKDIILTTYQSLQSDIKEEKKIDESARRSYKLLKNKFDLVIIDEAH  156 (184)
T ss_dssp             -EEEEE--GGGCCE-SEEETTTTEEEHHHHHCBSS-SEEEEEHHHHHHHHHH---------GCHHGGGGSESEEEEETGG
T ss_pred             -hhhcccccccccccccccccccccccccccccccccchhhHHHHHHhhcccccccccchhhhhhhccccCCEEEEehhh
Confidence             111110           0 1111112233345567899999999987764321           112467899999999


Q ss_pred             hhhccCcHHHHHHHHHhCCCCceEEEEeecCC
Q 015158          192 EMLSRGFKDQIYDIFQLLPPKIQVGVFSATMP  223 (412)
Q Consensus       192 ~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~  223 (412)
                      ++....-   +..+..  .+...+++|||||.
T Consensus       157 ~~~~~~~---~~~i~~--~~~~~~l~lTATp~  183 (184)
T PF04851_consen  157 HYPSDSS---YREIIE--FKAAFILGLTATPF  183 (184)
T ss_dssp             CTHHHHH---HHHHHH--SSCCEEEEEESS-S
T ss_pred             hcCCHHH---HHHHHc--CCCCeEEEEEeCcc
Confidence            8765431   344444  45777999999985

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 ....

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

Probab=99.78  E-value=7.9e-17  Score=162.47  Aligned_cols=285  Identities=14%  Similarity=0.146  Sum_probs=174.2

Q ss_pred             ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhc-
Q 015158           77 LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILS-  155 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-  155 (412)
                      +.++||..+|||||++.+..+-.... ....+++++|+.++.|-.|+.+.+..+........    ...+.......+. 
T Consensus       274 ~~G~IWHtqGSGKTlTm~~~A~~l~~-~~~~~~v~fvvDR~dLd~Q~~~~f~~~~~~~~~~~----~~~s~~~Lk~~l~~  348 (962)
T COG0610         274 KGGYIWHTQGSGKTLTMFKLARLLLE-LPKNPKVLFVVDRKDLDDQTSDEFQSFGKVAFNDP----KAESTSELKELLED  348 (962)
T ss_pred             CceEEEeecCCchHHHHHHHHHHHHh-ccCCCeEEEEechHHHHHHHHHHHHHHHHhhhhcc----cccCHHHHHHHHhc
Confidence            56999999999999987655544433 35678999999999999999999999865432222    2233334444444 


Q ss_pred             CCCcEEEeChHHHHHHHHcCC-C-CCCCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEeecCChHHHHH-HHH
Q 015158          156 SGVHVVVGTPGRVFDMLRRQS-L-RPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEI-TRK  232 (412)
Q Consensus       156 ~~~~iii~T~~~l~~~~~~~~-~-~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~-~~~  232 (412)
                      ....|+|||.++|........ . ..+.--+||+||||+- .  ++..-..+...++ +...+++|+||--..... ...
T Consensus       349 ~~~~ii~TTIQKf~~~~~~~~~~~~~~~~ivvI~DEaHRS-Q--~G~~~~~~~~~~~-~a~~~gFTGTPi~~~d~~tt~~  424 (962)
T COG0610         349 GKGKIIVTTIQKFNKAVKEDELELLKRKNVVVIIDEAHRS-Q--YGELAKLLKKALK-KAIFIGFTGTPIFKEDKDTTKD  424 (962)
T ss_pred             CCCcEEEEEecccchhhhcccccccCCCcEEEEEechhhc-c--ccHHHHHHHHHhc-cceEEEeeCCccccccccchhh
Confidence            345899999999988776531 1 1122238999999983 2  2233334444444 477999999996433333 355


Q ss_pred             hcCCCeEEEecCCccccCCceEEEEEec-cc-------------------------------------------hhhH--
Q 015158          233 FMNKPVRILVKRDELTLEGIKQFHVNVE-KE-------------------------------------------EWKL--  266 (412)
Q Consensus       233 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~-------------------------------------------~~~~--  266 (412)
                      .++.....+.......-..+-..++... ..                                           ....  
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            6666655554443332222212222111 00                                           0000  


Q ss_pred             --HHHHHHHH-hcCCCcEEEEEcchhHHHHHHHHHhcCCCe-----------------------eEEecCCCCHHHHHHH
Q 015158          267 --ETLCDLYE-TLAITQSVIFVNTRRKVDWLTDKMRSRDHT-----------------------VSATHGDMDQNTRDII  320 (412)
Q Consensus       267 --~~l~~~~~-~~~~~k~lif~~~~~~~~~~~~~L~~~~~~-----------------------~~~~~~~~~~~~r~~~  320 (412)
                        +.+..+.+ .....++++.+.++..+..+++........                       ....|.. ....+...
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              11111122 223367888888888555555554332100                       0000111 22233344


Q ss_pred             HHHH--hcCCCcEEEEcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccC
Q 015158          321 MREF--RSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRF  372 (412)
Q Consensus       321 ~~~f--~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~  372 (412)
                      ..+|  ....+++||+++++-+|+|.|.++++. ++-|.-...++|++.|+.|.
T Consensus       584 ~~r~~~~~d~~kilIV~dmlLTGFDaP~L~TmY-vDK~Lk~H~L~QAisRtNR~  636 (962)
T COG0610         584 IKRFKLKDDPLDLLIVVDMLLTGFDAPCLNTLY-VDKPLKYHNLIQAISRTNRV  636 (962)
T ss_pred             hhhhcCcCCCCCEEEEEccccccCCccccceEE-eccccccchHHHHHHHhccC
Confidence            4443  346889999999999999999888887 66778889999999999996

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

Probab=99.77  E-value=1.2e-16  Score=158.66  Aligned_cols=127  Identities=13%  Similarity=0.204  Sum_probs=89.0

Q ss_pred             HHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcCCCe-eEEecCCCCHHHHHHHHHHHhcCCC-cEEEEcCCCcCCCCCCC
Q 015158          269 LCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHT-VSATHGDMDQNTRDIIMREFRSGSS-RVLITTDLLARGIDVQQ  346 (412)
Q Consensus       269 l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~-~~~~~~~~~~~~r~~~~~~f~~g~~-~vlv~t~~~~~G~d~~~  346 (412)
                      +.+++...+ ++++||++|.+..+.+.+.+...... ....+|..   .+..+++.|.++.- .++|++..+.+|+|+|+
T Consensus       471 i~~~~~~~~-~~~lvlF~Sy~~l~~~~~~~~~~~~~~~v~~q~~~---~~~~~l~~f~~~~~~~~lv~~gsf~EGVD~~g  546 (654)
T COG1199         471 LREILKASP-GGVLVLFPSYEYLKRVAERLKDERSTLPVLTQGED---EREELLEKFKASGEGLILVGGGSFWEGVDFPG  546 (654)
T ss_pred             HHHHHhhcC-CCEEEEeccHHHHHHHHHHHhhcCccceeeecCCC---cHHHHHHHHHHhcCCeEEEeeccccCcccCCC
Confidence            334444444 68999999999999999999886653 33444443   34478888887544 79999999999999996


Q ss_pred             --CCEEEEccCCCC------------------------------hhhHHHhhhhcccCCCCceEEEEeccCcHH--HHHH
Q 015158          347 --VSLVINYDLPTQ------------------------------PENYLHRIGRSGRFGRKGVAINFVTRDDER--MLFD  392 (412)
Q Consensus       347 --~~~vi~~~~~~s------------------------------~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~--~~~~  392 (412)
                        ++.||+.+.|+-                              ...+.|.+||+.|...+..++++++..-..  .-+.
T Consensus       547 ~~l~~vvI~~lPfp~p~dp~~~~r~~~~~~~g~~~f~~~~l~~A~~~l~QavGRlIR~~~D~G~ivllD~R~~~~~y~~~  626 (654)
T COG1199         547 DALRLVVIVGLPFPNPDDPLLKARLEFLKRLGGDPFEEFYLPPAVIKLRQAVGRLIRSEDDRGVIVLLDKRYATKRYGKL  626 (654)
T ss_pred             CCeeEEEEEecCCCCCCCHHHHHHHHHHHHhcCCCceEeehHHHHHHHHHhhccccccCCCceEEEEecccchhhhHHHH
Confidence              578888887742                              446799999999986665555566654322  3344


Q ss_pred             HHHHhcc
Q 015158          393 IQKFYNV  399 (412)
Q Consensus       393 ~~~~~~~  399 (412)
                      +-+.+..
T Consensus       627 l~~~l~~  633 (654)
T COG1199         627 LLDSLPP  633 (654)
T ss_pred             HHHhCCC
Confidence            4444443

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=99.77  E-value=2e-16  Score=156.95  Aligned_cols=75  Identities=24%  Similarity=0.216  Sum_probs=63.2

Q ss_pred             HCCCCCChHHHHhhhhhhh----cCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 015158           56 AYGFEKPSAIQQRGIVPFC----KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRAL  130 (412)
Q Consensus        56 ~~~~~~l~~~Q~~a~~~~~----~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~  130 (412)
                      .++|..+||.|++.+..+.    .++++++.+|||+|||++.+.+++..........+++|.+.|.+-..|..+++++.
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            3678877999998887765    47899999999999999999999887654434468999999999999999999884

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).

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3

Probab=99.76  E-value=1.2e-16  Score=156.25  Aligned_cols=335  Identities=16%  Similarity=0.120  Sum_probs=198.3

Q ss_pred             HHHHHHCCCCCChHHHHhhhhhhhc--------CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHH
Q 015158           51 LRGIYAYGFEKPSAIQQRGIVPFCK--------GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQ  122 (412)
Q Consensus        51 ~~~l~~~~~~~l~~~Q~~a~~~~~~--------~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q  122 (412)
                      .+.+....-..-..||-+|+..+..        |--++..|.||+|||++=. -|+..+.....+.+..|..-.++|.-|
T Consensus       398 hk~~~~r~~~~rF~WQdkA~d~a~~~r~~~~~~GfF~vNMASTGcGKT~aNA-RImyaLsd~~~g~RfsiALGLRTLTLQ  476 (1110)
T TIGR02562       398 HKYFCQRSAHPRFRWQNKAFNLAQKLRQKSPEQGAFGVNMASTGCGKTLANA-RAMYALRDDKQGARFAIALGLRSLTLQ  476 (1110)
T ss_pred             hhhhccCCCCCCcchHHHHHHHHHHHHhhcccCCeEEEEecCCCcchHHHHH-HHHHHhCCCCCCceEEEEccccceecc
Confidence            3444433444457799999998775        3345668999999998754 344455566677789999999999988


Q ss_pred             HHHHHHHhhcccCcEEEEEEcCcchHHHHH-------------------------------------------Hhc----
Q 015158          123 IEKVMRALGDYLGVKVHACVGGTSVREDQR-------------------------------------------ILS----  155 (412)
Q Consensus       123 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------------------------------------------~~~----  155 (412)
                      +-+.+++-....+....++.|+.......+                                           .+.    
T Consensus       477 TGda~r~rL~L~~ddLAVlIGs~Av~~L~e~~~~~~~~~~~~GSeS~e~l~~e~~~~~~~~~~g~l~~~~l~~~l~~~~k  556 (1110)
T TIGR02562       477 TGHALKTRLNLSDDDLAVLIGGTAVQTLFDLSKEKIEQVDEDGSESAPIFLAEGQDCNLPDWDGPLDTIELLGRLSLDDK  556 (1110)
T ss_pred             chHHHHHhcCCCccceEEEECHHHHHHHHHHHhhhccccccCCCccchhhhcccCcCCeeeccCCccchhhhhhhccChh
Confidence            888887754444445555555443222110                                           000    


Q ss_pred             ----CCCcEEEeChHHHHHHHHcCC--CC-CC----CceEEEEeCCchhhccCcHHHHHHHHHh-CCCCceEEEEeecCC
Q 015158          156 ----SGVHVVVGTPGRVFDMLRRQS--LR-PD----NIRIFVLDEADEMLSRGFKDQIYDIFQL-LPPKIQVGVFSATMP  223 (412)
Q Consensus       156 ----~~~~iii~T~~~l~~~~~~~~--~~-~~----~~~~iiiDE~h~~~~~~~~~~~~~i~~~-~~~~~~~i~~SAT~~  223 (412)
                          -...++|+|++.++.......  .. ..    .-+.||+||+|-+....+ ..+..++.. -.-+.++++||||++
T Consensus       557 ~~rll~apv~V~TIDQlL~a~~~~r~~~~~l~ll~La~svlVlDEVHaYD~~~~-~~L~rlL~w~~~lG~~VlLmSATLP  635 (1110)
T TIGR02562       557 EKTLLAAPVLVCTIDHLIPATESHRGGHHIAPMLRLMSSDLILDEPDDYEPEDL-PALLRLVQLAGLLGSRVLLSSATLP  635 (1110)
T ss_pred             hhhhhcCCeEEecHHHHHHHhhhcccchhHHHHHHhcCCCEEEECCccCCHHHH-HHHHHHHHHHHHcCCCEEEEeCCCC
Confidence                013699999999987763211  11 01    125799999997654443 333333331 123678999999999


Q ss_pred             hHHHHHHHHh-----------cCC---CeEEEecC--C-cc----------------------------ccCCceEEEEE
Q 015158          224 PEALEITRKF-----------MNK---PVRILVKR--D-EL----------------------------TLEGIKQFHVN  258 (412)
Q Consensus       224 ~~~~~~~~~~-----------~~~---~~~~~~~~--~-~~----------------------------~~~~~~~~~~~  258 (412)
                      +.....+..-           .+.   +..+....  + ..                            .+.--.-....
T Consensus       636 ~~l~~~L~~Ay~~G~~~~q~~~g~~~~~~~i~CaW~DE~~~~~~~~~~~~~F~~~H~~Fv~~R~~~L~~~p~~R~a~i~~  715 (1110)
T TIGR02562       636 PALVKTLFRAYEAGRQMYQALYGQPKKPLNICCAWVDEPQVWQADCNQKSEFIQRHQDFLRDRAVQLAKKPVRRLAELLS  715 (1110)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCCCCcceeEEeecccCchhhhhcCHHHHHHHHHHHHHHHHHHHhcCcccceEEEee
Confidence            8765544322           232   22111111  0 00                            01001111122


Q ss_pred             eccch----hhHHHHH--------HHHHhc----C-CCc----EEEEEcchhHHHHHHHHHhcC------CCeeEEecCC
Q 015158          259 VEKEE----WKLETLC--------DLYETL----A-ITQ----SVIFVNTRRKVDWLTDKMRSR------DHTVSATHGD  311 (412)
Q Consensus       259 ~~~~~----~~~~~l~--------~~~~~~----~-~~k----~lif~~~~~~~~~~~~~L~~~------~~~~~~~~~~  311 (412)
                      ++...    .....+.        .+-..+    + .+|    .+|-.+++..+-.+++.|...      .+.+.+||+.
T Consensus       716 ~~~~~~~~~~~~~~~a~~i~~~~~~LH~~h~~~~~~sgk~VSfGliR~anI~p~V~~A~~L~~~~~~~~~~i~~~~yHSr  795 (1110)
T TIGR02562       716 LSSLPRENESTYLALAQSLLEGALRLHQAHAQTDPKSEKKVSVGLIRVANIDPLIRLAQFLYALLAEEKYQIHLCCYHAQ  795 (1110)
T ss_pred             cCCcccchhHHHHHHHHHHHHHHHHHHHHhCccCCCCCeEEEEEEEEEcCchHHHHHHHHHHhhccccCCceeEEEeccc
Confidence            22211    0111111        111211    1 122    478888888777777777543      3457889999


Q ss_pred             CCHHHHHHHHHHH----------------------hc----CCCcEEEEcCCCcCCCCCCCCCEEEEccCCCChhhHHHh
Q 015158          312 MDQNTRDIIMREF----------------------RS----GSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHR  365 (412)
Q Consensus       312 ~~~~~r~~~~~~f----------------------~~----g~~~vlv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~  365 (412)
                      .....|..++++.                      .+    +...|+|+|++++.|+|+ +.+.+|  .-+.+...++|+
T Consensus       796 ~~l~~Rs~~E~~Ld~~L~R~~~~~~~~~~~i~~~l~~~~~~~~~~i~v~Tqv~E~g~D~-dfd~~~--~~~~~~~sliQ~  872 (1110)
T TIGR02562       796 DPLLLRSYIERRLDQLLTRHKPEQLFQDDEIIDLMQNSPALNHLFIVLATPVEEVGRDH-DYDWAI--ADPSSMRSIIQL  872 (1110)
T ss_pred             ChHHHHHHHHHHHHHHhcccChhhhhchHHHHHHHhcccccCCCeEEEEeeeEEEEecc-cCCeee--eccCcHHHHHHH
Confidence            9888887777654                      12    356799999999999998 466664  346778999999


Q ss_pred             hhhcccCCCC--ceEEEEeccCcHHHH
Q 015158          366 IGRSGRFGRK--GVAINFVTRDDERML  390 (412)
Q Consensus       366 ~GR~~R~g~~--g~~~~~~~~~~~~~~  390 (412)
                      +||+.|.|..  +..-+++...+.+.+
T Consensus       873 aGR~~R~~~~~~~~~N~~i~~~N~r~l  899 (1110)
T TIGR02562       873 AGRVNRHRLEKVQQPNIVILQWNYRYL  899 (1110)
T ss_pred             hhcccccccCCCCCCcEEEeHhHHHHh
Confidence            9999998643  333344445555544

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.

>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=99.75  E-value=4.1e-18  Score=120.01  Aligned_cols=78  Identities=47%  Similarity=0.814  Sum_probs=75.4

Q ss_pred             HHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccCC
Q 015158          296 DKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFG  373 (412)
Q Consensus       296 ~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g  373 (412)
                      +.|+..++.+..+||+++..+|..+++.|.+++..+||+|+++++|+|+|.+++|+++++|+|+..|.|++||++|.|
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 ....

>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]

Probab=99.74  E-value=1.2e-15  Score=135.62  Aligned_cols=108  Identities=17%  Similarity=0.260  Sum_probs=94.7

Q ss_pred             CCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcC-CCc-EEEEcCCCcCCCCCCCCCEEEEccC
Q 015158          278 ITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSG-SSR-VLITTDLLARGIDVQQVSLVINYDL  355 (412)
Q Consensus       278 ~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g-~~~-vlv~t~~~~~G~d~~~~~~vi~~~~  355 (412)
                      .-|.|||.+.-...+-+.-.|.+.|..++.+.|+|++..|...++.|++. ... +|++-.+.+..+|+..+.+|+++++
T Consensus       638 t~KsIVFSQFTSmLDLi~~rL~kaGfscVkL~GsMs~~ardatik~F~nd~~c~vfLvSLkAGGVALNLteASqVFmmDP  717 (791)
T KOG1002|consen  638 TAKSIVFSQFTSMLDLIEWRLGKAGFSCVKLVGSMSPAARDATIKYFKNDIDCRVFLVSLKAGGVALNLTEASQVFMMDP  717 (791)
T ss_pred             chhhhhHHHHHHHHHHHHHHhhccCceEEEeccCCChHHHHHHHHHhccCCCeEEEEEEeccCceEeeechhceeEeecc
Confidence            35789999999999999999999999999999999999999999999986 444 4566789999999999999999999


Q ss_pred             CCChhhHHHhhhhcccCCCC--ceEEEEeccC
Q 015158          356 PTQPENYLHRIGRSGRFGRK--GVAINFVTRD  385 (412)
Q Consensus       356 ~~s~~~~~Q~~GR~~R~g~~--g~~~~~~~~~  385 (412)
                      .|+++.-.|.-.|+.|.|+.  -.++.|+-++
T Consensus       718 WWNpaVe~Qa~DRiHRIGQ~rPvkvvrf~iEn  749 (791)
T KOG1002|consen  718 WWNPAVEWQAQDRIHRIGQYRPVKVVRFCIEN  749 (791)
T ss_pred             cccHHHHhhhhhhHHhhcCccceeEEEeehhc
Confidence            99999999999999999964  4566666554

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=99.73  E-value=5.3e-15  Score=145.75  Aligned_cols=105  Identities=20%  Similarity=0.358  Sum_probs=78.4

Q ss_pred             CCCcEEEEEcchhHHHHHHHHHhcC-CCeeEEecCCCCHHHHHHHHHHHh----cCCCcEEEEcCCCcCCCCCCC--CCE
Q 015158          277 AITQSVIFVNTRRKVDWLTDKMRSR-DHTVSATHGDMDQNTRDIIMREFR----SGSSRVLITTDLLARGIDVQQ--VSL  349 (412)
Q Consensus       277 ~~~k~lif~~~~~~~~~~~~~L~~~-~~~~~~~~~~~~~~~r~~~~~~f~----~g~~~vlv~t~~~~~G~d~~~--~~~  349 (412)
                      ..+.++|+++|.+..+.+++.|... +.. ....|.   ..+.++++.|+    +++..||++|..+.+|||+|+  +++
T Consensus       533 ~~gg~LVlFtSy~~l~~v~~~l~~~~~~~-ll~Q~~---~~~~~ll~~f~~~~~~~~~~VL~g~~sf~EGVD~pGd~l~~  608 (697)
T PRK11747        533 KHKGSLVLFASRRQMQKVADLLPRDLRLM-LLVQGD---QPRQRLLEKHKKRVDEGEGSVLFGLQSFAEGLDLPGDYLTQ  608 (697)
T ss_pred             cCCCEEEEeCcHHHHHHHHHHHHHhcCCc-EEEeCC---chHHHHHHHHHHHhccCCCeEEEEeccccccccCCCCceEE
Confidence            3456999999999999999999743 333 333443   24667776666    467789999999999999996  788


Q ss_pred             EEEccCCCC-h-----------------------------hhHHHhhhhcccCCCCceEEEEeccC
Q 015158          350 VINYDLPTQ-P-----------------------------ENYLHRIGRSGRFGRKGVAINFVTRD  385 (412)
Q Consensus       350 vi~~~~~~s-~-----------------------------~~~~Q~~GR~~R~g~~g~~~~~~~~~  385 (412)
                      ||+.+.|+. +                             ..+.|.+||+.|...+..+++++++.
T Consensus       609 vII~kLPF~~p~dp~~~ar~~~~~~~g~~~F~~~~lP~A~~kl~Qg~GRlIRs~~D~G~i~ilD~R  674 (697)
T PRK11747        609 VIITKIPFAVPDSPVEATLAEWLKSRGGNPFMEISVPDASFKLIQAVGRLIRSEQDRGRVTILDRR  674 (697)
T ss_pred             EEEEcCCCCCCCCHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhccccccCCceEEEEEEccc
Confidence            998887742 1                             14689999999997665566666665

>KOG0388 consensus SNF2 family DNA-dependent ATPase [Replication, recombination and repair]

Probab=99.72  E-value=1.5e-16  Score=146.89  Aligned_cols=121  Identities=21%  Similarity=0.326  Sum_probs=102.9

Q ss_pred             hHHHHHHHHHhc--CCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCc-EEEEcCCCcCC
Q 015158          265 KLETLCDLYETL--AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSR-VLITTDLLARG  341 (412)
Q Consensus       265 ~~~~l~~~~~~~--~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~-vlv~t~~~~~G  341 (412)
                      +...|.+++.+.  .+.++|+|++-.+-..-+.++|.-+++....+.|.....+|..++++|+..++- +|++|.+.+-|
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            444455555554  346899999999999999999999999999999999999999999999997655 56789999999


Q ss_pred             CCCCCCCEEEEccCCCChhhHHHhhhhcccCCCCce--EEEEeccC
Q 015158          342 IDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGV--AINFVTRD  385 (412)
Q Consensus       342 ~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~--~~~~~~~~  385 (412)
                      +|+..+++||+++..|++..-.|++.|+.|.|+...  +|-++...
T Consensus      1109 INLTAADTViFYdSDWNPT~D~QAMDRAHRLGQTrdvtvyrl~~rg 1154 (1185)
T KOG0388|consen 1109 INLTAADTVIFYDSDWNPTADQQAMDRAHRLGQTRDVTVYRLITRG 1154 (1185)
T ss_pred             ccccccceEEEecCCCCcchhhHHHHHHHhccCccceeeeeecccc
Confidence            999999999999999999999999999999997654  55555554

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=99.72  E-value=6.7e-16  Score=150.40  Aligned_cols=122  Identities=18%  Similarity=0.231  Sum_probs=97.0

Q ss_pred             hhHHHHHHHHHh-c-CCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcC-CCcEEEEcCCCcC
Q 015158          264 WKLETLCDLYET-L-AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSG-SSRVLITTDLLAR  340 (412)
Q Consensus       264 ~~~~~l~~~~~~-~-~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g-~~~vlv~t~~~~~  340 (412)
                      .+...+.+-+.. + .+.|+||-+.|++..+.+++.|...|+...++++.....+. .|+.  ..| ...|.|+|+++++
T Consensus       612 eK~~Aii~ei~~~~~~GrPVLVGT~SVe~SE~lS~~L~~~gI~H~VLNAK~h~~EA-eIVA--~AG~~GaVTIATNMAGR  688 (1112)
T PRK12901        612 EKYNAVIEEITELSEAGRPVLVGTTSVEISELLSRMLKMRKIPHNVLNAKLHQKEA-EIVA--EAGQPGTVTIATNMAGR  688 (1112)
T ss_pred             HHHHHHHHHHHHHHHCCCCEEEEeCcHHHHHHHHHHHHHcCCcHHHhhccchhhHH-HHHH--hcCCCCcEEEeccCcCC
Confidence            344444444333 3 55799999999999999999999999998888886543332 3333  345 4459999999999


Q ss_pred             CCCCC--------CCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHH
Q 015158          341 GIDVQ--------QVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDER  388 (412)
Q Consensus       341 G~d~~--------~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~  388 (412)
                      |.|+.        +--+||....+.|...-.|..||+||-|.+|.+-.|++-.|.-
T Consensus       689 GTDIkLg~~V~e~GGL~VIgTerheSrRID~QLrGRaGRQGDPGsS~f~lSLEDdL  744 (1112)
T PRK12901        689 GTDIKLSPEVKAAGGLAIIGTERHESRRVDRQLRGRAGRQGDPGSSQFYVSLEDNL  744 (1112)
T ss_pred             CcCcccchhhHHcCCCEEEEccCCCcHHHHHHHhcccccCCCCCcceEEEEcccHH
Confidence            99988        4568888999999999999999999999999999998877653

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

Probab=99.71  E-value=8.6e-16  Score=148.51  Aligned_cols=108  Identities=17%  Similarity=0.244  Sum_probs=96.6

Q ss_pred             CCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCC--CcEEEEcCCCcCCCCCCCCCEEEEccC
Q 015158          278 ITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGS--SRVLITTDLLARGIDVQQVSLVINYDL  355 (412)
Q Consensus       278 ~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~--~~vlv~t~~~~~G~d~~~~~~vi~~~~  355 (412)
                      +.++|||.+-.+-.+.+...|+-+|+-...+.|..+-++|..++++|+.+.  .+.|++|...+.|||+.++++||+|+.
T Consensus      1276 ghRvLIfTQMtkmLDVLeqFLnyHgylY~RLDg~t~vEqRQaLmerFNaD~RIfcfILSTrSggvGiNLtgADTVvFYDs 1355 (1958)
T KOG0391|consen 1276 GHRVLIFTQMTKMLDVLEQFLNYHGYLYVRLDGNTSVEQRQALMERFNADRRIFCFILSTRSGGVGINLTGADTVVFYDS 1355 (1958)
T ss_pred             CceEEehhHHHHHHHHHHHHHhhcceEEEEecCCccHHHHHHHHHHhcCCCceEEEEEeccCCccccccccCceEEEecC
Confidence            357899999999999999999999999999999999999999999999874  467889999999999999999999999


Q ss_pred             CCChhhHHHhhhhcccCCCCc--eEEEEeccC
Q 015158          356 PTQPENYLHRIGRSGRFGRKG--VAINFVTRD  385 (412)
Q Consensus       356 ~~s~~~~~Q~~GR~~R~g~~g--~~~~~~~~~  385 (412)
                      .|++.--.|.-.|+.|.|+..  ..|-+++..
T Consensus      1356 DwNPtMDaQAQDrChRIGqtRDVHIYRLISe~ 1387 (1958)
T KOG0391|consen 1356 DWNPTMDAQAQDRCHRIGQTRDVHIYRLISER 1387 (1958)
T ss_pred             CCCchhhhHHHHHHHhhcCccceEEEEeeccc
Confidence            999999999999999998754  456666654

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

Probab=99.71  E-value=2.4e-16  Score=153.68  Aligned_cols=309  Identities=16%  Similarity=0.197  Sum_probs=204.8

Q ss_pred             ChHHHHhhhhhhhc-CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHH-hhcccCcEEE
Q 015158           62 PSAIQQRGIVPFCK-GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRA-LGDYLGVKVH  139 (412)
Q Consensus        62 l~~~Q~~a~~~~~~-~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~-~~~~~~~~~~  139 (412)
                      .++.|.+.++.+.+ +.++++.+|+|||||.|+.++++..    ....+++++.|..+.+..+++.+.. +....|..+.
T Consensus      1144 ~n~iqtqVf~~~y~~nd~v~vga~~gsgkt~~ae~a~l~~----~~~~~~vyi~p~~~i~~~~~~~w~~~f~~~~G~~~~ 1219 (1674)
T KOG0951|consen 1144 FNPIQTQVFTSLYNTNDNVLVGAPNGSGKTACAELALLRP----DTIGRAVYIAPLEEIADEQYRDWEKKFSKLLGLRIV 1219 (1674)
T ss_pred             cCCceEEEEeeeecccceEEEecCCCCchhHHHHHHhcCC----ccceEEEEecchHHHHHHHHHHHHHhhccccCceEE
Confidence            47889999998876 4688999999999999998888762    2445899999999988777666644 5555688888


Q ss_pred             EEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccC-----cHHHHHHHHHhCCCCce
Q 015158          140 ACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRG-----FKDQIYDIFQLLPPKIQ  214 (412)
Q Consensus       140 ~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~-----~~~~~~~i~~~~~~~~~  214 (412)
                      .++|.......   .....+|+|+||++|..+ .    ..+.+++.|+||.|.+.+..     ..-.+..+...+-++.+
T Consensus      1220 ~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~ir 1291 (1674)
T KOG0951|consen 1220 KLTGETSLDLK---LLQKGQVIISTPEQWDLL-Q----SIQQVDLFIVDELHLIGGVYGAVYEVICSMRYIASQLEKKIR 1291 (1674)
T ss_pred             ecCCccccchH---HhhhcceEEechhHHHHH-h----hhhhcceEeeehhhhhcccCCceEEEEeeHHHHHHHHHhhee
Confidence            88887764332   334458999999999665 2    45678999999999876321     00125566666667888


Q ss_pred             EEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccch--h----h-HHHHHHHHHhc-CCCcEEEEEc
Q 015158          215 VGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEE--W----K-LETLCDLYETL-AITQSVIFVN  286 (412)
Q Consensus       215 ~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~----~-~~~l~~~~~~~-~~~k~lif~~  286 (412)
                      ++++|..+.+. .+.  ........+.... ...+.........+....  .    . ...+..+.+.. ..++.+||++
T Consensus      1292 ~v~ls~~lana-~d~--ig~s~~~v~Nf~p-~~R~~Pl~i~i~~~~~~~~~~~~~am~~~~~~ai~~~a~~~k~~~vf~p 1367 (1674)
T KOG0951|consen 1292 VVALSSSLANA-RDL--IGASSSGVFNFSP-SVRPVPLEIHIQSVDISHFESRMLAMTKPTYTAIVRHAGNRKPAIVFLP 1367 (1674)
T ss_pred             EEEeehhhccc-hhh--ccccccceeecCc-ccCCCceeEEEEEeccchhHHHHHHhhhhHHHHHHHHhcCCCCeEEEec
Confidence            99999987542 222  1111111122222 111222222222222111  1    1 11222222221 4478999999


Q ss_pred             chhHHHHHHHHHhcC----------------------CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCC
Q 015158          287 TRRKVDWLTDKMRSR----------------------DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDV  344 (412)
Q Consensus       287 ~~~~~~~~~~~L~~~----------------------~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~  344 (412)
                      ++++|..++.-|-..                      .....+-|.++++.+..-+-.-|..|.+.|+|.... ..|+-.
T Consensus      1368 ~rk~~~~~a~~~~~~s~~~~~~~l~~~~e~~~~~l~e~l~~gvg~e~~s~~d~~iv~~l~e~g~i~v~v~s~~-~~~~~~ 1446 (1674)
T KOG0951|consen 1368 TRKHARLVAVDLVTFSHADEPDYLLSELEECDETLRESLKHGVGHEGLSSNDQEIVQQLFEAGAIQVCVMSRD-CYGTKL 1446 (1674)
T ss_pred             cchhhhhhhhccchhhccCcHHHHHHHHhcchHhhhhcccccccccccCcchHHHHHHHHhcCcEEEEEEEcc-cccccc
Confidence            999987665444211                      122333388899999999999999999999988776 667776


Q ss_pred             CCCCEEEEcc-----------CCCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHH
Q 015158          345 QQVSLVINYD-----------LPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLF  391 (412)
Q Consensus       345 ~~~~~vi~~~-----------~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~  391 (412)
                      . .+.||.++           .+.+.+...||.|++.|   .|+|+++....+...++
T Consensus      1447 ~-~~lVvvmgt~~ydg~e~~~~~y~i~~ll~m~G~a~~---~~k~vi~~~~~~k~yyk 1500 (1674)
T KOG0951|consen 1447 K-AHLVVVMGTQYYDGKEHSYEDYPIAELLQMVGLASG---AGKCVIMCHTPKKEYYK 1500 (1674)
T ss_pred             c-ceEEEEecceeecccccccccCchhHHHHHhhhhcC---CccEEEEecCchHHHHH
Confidence            5 34444333           35678999999999999   58899998888877543

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

Probab=99.70  E-value=6e-15  Score=140.93  Aligned_cols=293  Identities=12%  Similarity=0.103  Sum_probs=187.9

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhc
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILS  155 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  155 (412)
                      +.-.+|.+|+|||||....-++...+.  .+..+++++..+++|+.+..+.++...- .++.. ....+.     .....
T Consensus        49 ~~V~vVRSpMGTGKTtaLi~wLk~~l~--~~~~~VLvVShRrSL~~sL~~rf~~~~l-~gFv~-Y~d~~~-----~~i~~  119 (824)
T PF02399_consen   49 RGVLVVRSPMGTGKTTALIRWLKDALK--NPDKSVLVVSHRRSLTKSLAERFKKAGL-SGFVN-YLDSDD-----YIIDG  119 (824)
T ss_pred             CCeEEEECCCCCCcHHHHHHHHHHhcc--CCCCeEEEEEhHHHHHHHHHHHHhhcCC-Cccee-eecccc-----ccccc
Confidence            345688999999999887776665543  2446899999999999999998876421 12221 111110     11111


Q ss_pred             CCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcH-------HHHHHHHHhCCCCceEEEEeecCChHHHH
Q 015158          156 SGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFK-------DQIYDIFQLLPPKIQVGVFSATMPPEALE  228 (412)
Q Consensus       156 ~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~-------~~~~~i~~~~~~~~~~i~~SAT~~~~~~~  228 (412)
                      ..++-++++.++|.+...   ..++++|+||+||+-.+...-+.       ..+..+...+.....+|++-|++.....+
T Consensus       120 ~~~~rLivqIdSL~R~~~---~~l~~yDvVIIDEv~svL~qL~S~Tm~~~~~v~~~L~~lI~~ak~VI~~DA~ln~~tvd  196 (824)
T PF02399_consen  120 RPYDRLIVQIDSLHRLDG---SLLDRYDVVIIDEVMSVLNQLFSPTMRQREEVDNLLKELIRNAKTVIVMDADLNDQTVD  196 (824)
T ss_pred             cccCeEEEEehhhhhccc---ccccccCEEEEehHHHHHHHHhHHHHhhHHHHHHHHHHHHHhCCeEEEecCCCCHHHHH
Confidence            245788888898876542   23457899999999876644222       22233445556788899999999999999


Q ss_pred             HHHHhcCCCeEEEecCCccccCCceEEEEEecc-----------------------------------chhhHHHHHHHH
Q 015158          229 ITRKFMNKPVRILVKRDELTLEGIKQFHVNVEK-----------------------------------EEWKLETLCDLY  273 (412)
Q Consensus       229 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----------------------------------~~~~~~~l~~~~  273 (412)
                      +++.+.+......+..+...+.-........+.                                   ..........+.
T Consensus       197 Fl~~~Rp~~~i~vI~n~y~~~~fs~R~~~~~~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~tF~~~L~  276 (824)
T PF02399_consen  197 FLASCRPDENIHVIVNTYASPGFSNRRCTFLRSLGTDTLAAALNPEDENADTSPTPKHSPDPTATAAISNDETTFFSELL  276 (824)
T ss_pred             HHHHhCCCCcEEEEEeeeecCCcccceEEEecccCcHHHHHHhCCcccccccCCCcCCCCccccccccccchhhHHHHHH
Confidence            999876544333222221111000000000000                                   011223444444


Q ss_pred             Hhc-CCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCC--CCEE
Q 015158          274 ETL-AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQ--VSLV  350 (412)
Q Consensus       274 ~~~-~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~--~~~v  350 (412)
                      ... .++++.||+++...++.+++........+.++++.-+..+   + +.  -++++|++-|+++..|+++..  .+.|
T Consensus       277 ~~L~~gknIcvfsSt~~~~~~v~~~~~~~~~~Vl~l~s~~~~~d---v-~~--W~~~~VviYT~~itvG~Sf~~~HF~~~  350 (824)
T PF02399_consen  277 ARLNAGKNICVFSSTVSFAEIVARFCARFTKKVLVLNSTDKLED---V-ES--WKKYDVVIYTPVITVGLSFEEKHFDSM  350 (824)
T ss_pred             HHHhCCCcEEEEeChHHHHHHHHHHHHhcCCeEEEEcCCCCccc---c-cc--ccceeEEEEeceEEEEeccchhhceEE
Confidence            443 4467888999999999999999888889999988755442   2 21  457999999999999999864  4445


Q ss_pred             EEccCC----CChhhHHHhhhhcccCCCCceEEEEeccCcH
Q 015158          351 INYDLP----TQPENYLHRIGRSGRFGRKGVAINFVTRDDE  387 (412)
Q Consensus       351 i~~~~~----~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~  387 (412)
                      +.+-.|    .++.+..|++||+-.. ...+.+++++....
T Consensus       351 f~yvk~~~~gpd~~s~~Q~lgRvR~l-~~~ei~v~~d~~~~  390 (824)
T PF02399_consen  351 FAYVKPMSYGPDMVSVYQMLGRVRSL-LDNEIYVYIDASGA  390 (824)
T ss_pred             EEEecCCCCCCcHHHHHHHHHHHHhh-ccCeEEEEEecccc
Confidence            444222    3456789999999444 56788888877543

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=99.65  E-value=2.6e-14  Score=138.38  Aligned_cols=138  Identities=19%  Similarity=0.189  Sum_probs=97.6

Q ss_pred             EEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHH----HHHHhc
Q 015158           80 IQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVRE----DQRILS  155 (412)
Q Consensus        80 lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~  155 (412)
                      +..+-+|||||.+|+-.+...+..++   .+|+++|...|..|+.+.|++...  +..+..++++.+...    +.....
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            33344699999999988888777654   899999999999999999998653  256778887776553    345556


Q ss_pred             CCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccC-----c-HHHHHHHHHhCCCCceEEEEeecCChHHHHH
Q 015158          156 SGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRG-----F-KDQIYDIFQLLPPKIQVGVFSATMPPEALEI  229 (412)
Q Consensus       156 ~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~-----~-~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~  229 (412)
                      +...|+|+|-..++       ..+.++++||+||=|.-.-..     | ...+-.... ...+..+|+.||||+-+....
T Consensus       239 G~~~IViGtRSAvF-------aP~~~LgLIIvdEEhd~sykq~~~p~yhaRdvA~~Ra-~~~~~~lvLgSaTPSles~~~  310 (665)
T PRK14873        239 GQARVVVGTRSAVF-------APVEDLGLVAIWDDGDDLLAEPRAPYPHAREVALLRA-HQHGCALLIGGHARTAEAQAL  310 (665)
T ss_pred             CCCcEEEEcceeEE-------eccCCCCEEEEEcCCchhhcCCCCCCccHHHHHHHHH-HHcCCcEEEECCCCCHHHHHH
Confidence            77899999944443       234689999999999643111     1 123333333 335788999999998765444


Q ss_pred             H
Q 015158          230 T  230 (412)
Q Consensus       230 ~  230 (412)
                      .
T Consensus       311 ~  311 (665)
T PRK14873        311 V  311 (665)
T ss_pred             H
Confidence            3

>KOG1015 consensus Transcription regulator XNP/ATRX, DEAD-box superfamily [Transcription]

Probab=99.64  E-value=2.6e-14  Score=136.06  Aligned_cols=118  Identities=19%  Similarity=0.229  Sum_probs=98.5

Q ss_pred             hHHHHHHHHHhc--CCCcEEEEEcchhHHHHHHHHHhcC----------------------CCeeEEecCCCCHHHHHHH
Q 015158          265 KLETLCDLYETL--AITQSVIFVNTRRKVDWLTDKMRSR----------------------DHTVSATHGDMDQNTRDII  320 (412)
Q Consensus       265 ~~~~l~~~~~~~--~~~k~lif~~~~~~~~~~~~~L~~~----------------------~~~~~~~~~~~~~~~r~~~  320 (412)
                      ++..|.++++..  .++|.|||.+|.....-+..+|.-.                      |.+...+.|......|.+.
T Consensus      1127 KmiLLleIL~mceeIGDKlLVFSQSL~SLdLIe~fLe~v~r~gk~~~d~~~~~~~eGkW~~GkDyyriDGst~s~~R~k~ 1206 (1567)
T KOG1015|consen 1127 KMILLLEILRMCEEIGDKLLVFSQSLISLDLIEDFLELVSREGKEDKDKPLIYKGEGKWLRGKDYYRLDGSTTSQSRKKW 1206 (1567)
T ss_pred             ceehHHHHHHHHHHhcceeEEeecccchhHHHHHHHHhhcccCccccccccccccccceecCCceEEecCcccHHHHHHH
Confidence            344555665554  4479999999999888888877521                      5678889999999999999


Q ss_pred             HHHHhcC-C---CcEEEEcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEe
Q 015158          321 MREFRSG-S---SRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFV  382 (412)
Q Consensus       321 ~~~f~~g-~---~~vlv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~  382 (412)
                      .++|++. +   ...||+|.+.+-|+|+-.++.||+++..|++..-.|.|=|+-|.|+...||+|=
T Consensus      1207 ~~~FNdp~NlRaRl~LISTRAGsLGiNLvAANRVIIfDasWNPSyDtQSIFRvyRfGQtKPvyiYR 1272 (1567)
T KOG1015|consen 1207 AEEFNDPTNLRARLFLISTRAGSLGINLVAANRVIIFDASWNPSYDTQSIFRVYRFGQTKPVYIYR 1272 (1567)
T ss_pred             HHHhcCcccceeEEEEEeeccCccccceeecceEEEEecccCCccchHHHHHHHhhcCcCceeehh
Confidence            9999874 2   248899999999999999999999999999999999999999999887777653

>smart00490 HELICc helicase superfamily c-terminal domain

Probab=99.63  E-value=1.2e-15  Score=108.80  Aligned_cols=81  Identities=41%  Similarity=0.749  Sum_probs=77.1

Q ss_pred             HHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccC
Q 015158          293 WLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRF  372 (412)
Q Consensus       293 ~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~  372 (412)
                      .+++.|+..+..+..+||+++..+|..+++.|.++...++++|+++++|+|+|.+++|++++++++...+.|++||++|.
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            46778888899999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             C
Q 015158          373 G  373 (412)
Q Consensus       373 g  373 (412)
                      |
T Consensus        82 g   82 (82)
T smart00490       82 G   82 (82)
T ss_pred             C
Confidence            5

>COG0553 HepA Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]

Probab=99.57  E-value=4.8e-13  Score=138.31  Aligned_cols=318  Identities=19%  Similarity=0.201  Sum_probs=205.9

Q ss_pred             CCChHHHHhhhhhhhc-----CccEEEECCCCCCchhHhHHHHHHhhccCCC-ceeEEEEcCCHHHHHHHHHHHHHhhcc
Q 015158           60 EKPSAIQQRGIVPFCK-----GLDVIQQAQSGTGKTATFCSGILQQLDYGLV-ECQALVLAPTRELAQQIEKVMRALGDY  133 (412)
Q Consensus        60 ~~l~~~Q~~a~~~~~~-----~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~-~~~~lil~P~~~L~~q~~~~~~~~~~~  133 (412)
                      ..++++|.+.++.+..     +.+.++...+|.|||...+..+......... .+..+++||+ +++.+|.+++.++...
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            4589999999988662     5678889999999998776666542222222 4579999996 6677799999888764


Q ss_pred             cCcEEEEEEcCcc-----hHHHHHHhcC----CCcEEEeChHHHHHHH-HcCCCCCCCceEEEEeCCchhhccCcHHHHH
Q 015158          134 LGVKVHACVGGTS-----VREDQRILSS----GVHVVVGTPGRVFDML-RRQSLRPDNIRIFVLDEADEMLSRGFKDQIY  203 (412)
Q Consensus       134 ~~~~~~~~~~~~~-----~~~~~~~~~~----~~~iii~T~~~l~~~~-~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~  203 (412)
                      ... +...+|...     ..........    .++++++|++.+.... ....+....++.+|+||+|.+.+.. .....
T Consensus       416 ~~~-~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~v~itty~~l~~~~~~~~~l~~~~~~~~v~DEa~~ikn~~-s~~~~  493 (866)
T COG0553         416 LRL-VLVYHGEKSELDKKREALRDLLKLHLVIIFDVVITTYELLRRFLVDHGGLKKIEWDRVVLDEAHRIKNDQ-SSEGK  493 (866)
T ss_pred             ccc-eeeeeCCcccccHHHHHHHHHhhhcccceeeEEechHHHHHHhhhhHHHHhhceeeeeehhhHHHHhhhh-hHHHH
Confidence            443 666666554     1222222222    2789999999997732 1223445678999999999976543 22222


Q ss_pred             HHHHhCCCCceEEEEeecCChHHHH----HHH----------------HhcCCCeEEEec--------------------
Q 015158          204 DIFQLLPPKIQVGVFSATMPPEALE----ITR----------------KFMNKPVRILVK--------------------  243 (412)
Q Consensus       204 ~i~~~~~~~~~~i~~SAT~~~~~~~----~~~----------------~~~~~~~~~~~~--------------------  243 (412)
                      .+. .+.... .+.+|+||-.+-..    .+.                ..+..+......                    
T Consensus       494 ~l~-~~~~~~-~~~LtgTPlen~l~eL~sl~~~f~~p~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~  571 (866)
T COG0553         494 ALQ-FLKALN-RLDLTGTPLENRLGELWSLLQEFLNPGLLGTSFAIFTRLFEKPIQAEEDIGPLEARELGIELLRKLLSP  571 (866)
T ss_pred             HHH-HHhhcc-eeeCCCChHhhhHHHHHHHHHHHhCCccccchHHHHHHHHhhhhhhcccccchhhHHHHHHHHHHHHHH
Confidence            222 332222 37777776211000    000                000000000000                    


Q ss_pred             ------CCc--c----------------------------c-------------cCC----------------------c
Q 015158          244 ------RDE--L----------------------------T-------------LEG----------------------I  252 (412)
Q Consensus       244 ------~~~--~----------------------------~-------------~~~----------------------~  252 (412)
                            ...  .                            .             ...                      +
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                  000  0                            0             000                      0


Q ss_pred             eE-EEEEecc---------------------------ch-hhHHHHHHHH-Hhc--CCC--cEEEEEcchhHHHHHHHHH
Q 015158          253 KQ-FHVNVEK---------------------------EE-WKLETLCDLY-ETL--AIT--QSVIFVNTRRKVDWLTDKM  298 (412)
Q Consensus       253 ~~-~~~~~~~---------------------------~~-~~~~~l~~~~-~~~--~~~--k~lif~~~~~~~~~~~~~L  298 (412)
                      .. .......                           .. .+...+.+++ ...  ...  ++++|++......-+...+
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            00 0000000                           00 3455555666 222  334  8999999999999999999


Q ss_pred             hcCCCeeEEecCCCCHHHHHHHHHHHhcC--CCcEEEEcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccCCCCc
Q 015158          299 RSRDHTVSATHGDMDQNTRDIIMREFRSG--SSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKG  376 (412)
Q Consensus       299 ~~~~~~~~~~~~~~~~~~r~~~~~~f~~g--~~~vlv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g  376 (412)
                      +..++....++|.++...|...+++|.++  ...+++++.+.+.|+|+..+++||++++.|++....|+..|+.|.|+..
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            99998899999999999999999999996  3446667789999999999999999999999999999999999999876


Q ss_pred             eEEEEe
Q 015158          377 VAINFV  382 (412)
Q Consensus       377 ~~~~~~  382 (412)
                      .+.++-
T Consensus       812 ~v~v~r  817 (866)
T COG0553         812 PVKVYR  817 (866)
T ss_pred             eeEEEE
Confidence            654444

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

Probab=99.57  E-value=1.6e-14  Score=109.40  Aligned_cols=134  Identities=21%  Similarity=0.253  Sum_probs=81.6

Q ss_pred             cCccEEEECCCCCCchhHhHHHHHHh-hccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHH
Q 015158           75 KGLDVIQQAQSGTGKTATFCSGILQQ-LDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRI  153 (412)
Q Consensus        75 ~~~~~lv~~~tGsGKT~~~~~~~~~~-~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  153 (412)
                      +|+-.++..++|+|||.-.+..++.. +..+   .++|++.||+.+++.+.+.++..    ++.+  ...-..     ..
T Consensus         3 kg~~~~~d~hpGaGKTr~vlp~~~~~~i~~~---~rvLvL~PTRvva~em~~aL~~~----~~~~--~t~~~~-----~~   68 (148)
T PF07652_consen    3 KGELTVLDLHPGAGKTRRVLPEIVREAIKRR---LRVLVLAPTRVVAEEMYEALKGL----PVRF--HTNARM-----RT   68 (148)
T ss_dssp             TTEEEEEE--TTSSTTTTHHHHHHHHHHHTT-----EEEEESSHHHHHHHHHHTTTS----SEEE--ESTTSS-------
T ss_pred             CCceeEEecCCCCCCcccccHHHHHHHHHcc---CeEEEecccHHHHHHHHHHHhcC----Cccc--Cceeee-----cc
Confidence            56677899999999998766655543 3333   58999999999999888877653    2222  111110     01


Q ss_pred             hcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccC--cHHHHHHHHHhCCCCceEEEEeecCChH
Q 015158          154 LSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRG--FKDQIYDIFQLLPPKIQVGVFSATMPPE  225 (412)
Q Consensus       154 ~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~--~~~~~~~i~~~~~~~~~~i~~SAT~~~~  225 (412)
                      ..++.-|-++|+..+.+.+.+ .....++++||+||||.....+  +...+... ... ...++|+|||||+..
T Consensus        69 ~~g~~~i~vMc~at~~~~~~~-p~~~~~yd~II~DEcH~~Dp~sIA~rg~l~~~-~~~-g~~~~i~mTATPPG~  139 (148)
T PF07652_consen   69 HFGSSIIDVMCHATYGHFLLN-PCRLKNYDVIIMDECHFTDPTSIAARGYLREL-AES-GEAKVIFMTATPPGS  139 (148)
T ss_dssp             --SSSSEEEEEHHHHHHHHHT-SSCTTS-SEEEECTTT--SHHHHHHHHHHHHH-HHT-TS-EEEEEESS-TT-
T ss_pred             ccCCCcccccccHHHHHHhcC-cccccCccEEEEeccccCCHHHHhhheeHHHh-hhc-cCeeEEEEeCCCCCC
Confidence            234567899999999887766 5556899999999999743332  11222222 111 246799999999864

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 ....

>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=99.53  E-value=7.5e-14  Score=125.74  Aligned_cols=152  Identities=18%  Similarity=0.096  Sum_probs=95.2

Q ss_pred             HHHhhhhhhh-------------cCccEEEECCCCCCchhHhHHHHHHhhccCC--CceeEEEEcCCHHHHHHHHHHHHH
Q 015158           65 IQQRGIVPFC-------------KGLDVIQQAQSGTGKTATFCSGILQQLDYGL--VECQALVLAPTRELAQQIEKVMRA  129 (412)
Q Consensus        65 ~Q~~a~~~~~-------------~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~--~~~~~lil~P~~~L~~q~~~~~~~  129 (412)
                      ||.+++..+.             ..+.+++..++|+|||..++..+........  ....+||+||. .+..+|.+++.+
T Consensus         1 ~Q~~~v~~m~~~~~~~~~~~~~~~~~g~lL~de~GlGKT~~~i~~~~~l~~~~~~~~~~~~LIv~P~-~l~~~W~~E~~~   79 (299)
T PF00176_consen    1 HQLEAVRWMLDRELVEEYPNSESPPRGGLLADEMGLGKTITAIALISYLKNEFPQRGEKKTLIVVPS-SLLSQWKEEIEK   79 (299)
T ss_dssp             HHHHHHHHHHHHH----TTSSSTTT-EEEE---TTSSHHHHHHHHHHHHHHCCTTSS-S-EEEEE-T-TTHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHhhhhcccccccCCCCEEEEECCCCCchhhhhhhhhhhhhccccccccceeEeecc-chhhhhhhhhcc
Confidence            5777776653             3467899999999999887665553222221  11259999999 888999999999


Q ss_pred             hhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHH--------HHHHcCCCCCCCceEEEEeCCchhhccCcHHH
Q 015158          130 LGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVF--------DMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQ  201 (412)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~--------~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~  201 (412)
                      +.......+..+.+...............+++|+|++.+.        ..+.     ..++++||+||+|.+.+..  ..
T Consensus        80 ~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~vvi~ty~~~~~~~~~~~~~~l~-----~~~~~~vIvDEaH~~k~~~--s~  152 (299)
T PF00176_consen   80 WFDPDSLRVIIYDGDSERRRLSKNQLPKYDVVITTYETLRKARKKKDKEDLK-----QIKWDRVIVDEAHRLKNKD--SK  152 (299)
T ss_dssp             HSGT-TS-EEEESSSCHHHHTTSSSCCCSSEEEEEHHHHH--TSTHTTHHHH-----TSEEEEEEETTGGGGTTTT--SH
T ss_pred             ccccccccccccccccccccccccccccceeeeccccccccccccccccccc-----cccceeEEEeccccccccc--cc
Confidence            9865456777777665222222223456799999999998        2222     1358999999999985443  33


Q ss_pred             HHHHHHhCCCCceEEEEeecCChH
Q 015158          202 IYDIFQLLPPKIQVGVFSATMPPE  225 (412)
Q Consensus       202 ~~~i~~~~~~~~~~i~~SAT~~~~  225 (412)
                      ....+..+. ...++++||||-.+
T Consensus       153 ~~~~l~~l~-~~~~~lLSgTP~~n  175 (299)
T PF00176_consen  153 RYKALRKLR-ARYRWLLSGTPIQN  175 (299)
T ss_dssp             HHHHHHCCC-ECEEEEE-SS-SSS
T ss_pred             ccccccccc-cceEEeeccccccc
Confidence            333444454 66689999998643

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.

>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=99.50  E-value=7.7e-11  Score=107.50  Aligned_cols=293  Identities=14%  Similarity=0.195  Sum_probs=198.7

Q ss_pred             ccCCCceeEEEEcCCHHHHHHHHHHHHHhhccc-------------CcE-------EEEEEcCcchHHHHHHh-------
Q 015158          102 DYGLVECQALVLAPTRELAQQIEKVMRALGDYL-------------GVK-------VHACVGGTSVREDQRIL-------  154 (412)
Q Consensus       102 ~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~-------------~~~-------~~~~~~~~~~~~~~~~~-------  154 (412)
                      .++-..++|||++|++..+-++.+.+.++....             +..       ...-.....+......+       
T Consensus        32 DQGftRPkVLIL~P~R~~A~~~V~~Li~l~~~~~~~~nk~RF~~efg~~~~~~~~~~~~~~~~~kP~D~~~~F~GN~DD~  111 (442)
T PF06862_consen   32 DQGFTRPKVLILLPFRNSALRIVETLISLLPPGKQVENKKRFEEEFGLPEDEDDDEEPPEFKKSKPEDFKALFSGNNDDC  111 (442)
T ss_pred             ccCCCCceEEEEcccHHHHHHHHHHHHHHcCccchHHHHHHHHHHcCCCccccchhhhccccCCCchhHHHhcCCCccce
Confidence            345566899999999999999998887765431             100       00000011122222222       


Q ss_pred             -----------------cCCCcEEEeChHHHHHHHHcC------CCCCCCceEEEEeCCchhhc--cCcHHHHHHHHHhC
Q 015158          155 -----------------SSGVHVVVGTPGRVFDMLRRQ------SLRPDNIRIFVLDEADEMLS--RGFKDQIYDIFQLL  209 (412)
Q Consensus       155 -----------------~~~~~iii~T~~~l~~~~~~~------~~~~~~~~~iiiDE~h~~~~--~~~~~~~~~i~~~~  209 (412)
                                       ..+.||||+||=.|...+...      .-.++.+.++|+|.+|.+.-  |.....+...+...
T Consensus       112 FrlGik~trk~ikLys~Fy~SDIIiASPLGLr~~i~~~~~~~~d~DFLSSIEv~iiD~ad~l~MQNW~Hv~~v~~~lN~~  191 (442)
T PF06862_consen  112 FRLGIKFTRKSIKLYSDFYSSDIIIASPLGLRMIIGEEGEKKRDYDFLSSIEVLIIDQADVLLMQNWEHVLHVFEHLNLQ  191 (442)
T ss_pred             EEEeEEEecCeeeeecccccCCEEEEChHHHHHHhccccccccccchhheeeeEeechhhHHHHhhHHHHHHHHHHhccC
Confidence                             123589999999988777642      22357788999999998763  33333333333333


Q ss_pred             CC---------------------CceEEEEeecCChHHHHHHHHhcCC-CeEEEe--cCC-----ccccCCceEEEEEec
Q 015158          210 PP---------------------KIQVGVFSATMPPEALEITRKFMNK-PVRILV--KRD-----ELTLEGIKQFHVNVE  260 (412)
Q Consensus       210 ~~---------------------~~~~i~~SAT~~~~~~~~~~~~~~~-~~~~~~--~~~-----~~~~~~~~~~~~~~~  260 (412)
                      |.                     -.|.|++|+...++........+.+ .-.+..  ...     ......+.+.+..++
T Consensus       192 P~~~~~~DfsRVR~w~Ldg~a~~~RQtii~S~~~~pe~~slf~~~~~N~~G~v~~~~~~~~~g~i~~v~~~v~Q~F~r~~  271 (442)
T PF06862_consen  192 PKKSHDTDFSRVRPWYLDGQAKYYRQTIIFSSFQTPEINSLFNRHCQNYAGKVRLKPPYEASGVISQVVVQVRQVFQRFD  271 (442)
T ss_pred             CCCCCCCCHHHHHHHHHcCcchheeEeEEecCCCCHHHHHHHHhhCcCccceEEEeeccccceeeeccccCCceEEEEec
Confidence            32                     2489999999999887777763322 111221  111     123345566666544


Q ss_pred             cch------hhHHH----HHHHHH-hcCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCC
Q 015158          261 KEE------WKLET----LCDLYE-TLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSS  329 (412)
Q Consensus       261 ~~~------~~~~~----l~~~~~-~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~  329 (412)
                      ...      .....    +...+. ....+.+|||++|.-+--.+..+|++.+.....++...+..+-...-..|.+|+.
T Consensus       272 ~~s~~~~~d~Rf~yF~~~iLP~l~~~~~~~~~LIfIPSYfDfVRlRN~lk~~~~sF~~i~EYts~~~isRAR~~F~~G~~  351 (442)
T PF06862_consen  272 CSSPADDPDARFKYFTKKILPQLKRDSKMSGTLIFIPSYFDFVRLRNYLKKENISFVQISEYTSNSDISRARSQFFHGRK  351 (442)
T ss_pred             CCCcchhhhHHHHHHHHHHHHHhhhccCCCcEEEEecchhhhHHHHHHHHhcCCeEEEecccCCHHHHHHHHHHHHcCCc
Confidence            322      11111    122223 4455789999999999999999999999999999999999999999999999999


Q ss_pred             cEEEEcCCC--cCCCCCCCCCEEEEccCCCChhhHHHhhhhcccCCC------CceEEEEeccCcHHHHHHHH
Q 015158          330 RVLITTDLL--ARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGR------KGVAINFVTRDDERMLFDIQ  394 (412)
Q Consensus       330 ~vlv~t~~~--~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~------~g~~~~~~~~~~~~~~~~~~  394 (412)
                      ++|+.|.-+  -.-..+.++++||++++|..+.-|...+.-.+....      ...|.++++.-|.-.++.+.
T Consensus       352 ~iLL~TER~HFfrRy~irGi~~viFY~~P~~p~fY~El~n~~~~~~~~~~~~~~~~~~~lysk~D~~~LErIV  424 (442)
T PF06862_consen  352 PILLYTERFHFFRRYRIRGIRHVIFYGPPENPQFYSELLNMLDESSGGEVDAADATVTVLYSKYDALRLERIV  424 (442)
T ss_pred             eEEEEEhHHhhhhhceecCCcEEEEECCCCChhHHHHHHhhhcccccccccccCceEEEEecHhHHHHHHHHh
Confidence            999999844  466778999999999999999988888765555432      57899999998887766553

; GO: 0005634 nucleus

>COG0653 SecA Preprotein translocase subunit SecA (ATPase, RNA helicase) [Intracellular trafficking and secretion]

Probab=99.45  E-value=2.3e-12  Score=124.26  Aligned_cols=316  Identities=21%  Similarity=0.261  Sum_probs=194.4

Q ss_pred             CCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcE
Q 015158           58 GFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVK  137 (412)
Q Consensus        58 ~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~  137 (412)
                      |+. ++..|.-..-.+..|  -+..+-||-|||+++.+++.-....+   ..+.+++.+.-|+..-++++..+....|+.
T Consensus        78 g~~-~~dVQliG~i~lh~g--~iaEM~TGEGKTL~atlp~ylnaL~g---kgVhvVTvNdYLA~RDae~m~~l~~~LGls  151 (822)
T COG0653          78 GMR-HFDVQLLGGIVLHLG--DIAEMRTGEGKTLVATLPAYLNALAG---KGVHVVTVNDYLARRDAEWMGPLYEFLGLS  151 (822)
T ss_pred             CCC-hhhHHHhhhhhhcCC--ceeeeecCCchHHHHHHHHHHHhcCC---CCcEEeeehHHhhhhCHHHHHHHHHHcCCc
Confidence            444 566666655555544  48899999999999988776554433   478899999999999999999999999999


Q ss_pred             EEEEEcCcchHHHHHHhcCCCcEEEeChHHHH-HHHH------cCCCCCCCceEEEEeCCchhh----------cc----
Q 015158          138 VHACVGGTSVREDQRILSSGVHVVVGTPGRVF-DMLR------RQSLRPDNIRIFVLDEADEML----------SR----  196 (412)
Q Consensus       138 ~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~-~~~~------~~~~~~~~~~~iiiDE~h~~~----------~~----  196 (412)
                      +.....+.......  ..-.++|.++|...|- ..+.      ......+...+.|+||++.+.          ++    
T Consensus       152 vG~~~~~m~~~ek~--~aY~~DItY~TnnElGFDYLRDNm~~~~ee~vqr~~~faIvDEvDSILIDEARtPLiISG~~~~  229 (822)
T COG0653         152 VGVILAGMSPEEKR--AAYACDITYGTNNELGFDYLRDNMVTSQEEKVQRGLNFAIVDEVDSILIDEARTPLIISGPAED  229 (822)
T ss_pred             eeeccCCCChHHHH--HHHhcCceeccccccCcchhhhhhhccHHHhhhccCCeEEEcchhheeeeccccceeeeccccc
Confidence            99988877644433  3345789999976651 1111      111223456778888888643          11    


Q ss_pred             --CcHHHHHHHHHhCCCC--------------------------------------------------------------
Q 015158          197 --GFKDQIYDIFQLLPPK--------------------------------------------------------------  212 (412)
Q Consensus       197 --~~~~~~~~i~~~~~~~--------------------------------------------------------------  212 (412)
                        ..+..+..+...+...                                                              
T Consensus       230 ~~~~Y~~~~~~v~~l~~~~d~~iDek~k~v~lte~G~~kae~~f~~~~Ly~~en~~~~h~~~~alrA~~l~~~D~dYIVr  309 (822)
T COG0653         230 SSELYKKVDDLVRLLSEDEDFTIDEKSKNVSLTESGLEKAEELLGIENLYDLENVNLVHHLNQALRAHILFFRDVDYIVR  309 (822)
T ss_pred             CchHHHHHHHHHHHhccccceeecchhcccccchhhHHHHHHHhCcccccchhhHHHHhhHHHHHHHHHHhhcCCeeEEe
Confidence              1122233333222100                                                              


Q ss_pred             -------------------------------------------------------ceEEEEeecCChHHHHHHHHhcCCC
Q 015158          213 -------------------------------------------------------IQVGVFSATMPPEALEITRKFMNKP  237 (412)
Q Consensus       213 -------------------------------------------------------~~~i~~SAT~~~~~~~~~~~~~~~~  237 (412)
                                                                             .+..+||+|...+..++..-+....
T Consensus       310 d~ev~IvD~ftGR~m~gRr~s~GLhQAiEAKEgv~i~~e~~tlatITfQn~fR~y~kl~gmTGTa~te~~EF~~iY~l~v  389 (822)
T COG0653         310 DGEVVIVDEFTGRMMEGRRWSDGLHQAIEAKEGVEIQEENQTLATITFQNLFRLYPKLAGMTGTADTEEEEFDVIYGLDV  389 (822)
T ss_pred             cCeEEEEecccCCcccCcCCCchhHHHHHHhcCCcccccceeehhhhHHHHHhhhhhhcCCCCcchhhhhhhhhccCCce
Confidence                                                                   1233333333222222222111111


Q ss_pred             eEEEecCCccccCCceEEEEEeccchhhHHHHHH-HHHhc-CCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHH
Q 015158          238 VRILVKRDELTLEGIKQFHVNVEKEEWKLETLCD-LYETL-AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQN  315 (412)
Q Consensus       238 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~-~~~~~-~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~  315 (412)
                      +.+.....-...+.-..   .......+...+.+ +...+ .+.|+||-+.+++..+.+.+.|.+.|++..+++......
T Consensus       390 v~iPTnrp~~R~D~~D~---vy~t~~~K~~Aiv~~I~~~~~~gqPvLvgT~sie~SE~ls~~L~~~~i~h~VLNAk~h~~  466 (822)
T COG0653         390 VVIPTNRPIIRLDEPDL---VYKTEEEKFKAIVEDIKERHEKGQPVLVGTVSIEKSELLSKLLRKAGIPHNVLNAKNHAR  466 (822)
T ss_pred             eeccCCCcccCCCCccc---cccchHHHHHHHHHHHHHHHhcCCCEEEcCcceecchhHHHHHHhcCCCceeeccccHHH
Confidence            11111111111111111   11122334444444 44444 568999999999999999999999999998888876533


Q ss_pred             HHHHHHHHHhcCCC-cEEEEcCCCcCCCCCCCCC-----------EEEEccCCCChhhHHHhhhhcccCCCCceEEEEec
Q 015158          316 TRDIIMREFRSGSS-RVLITTDLLARGIDVQQVS-----------LVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVT  383 (412)
Q Consensus       316 ~r~~~~~~f~~g~~-~vlv~t~~~~~G~d~~~~~-----------~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~  383 (412)
                      +-+.+-   .+|.. -|-|+|+++++|.|+.--.           +||-....-|...-.|.-||+||.|.+|.+-.|++
T Consensus       467 EA~Iia---~AG~~gaVTiATNMAGRGTDIkLg~~~~~V~~lGGL~VIgTERhESRRIDnQLRGRsGRQGDpG~S~F~lS  543 (822)
T COG0653         467 EAEIIA---QAGQPGAVTIATNMAGRGTDIKLGGNPEFVMELGGLHVIGTERHESRRIDNQLRGRAGRQGDPGSSRFYLS  543 (822)
T ss_pred             HHHHHh---hcCCCCccccccccccCCcccccCCCHHHHHHhCCcEEEecccchhhHHHHHhhcccccCCCcchhhhhhh
Confidence            322222   34544 4889999999999987322           45556666677777799999999999999887776


Q ss_pred             cCcH
Q 015158          384 RDDE  387 (412)
Q Consensus       384 ~~~~  387 (412)
                      -.|.
T Consensus       544 leD~  547 (822)
T COG0653         544 LEDD  547 (822)
T ss_pred             hHHH
Confidence            5544

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=99.30  E-value=2e-11  Score=107.79  Aligned_cols=73  Identities=23%  Similarity=0.209  Sum_probs=57.7

Q ss_pred             CCCCCChHHHHhhhh----hhhcCccEEEECCCCCCchhHhHHHHHHhhccCCC---ceeEEEEcCCHHHHHHHHHHHHH
Q 015158           57 YGFEKPSAIQQRGIV----PFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLV---ECQALVLAPTRELAQQIEKVMRA  129 (412)
Q Consensus        57 ~~~~~l~~~Q~~a~~----~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~---~~~~lil~P~~~L~~q~~~~~~~  129 (412)
                      ++|. |||.|.+.+.    .+..|+++++.+|||+|||++++.+++..+.....   ..+++|.++|.++.+|...++++
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            5777 7999999444    45568899999999999999999999866544322   23799999999998888777765


Q ss_pred             h
Q 015158          130 L  130 (412)
Q Consensus       130 ~  130 (412)
                      .
T Consensus        84 ~   84 (289)
T smart00488       84 L   84 (289)
T ss_pred             c
Confidence            4

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=99.30  E-value=2e-11  Score=107.79  Aligned_cols=73  Identities=23%  Similarity=0.209  Sum_probs=57.7

Q ss_pred             CCCCCChHHHHhhhh----hhhcCccEEEECCCCCCchhHhHHHHHHhhccCCC---ceeEEEEcCCHHHHHHHHHHHHH
Q 015158           57 YGFEKPSAIQQRGIV----PFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLV---ECQALVLAPTRELAQQIEKVMRA  129 (412)
Q Consensus        57 ~~~~~l~~~Q~~a~~----~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~---~~~~lil~P~~~L~~q~~~~~~~  129 (412)
                      ++|. |||.|.+.+.    .+..|+++++.+|||+|||++++.+++..+.....   ..+++|.++|.++.+|...++++
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            5777 7999999444    45568899999999999999999999866544322   23799999999998888777765


Q ss_pred             h
Q 015158          130 L  130 (412)
Q Consensus       130 ~  130 (412)
                      .
T Consensus        84 ~   84 (289)
T smart00489       84 L   84 (289)
T ss_pred             c
Confidence            4

>PRK15483 type III restriction-modification system StyLTI enzyme res; Provisional

Probab=99.25  E-value=1.7e-09  Score=107.12  Aligned_cols=143  Identities=14%  Similarity=0.236  Sum_probs=86.4

Q ss_pred             ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHH---------HhhcccCcEEEEEEcCc--
Q 015158           77 LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMR---------ALGDYLGVKVHACVGGT--  145 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~---------~~~~~~~~~~~~~~~~~--  145 (412)
                      .++.+.++||+|||.+|+..++..... ....++||+||+.+..+.+...+.         .......+....+.+..  
T Consensus        60 ~n~~~~M~TGtGKT~~~~~~i~~l~~~-~~~~~fii~vp~~aI~egv~~~l~s~~~k~hF~~~y~~~~~~~~~~~S~k~~  138 (986)
T PRK15483         60 ANIDIKMETGTGKTYVYTRLMYELHQK-YGLFKFIIVVPTPAIKEGTRNFIQSDYAKQHFSQFYENTRIELYVINAGDKK  138 (986)
T ss_pred             ceEEEEeCCCCCHHHHHHHHHHHHHHH-cCCcEEEEEeCCHHHHHHHHHHhhHHHHHHHHHHHcCCceeEEEEEecCccc
Confidence            478999999999999998888765443 234689999999998877765554         11222234444454332  


Q ss_pred             -----chHHHHHHhc-------CCCcEEEeChHHHHHHHH--cC--CC----CCCCc-------eEEEEeCCchhhccCc
Q 015158          146 -----SVREDQRILS-------SGVHVVVGTPGRVFDMLR--RQ--SL----RPDNI-------RIFVLDEADEMLSRGF  198 (412)
Q Consensus       146 -----~~~~~~~~~~-------~~~~iii~T~~~l~~~~~--~~--~~----~~~~~-------~~iiiDE~h~~~~~~~  198 (412)
                           ........+.       +...|+++|.+.|.....  ..  .+    ....+       -+||+||.|++...  
T Consensus       139 k~gr~~~~~~i~~Fa~~~~~~~~~I~Ilv~niqa~n~~~~~~~~~D~~l~~g~~~p~~~i~~~~PivIiDEPh~~~~~--  216 (986)
T PRK15483        139 KSGRKNFPAQLSNFVKASRQNSNTIHVLLINAGMLNSASMTRDDYDQTLLGGFTSPVDALAATRPVVIIDEPHRFPRD--  216 (986)
T ss_pred             ccccccChHHHHHHHhccccCCCceEEEEEehHHhcccccccchhhhhhccCCCChHHHHHhCCCEEEEECCCCCCcc--
Confidence                 1111211121       146899999998865221  00  00    00111       27999999997543  


Q ss_pred             HHHHHHHHHhCCCCceEEEEeecCCh
Q 015158          199 KDQIYDIFQLLPPKIQVGVFSATMPP  224 (412)
Q Consensus       199 ~~~~~~i~~~~~~~~~~i~~SAT~~~  224 (412)
                      ...+..+ ..+.+.. ++..|||.+.
T Consensus       217 ~k~~~~i-~~lnpl~-~lrysAT~~~  240 (986)
T PRK15483        217 NKFYQAI-EALKPQM-IIRFGATFPD  240 (986)
T ss_pred             hHHHHHH-HhcCccc-EEEEeeecCC
Confidence            2344555 4454444 5669999865

>KOG1016 consensus Predicted DNA helicase, DEAD-box superfamily [General function prediction only]

Probab=99.17  E-value=4.3e-09  Score=99.26  Aligned_cols=106  Identities=18%  Similarity=0.291  Sum_probs=87.8

Q ss_pred             CcEEEEEcchhHHHHHHHHHhcC------------------CCeeEEecCCCCHHHHHHHHHHHhcC--CC-cEEEEcCC
Q 015158          279 TQSVIFVNTRRKVDWLTDKMRSR------------------DHTVSATHGDMDQNTRDIIMREFRSG--SS-RVLITTDL  337 (412)
Q Consensus       279 ~k~lif~~~~~~~~~~~~~L~~~------------------~~~~~~~~~~~~~~~r~~~~~~f~~g--~~-~vlv~t~~  337 (412)
                      .++|||.++.....-+.+.|.++                  +.....+.|..+..+|++++.+|+..  -. -++++|.+
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            37899999998888888888765                  12344567778889999999999873  22 36778999


Q ss_pred             CcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEecc
Q 015158          338 LARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTR  384 (412)
Q Consensus       338 ~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~  384 (412)
                      ...|+|+-..+.+++++..|++..-.|++.|+-|.|+...|+++=.-
T Consensus       800 g~lGinLIsanr~~ifda~wnpchdaqavcRvyrYGQ~KpcfvYRlV  846 (1387)
T KOG1016|consen  800 GSLGINLISANRCIIFDACWNPCHDAQAVCRVYRYGQQKPCFVYRLV  846 (1387)
T ss_pred             ccccceeeccceEEEEEeecCccccchhhhhhhhhcCcCceeEEeeh
Confidence            99999999888899999999999999999999999998888876543

>KOG1133 consensus Helicase of the DEAD superfamily [Replication, recombination and repair]

Probab=99.15  E-value=1.4e-07  Score=88.53  Aligned_cols=104  Identities=14%  Similarity=0.204  Sum_probs=74.2

Q ss_pred             CcEEEEEcchhHHHHHHHHHhcCCC-------eeEEecCCCCHHHHHHHHHHHhc----CCCcEEEEc--CCCcCCCCCC
Q 015158          279 TQSVIFVNTRRKVDWLTDKMRSRDH-------TVSATHGDMDQNTRDIIMREFRS----GSSRVLITT--DLLARGIDVQ  345 (412)
Q Consensus       279 ~k~lif~~~~~~~~~~~~~L~~~~~-------~~~~~~~~~~~~~r~~~~~~f~~----g~~~vlv~t--~~~~~G~d~~  345 (412)
                      +.+++|++|.+....+.+.+.+.|+       +-+++-..-+   -+.+++.+..    |...+|++.  .-+++|||+.
T Consensus       630 gGvV~FfPSy~yL~~v~k~w~~~gil~ri~~kK~vF~E~k~~---~~dvl~~Ya~a~~~g~GaiLlaVVGGKlSEGINF~  706 (821)
T KOG1133|consen  630 GGVVCFFPSYAYLGQVRKRWEQNGILARIVGKKKVFYEPKDT---VEDVLEGYAEAAERGRGAILLAVVGGKLSEGINFS  706 (821)
T ss_pred             CcEEEEeccHHHHHHHHHHHHhcchHHHhhccchhhccCccc---HHHHHHHHHHHhhcCCCeEEEEEeccccccccccc
Confidence            7899999999999999999987643       2222322222   3556666643    555677654  5889999998


Q ss_pred             C--CCEEEEccCCCC--------------------------------hhhHHHhhhhcccCCCCceEEEEeccC
Q 015158          346 Q--VSLVINYDLPTQ--------------------------------PENYLHRIGRSGRFGRKGVAINFVTRD  385 (412)
Q Consensus       346 ~--~~~vi~~~~~~s--------------------------------~~~~~Q~~GR~~R~g~~g~~~~~~~~~  385 (412)
                      +  ++.|+.+++|+.                                +....|.+|||.|..++--++++++..
T Consensus       707 D~LgRaVvvVGlPyPN~~s~EL~er~k~l~~k~~~~gagke~yEnlCMkAVNQsIGRAIRH~~DYA~i~LlD~R  780 (821)
T KOG1133|consen  707 DDLGRAVVVVGLPYPNIQSVELQERMKHLDGKLPTPGAGKELYENLCMKAVNQSIGRAIRHRKDYASIYLLDKR  780 (821)
T ss_pred             cccccEEEEeecCCCCCCCHHHHHHHHHhhhccCCCCchHHHHHHHHHHHHHHHHHHHHhhhccceeEEEehhh
Confidence            6  788888888742                                224579999999997777777777654

>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=99.06  E-value=2.7e-09  Score=91.65  Aligned_cols=130  Identities=23%  Similarity=0.302  Sum_probs=96.1

Q ss_pred             CCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCc
Q 015158           57 YGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGV  136 (412)
Q Consensus        57 ~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~  136 (412)
                      .|+. |++.|.-+.-.+.+|+  ++.+.||-|||+++.++++-....+   ..|=|++.+..|+..-++++..+...+|+
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 LGLR-PYDVQLLGALALHKGR--LAEMKTGEGKTLIAALPAALNALQG---KGVHVVTSNDYLAKRDAEEMRPFYEFLGL  147 (266)
T ss_dssp             TS-----HHHHHHHHHHHTTS--EEEESTTSHHHHHHHHHHHHHHTTS---S-EEEEESSHHHHHHHHHHHHHHHHHTT-
T ss_pred             cCCc-ccHHHHhhhhhcccce--eEEecCCCCcHHHHHHHHHHHHHhc---CCcEEEeccHHHhhccHHHHHHHHHHhhh
Confidence            4666 9999999998887776  9999999999988877766555444   47999999999999999999999999999


Q ss_pred             EEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCC-------CCCCceEEEEeCCchhh
Q 015158          137 KVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSL-------RPDNIRIFVLDEADEML  194 (412)
Q Consensus       137 ~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~-------~~~~~~~iiiDE~h~~~  194 (412)
                      .+....++.+........  .++|+++|...|..-+.+..+       ..+.++++|+||++.++
T Consensus       148 sv~~~~~~~~~~~r~~~Y--~~dI~Y~t~~~~~fD~Lrd~~~~~~~~~~~r~~~~~ivDEvDs~L  210 (266)
T PF07517_consen  148 SVGIITSDMSSEERREAY--AADIVYGTNSEFGFDYLRDNLALSKNEQVQRGFDFAIVDEVDSIL  210 (266)
T ss_dssp             -EEEEETTTEHHHHHHHH--HSSEEEEEHHHHHHHHHHHTT-SSGGG--SSSSSEEEECTHHHHT
T ss_pred             ccccCccccCHHHHHHHH--hCcccccccchhhHHHHHHHHhhccchhccCCCCEEEEeccceEE
Confidence            999999887754433333  357999999988653322221       13678899999999865

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 ....

>KOG2340 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.06  E-value=1.3e-08  Score=92.29  Aligned_cols=334  Identities=18%  Similarity=0.217  Sum_probs=198.5

Q ss_pred             CCCCChHHHHhhhhhhhcCccEEE-ECCCCCCc--hhHhHHHHHHhh----------------------------ccCCC
Q 015158           58 GFEKPSAIQQRGIVPFCKGLDVIQ-QAQSGTGK--TATFCSGILQQL----------------------------DYGLV  106 (412)
Q Consensus        58 ~~~~l~~~Q~~a~~~~~~~~~~lv-~~~tGsGK--T~~~~~~~~~~~----------------------------~~~~~  106 (412)
                      .-.++++.|.+.+....+.++++- ....+.|+  +-.|.+.+++++                            .++-.
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            345689999999999888888764 23334555  345556666554                            11223


Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhhcccCc-EE---------EEEEcC-------cchHHH-HHHh--------------
Q 015158          107 ECQALVLAPTRELAQQIEKVMRALGDYLGV-KV---------HACVGG-------TSVRED-QRIL--------------  154 (412)
Q Consensus       107 ~~~~lil~P~~~L~~q~~~~~~~~~~~~~~-~~---------~~~~~~-------~~~~~~-~~~~--------------  154 (412)
                      .++||||||++.-+-...+.+..+....+- +.         ..+.|.       .+.+.+ ...+              
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            568999999999999988888776322110 00         001110       000111 1111              


Q ss_pred             ----------cCCCcEEEeChHHHHHHHHcCCC------CCCCceEEEEeCCchhhccCcHHHHHHHHHhCCC---C---
Q 015158          155 ----------SSGVHVVVGTPGRVFDMLRRQSL------RPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPP---K---  212 (412)
Q Consensus       155 ----------~~~~~iii~T~~~l~~~~~~~~~------~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~---~---  212 (412)
                                ....+|+||+|=.|...+.+.+-      .++.+.++|+|.+|.+...+ ...+..++..++.   .   
T Consensus       373 tkKtikLys~fy~SDIlVaSPLGLRmil~n~gdkkrd~dfLSSIEl~iIDQa~~~l~QN-wEhl~~ifdHLn~~P~k~h~  451 (698)
T KOG2340|consen  373 TKKTIKLYSKFYKSDILVASPLGLRMILGNTGDKKRDFDFLSSIELLIIDQADIMLMQN-WEHLLHIFDHLNLQPSKQHD  451 (698)
T ss_pred             HHHHHHHHhhhcccCeEEecchhhhhhhcCCCcccccchhhhhhhhhhhhhHHHHHHhh-HHHHHHHHHHhhcCcccccC
Confidence                      13458999999988777763221      24567899999999877554 3445555555431   1   


Q ss_pred             ------------------ceEEEEeecCChHHHHHHHHhcCCC---eEEEecCCccccC----CceEEE--EEecc----
Q 015158          213 ------------------IQVGVFSATMPPEALEITRKFMNKP---VRILVKRDELTLE----GIKQFH--VNVEK----  261 (412)
Q Consensus       213 ------------------~~~i~~SAT~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~----~~~~~~--~~~~~----  261 (412)
                                        .|.+++|+--.+.....+...+.+.   +........-...    .+.+.+  ..+..    
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                              1333444433333333222222111   1111111110000    011111  11111    


Q ss_pred             chhhHHHH-HHHHHhc---CCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCC
Q 015158          262 EEWKLETL-CDLYETL---AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDL  337 (412)
Q Consensus       262 ~~~~~~~l-~~~~~~~---~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~  337 (412)
                      .+.....+ ..++...   ...-+|||.||.-.--++..++++..+....++...+...-...-+.|..|...+++-|.-
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            11122221 1222221   2245799999999999999999999888888888878777788889999999999999985


Q ss_pred             C--cCCCCCCCCCEEEEccCCCChhhH---HHhhhhcccCC----CCceEEEEeccCcHHHHHH
Q 015158          338 L--ARGIDVQQVSLVINYDLPTQPENY---LHRIGRSGRFG----RKGVAINFVTRDDERMLFD  392 (412)
Q Consensus       338 ~--~~G~d~~~~~~vi~~~~~~s~~~~---~Q~~GR~~R~g----~~g~~~~~~~~~~~~~~~~  392 (412)
                      +  -+-.++++++.||++.+|..+.-|   +.+++|..-.|    ..-.|.++++.-|.-.+..
T Consensus       612 ~hffrR~~ikGVk~vVfYqpP~~P~FYsEiinm~~k~~~~gn~d~d~~t~~ilytKyD~i~Le~  675 (698)
T KOG2340|consen  612 AHFFRRYHIKGVKNVVFYQPPNNPHFYSEIINMSDKTTSQGNTDLDIFTVRILYTKYDRIRLEN  675 (698)
T ss_pred             hhhhhhheecceeeEEEecCCCCcHHHHHHHhhhhhhhccCCccccceEEEEEeechhhHHHHH
Confidence            4  577889999999999999987654   66777765443    2356888888876654433

>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]

Probab=99.03  E-value=2.7e-09  Score=103.27  Aligned_cols=102  Identities=17%  Similarity=0.168  Sum_probs=90.7

Q ss_pred             CcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCC-Cc-EEEEcCCCcCCCCCCCCCEEEEccCC
Q 015158          279 TQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGS-SR-VLITTDLLARGIDVQQVSLVINYDLP  356 (412)
Q Consensus       279 ~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~-~~-vlv~t~~~~~G~d~~~~~~vi~~~~~  356 (412)
                      .+++||++-...+..+...|...+.....+.|.++...|.+.+..|..+. .. .+++..+.+.|+|+..+.+|+..++.
T Consensus       540 ~kiiifsq~~~~l~l~~~~l~~~~~~~~~~~g~~~~~~r~~s~~~~~~~~~~~vll~Slkag~~glnlt~a~~v~~~d~~  619 (674)
T KOG1001|consen  540 PKIVIFSQLIWGLALVCLRLFFKGFVFLRYDGEMLMKIRTKSFTDFPCDPLVTALLMSLKAGKVGLNLTAASHVLLMDPW  619 (674)
T ss_pred             CceeeehhHHHHHHHhhhhhhhcccccchhhhhhHHHHHHhhhcccccCccHHHHHHHHHHhhhhhchhhhhHHHhhchh
Confidence            48999999999999999999888889999999999999999999998653 33 34567899999999999999999999


Q ss_pred             CChhhHHHhhhhcccCCCCceEEE
Q 015158          357 TQPENYLHRIGRSGRFGRKGVAIN  380 (412)
Q Consensus       357 ~s~~~~~Q~~GR~~R~g~~g~~~~  380 (412)
                      |++....|.+-|+.|.|+...+.+
T Consensus       620 wnp~~eeQaidR~hrigq~k~v~v  643 (674)
T KOG1001|consen  620 WNPAVEEQAIDRAHRIGQTKPVKV  643 (674)
T ss_pred             cChHHHHHHHHHHHHhcccceeee
Confidence            999999999999999998776655

>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]

Probab=99.02  E-value=1.8e-09  Score=103.37  Aligned_cols=310  Identities=15%  Similarity=0.205  Sum_probs=182.3

Q ss_pred             HHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCc--eeEEEEcCCHHHHHHHHHHHHH-----hhcccCcE
Q 015158           65 IQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVE--CQALVLAPTRELAQQIEKVMRA-----LGDYLGVK  137 (412)
Q Consensus        65 ~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~--~~~lil~P~~~L~~q~~~~~~~-----~~~~~~~~  137 (412)
                      +-.+.+..+..+..+++.+.||.|||..+...++..+.....+  ..+.+.-|++..+.-+++.+..     .+...+.+
T Consensus       382 ~~~~i~q~v~dn~v~~I~getgcgk~tq~aq~iLe~~~~ns~g~~~na~v~qprrisaisiaerva~er~e~~g~tvgy~  461 (1282)
T KOG0921|consen  382 YRSEILQAVAENRVVIIKGETGCGKSTQVAQFLLESFLENSNGASFNAVVSQPRRISAISLAERVANERGEEVGETCGYN  461 (1282)
T ss_pred             HHHHHHHHHhcCceeeEeecccccchhHHHHHHHHHHhhccccccccceeccccccchHHHHHHHHHhhHHhhccccccc
Confidence            3445555666678889999999999999988888887655322  2355666777665555554432     33222333


Q ss_pred             EEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhcc-CcHHHHHHHHHhCCCCceEE
Q 015158          138 VHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSR-GFKDQIYDIFQLLPPKIQVG  216 (412)
Q Consensus       138 ~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~-~~~~~~~~i~~~~~~~~~~i  216 (412)
                      +.....-..         ..-.|..+|.+-+.+..+...   ..+.++|+||+|+.--. .|...+.+=+....+...++
T Consensus       462 vRf~Sa~pr---------pyg~i~fctvgvllr~~e~gl---rg~sh~i~deiherdv~~dfll~~lr~m~~ty~dl~v~  529 (1282)
T KOG0921|consen  462 VRFDSATPR---------PYGSIMFCTVGVLLRMMENGL---RGISHVIIDEIHERDVDTDFVLIVLREMISTYRDLRVV  529 (1282)
T ss_pred             ccccccccc---------cccceeeeccchhhhhhhhcc---cccccccchhhhhhccchHHHHHHHHhhhccchhhhhh
Confidence            322211110         112588999999988877654   46789999999974322 23322222222223455667


Q ss_pred             EEeecCChHHH--------------------HHHHHhcCCCeEE-Eec---------CCccccCC------c--------
Q 015158          217 VFSATMPPEAL--------------------EITRKFMNKPVRI-LVK---------RDELTLEG------I--------  252 (412)
Q Consensus       217 ~~SAT~~~~~~--------------------~~~~~~~~~~~~~-~~~---------~~~~~~~~------~--------  252 (412)
                      ++|||+..+..                    .+....+..+... ...         ..+..++.      .        
T Consensus       530 lmsatIdTd~f~~~f~~~p~~~~~grt~pvq~F~led~~~~~~~vp~~~~~~k~k~~~~~~~~~~ddK~~n~n~~~dd~~  609 (1282)
T KOG0921|consen  530 LMSATIDTDLFTNFFSSIPDVTVHGRTFPVQSFFLEDIIQMTQFVPSEPSQKKRKKDDDEEDEEVDDKGRNMNILCDPSY  609 (1282)
T ss_pred             hhhcccchhhhhhhhccccceeeccccccHHHHHHHHhhhhhhccCCCcCccchhhcccccCchhhhcccccccccChhh
Confidence            77777653211                    1111111111100 000         00000000      0        


Q ss_pred             ----eEEEEEeccchhhHHHHHHHH----HhcCCCcEEEEEcchhHHHHHHHHHhcC-------CCeeEEecCCCCHHHH
Q 015158          253 ----KQFHVNVEKEEWKLETLCDLY----ETLAITQSVIFVNTRRKVDWLTDKMRSR-------DHTVSATHGDMDQNTR  317 (412)
Q Consensus       253 ----~~~~~~~~~~~~~~~~l~~~~----~~~~~~k~lif~~~~~~~~~~~~~L~~~-------~~~~~~~~~~~~~~~r  317 (412)
                          ...+............+..++    ...-.+-+++|.+.-...-.++..|..+       ...+...|+.....+.
T Consensus       610 ~~~~~~am~~~se~d~~f~l~Eal~~~i~s~~i~gailvflpgwa~i~~L~~~ll~~~~fg~~~~y~ilp~Hsq~~~~eq  689 (1282)
T KOG0921|consen  610 NESTRTAMSRLSEKDIPFGLIEALLNDIASRNIDGAVLVFLPGWAEIMTLCNRLLEHQEFGQANKYEILPLHSQLTSQEQ  689 (1282)
T ss_pred             cchhhhhhhcchhhcchhHHHHHHHhhhcccCCccceeeecCchHHhhhhhhhhhhhhhhccchhcccccchhhcccHhh
Confidence                000000000000011111111    2223367889999888888888877654       4567888998888888


Q ss_pred             HHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEcc------------------CCCChhhHHHhhhhcccCCCCceEE
Q 015158          318 DIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYD------------------LPTQPENYLHRIGRSGRFGRKGVAI  379 (412)
Q Consensus       318 ~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~------------------~~~s~~~~~Q~~GR~~R~g~~g~~~  379 (412)
                      .++.+....|..++|++|.+..+.+.+.++..|++.+                  ...|....+|+.||+||. .+|.|.
T Consensus       690 rkvf~~~p~gv~kii~stniaetsiTidd~v~vid~cka~~~~~~s~nn~~~~Atvw~sktn~eqr~gr~grv-R~G~~f  768 (1282)
T KOG0921|consen  690 RKVFEPVPEGVTKIILSTNIAETSITIDDVVYVIDSCKAKEKLFTSHNNMTHYATVWASKTNLEQRKGRAGRV-RPGFCF  768 (1282)
T ss_pred             hhccCcccccccccccccceeeEeeeecceeEEEeeeeeeeeeeccccceeeeeeecccccchHhhcccCcee-cccccc
Confidence            8999888889999999999999888887766665332                  235778899999999998 678888


Q ss_pred             EEeccCcH
Q 015158          380 NFVTRDDE  387 (412)
Q Consensus       380 ~~~~~~~~  387 (412)
                      .+.+....
T Consensus       769 ~lcs~arF  776 (1282)
T KOG0921|consen  769 HLCSRARF  776 (1282)
T ss_pred             cccHHHHH
Confidence            77765443

>COG3587 Restriction endonuclease [Defense mechanisms]

Probab=98.94  E-value=4.1e-08  Score=94.15  Aligned_cols=72  Identities=19%  Similarity=0.237  Sum_probs=55.5

Q ss_pred             CCCcEEEEcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccC--CCCce-----------EEEEeccCcHHHHHHH
Q 015158          327 GSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRF--GRKGV-----------AINFVTRDDERMLFDI  393 (412)
Q Consensus       327 g~~~vlv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~--g~~g~-----------~~~~~~~~~~~~~~~~  393 (412)
                      ...+.|++..++.+|+|-|++=+++-+....|...=.|.+||+-|.  .+.|.           -.+++......++..+
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            4578999999999999999999999999999999999999999994  22222           2345555666666666


Q ss_pred             HHHhc
Q 015158          394 QKFYN  398 (412)
Q Consensus       394 ~~~~~  398 (412)
                      ++...
T Consensus       562 qkEI~  566 (985)
T COG3587         562 QKEIN  566 (985)
T ss_pred             HHHHH
Confidence            65443

>PF13872 AAA_34: P-loop containing NTP hydrolase pore-1

Probab=98.93  E-value=1.8e-08  Score=86.79  Aligned_cols=155  Identities=20%  Similarity=0.201  Sum_probs=103.3

Q ss_pred             ChHHHHhhhhhhhc----------CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhh
Q 015158           62 PSAIQQRGIVPFCK----------GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALG  131 (412)
Q Consensus        62 l~~~Q~~a~~~~~~----------~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~  131 (412)
                      +...|.+++-...+          +..+++-..||.||-......++.....++  .+.|++..+..|..+..+.++.+.
T Consensus        38 LS~~QLEaV~yA~q~h~~~Lp~~~R~Gf~lGDGtGvGKGR~iAgiI~~n~l~Gr--~r~vwvS~s~dL~~Da~RDl~DIG  115 (303)
T PF13872_consen   38 LSALQLEAVIYACQRHEQILPGGSRAGFFLGDGTGVGKGRQIAGIILENWLRGR--KRAVWVSVSNDLKYDAERDLRDIG  115 (303)
T ss_pred             ccHHHHHHHHHHHHHHHhhcccccCcEEEeccCCCcCccchhHHHHHHHHHcCC--CceEEEECChhhhhHHHHHHHHhC
Confidence            67788887766542          346788889999999888777777766653  479999999999999999999875


Q ss_pred             cccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcC---CCC---------CCCceEEEEeCCchhhccCc-
Q 015158          132 DYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQ---SLR---------PDNIRIFVLDEADEMLSRGF-  198 (412)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~---~~~---------~~~~~~iiiDE~h~~~~~~~-  198 (412)
                      .. .+.+..+..-..    .....-+..|+++||..|.......   ...         ...=++||+||||...+... 
T Consensus       116 ~~-~i~v~~l~~~~~----~~~~~~~~GvlF~TYs~L~~~~~~~~~~~sRl~ql~~W~g~dfdgvivfDEcH~akn~~~~  190 (303)
T PF13872_consen  116 AD-NIPVHPLNKFKY----GDIIRLKEGVLFSTYSTLISESQSGGKYRSRLDQLVDWCGEDFDGVIVFDECHKAKNLSSG  190 (303)
T ss_pred             CC-cccceechhhcc----CcCCCCCCCccchhHHHHHhHHhccCCccchHHHHHHHHhcCCCceEEeccchhcCCCCcc
Confidence            43 333332221110    0111224579999999987764321   100         11225899999999765432 


Q ss_pred             -------HHHHHHHHHhCCCCceEEEEeecCCh
Q 015158          199 -------KDQIYDIFQLLPPKIQVGVFSATMPP  224 (412)
Q Consensus       199 -------~~~~~~i~~~~~~~~~~i~~SAT~~~  224 (412)
                             ...+..+.+.+| +.+++.+|||--.
T Consensus       191 ~~~~sk~g~avl~LQ~~LP-~ARvvY~SATgas  222 (303)
T PF13872_consen  191 SKKPSKTGIAVLELQNRLP-NARVVYASATGAS  222 (303)
T ss_pred             CccccHHHHHHHHHHHhCC-CCcEEEecccccC
Confidence                   134445556664 7779999999643

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

Probab=98.86  E-value=2.5e-09  Score=104.22  Aligned_cols=259  Identities=17%  Similarity=0.172  Sum_probs=156.0

Q ss_pred             ChHHHHhhhhhhhc-CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEE
Q 015158           62 PSAIQQRGIVPFCK-GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHA  140 (412)
Q Consensus        62 l~~~Q~~a~~~~~~-~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~  140 (412)
                      ..|.|...+..+.. ..++++-+|||+|||.++..++...+... +..++++++|.++|+....+.++......|+++..
T Consensus       928 fn~~q~~if~~~y~td~~~~~g~ptgsgkt~~ae~a~~~~~~~~-p~~kvvyIap~kalvker~~Dw~~r~~~~g~k~ie 1006 (1230)
T KOG0952|consen  928 FNPIQTQIFHCLYHTDLNFLLGAPTGSGKTVVAELAIFRALSYY-PGSKVVYIAPDKALVKERSDDWSKRDELPGIKVIE 1006 (1230)
T ss_pred             cCCccceEEEEEeecchhhhhcCCccCcchhHHHHHHHHHhccC-CCccEEEEcCCchhhcccccchhhhcccCCceeEe
Confidence            45567777766554 36789999999999999999888776654 55789999999999998888887765555889999


Q ss_pred             EEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCC--CCCCCceEEEEeCCchhhccCcHHHHHHHH-------HhCCC
Q 015158          141 CVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQS--LRPDNIRIFVLDEADEMLSRGFKDQIYDIF-------QLLPP  211 (412)
Q Consensus       141 ~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~--~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~-------~~~~~  211 (412)
                      ++|+...+..   .-...+++|+||+++....+.+.  ...+++..+|+||.|.+... +...+..+.       ...++
T Consensus      1007 ~tgd~~pd~~---~v~~~~~~ittpek~dgi~Rsw~~r~~v~~v~~iv~de~hllg~~-rgPVle~ivsr~n~~s~~t~~ 1082 (1230)
T KOG0952|consen 1007 LTGDVTPDVK---AVREADIVITTPEKWDGISRSWQTRKYVQSVSLIVLDEIHLLGED-RGPVLEVIVSRMNYISSQTEE 1082 (1230)
T ss_pred             ccCccCCChh---heecCceEEcccccccCccccccchhhhccccceeecccccccCC-CcceEEEEeeccccCccccCc
Confidence            9988775522   22346899999999988777443  34678899999999975543 222222222       22234


Q ss_pred             CceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEE------EEeccch-hhHHHHHHHHHhcCCCcEEEE
Q 015158          212 KIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFH------VNVEKEE-WKLETLCDLYETLAITQSVIF  284 (412)
Q Consensus       212 ~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~-~~~~~l~~~~~~~~~~k~lif  284 (412)
                      ..+++++|--+. +..+...++.-.+. + ..+....+-.....+      +..+... .....+..+....+..+++||
T Consensus      1083 ~vr~~glsta~~-na~dla~wl~~~~~-~-nf~~svrpvp~~~~i~gfp~~~~cprm~smnkpa~qaik~~sp~~p~lif 1159 (1230)
T KOG0952|consen 1083 PVRYLGLSTALA-NANDLADWLNIKDM-Y-NFRPSVRPVPLEVHIDGFPGQHYCPRMMSMNKPAFQAIKTHSPIKPVLIF 1159 (1230)
T ss_pred             chhhhhHhhhhh-ccHHHHHHhCCCCc-C-CCCcccccCCceEeecCCCchhcchhhhhcccHHHHHHhcCCCCCceEEE
Confidence            556666665543 22333333322222 1 111111111111111      1112212 223344444444566899999


Q ss_pred             EcchhHHH----HHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCc
Q 015158          285 VNTRRKVD----WLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSR  330 (412)
Q Consensus       285 ~~~~~~~~----~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~  330 (412)
                      +.++++..    .+...+....-+..+++.+  ..+-+.++...+...++
T Consensus      1160 v~srrqtrlta~~li~~~~~~~~p~~fl~~d--e~e~e~~~~~~~d~~Lk 1207 (1230)
T KOG0952|consen 1160 VSSRRQTRLTALDLIASCATEDNPKQFLNMD--ELELEIIMSKVRDTNLK 1207 (1230)
T ss_pred             eecccccccchHhHHhhccCCCCchhccCCC--HHHHHHHHHHhcccchh
Confidence            99887543    3333333333344555443  56666666666655443

>PF13307 Helicase_C_2: Helicase C-terminal domain; PDB: 4A15_A 2VSF_A 3CRV_A 3CRW_1 2VL7_A

Probab=98.83  E-value=1.5e-08  Score=82.11  Aligned_cols=112  Identities=20%  Similarity=0.337  Sum_probs=77.6

Q ss_pred             HHHHhcCCCcEEEEEcchhHHHHHHHHHhcCCC--eeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcC--CCcCCCCCCC
Q 015158          271 DLYETLAITQSVIFVNTRRKVDWLTDKMRSRDH--TVSATHGDMDQNTRDIIMREFRSGSSRVLITTD--LLARGIDVQQ  346 (412)
Q Consensus       271 ~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~~--~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~--~~~~G~d~~~  346 (412)
                      ++++..+ +.+|||++|.+..+.+.+.+++...  .+.++..  +..++..+++.|++++..||+++.  .+.+|+|+++
T Consensus         3 ~l~~~~~-g~~lv~f~Sy~~l~~~~~~~~~~~~~~~~~v~~q--~~~~~~~~l~~~~~~~~~il~~v~~g~~~EGiD~~~   79 (167)
T PF13307_consen    3 ELISAVP-GGVLVFFPSYRRLEKVYERLKERLEEKGIPVFVQ--GSKSRDELLEEFKRGEGAILLAVAGGSFSEGIDFPG   79 (167)
T ss_dssp             HHHHCCS-SEEEEEESSHHHHHHHHTT-TSS-E-ETSCEEES--TCCHHHHHHHHHCCSSSEEEEEETTSCCGSSS--EC
T ss_pred             HHHhcCC-CCEEEEeCCHHHHHHHHHHHHhhcccccceeeec--CcchHHHHHHHHHhccCeEEEEEecccEEEeecCCC
Confidence            3444444 8999999999999999999987642  2222222  345788999999999999999998  9999999996


Q ss_pred             --CCEEEEccCCCC------------------------------hhhHHHhhhhcccCCCCceEEEEeccC
Q 015158          347 --VSLVINYDLPTQ------------------------------PENYLHRIGRSGRFGRKGVAINFVTRD  385 (412)
Q Consensus       347 --~~~vi~~~~~~s------------------------------~~~~~Q~~GR~~R~g~~g~~~~~~~~~  385 (412)
                        ++.||+.+.|..                              .....|.+||+.|..++--++++++..
T Consensus        80 ~~~r~vii~glPfp~~~d~~~~~~~~~~~~~~~~~~~~~~~~~a~~~l~Qa~GR~iR~~~D~g~i~llD~R  150 (167)
T PF13307_consen   80 DLLRAVIIVGLPFPPPSDPLVQAKREYLDKQGKNPFRDWYLPPAIRKLKQAIGRLIRSEDDYGVIILLDSR  150 (167)
T ss_dssp             ESEEEEEEES-----TTCHHHHHHHHHHHHCCTTCHHHHTHHHHHHHHHHHHHCC--STT-EEEEEEESGG
T ss_pred             chhheeeecCCCCCCCCCHHHHHHHHHHHHHhccchhhHhhHHHHHHHhhhcCcceeccCCcEEEEEEcCc
Confidence              778999888742                              123589999999997766666666664

>PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A

Probab=98.81  E-value=1.2e-08  Score=88.48  Aligned_cols=69  Identities=26%  Similarity=0.262  Sum_probs=51.1

Q ss_pred             CChHHHHhhhhhhhcCcc-EEEECCCCCCchhHhHHHHHHhh-----ccCCCceeEEEEcCCHHHHHHHHHHHHH
Q 015158           61 KPSAIQQRGIVPFCKGLD-VIQQAQSGTGKTATFCSGILQQL-----DYGLVECQALVLAPTRELAQQIEKVMRA  129 (412)
Q Consensus        61 ~l~~~Q~~a~~~~~~~~~-~lv~~~tGsGKT~~~~~~~~~~~-----~~~~~~~~~lil~P~~~L~~q~~~~~~~  129 (412)
                      ++++.|++|+..++.... .+|+||+|+|||.+....+....     .....+.++|+++|+..-+++..+.+.+
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            378999999999999888 99999999999966554444331     1234567899999999999999888877

>KOG1802 consensus RNA helicase nonsense mRNA reducing factor (pNORF1) [RNA processing and modification]

Probab=98.74  E-value=3.5e-07  Score=85.50  Aligned_cols=85  Identities=22%  Similarity=0.200  Sum_probs=67.7

Q ss_pred             HHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhh
Q 015158           52 RGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALG  131 (412)
Q Consensus        52 ~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~  131 (412)
                      +.+...++.+|+.-|..|+.+++.+.-.+|++|+|+|||.+....++.....  ...++|+++|+..-++|+++.+.+- 
T Consensus       401 ~~~s~~~lpkLN~SQ~~AV~~VL~rplsLIQGPPGTGKTvtsa~IVyhl~~~--~~~~VLvcApSNiAVDqLaeKIh~t-  477 (935)
T KOG1802|consen  401 RRFSVPNLPKLNASQSNAVKHVLQRPLSLIQGPPGTGKTVTSATIVYHLARQ--HAGPVLVCAPSNIAVDQLAEKIHKT-  477 (935)
T ss_pred             hhhcCCCchhhchHHHHHHHHHHcCCceeeecCCCCCceehhHHHHHHHHHh--cCCceEEEcccchhHHHHHHHHHhc-
Confidence            3555668889999999999999999999999999999998765555544433  3457999999999999999888764 


Q ss_pred             cccCcEEEEEE
Q 015158          132 DYLGVKVHACV  142 (412)
Q Consensus       132 ~~~~~~~~~~~  142 (412)
                         |+++..+.
T Consensus       478 ---gLKVvRl~  485 (935)
T KOG1802|consen  478 ---GLKVVRLC  485 (935)
T ss_pred             ---CceEeeee
Confidence               55555554

>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=4.3e-06  Score=76.26  Aligned_cols=75  Identities=15%  Similarity=0.055  Sum_probs=51.0

Q ss_pred             HCCCCCChHHHHhhhhhhhc----CccEEEECCCCCCchhHhHHHHHHhhccCC-CceeEEEEcCCHHHHHHHHHHHHHh
Q 015158           56 AYGFEKPSAIQQRGIVPFCK----GLDVIQQAQSGTGKTATFCSGILQQLDYGL-VECQALVLAPTRELAQQIEKVMRAL  130 (412)
Q Consensus        56 ~~~~~~l~~~Q~~a~~~~~~----~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~-~~~~~lil~P~~~L~~q~~~~~~~~  130 (412)
                      -+++...+|-|-+=...+..    +.+.++.+|+|+|||.+.+..+.....+-. ...+.++..-|..-.+....+++.+
T Consensus        11 ~FPY~~iYPEQ~~YM~elKrsLDakGh~llEMPSGTGKTvsLLSli~aYq~~~p~~~~KliYCSRTvpEieK~l~El~~l   90 (755)
T KOG1131|consen   11 YFPYDYIYPEQYEYMRELKRSLDAKGHCLLEMPSGTGKTVSLLSLIIAYQLHYPDEHRKLIYCSRTVPEIEKALEELKRL   90 (755)
T ss_pred             ecCCcccCHHHHHHHHHHHHhhccCCcEEEECCCCCCcchHHHHHHHHHHHhCCcccceEEEecCcchHHHHHHHHHHHH
Confidence            35777788888776665543    578999999999999887766665544332 2345666666666666666666543

>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=98.65  E-value=2.7e-08  Score=82.09  Aligned_cols=146  Identities=15%  Similarity=0.186  Sum_probs=74.3

Q ss_pred             CCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHH-------HHHHHHHhhc
Q 015158           60 EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQ-------IEKVMRALGD  132 (412)
Q Consensus        60 ~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q-------~~~~~~~~~~  132 (412)
                      ...+..|+.++..+.....+++.+|.|||||+.++..++..+..+ .-.+++++-|.....++       ..+.+..+..
T Consensus         3 ~p~~~~Q~~~~~al~~~~~v~~~G~AGTGKT~LA~a~Al~~v~~g-~~~kiii~Rp~v~~~~~lGflpG~~~eK~~p~~~   81 (205)
T PF02562_consen    3 KPKNEEQKFALDALLNNDLVIVNGPAGTGKTFLALAAALELVKEG-EYDKIIITRPPVEAGEDLGFLPGDLEEKMEPYLR   81 (205)
T ss_dssp             ---SHHHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHTT-S-SEEEEEE-S--TT----SS---------TTTH
T ss_pred             cCCCHHHHHHHHHHHhCCeEEEECCCCCcHHHHHHHHHHHHHHhC-CCcEEEEEecCCCCccccccCCCCHHHHHHHHHH
Confidence            346889999999999888899999999999999999888887764 44578888887653111       1111111100


Q ss_pred             ccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCCCC
Q 015158          133 YLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPK  212 (412)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~  212 (412)
                      ..-.....+.+....   .. ......|-+.+...+    +-..+  + -.+||+|||+.+.    ..++..++.++..+
T Consensus        82 p~~d~l~~~~~~~~~---~~-~~~~~~Ie~~~~~~i----RGrt~--~-~~~iIvDEaQN~t----~~~~k~ilTR~g~~  146 (205)
T PF02562_consen   82 PIYDALEELFGKEKL---EE-LIQNGKIEIEPLAFI----RGRTF--D-NAFIIVDEAQNLT----PEELKMILTRIGEG  146 (205)
T ss_dssp             HHHHHHTTTS-TTCH---HH-HHHTTSEEEEEGGGG----TT--B----SEEEEE-SGGG------HHHHHHHHTTB-TT
T ss_pred             HHHHHHHHHhChHhH---HH-HhhcCeEEEEehhhh----cCccc--c-ceEEEEecccCCC----HHHHHHHHcccCCC
Confidence            000000000011111   11 112234555553332    11111  2 3799999999753    56788888888888


Q ss_pred             ceEEEEeec
Q 015158          213 IQVGVFSAT  221 (412)
Q Consensus       213 ~~~i~~SAT  221 (412)
                      .+++++.-.
T Consensus       147 skii~~GD~  155 (205)
T PF02562_consen  147 SKIIITGDP  155 (205)
T ss_dssp             -EEEEEE--
T ss_pred             cEEEEecCc
Confidence            887776655

; GO: 0005524 ATP binding; PDB: 3B85_A.

>TIGR00596 rad1 DNA repair protein (rad1)

Probab=98.60  E-value=2.7e-06  Score=84.79  Aligned_cols=66  Identities=14%  Similarity=0.079  Sum_probs=57.0

Q ss_pred             CcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEeecCC
Q 015158          158 VHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMP  223 (412)
Q Consensus       158 ~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~  223 (412)
                      ..|+++||..+.+-+....+....+..||+||||++....-..-+-+++...++...+.++||.|.
T Consensus         8 ggi~~~T~rIl~~DlL~~ri~~~~itgiiv~~Ahr~~~~~~eaFI~rlyr~~n~~gfIkafSdsP~   73 (814)
T TIGR00596         8 GGIFSITSRILVVDLLTGIIPPELITGILVLRADRIIESSQEAFILRLYRQKNKTGFIKAFSDNPE   73 (814)
T ss_pred             CCEEEEechhhHhHHhcCCCCHHHccEEEEeecccccccccHHHHHHHHHHhCCCcceEEecCCCc
Confidence            479999999999999999999999999999999998866656666677776677778999999986

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

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A

Probab=98.60  E-value=2.3e-07  Score=77.31  Aligned_cols=122  Identities=16%  Similarity=0.228  Sum_probs=71.4

Q ss_pred             ChHHHHhhhhhhhcC--ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEE
Q 015158           62 PSAIQQRGIVPFCKG--LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVH  139 (412)
Q Consensus        62 l~~~Q~~a~~~~~~~--~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~  139 (412)
                      |++-|++|+..++.+  +-.++.++.|+|||.+. ..+...+...  +.++++++||...+..+.+..       +..  
T Consensus         2 L~~~Q~~a~~~~l~~~~~~~~l~G~aGtGKT~~l-~~~~~~~~~~--g~~v~~~apT~~Aa~~L~~~~-------~~~--   69 (196)
T PF13604_consen    2 LNEEQREAVRAILTSGDRVSVLQGPAGTGKTTLL-KALAEALEAA--GKRVIGLAPTNKAAKELREKT-------GIE--   69 (196)
T ss_dssp             S-HHHHHHHHHHHHCTCSEEEEEESTTSTHHHHH-HHHHHHHHHT--T--EEEEESSHHHHHHHHHHH-------TS---
T ss_pred             CCHHHHHHHHHHHhcCCeEEEEEECCCCCHHHHH-HHHHHHHHhC--CCeEEEECCcHHHHHHHHHhh-------Ccc--
Confidence            788999999999754  35778899999999764 3344444432  368999999998777655541       111  


Q ss_pred             EEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCC----CCCCCceEEEEeCCchhhccCcHHHHHHHHHhCCC-Cce
Q 015158          140 ACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQS----LRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPP-KIQ  214 (412)
Q Consensus       140 ~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~----~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~-~~~  214 (412)
                                            ..|..+++.......    ......++|||||+-.+.    ...+..++...+. +.+
T Consensus        70 ----------------------a~Ti~~~l~~~~~~~~~~~~~~~~~~vliVDEasmv~----~~~~~~ll~~~~~~~~k  123 (196)
T PF13604_consen   70 ----------------------AQTIHSFLYRIPNGDDEGRPELPKKDVLIVDEASMVD----SRQLARLLRLAKKSGAK  123 (196)
T ss_dssp             ----------------------EEEHHHHTTEECCEECCSSCC-TSTSEEEESSGGG-B----HHHHHHHHHHS-T-T-E
T ss_pred             ----------------------hhhHHHHHhcCCcccccccccCCcccEEEEecccccC----HHHHHHHHHHHHhcCCE
Confidence                                  122222211111100    003456799999999753    3456677777665 666


Q ss_pred             EEEEeec
Q 015158          215 VGVFSAT  221 (412)
Q Consensus       215 ~i~~SAT  221 (412)
                      ++++--+
T Consensus       124 lilvGD~  130 (196)
T PF13604_consen  124 LILVGDP  130 (196)
T ss_dssp             EEEEE-T
T ss_pred             EEEECCc
Confidence            6666655

>PRK10536 hypothetical protein; Provisional

Probab=98.47  E-value=8.1e-07  Score=75.43  Aligned_cols=146  Identities=16%  Similarity=0.116  Sum_probs=85.1

Q ss_pred             CCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHH-----------HHHHH
Q 015158           57 YGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELA-----------QQIEK  125 (412)
Q Consensus        57 ~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~-----------~q~~~  125 (412)
                      .++...+..|...+..+.++..+++.+|+|+|||+.+...++..+..+ .-.++++.=|.....           +...-
T Consensus        55 ~~i~p~n~~Q~~~l~al~~~~lV~i~G~aGTGKT~La~a~a~~~l~~~-~~~kIiI~RP~v~~ge~LGfLPG~~~eK~~p  133 (262)
T PRK10536         55 SPILARNEAQAHYLKAIESKQLIFATGEAGCGKTWISAAKAAEALIHK-DVDRIIVTRPVLQADEDLGFLPGDIAEKFAP  133 (262)
T ss_pred             ccccCCCHHHHHHHHHHhcCCeEEEECCCCCCHHHHHHHHHHHHHhcC-CeeEEEEeCCCCCchhhhCcCCCCHHHHHHH
Confidence            355667889999999999888899999999999998877777665443 244666666664321           11111


Q ss_pred             HHHHhhcccCcEEEEEEcCcchHHHHHHh-cCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHH
Q 015158          126 VMRALGDYLGVKVHACVGGTSVREDQRIL-SSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYD  204 (412)
Q Consensus       126 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~  204 (412)
                      .+..+......    +.+..   ...... .....|-+....    +++...+   .-++||+|||+.+.    ..++..
T Consensus       134 ~~~pi~D~L~~----~~~~~---~~~~~~~~~~~~Iei~~l~----ymRGrtl---~~~~vIvDEaqn~~----~~~~k~  195 (262)
T PRK10536        134 YFRPVYDVLVR----RLGAS---FMQYCLRPEIGKVEIAPFA----YMRGRTF---ENAVVILDEAQNVT----AAQMKM  195 (262)
T ss_pred             HHHHHHHHHHH----HhChH---HHHHHHHhccCcEEEecHH----HhcCCcc---cCCEEEEechhcCC----HHHHHH
Confidence            11221111110    01111   111111 112345566522    2222222   23799999999753    367778


Q ss_pred             HHHhCCCCceEEEEeec
Q 015158          205 IFQLLPPKIQVGVFSAT  221 (412)
Q Consensus       205 i~~~~~~~~~~i~~SAT  221 (412)
                      ++..+..+.++|++.-.
T Consensus       196 ~ltR~g~~sk~v~~GD~  212 (262)
T PRK10536        196 FLTRLGENVTVIVNGDI  212 (262)
T ss_pred             HHhhcCCCCEEEEeCCh
Confidence            88888888876655443

>KOG1803 consensus DNA helicase [Replication, recombination and repair]

Probab=98.35  E-value=2.9e-06  Score=79.02  Aligned_cols=64  Identities=23%  Similarity=0.212  Sum_probs=53.6

Q ss_pred             ChHHHHhhhhhhhcCc-cEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHH
Q 015158           62 PSAIQQRGIVPFCKGL-DVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMR  128 (412)
Q Consensus        62 l~~~Q~~a~~~~~~~~-~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~  128 (412)
                      +.+-|+.|+......+ -.++.||+|+|||.+....+...+..+   .++|+.+|+..-++.+.+.+.
T Consensus       186 ln~SQk~Av~~~~~~k~l~~I~GPPGTGKT~TlvEiI~qlvk~~---k~VLVcaPSn~AVdNiverl~  250 (649)
T KOG1803|consen  186 LNSSQKAAVSFAINNKDLLIIHGPPGTGKTRTLVEIISQLVKQK---KRVLVCAPSNVAVDNIVERLT  250 (649)
T ss_pred             ccHHHHHHHHHHhccCCceEeeCCCCCCceeeHHHHHHHHHHcC---CeEEEEcCchHHHHHHHHHhc
Confidence            8889999999988875 467899999999998877777777665   499999999998888887643

>KOG1132 consensus Helicase of the DEAD superfamily [Replication, recombination and repair]

Probab=98.34  E-value=3.2e-06  Score=81.86  Aligned_cols=105  Identities=16%  Similarity=0.138  Sum_probs=65.3

Q ss_pred             CcEEEEEcchhHHHHHHHHHhcC-------CCeeEEecCCCCHHHHHHHHHHHhcC--------CCcEEEEcCCCcCCCC
Q 015158          279 TQSVIFVNTRRKVDWLTDKMRSR-------DHTVSATHGDMDQNTRDIIMREFRSG--------SSRVLITTDLLARGID  343 (412)
Q Consensus       279 ~k~lif~~~~~~~~~~~~~L~~~-------~~~~~~~~~~~~~~~r~~~~~~f~~g--------~~~vlv~t~~~~~G~d  343 (412)
                      ..+|||+++....+.+.......       +..-.++--. +..+-.+++.+|.+.        -.-+.||-...++|+|
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            45899999998777775554432       1112222211 444455566666542        2234456668899999


Q ss_pred             CCC--CCEEEEccCCCC--------------------------------------hhhHHHhhhhcccCCCCceEEEEec
Q 015158          344 VQQ--VSLVINYDLPTQ--------------------------------------PENYLHRIGRSGRFGRKGVAINFVT  383 (412)
Q Consensus       344 ~~~--~~~vi~~~~~~s--------------------------------------~~~~~Q~~GR~~R~g~~g~~~~~~~  383 (412)
                      +.+  .+.||..|.|+-                                      ...+.|++||+.|..++=.++++++
T Consensus       641 FsD~~~RaVI~tGlPyP~~~D~~V~lK~~y~D~~~~~~g~~s~~lsg~eWY~~qA~RAvNQAiGRviRHR~D~Gav~l~D  720 (945)
T KOG1132|consen  641 FSDDNGRAVIITGLPYPPVMDPRVKLKKQYLDENSSLKGAKSQLLSGQEWYSQQAYRAVNQAIGRVIRHRNDYGAVILCD  720 (945)
T ss_pred             ccccCCceeEEecCCCCCCCCHHHHHHHHhhhhhccccccccccccchHHHHhhHHHHHHHHHHHHHhhhcccceeeEee
Confidence            985  778888887631                                      2346899999999866644454554


Q ss_pred             c
Q 015158          384 R  384 (412)
Q Consensus       384 ~  384 (412)
                      .
T Consensus       721 ~  721 (945)
T KOG1132|consen  721 D  721 (945)
T ss_pred             c
Confidence            4

>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function

Probab=98.32  E-value=3.4e-06  Score=77.36  Aligned_cols=108  Identities=14%  Similarity=0.155  Sum_probs=66.8

Q ss_pred             cEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCC
Q 015158           78 DVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSG  157 (412)
Q Consensus        78 ~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  157 (412)
                      -++|.|.+|||||+.++-.+... .....+.+++++|++..|.....+.+..-.          ..            ..
T Consensus         3 v~~I~G~aGTGKTvla~~l~~~l-~~~~~~~~~~~l~~n~~l~~~l~~~l~~~~----------~~------------~~   59 (352)
T PF09848_consen    3 VILITGGAGTGKTVLALNLAKEL-QNSEEGKKVLYLCGNHPLRNKLREQLAKKY----------NP------------KL   59 (352)
T ss_pred             EEEEEecCCcCHHHHHHHHHHHh-hccccCCceEEEEecchHHHHHHHHHhhhc----------cc------------ch
Confidence            46899999999998876544433 222344689999999999888877776632          00            00


Q ss_pred             CcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccC-------cHHHHHHHHHh
Q 015158          158 VHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRG-------FKDQIYDIFQL  208 (412)
Q Consensus       158 ~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~-------~~~~~~~i~~~  208 (412)
                      ....+..+..+.+...........+++||+||||++....       ....+..++..
T Consensus        60 ~~~~~~~~~~~i~~~~~~~~~~~~~DviivDEAqrl~~~~~~~~~~~~~~~L~~i~~~  117 (352)
T PF09848_consen   60 KKSDFRKPTSFINNYSESDKEKNKYDVIIVDEAQRLRTKGDQYNNFSEPNQLDEIIKR  117 (352)
T ss_pred             hhhhhhhhHHHHhhcccccccCCcCCEEEEehhHhhhhccccccccccHHHHHHHHhc
Confidence            1233334444433332222334678999999999987632       23455555554

It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].

>PF13245 AAA_19: Part of AAA domain

Probab=98.31  E-value=2.4e-06  Score=58.74  Aligned_cols=52  Identities=33%  Similarity=0.392  Sum_probs=39.5

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhcc-CCCceeEEEEcCCHHHHHHHHHHH
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDY-GLVECQALVLAPTRELAQQIEKVM  127 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~-~~~~~~~lil~P~~~L~~q~~~~~  127 (412)
                      +.-++|.+|+|||||.+.+-.+...+.. ...+.++++++|++..++++.+.+
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            4445669999999998776666666532 122568999999999999888877

>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=98.30  E-value=1.7e-05  Score=66.17  Aligned_cols=152  Identities=21%  Similarity=0.249  Sum_probs=93.9

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhc---CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCC
Q 015158           40 TFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCK---GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPT  116 (412)
Q Consensus        40 ~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~---~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~  116 (412)
                      +|+....+..+.=.+. .++. +|+.|.+....+.+   |.+.+.++-+|.|||.+.+..++..+.++.  .-+.+++| 
T Consensus         4 ~w~p~~~P~wLl~E~e-~~il-iR~~Q~~ia~~mi~~~~~~n~v~QlnMGeGKTsVI~Pmla~~LAdg~--~LvrviVp-   78 (229)
T PF12340_consen    4 NWDPMEYPDWLLFEIE-SNIL-IRPVQVEIAREMISPPSGKNSVMQLNMGEGKTSVIVPMLALALADGS--RLVRVIVP-   78 (229)
T ss_pred             CCCchhChHHHHHHHH-cCce-eeHHHHHHHHHHhCCCCCCCeEeeecccCCccchHHHHHHHHHcCCC--cEEEEEcC-
Confidence            5666666666666663 4666 89999999999886   478999999999999887555554444432  34666677 


Q ss_pred             HHHHHHHHHHHHHh-hcccCcEEEEEE--cCcchHH-----H---HHHhcCCCcEEEeChHHHHHHHHcC-------CCC
Q 015158          117 RELAQQIEKVMRAL-GDYLGVKVHACV--GGTSVRE-----D---QRILSSGVHVVVGTPGRVFDMLRRQ-------SLR  178 (412)
Q Consensus       117 ~~L~~q~~~~~~~~-~~~~~~~~~~~~--~~~~~~~-----~---~~~~~~~~~iii~T~~~l~~~~~~~-------~~~  178 (412)
                      ++|.+|+.+.+... +...+-.+..+.  -......     .   .......-.|+++||+.+.......       ...
T Consensus        79 k~Ll~q~~~~L~~~lg~l~~r~i~~lpFsR~~~~~~~~~~~~~~l~~~~~~~~gill~~PEhilSf~L~~le~l~~~~~~  158 (229)
T PF12340_consen   79 KALLEQMRQMLRSRLGGLLNRRIYHLPFSRSTPLTPETLEKIRQLLEECMRSGGILLATPEHILSFKLKGLERLQDGKPE  158 (229)
T ss_pred             HHHHHHHHHHHHHHHHHHhCCeeEEecccCCCCCCHHHHHHHHHHHHHHHHcCCEEEeChHHHHHHHHHHHHHHHhcCHH
Confidence            68999998888663 333344444332  1111111     1   1112234479999999876533211       100


Q ss_pred             -----------CCCceEEEEeCCchhhcc
Q 015158          179 -----------PDNIRIFVLDEADEMLSR  196 (412)
Q Consensus       179 -----------~~~~~~iiiDE~h~~~~~  196 (412)
                                 ++....=|+||+|.++..
T Consensus       159 ~~~~l~~~q~~l~~~~rdilDEsDe~L~~  187 (229)
T PF12340_consen  159 EARELLKIQKWLDEHSRDILDESDEILSV  187 (229)
T ss_pred             HHHHHHHHHHHHHhcCCeEeECchhccCc
Confidence                       122345689999986543

There are two conserved sequence motifs: LLE and NMG.

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=98.27  E-value=8.8e-06  Score=79.05  Aligned_cols=141  Identities=18%  Similarity=0.197  Sum_probs=86.5

Q ss_pred             hHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhcc-CCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEE
Q 015158           63 SAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY-GLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHAC  141 (412)
Q Consensus        63 ~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~-~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~  141 (412)
                      .++|+.|+...+.++-.+|.+++|+|||.+....+...... .....++++++||..-+..+.+.+.......+..    
T Consensus       154 ~d~Qk~Av~~a~~~~~~vItGgpGTGKTt~v~~ll~~l~~~~~~~~~~i~l~APTgkAA~rL~e~~~~~~~~~~~~----  229 (615)
T PRK10875        154 VDWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQLADGERCRIRLAAPTGKAAARLTESLGKALRQLPLT----  229 (615)
T ss_pred             CHHHHHHHHHHhcCCeEEEEeCCCCCHHHHHHHHHHHHHHhcCCCCcEEEEECCcHHHHHHHHHHHHhhhhccccc----
Confidence            47999999999999999999999999997753322221111 1123578899999887777777665432211110    


Q ss_pred             EcCcchHHHHHHhcCCCcEEEeChHHHHHHHHc------CCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceE
Q 015158          142 VGGTSVREDQRILSSGVHVVVGTPGRVFDMLRR------QSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQV  215 (412)
Q Consensus       142 ~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~------~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~  215 (412)
                            ....    .....-..|.++|+.....      ...+.-.++++|+||+-.+.    ...+..++..++++.++
T Consensus       230 ------~~~~----~~~~~~a~TiHrlLg~~~~~~~~~~~~~~~l~~dvlIvDEaSMvd----~~lm~~ll~al~~~~rl  295 (615)
T PRK10875        230 ------DEQK----KRIPEEASTLHRLLGAQPGSQRLRYHAGNPLHLDVLVVDEASMVD----LPMMARLIDALPPHARV  295 (615)
T ss_pred             ------hhhh----hcCCCchHHHHHHhCcCCCccchhhccccCCCCCeEEEChHhccc----HHHHHHHHHhcccCCEE
Confidence                  0000    0001123444444322111      11122346899999999652    35667788889999998


Q ss_pred             EEEeec
Q 015158          216 GVFSAT  221 (412)
Q Consensus       216 i~~SAT  221 (412)
                      |++.-.
T Consensus       296 IlvGD~  301 (615)
T PRK10875        296 IFLGDR  301 (615)
T ss_pred             EEecch
Confidence            888766

>TIGR00376 DNA helicase, putative

Probab=98.26  E-value=8.2e-06  Score=80.19  Aligned_cols=66  Identities=21%  Similarity=0.202  Sum_probs=54.1

Q ss_pred             CChHHHHhhhhhhhcC-ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHH
Q 015158           61 KPSAIQQRGIVPFCKG-LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRA  129 (412)
Q Consensus        61 ~l~~~Q~~a~~~~~~~-~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~  129 (412)
                      .+++.|++|+..++.. ...+|.||+|+|||.+....+...+..+   .++++++|+..-+.++.+.+..
T Consensus       157 ~ln~~Q~~Av~~~l~~~~~~lI~GpPGTGKT~t~~~ii~~~~~~g---~~VLv~a~sn~Avd~l~e~l~~  223 (637)
T TIGR00376       157 NLNESQKEAVSFALSSKDLFLIHGPPGTGKTRTLVELIRQLVKRG---LRVLVTAPSNIAVDNLLERLAL  223 (637)
T ss_pred             CCCHHHHHHHHHHhcCCCeEEEEcCCCCCHHHHHHHHHHHHHHcC---CCEEEEcCcHHHHHHHHHHHHh
Confidence            4799999999998876 6788999999999987765555555443   4899999999988888888776

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.

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit

Probab=98.26  E-value=1.4e-05  Score=77.53  Aligned_cols=141  Identities=18%  Similarity=0.179  Sum_probs=85.7

Q ss_pred             hHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHH--HhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEE
Q 015158           63 SAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGIL--QQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHA  140 (412)
Q Consensus        63 ~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~--~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~  140 (412)
                      .++|+.|+...+.++-.+|.|++|+|||.+....+.  ..........++++++||-.-+..+.+............   
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            379999999999999999999999999976533222  121111112479999999877776666554432111110   


Q ss_pred             EEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHc------CCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCCCCce
Q 015158          141 CVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRR------QSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQ  214 (412)
Q Consensus       141 ~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~------~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~  214 (412)
                            . ...    ....+-..|.++|+.....      ...+...+++||+||+-.+.    ...+..++..++++.+
T Consensus       224 ------~-~~~----~~~~~~a~TiHrlLg~~~~~~~~~~~~~~~l~~dvlIiDEaSMvd----~~l~~~ll~al~~~~r  288 (586)
T TIGR01447       224 ------E-ALI----AALPSEAVTIHRLLGIKPDTKRFRHHERNPLPLDVLVVDEASMVD----LPLMAKLLKALPPNTK  288 (586)
T ss_pred             ------h-hhh----hccccccchhhhhhcccCCcchhhhcccCCCcccEEEEcccccCC----HHHHHHHHHhcCCCCE
Confidence                  0 000    0011224555554432211      01122357899999999653    3456777888888888


Q ss_pred             EEEEeec
Q 015158          215 VGVFSAT  221 (412)
Q Consensus       215 ~i~~SAT  221 (412)
                      +|++.-.
T Consensus       289 lIlvGD~  295 (586)
T TIGR01447       289 LILLGDK  295 (586)
T ss_pred             EEEECCh
Confidence            8877665

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.

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=98.24  E-value=1.6e-05  Score=79.39  Aligned_cols=128  Identities=20%  Similarity=0.167  Sum_probs=79.4

Q ss_pred             CCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCc
Q 015158           57 YGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGV  136 (412)
Q Consensus        57 ~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~  136 (412)
                      .++. +++.|++|+..+..++..++.+++|+|||.+. -.++..+........+++++||-.-+..+.+..       +.
T Consensus       320 ~~~~-l~~~Q~~Ai~~~~~~~~~iitGgpGTGKTt~l-~~i~~~~~~~~~~~~v~l~ApTg~AA~~L~e~~-------g~  390 (720)
T TIGR01448       320 LRKG-LSEEQKQALDTAIQHKVVILTGGPGTGKTTIT-RAIIELAEELGGLLPVGLAAPTGRAAKRLGEVT-------GL  390 (720)
T ss_pred             cCCC-CCHHHHHHHHHHHhCCeEEEECCCCCCHHHHH-HHHHHHHHHcCCCceEEEEeCchHHHHHHHHhc-------CC
Confidence            3444 99999999999998889999999999999765 333333332211246888999977655443221       21


Q ss_pred             EEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHc-----CCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCCC
Q 015158          137 KVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRR-----QSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPP  211 (412)
Q Consensus       137 ~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~-----~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~  211 (412)
                      ..                        .|.++++.....     ........++||+||++.+..    ..+..++..++.
T Consensus       391 ~a------------------------~Tih~lL~~~~~~~~~~~~~~~~~~~llIvDEaSMvd~----~~~~~Ll~~~~~  442 (720)
T TIGR01448       391 TA------------------------STIHRLLGYGPDTFRHNHLEDPIDCDLLIVDESSMMDT----WLALSLLAALPD  442 (720)
T ss_pred             cc------------------------ccHHHHhhccCCccchhhhhccccCCEEEEeccccCCH----HHHHHHHHhCCC
Confidence            11                        111111111000     000123568999999997643    345666777888


Q ss_pred             CceEEEEeec
Q 015158          212 KIQVGVFSAT  221 (412)
Q Consensus       212 ~~~~i~~SAT  221 (412)
                      +.++|++.-+
T Consensus       443 ~~rlilvGD~  452 (720)
T TIGR01448       443 HARLLLVGDT  452 (720)
T ss_pred             CCEEEEECcc
Confidence            8888887665

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.

>COG3421 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=98.22  E-value=2.5e-05  Score=72.67  Aligned_cols=135  Identities=16%  Similarity=0.214  Sum_probs=77.8

Q ss_pred             EECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHH-----h--hccc-----CcEEEEEEcCcchH
Q 015158           81 QQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRA-----L--GDYL-----GVKVHACVGGTSVR  148 (412)
Q Consensus        81 v~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~-----~--~~~~-----~~~~~~~~~~~~~~  148 (412)
                      ..++||||||+++...++.....+.  ...|+.|......+.+...+..     +  ....     .+++..+..     
T Consensus         2 f~matgsgkt~~ma~lil~~y~kgy--r~flffvnq~nilekt~~nftd~~s~kylf~e~i~~~d~~i~ikkvn~-----   74 (812)
T COG3421           2 FEMATGSGKTLVMAGLILECYKKGY--RNFLFFVNQANILEKTKLNFTDSVSSKYLFSENININDENIEIKKVNN-----   74 (812)
T ss_pred             cccccCCChhhHHHHHHHHHHHhch--hhEEEEecchhHHHHHHhhcccchhhhHhhhhhhhcCCceeeeeeecc-----
Confidence            4689999999998888887766543  4577778777776666554422     1  0000     111211111     


Q ss_pred             HHHHHhcCCCcEEEeChHHHHHHHHcCCCCC------CCce-EEEEeCCchhhccC---------cHHHHHHHH-Hh--C
Q 015158          149 EDQRILSSGVHVVVGTPGRVFDMLRRQSLRP------DNIR-IFVLDEADEMLSRG---------FKDQIYDIF-QL--L  209 (412)
Q Consensus       149 ~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~------~~~~-~iiiDE~h~~~~~~---------~~~~~~~i~-~~--~  209 (412)
                        ..-......|+++|.+.|...+.+.+.+.      .+.. +++-||+|++-...         ....|.... ..  -
T Consensus        75 --fsehnd~iei~fttiq~l~~d~~~~ken~itledl~~~klvfl~deahhln~~tkkk~~de~~~~~~we~~v~la~~~  152 (812)
T COG3421          75 --FSEHNDAIEIYFTTIQGLFSDFTRAKENAITLEDLKDQKLVFLADEAHHLNTETKKKLNDEASEKRNWESVVKLALEQ  152 (812)
T ss_pred             --cCccCCceEEEEeehHHHHHHHHhhccccccHhhHhhCceEEEechhhhhhhhhhhhcccHHHHHhhHHHHHHHHHhc
Confidence              11133456899999999988877654331      2222 57789999975321         112222221 11  2


Q ss_pred             CCCceEEEEeecCCh
Q 015158          210 PPKIQVGVFSATMPP  224 (412)
Q Consensus       210 ~~~~~~i~~SAT~~~  224 (412)
                      .+.--++..|||.+.
T Consensus       153 nkd~~~lef~at~~k  167 (812)
T COG3421         153 NKDNLLLEFSATIPK  167 (812)
T ss_pred             CCCceeehhhhcCCc
Confidence            234457888999874

>smart00492 HELICc3 helicase superfamily c-terminal domain

Probab=98.12  E-value=2.1e-05  Score=61.42  Aligned_cols=73  Identities=16%  Similarity=0.243  Sum_probs=54.4

Q ss_pred             CCHHHHHHHHHHHhcCC-CcEEEEcCCCcCCCCCCC--CCEEEEccCCCC------------------------------
Q 015158          312 MDQNTRDIIMREFRSGS-SRVLITTDLLARGIDVQQ--VSLVINYDLPTQ------------------------------  358 (412)
Q Consensus       312 ~~~~~r~~~~~~f~~g~-~~vlv~t~~~~~G~d~~~--~~~vi~~~~~~s------------------------------  358 (412)
                      .+..+...+++.|.+.. ..||+++..+.+|+|+|+  ++.||+.+.|..                              
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            44446788999998754 379999988999999996  678888887631                              


Q ss_pred             -hhhHHHhhhhcccCCCCceEEEEecc
Q 015158          359 -PENYLHRIGRSGRFGRKGVAINFVTR  384 (412)
Q Consensus       359 -~~~~~Q~~GR~~R~g~~g~~~~~~~~  384 (412)
                       ...+.|.+||+.|...+-.++++++.
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             23468999999998766555656554

>COG1875 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]

Probab=98.07  E-value=1.6e-05  Score=69.87  Aligned_cols=146  Identities=16%  Similarity=0.139  Sum_probs=88.0

Q ss_pred             HCCCCCChHHHHhhhhhhhcCc--cEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcc
Q 015158           56 AYGFEKPSAIQQRGIVPFCKGL--DVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDY  133 (412)
Q Consensus        56 ~~~~~~l~~~Q~~a~~~~~~~~--~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~  133 (412)
                      .+|+...+..|+-|+..++...  -+.+.++.|||||+.++.+.+......+.-.++++.=|+..+.+++          
T Consensus       223 vwGi~prn~eQ~~ALdlLld~dI~lV~L~G~AGtGKTlLALaAgleqv~e~~~y~KiiVtRp~vpvG~dI----------  292 (436)
T COG1875         223 VWGIRPRNAEQRVALDLLLDDDIDLVSLGGKAGTGKTLLALAAGLEQVLERKRYRKIIVTRPTVPVGEDI----------  292 (436)
T ss_pred             hhccCcccHHHHHHHHHhcCCCCCeEEeeccCCccHhHHHHHHHHHHHHHHhhhceEEEecCCcCccccc----------
Confidence            4688878889999999999863  4567899999999999888888877666666888888877654321          


Q ss_pred             cCcEEEEEEcCcchH--HHHHHhcCCCcEEE----eChHHHHHHHHcCCCCC--------C--CceEEEEeCCchhhccC
Q 015158          134 LGVKVHACVGGTSVR--EDQRILSSGVHVVV----GTPGRVFDMLRRQSLRP--------D--NIRIFVLDEADEMLSRG  197 (412)
Q Consensus       134 ~~~~~~~~~~~~~~~--~~~~~~~~~~~iii----~T~~~l~~~~~~~~~~~--------~--~~~~iiiDE~h~~~~~~  197 (412)
                           ..+.|....+  .|-.....+-..+.    ++.+.+...+.+..+..        +  .-.+||+|||+.+.   
T Consensus       293 -----GfLPG~eEeKm~PWmq~i~DnLE~L~~~~~~~~~~l~~~l~~~~iev~alt~IRGRSl~~~FiIIDEaQNLT---  364 (436)
T COG1875         293 -----GFLPGTEEEKMGPWMQAIFDNLEVLFSPNEPGDRALEEILSRGRIEVEALTYIRGRSLPDSFIIIDEAQNLT---  364 (436)
T ss_pred             -----CcCCCchhhhccchHHHHHhHHHHHhcccccchHHHHHHHhccceeeeeeeeecccccccceEEEehhhccC---
Confidence                 1111111100  00000000000000    11333444433332221        1  12489999999863   


Q ss_pred             cHHHHHHHHHhCCCCceEEEEee
Q 015158          198 FKDQIYDIFQLLPPKIQVGVFSA  220 (412)
Q Consensus       198 ~~~~~~~i~~~~~~~~~~i~~SA  220 (412)
                       ..++..++....++.+++++.-
T Consensus       365 -pheikTiltR~G~GsKIVl~gd  386 (436)
T COG1875         365 -PHELKTILTRAGEGSKIVLTGD  386 (436)
T ss_pred             -HHHHHHHHHhccCCCEEEEcCC
Confidence             5678888888888887666543

>smart00491 HELICc2 helicase superfamily c-terminal domain

Probab=98.06  E-value=1.9e-05  Score=61.78  Aligned_cols=93  Identities=14%  Similarity=0.257  Sum_probs=61.4

Q ss_pred             HHHHHHHHhcCCC----eeEEecCCCCHHHHHHHHHHHhcCCC---cEEEEcCC--CcCCCCCCC--CCEEEEccCCCC-
Q 015158          291 VDWLTDKMRSRDH----TVSATHGDMDQNTRDIIMREFRSGSS---RVLITTDL--LARGIDVQQ--VSLVINYDLPTQ-  358 (412)
Q Consensus       291 ~~~~~~~L~~~~~----~~~~~~~~~~~~~r~~~~~~f~~g~~---~vlv~t~~--~~~G~d~~~--~~~vi~~~~~~s-  358 (412)
                      .+.+++.+++.+.    ...+.-+. ...+...+++.|++..-   .||+++..  +.+|+|+|+  ++.||+.+.|.. 
T Consensus         4 m~~v~~~~~~~~~~~~~~~i~~e~~-~~~~~~~~l~~f~~~~~~~g~iL~~v~~G~~~EGiD~~g~~~r~vii~glPfp~   82 (142)
T smart00491        4 LEQVVEYWKENGILEINKPVFIEGK-DSGETEELLEKYSAACEARGALLLAVARGKVSEGIDFPDDLGRAVIIVGIPFPN   82 (142)
T ss_pred             HHHHHHHHHhcCccccCceEEEECC-CCchHHHHHHHHHHhcCCCCEEEEEEeCCeeecceecCCCccEEEEEEecCCCC
Confidence            4556666655432    12222222 22344788888887533   68888876  999999996  678888887731 


Q ss_pred             ------------------------------hhhHHHhhhhcccCCCCceEEEEecc
Q 015158          359 ------------------------------PENYLHRIGRSGRFGRKGVAINFVTR  384 (412)
Q Consensus       359 ------------------------------~~~~~Q~~GR~~R~g~~g~~~~~~~~  384 (412)
                                                    ...+.|.+||+.|...+-.++++++.
T Consensus        83 ~~d~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~Qa~GR~iR~~~D~g~i~l~D~  138 (142)
T smart00491       83 PDSPILRARLEYLDEKGGIRPFDEVYLFDAMRALAQAIGRAIRHKNDYGVVVLLDK  138 (142)
T ss_pred             CCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHHHHhCccccCccceEEEEEEec
Confidence                                          12458999999999766556666654

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=98.02  E-value=0.00013  Score=65.83  Aligned_cols=133  Identities=17%  Similarity=0.203  Sum_probs=82.2

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhc
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILS  155 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  155 (412)
                      ++.+.++||||.|||++..=.++..........-.||.+.|=-.+  ..++++.++..+++++                 
T Consensus       203 ~~vi~LVGPTGVGKTTTlAKLAar~~~~~~~~kVaiITtDtYRIG--A~EQLk~Ya~im~vp~-----------------  263 (407)
T COG1419         203 KRVIALVGPTGVGKTTTLAKLAARYVMLKKKKKVAIITTDTYRIG--AVEQLKTYADIMGVPL-----------------  263 (407)
T ss_pred             CcEEEEECCCCCcHHHHHHHHHHHHHhhccCcceEEEEeccchhh--HHHHHHHHHHHhCCce-----------------
Confidence            567889999999999876544444442222233455555543322  2455666666556655                 


Q ss_pred             CCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCch-hhccCcHHHHHHHHHhCCCCceEEEEeecCCh-HHHHHHHHh
Q 015158          156 SGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADE-MLSRGFKDQIYDIFQLLPPKIQVGVFSATMPP-EALEITRKF  233 (412)
Q Consensus       156 ~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~-~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~-~~~~~~~~~  233 (412)
                          .++-++.-|...+..    +.+.++|.+|=+-+ ..+......+..+.....+....+.+|||... ++.+.+..+
T Consensus       264 ----~vv~~~~el~~ai~~----l~~~d~ILVDTaGrs~~D~~~i~el~~~~~~~~~i~~~Lvlsat~K~~dlkei~~~f  335 (407)
T COG1419         264 ----EVVYSPKELAEAIEA----LRDCDVILVDTAGRSQYDKEKIEELKELIDVSHSIEVYLVLSATTKYEDLKEIIKQF  335 (407)
T ss_pred             ----EEecCHHHHHHHHHH----hhcCCEEEEeCCCCCccCHHHHHHHHHHHhccccceEEEEEecCcchHHHHHHHHHh
Confidence                455566666555542    34679999997664 33444556777777777666678999999865 445555555


Q ss_pred             cC
Q 015158          234 MN  235 (412)
Q Consensus       234 ~~  235 (412)
                      ..
T Consensus       336 ~~  337 (407)
T COG1419         336 SL  337 (407)
T ss_pred             cc
Confidence            43

>PF00580 UvrD-helicase: UvrD/REP helicase N-terminal domain; InterPro: IPR000212 Members of this family are helicases that catalyse ATP dependent unwinding of double stranded DNA to single stranded DNA

Probab=97.96  E-value=2.2e-05  Score=71.15  Aligned_cols=122  Identities=24%  Similarity=0.162  Sum_probs=77.1

Q ss_pred             ChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccC-CCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEE
Q 015158           62 PSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYG-LVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHA  140 (412)
Q Consensus        62 l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~-~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~  140 (412)
                      +++-|.+++..  ..+.++|.|+.|||||.+.+.-+...+... ....+++++++|+..+.++.+.+...........  
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  667899999999999999887777666554 4556899999999999999888887543221100  


Q ss_pred             EEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCC--CCceEEEEeCCc
Q 015158          141 CVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRP--DNIRIFVLDEAD  191 (412)
Q Consensus       141 ~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~--~~~~~iiiDE~h  191 (412)
                          ...............+.|.|.+.|...+.+.....  -.-.+-++|+..
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                00001112222335689999988866443311110  112356666665

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 ....

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=97.91  E-value=0.00023  Score=71.55  Aligned_cols=125  Identities=14%  Similarity=0.107  Sum_probs=74.4

Q ss_pred             CCCCChHHHHhhhhhhhcC-ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCc
Q 015158           58 GFEKPSAIQQRGIVPFCKG-LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGV  136 (412)
Q Consensus        58 ~~~~l~~~Q~~a~~~~~~~-~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~  136 (412)
                      ++. +++-|++|+..++.+ +-.+|.+++|+|||.+.- ++...+..  .+.++++++||-.-+..+.+.       .+.
T Consensus       350 ~~~-Ls~~Q~~Av~~i~~s~~~~il~G~aGTGKTtll~-~i~~~~~~--~g~~V~~~ApTg~Aa~~L~~~-------~g~  418 (744)
T TIGR02768       350 HYR-LSEEQYEAVRHVTGSGDIAVVVGRAGTGKSTMLK-AAREAWEA--AGYRVIGAALSGKAAEGLQAE-------SGI  418 (744)
T ss_pred             cCC-CCHHHHHHHHHHhcCCCEEEEEecCCCCHHHHHH-HHHHHHHh--CCCeEEEEeCcHHHHHHHHhc-------cCC
Confidence            444 899999999999874 667899999999997643 33333322  245799999997655444321       122


Q ss_pred             EEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHh-CCCCceE
Q 015158          137 KVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQL-LPPKIQV  215 (412)
Q Consensus       137 ~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~-~~~~~~~  215 (412)
                      ...                        |..++...+..........++||+||+-.+....    +..++.. ...+.++
T Consensus       419 ~a~------------------------Ti~~~~~~~~~~~~~~~~~~llIvDEasMv~~~~----~~~Ll~~~~~~~~kl  470 (744)
T TIGR02768       419 ESR------------------------TLASLEYAWANGRDLLSDKDVLVIDEAGMVGSRQ----MARVLKEAEEAGAKV  470 (744)
T ss_pred             cee------------------------eHHHHHhhhccCcccCCCCcEEEEECcccCCHHH----HHHHHHHHHhcCCEE
Confidence            211                        2222211112222223567899999999765433    3344442 2346667


Q ss_pred             EEEeec
Q 015158          216 GVFSAT  221 (412)
Q Consensus       216 i~~SAT  221 (412)
                      |++.-+
T Consensus       471 iLVGD~  476 (744)
T TIGR02768       471 VLVGDP  476 (744)
T ss_pred             EEECCh
Confidence            666644

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.

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.85  E-value=0.00032  Score=64.37  Aligned_cols=122  Identities=14%  Similarity=0.102  Sum_probs=67.2

Q ss_pred             ccEEEECCCCCCchhHhHHHHHHhhcc-CCCceeEEEEc-CC-HHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHH
Q 015158           77 LDVIQQAQSGTGKTATFCSGILQQLDY-GLVECQALVLA-PT-RELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRI  153 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~~~~~~~~~~-~~~~~~~lil~-P~-~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  153 (412)
                      +.+++.+|||+|||.+..-.+...... ...+.++.+++ .+ +.-+   .+++..++...++++..             
T Consensus       175 ~vi~lvGptGvGKTTT~aKLA~~~~~~~~~~g~~V~lit~Dt~R~aa---~eQL~~~a~~lgvpv~~-------------  238 (388)
T PRK12723        175 RVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIGA---KKQIQTYGDIMGIPVKA-------------  238 (388)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHhhhccCCCeEEEEeccCccHHH---HHHHHHHhhcCCcceEe-------------
Confidence            567889999999998875444332211 11233455544 33 2222   22245555444554421             


Q ss_pred             hcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccC-cHHHHHHHHHhCCCC-ceEEEEeecCChHH
Q 015158          154 LSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRG-FKDQIYDIFQLLPPK-IQVGVFSATMPPEA  226 (412)
Q Consensus       154 ~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~-~~~~~~~i~~~~~~~-~~~i~~SAT~~~~~  226 (412)
                              +-+++.+...+..    ..+.++|++|++.+..... ....+..++...... ..++.+|||.....
T Consensus       239 --------~~~~~~l~~~L~~----~~~~DlVLIDTaGr~~~~~~~l~el~~~l~~~~~~~e~~LVlsat~~~~~  301 (388)
T PRK12723        239 --------IESFKDLKEEITQ----SKDFDLVLVDTIGKSPKDFMKLAEMKELLNACGRDAEFHLAVSSTTKTSD  301 (388)
T ss_pred             --------eCcHHHHHHHHHH----hCCCCEEEEcCCCCCccCHHHHHHHHHHHHhcCCCCeEEEEEcCCCCHHH
Confidence                    1133444444432    2468999999999754221 223455555544433 56899999987543

>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]

Probab=97.84  E-value=5.2e-05  Score=76.48  Aligned_cols=145  Identities=18%  Similarity=0.034  Sum_probs=97.2

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhccC---------------CCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEE
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDYG---------------LVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHA  140 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~~---------------~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~  140 (412)
                      |+.+++.-..|+|||...+...+......               ...+..|||||. ++..||.+++..-.... +.+..
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            56778899999999977655444332111               112469999996 77888999998876543 67777


Q ss_pred             EEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCC---------C-----------CceEEEEeCCchhhccCcHH
Q 015158          141 CVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRP---------D-----------NIRIFVLDEADEMLSRGFKD  200 (412)
Q Consensus       141 ~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~---------~-----------~~~~iiiDE~h~~~~~~~~~  200 (412)
                      +.|-.+...........+|||+|||+.|.+.+.....+.         +           .|=.|++||++.+-..  ..
T Consensus       452 Y~Girk~~~~~~~el~~yDIVlTtYdiLr~El~hte~~~~~R~lR~qsr~~~~~SPL~~v~wWRIclDEaQMvess--sS  529 (1394)
T KOG0298|consen  452 YFGIRKTFWLSPFELLQYDIVLTTYDILRNELYHTEDFGSDRQLRHQSRYMRPNSPLLMVNWWRICLDEAQMVESS--SS  529 (1394)
T ss_pred             EechhhhcccCchhhhccCEEEeehHHHHhHhhcccccCChhhhhcccCCCCCCCchHHHHHHHHhhhHHHhhcch--HH
Confidence            777665544444445678999999999987665431110         0           1225999999976543  35


Q ss_pred             HHHHHHHhCCCCceEEEEeecCChH
Q 015158          201 QIYDIFQLLPPKIQVGVFSATMPPE  225 (412)
Q Consensus       201 ~~~~i~~~~~~~~~~i~~SAT~~~~  225 (412)
                      ...+....++ ....=++|+||-..
T Consensus       530 ~~a~M~~rL~-~in~W~VTGTPiq~  553 (1394)
T KOG0298|consen  530 AAAEMVRRLH-AINRWCVTGTPIQK  553 (1394)
T ss_pred             HHHHHHHHhh-hhceeeecCCchhh
Confidence            5556666665 44478999998654

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=97.84  E-value=5e-05  Score=58.95  Aligned_cols=37  Identities=24%  Similarity=0.254  Sum_probs=25.8

Q ss_pred             eEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEeecC
Q 015158          183 RIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATM  222 (412)
Q Consensus       183 ~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~  222 (412)
                      .+||+||+|++.  . ...+..+........-.+.+++++
T Consensus        89 ~~lviDe~~~l~--~-~~~l~~l~~l~~~~~~~vvl~G~~  125 (131)
T PF13401_consen   89 VLLVIDEADHLF--S-DEFLEFLRSLLNESNIKVVLVGTP  125 (131)
T ss_dssp             EEEEEETTHHHH--T-HHHHHHHHHHTCSCBEEEEEEESS
T ss_pred             eEEEEeChHhcC--C-HHHHHHHHHHHhCCCCeEEEEECh
Confidence            689999999964  2 455555555555555567777776

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.77  E-value=0.0005  Score=62.57  Aligned_cols=170  Identities=19%  Similarity=0.179  Sum_probs=87.5

Q ss_pred             CChhhhccccccCCCCHHHHHHHHHC-C----CC---CChHHHHhhhhh-----------hhcCccEEEECCCCCCchhH
Q 015158           32 TSYDEVYDTFDAMGLQENLLRGIYAY-G----FE---KPSAIQQRGIVP-----------FCKGLDVIQQAQSGTGKTAT   92 (412)
Q Consensus        32 ~~~~~~~~~f~~~~l~~~~~~~l~~~-~----~~---~l~~~Q~~a~~~-----------~~~~~~~lv~~~tGsGKT~~   92 (412)
                      +.....+..+...++++.+.+.|-.. +    ..   ..+.+....+..           +.++..+++.+|||+|||++
T Consensus        74 p~~~~l~~~L~~~g~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~g~ii~lvGptGvGKTTt  153 (374)
T PRK14722         74 PVHGALTKYLFAAGFSAQLVRMIVDNLPEGEGYDTLDAAADWAQSVLAANLPVLDSEDALMERGGVFALMGPTGVGKTTT  153 (374)
T ss_pred             cHHHHHHHHHHHCCCCHHHHHHHHHhhhhhcccCCHHHHHHHHHHHHHhcchhhcCCCccccCCcEEEEECCCCCCHHHH
Confidence            33445567788889998888877442 1    11   123333333322           11256789999999999987


Q ss_pred             hHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHH
Q 015158           93 FCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDML  172 (412)
Q Consensus        93 ~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~  172 (412)
                      ....+....... ...++.+++. ...-.--.++++.++...++.+...                     -+...+...+
T Consensus       154 iakLA~~~~~~~-G~~~V~lit~-D~~R~ga~EqL~~~a~~~gv~~~~~---------------------~~~~~l~~~l  210 (374)
T PRK14722        154 TAKLAARCVMRF-GASKVALLTT-DSYRIGGHEQLRIFGKILGVPVHAV---------------------KDGGDLQLAL  210 (374)
T ss_pred             HHHHHHHHHHhc-CCCeEEEEec-ccccccHHHHHHHHHHHcCCceEec---------------------CCcccHHHHH
Confidence            755444333221 1124544442 2221112344444444445444322                     2222232223


Q ss_pred             HcCCCCCCCceEEEEeCCchhhc-cCcHHHHHHHHHhCCCCceEEEEeecCChHHHH
Q 015158          173 RRQSLRPDNIRIFVLDEADEMLS-RGFKDQIYDIFQLLPPKIQVGVFSATMPPEALE  228 (412)
Q Consensus       173 ~~~~~~~~~~~~iiiDE~h~~~~-~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~  228 (412)
                      .+    ..+.++|+||++-.... ......+..+.....+...++.+|||...+...
T Consensus       211 ~~----l~~~DlVLIDTaG~~~~d~~l~e~La~L~~~~~~~~~lLVLsAts~~~~l~  263 (374)
T PRK14722        211 AE----LRNKHMVLIDTIGMSQRDRTVSDQIAMLHGADTPVQRLLLLNATSHGDTLN  263 (374)
T ss_pred             HH----hcCCCEEEEcCCCCCcccHHHHHHHHHHhccCCCCeEEEEecCccChHHHH
Confidence            21    23568999999975321 112233333333233345689999998765544

>PRK13889 conjugal transfer relaxase TraA; Provisional

Probab=97.77  E-value=0.00058  Score=69.92  Aligned_cols=126  Identities=17%  Similarity=0.105  Sum_probs=76.3

Q ss_pred             CCCCCChHHHHhhhhhhhcCc-cEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccC
Q 015158           57 YGFEKPSAIQQRGIVPFCKGL-DVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLG  135 (412)
Q Consensus        57 ~~~~~l~~~Q~~a~~~~~~~~-~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~  135 (412)
                      .++. |++-|++|+..++.++ .++|.++.|+|||.+. -.+...+..  .+.+++.++||-.-+..+.+       ..+
T Consensus       343 ~g~~-Ls~eQr~Av~~il~s~~v~vv~G~AGTGKTT~l-~~~~~~~e~--~G~~V~~~ApTGkAA~~L~e-------~tG  411 (988)
T PRK13889        343 RGLV-LSGEQADALAHVTDGRDLGVVVGYAGTGKSAML-GVAREAWEA--AGYEVRGAALSGIAAENLEG-------GSG  411 (988)
T ss_pred             cCCC-CCHHHHHHHHHHhcCCCeEEEEeCCCCCHHHHH-HHHHHHHHH--cCCeEEEecCcHHHHHHHhh-------ccC
Confidence            4555 9999999999999854 5789999999999763 334433332  24579999998765443322       112


Q ss_pred             cEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhC-CCCce
Q 015158          136 VKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLL-PPKIQ  214 (412)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~-~~~~~  214 (412)
                      +..                        .|..+|..-...........++|||||+-.+...    .+..++... +.+.+
T Consensus       412 i~a------------------------~TI~sll~~~~~~~~~l~~~~vlIVDEASMv~~~----~m~~LL~~a~~~gar  463 (988)
T PRK13889        412 IAS------------------------RTIASLEHGWGQGRDLLTSRDVLVIDEAGMVGTR----QLERVLSHAADAGAK  463 (988)
T ss_pred             cch------------------------hhHHHHHhhhcccccccccCcEEEEECcccCCHH----HHHHHHHhhhhCCCE
Confidence            211                        1222332211122222345689999999976433    344455433 45677


Q ss_pred             EEEEeec
Q 015158          215 VGVFSAT  221 (412)
Q Consensus       215 ~i~~SAT  221 (412)
                      +|++.-+
T Consensus       464 vVLVGD~  470 (988)
T PRK13889        464 VVLVGDP  470 (988)
T ss_pred             EEEECCH
Confidence            7777666

>PRK04296 thymidine kinase; Provisional

Probab=97.76  E-value=6.5e-05  Score=62.34  Aligned_cols=36  Identities=17%  Similarity=0.205  Sum_probs=25.8

Q ss_pred             ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcC
Q 015158           77 LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAP  115 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P  115 (412)
                      .-.++.+|+|+|||..++..+......+   .+++++-|
T Consensus         3 ~i~litG~~GsGKTT~~l~~~~~~~~~g---~~v~i~k~   38 (190)
T PRK04296          3 KLEFIYGAMNSGKSTELLQRAYNYEERG---MKVLVFKP   38 (190)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHHcC---CeEEEEec
Confidence            3468899999999987766665554433   47887766

>KOG1805 consensus DNA replication helicase [Replication, recombination and repair]

Probab=97.74  E-value=0.00014  Score=71.66  Aligned_cols=123  Identities=17%  Similarity=0.167  Sum_probs=79.8

Q ss_pred             CChHHHHhhhhhhhcC-ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEE
Q 015158           61 KPSAIQQRGIVPFCKG-LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVH  139 (412)
Q Consensus        61 ~l~~~Q~~a~~~~~~~-~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~  139 (412)
                      .|+..|++|+..++.. ...+|.|=+|+|||.+....+-.....+   +++|+.+-|..-++.+.-.+..+    ++...
T Consensus       669 ~LN~dQr~A~~k~L~aedy~LI~GMPGTGKTTtI~~LIkiL~~~g---kkVLLtsyThsAVDNILiKL~~~----~i~~l  741 (1100)
T KOG1805|consen  669 RLNNDQRQALLKALAAEDYALILGMPGTGKTTTISLLIKILVALG---KKVLLTSYTHSAVDNILIKLKGF----GIYIL  741 (1100)
T ss_pred             hcCHHHHHHHHHHHhccchheeecCCCCCchhhHHHHHHHHHHcC---CeEEEEehhhHHHHHHHHHHhcc----Cccee
Confidence            5889999999997765 4578899999999977655444333333   48998888877777776666664    33333


Q ss_pred             EEEcCcchHHH-----------------HHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhh
Q 015158          140 ACVGGTSVRED-----------------QRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEML  194 (412)
Q Consensus       140 ~~~~~~~~~~~-----------------~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~  194 (412)
                      .+-........                 ...+-+...||.+|.-.+.+.+.    ..+.||+.|+|||-++.
T Consensus       742 RLG~~~kih~~v~e~~~~~~~s~ks~~~l~~~~~~~~IVa~TClgi~~plf----~~R~FD~cIiDEASQI~  809 (1100)
T KOG1805|consen  742 RLGSEEKIHPDVEEFTLTNETSEKSYADLKKFLDQTSIVACTCLGINHPLF----VNRQFDYCIIDEASQIL  809 (1100)
T ss_pred             ecCCccccchHHHHHhcccccchhhHHHHHHHhCCCcEEEEEccCCCchhh----hccccCEEEEccccccc
Confidence            22222221111                 12233556788888655544333    34579999999999864

>PRK08181 transposase; Validated

Probab=97.64  E-value=0.00061  Score=59.45  Aligned_cols=119  Identities=16%  Similarity=0.182  Sum_probs=64.8

Q ss_pred             ChHHHHhhhh----hhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcE
Q 015158           62 PSAIQQRGIV----PFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVK  137 (412)
Q Consensus        62 l~~~Q~~a~~----~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~  137 (412)
                      +...|..++.    .+..++++++.||+|+|||..+..........+   .+++++ +...|..+.......        
T Consensus        88 ~~~~~~~~L~~~~~~~~~~~nlll~Gp~GtGKTHLa~Aia~~a~~~g---~~v~f~-~~~~L~~~l~~a~~~--------  155 (269)
T PRK08181         88 VSKAQVMAIAAGDSWLAKGANLLLFGPPGGGKSHLAAAIGLALIENG---WRVLFT-RTTDLVQKLQVARRE--------  155 (269)
T ss_pred             CCHHHHHHHHHHHHHHhcCceEEEEecCCCcHHHHHHHHHHHHHHcC---Cceeee-eHHHHHHHHHHHHhC--------
Confidence            3456666663    334678999999999999966544333333332   355554 334444433211000        


Q ss_pred             EEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccC-cHHHHHHHHHhCCCCceEE
Q 015158          138 VHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRG-FKDQIYDIFQLLPPKIQVG  216 (412)
Q Consensus       138 ~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~-~~~~~~~i~~~~~~~~~~i  216 (412)
                                               .+.+.+...+       ...+++|+||.+...... ....+..+++......++|
T Consensus       156 -------------------------~~~~~~l~~l-------~~~dLLIIDDlg~~~~~~~~~~~Lf~lin~R~~~~s~I  203 (269)
T PRK08181        156 -------------------------LQLESAIAKL-------DKFDLLILDDLAYVTKDQAETSVLFELISARYERRSIL  203 (269)
T ss_pred             -------------------------CcHHHHHHHH-------hcCCEEEEeccccccCCHHHHHHHHHHHHHHHhCCCEE
Confidence                                     1222222222       257899999999754332 2345666666554445555


Q ss_pred             EEeecCCh
Q 015158          217 VFSATMPP  224 (412)
Q Consensus       217 ~~SAT~~~  224 (412)
                      ..|-.++.
T Consensus       204 iTSN~~~~  211 (269)
T PRK08181        204 ITANQPFG  211 (269)
T ss_pred             EEcCCCHH
Confidence            55555543

>PF13871 Helicase_C_4: Helicase_C-like

Probab=97.61  E-value=0.00022  Score=61.63  Aligned_cols=65  Identities=22%  Similarity=0.350  Sum_probs=53.1

Q ss_pred             HHHHHHHhcCCCcEEEEcCCCcCCCCCCC--------CCEEEEccCCCChhhHHHhhhhcccCCCCc-eEEEEe
Q 015158          318 DIIMREFRSGSSRVLITTDLLARGIDVQQ--------VSLVINYDLPTQPENYLHRIGRSGRFGRKG-VAINFV  382 (412)
Q Consensus       318 ~~~~~~f~~g~~~vlv~t~~~~~G~d~~~--------~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g-~~~~~~  382 (412)
                      ....+.|.+|+.+|+|.+.+.++|+.+..        -++.|...+|||....+|..||+.|.|+.. ..|.++
T Consensus        51 ~~e~~~F~~g~k~v~iis~AgstGiSlHAd~~~~nqr~Rv~i~le~pwsad~aiQ~~GR~hRsnQ~~~P~y~~l  124 (278)
T PF13871_consen   51 IAEKQAFMDGEKDVAIISDAGSTGISLHADRRVKNQRRRVHITLELPWSADKAIQQFGRTHRSNQVSAPEYRFL  124 (278)
T ss_pred             HHHHHHHhCCCceEEEEecccccccchhccccCCCCCceEEEEeeCCCCHHHHHHHhccccccccccCCEEEEe
Confidence            35678899999999999999999999763        345678899999999999999999998743 334433

>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=97.60  E-value=0.00025  Score=58.90  Aligned_cols=132  Identities=18%  Similarity=0.228  Sum_probs=72.2

Q ss_pred             cEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCC
Q 015158           78 DVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSG  157 (412)
Q Consensus        78 ~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  157 (412)
                      -+++++|||+|||.+..-.+......   +.++.+++--.-- .--.++++.++...++++........           
T Consensus         3 vi~lvGptGvGKTTt~aKLAa~~~~~---~~~v~lis~D~~R-~ga~eQL~~~a~~l~vp~~~~~~~~~-----------   67 (196)
T PF00448_consen    3 VIALVGPTGVGKTTTIAKLAARLKLK---GKKVALISADTYR-IGAVEQLKTYAEILGVPFYVARTESD-----------   67 (196)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHHT---T--EEEEEESTSS-THHHHHHHHHHHHHTEEEEESSTTSC-----------
T ss_pred             EEEEECCCCCchHhHHHHHHHHHhhc---cccceeecCCCCC-ccHHHHHHHHHHHhccccchhhcchh-----------
Confidence            46889999999998875544444333   3455555532111 11244455555545665543221111           


Q ss_pred             CcEEEeChHH-HHHHHHcCCCCCCCceEEEEeCCchhh-ccCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHh
Q 015158          158 VHVVVGTPGR-VFDMLRRQSLRPDNIRIFVLDEADEML-SRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKF  233 (412)
Q Consensus       158 ~~iii~T~~~-l~~~~~~~~~~~~~~~~iiiDE~h~~~-~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~  233 (412)
                             +.. +...++.  ...+++++|++|-+-+.. +......+..+.....+....+.+|||...+.......+
T Consensus        68 -------~~~~~~~~l~~--~~~~~~D~vlIDT~Gr~~~d~~~~~el~~~~~~~~~~~~~LVlsa~~~~~~~~~~~~~  136 (196)
T PF00448_consen   68 -------PAEIAREALEK--FRKKGYDLVLIDTAGRSPRDEELLEELKKLLEALNPDEVHLVLSATMGQEDLEQALAF  136 (196)
T ss_dssp             -------HHHHHHHHHHH--HHHTTSSEEEEEE-SSSSTHHHHHHHHHHHHHHHSSSEEEEEEEGGGGGHHHHHHHHH
T ss_pred             -------hHHHHHHHHHH--HhhcCCCEEEEecCCcchhhHHHHHHHHHHhhhcCCccceEEEecccChHHHHHHHHH
Confidence                   111 1122221  111357899999886533 223456677777777777789999999987655544444

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 ....

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.60  E-value=0.0014  Score=59.59  Aligned_cols=128  Identities=16%  Similarity=0.205  Sum_probs=68.0

Q ss_pred             ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcC-CH--HHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHH
Q 015158           77 LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAP-TR--ELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRI  153 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P-~~--~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  153 (412)
                      +.+++.||+|+|||......+......   +.++.++.. +.  +-.+|    ++.+....++.+               
T Consensus       242 ~vI~LVGptGvGKTTTiaKLA~~L~~~---GkkVglI~aDt~RiaAvEQ----Lk~yae~lgipv---------------  299 (436)
T PRK11889        242 QTIALIGPTGVGKTTTLAKMAWQFHGK---KKTVGFITTDHSRIGTVQQ----LQDYVKTIGFEV---------------  299 (436)
T ss_pred             cEEEEECCCCCcHHHHHHHHHHHHHHc---CCcEEEEecCCcchHHHHH----HHHHhhhcCCcE---------------
Confidence            467899999999998765544433322   234554443 22  23333    334433223332               


Q ss_pred             hcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhcc-CcHHHHHHHHHhCCCCceEEEEeecCCh-HHHHHHH
Q 015158          154 LSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSR-GFKDQIYDIFQLLPPKIQVGVFSATMPP-EALEITR  231 (412)
Q Consensus       154 ~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~-~~~~~~~~i~~~~~~~~~~i~~SAT~~~-~~~~~~~  231 (412)
                            +...++..+...+..... ..++++|++|-+-+.... .....+..++....+...++.+|||... +....+.
T Consensus       300 ------~v~~d~~~L~~aL~~lk~-~~~~DvVLIDTaGRs~kd~~lm~EL~~~lk~~~PdevlLVLsATtk~~d~~~i~~  372 (436)
T PRK11889        300 ------IAVRDEAAMTRALTYFKE-EARVDYILIDTAGKNYRASETVEEMIETMGQVEPDYICLTLSASMKSKDMIEIIT  372 (436)
T ss_pred             ------EecCCHHHHHHHHHHHHh-ccCCCEEEEeCccccCcCHHHHHHHHHHHhhcCCCeEEEEECCccChHHHHHHHH
Confidence                  223355556554432211 125799999988663322 2234455555544445557779998765 3344444


Q ss_pred             Hh
Q 015158          232 KF  233 (412)
Q Consensus       232 ~~  233 (412)
                      .+
T Consensus       373 ~F  374 (436)
T PRK11889        373 NF  374 (436)
T ss_pred             Hh
Confidence            43

>PRK13826 Dtr system oriT relaxase; Provisional

Probab=97.58  E-value=0.0018  Score=66.87  Aligned_cols=137  Identities=18%  Similarity=0.140  Sum_probs=79.9

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHhhhhhhhc-CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHH
Q 015158           46 LQENLLRGIYAYGFEKPSAIQQRGIVPFCK-GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIE  124 (412)
Q Consensus        46 l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~-~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~  124 (412)
                      .++.........++. |++-|++|+..+.. ++-.+|.|+.|+|||.+.- .+...+..  .+.+++.++|+-.-+..+.
T Consensus       367 v~~~~l~a~~~~~~~-Ls~eQ~~Av~~i~~~~r~~~v~G~AGTGKTt~l~-~~~~~~e~--~G~~V~g~ApTgkAA~~L~  442 (1102)
T PRK13826        367 VREAVLAATFARHAR-LSDEQKTAIEHVAGPARIAAVVGRAGAGKTTMMK-AAREAWEA--AGYRVVGGALAGKAAEGLE  442 (1102)
T ss_pred             CCHHHHHHHHhcCCC-CCHHHHHHHHHHhccCCeEEEEeCCCCCHHHHHH-HHHHHHHH--cCCeEEEEcCcHHHHHHHH
Confidence            334444444344554 99999999999865 4667899999999997653 33333322  2457999999876554433


Q ss_pred             HHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHH
Q 015158          125 KVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYD  204 (412)
Q Consensus       125 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~  204 (412)
                          +-   .|+..                        .|..+|..........+..-++|||||+..+..    ..+..
T Consensus       443 ----e~---~Gi~a------------------------~TIas~ll~~~~~~~~l~~~~vlVIDEAsMv~~----~~m~~  487 (1102)
T PRK13826        443 ----KE---AGIQS------------------------RTLSSWELRWNQGRDQLDNKTVFVLDEAGMVAS----RQMAL  487 (1102)
T ss_pred             ----Hh---hCCCe------------------------eeHHHHHhhhccCccCCCCCcEEEEECcccCCH----HHHHH
Confidence                21   13222                        122222111111112234567999999997543    34445


Q ss_pred             HHHhCC-CCceEEEEeec
Q 015158          205 IFQLLP-PKIQVGVFSAT  221 (412)
Q Consensus       205 i~~~~~-~~~~~i~~SAT  221 (412)
                      ++...+ .+.++|++.-+
T Consensus       488 Ll~~~~~~garvVLVGD~  505 (1102)
T PRK13826        488 FVEAVTRAGAKLVLVGDP  505 (1102)
T ss_pred             HHHHHHhcCCEEEEECCH
Confidence            555543 46777777666

>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=97.57  E-value=0.0012  Score=52.11  Aligned_cols=19  Identities=26%  Similarity=0.295  Sum_probs=16.1

Q ss_pred             CccEEEECCCCCCchhHhH
Q 015158           76 GLDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~   94 (412)
                      ++.+++.||+|+|||..+.
T Consensus        19 ~~~v~i~G~~G~GKT~l~~   37 (151)
T cd00009          19 PKNLLLYGPPGTGKTTLAR   37 (151)
T ss_pred             CCeEEEECCCCCCHHHHHH
Confidence            5789999999999996553

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.

>PRK06526 transposase; Provisional

Probab=97.55  E-value=0.00043  Score=60.03  Aligned_cols=111  Identities=13%  Similarity=0.052  Sum_probs=58.8

Q ss_pred             hhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHH
Q 015158           72 PFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQ  151 (412)
Q Consensus        72 ~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  151 (412)
                      .+..+.++++.||+|+|||..+..........+   .+++++.. ..+.++    +....          .         
T Consensus        94 fi~~~~nlll~Gp~GtGKThLa~al~~~a~~~g---~~v~f~t~-~~l~~~----l~~~~----------~---------  146 (254)
T PRK06526         94 FVTGKENVVFLGPPGTGKTHLAIGLGIRACQAG---HRVLFATA-AQWVAR----LAAAH----------H---------  146 (254)
T ss_pred             hhhcCceEEEEeCCCCchHHHHHHHHHHHHHCC---CchhhhhH-HHHHHH----HHHHH----------h---------
Confidence            344568999999999999977654444333333   35555322 233332    22110          0         


Q ss_pred             HHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccC-cHHHHHHHHHhCCCCceEEEEeecCChHH
Q 015158          152 RILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRG-FKDQIYDIFQLLPPKIQVGVFSATMPPEA  226 (412)
Q Consensus       152 ~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~-~~~~~~~i~~~~~~~~~~i~~SAT~~~~~  226 (412)
                          .      .+.......       ....+++|+||+|...... ....+..++.....+..+|+.|..+....
T Consensus       147 ----~------~~~~~~l~~-------l~~~dlLIIDD~g~~~~~~~~~~~L~~li~~r~~~~s~IitSn~~~~~w  205 (254)
T PRK06526        147 ----A------GRLQAELVK-------LGRYPLLIVDEVGYIPFEPEAANLFFQLVSSRYERASLIVTSNKPFGRW  205 (254)
T ss_pred             ----c------CcHHHHHHH-------hccCCEEEEcccccCCCCHHHHHHHHHHHHHHHhcCCEEEEcCCCHHHH
Confidence                0      011111111       1356899999999754222 22345555544333455777777765543

>PRK14974 cell division protein FtsY; Provisional

Probab=97.54  E-value=0.0019  Score=58.24  Aligned_cols=130  Identities=24%  Similarity=0.341  Sum_probs=72.2

Q ss_pred             ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCC---HHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHH
Q 015158           77 LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPT---RELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRI  153 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~---~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  153 (412)
                      .-+++.+++|+|||.+..-.+. .+..  .+.+++++...   ..-.+|+..    +....++.+.....+..       
T Consensus       141 ~vi~~~G~~GvGKTTtiakLA~-~l~~--~g~~V~li~~Dt~R~~a~eqL~~----~a~~lgv~v~~~~~g~d-------  206 (336)
T PRK14974        141 VVIVFVGVNGTGKTTTIAKLAY-YLKK--NGFSVVIAAGDTFRAGAIEQLEE----HAERLGVKVIKHKYGAD-------  206 (336)
T ss_pred             eEEEEEcCCCCCHHHHHHHHHH-HHHH--cCCeEEEecCCcCcHHHHHHHHH----HHHHcCCceecccCCCC-------
Confidence            3577899999999986544333 2322  22356555432   233444433    33333544432111111       


Q ss_pred             hcCCCcEEEeChHH-HHHHHHcCCCCCCCceEEEEeCCchhh-ccCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHH
Q 015158          154 LSSGVHVVVGTPGR-VFDMLRRQSLRPDNIRIFVLDEADEML-SRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITR  231 (412)
Q Consensus       154 ~~~~~~iii~T~~~-l~~~~~~~~~~~~~~~~iiiDE~h~~~-~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~  231 (412)
                                 |.. +...+....  ..+.++|++|.+++.. +......+..+.....+...++.++||...+......
T Consensus       207 -----------p~~v~~~ai~~~~--~~~~DvVLIDTaGr~~~~~~lm~eL~~i~~~~~pd~~iLVl~a~~g~d~~~~a~  273 (336)
T PRK14974        207 -----------PAAVAYDAIEHAK--ARGIDVVLIDTAGRMHTDANLMDELKKIVRVTKPDLVIFVGDALAGNDAVEQAR  273 (336)
T ss_pred             -----------HHHHHHHHHHHHH--hCCCCEEEEECCCccCCcHHHHHHHHHHHHhhCCceEEEeeccccchhHHHHHH
Confidence                       111 112121111  1356899999999865 3335567777777777788889999998766555555


Q ss_pred             Hh
Q 015158          232 KF  233 (412)
Q Consensus       232 ~~  233 (412)
                      .+
T Consensus       274 ~f  275 (336)
T PRK14974        274 EF  275 (336)
T ss_pred             HH
Confidence            44

>KOG0383 consensus Predicted helicase [General function prediction only]

Probab=97.51  E-value=1e-05  Score=78.06  Aligned_cols=74  Identities=18%  Similarity=0.245  Sum_probs=58.5

Q ss_pred             HHHHHHHHhc--CCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhc---CCCcEEEEcCCCcCC
Q 015158          267 ETLCDLYETL--AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRS---GSSRVLITTDLLARG  341 (412)
Q Consensus       267 ~~l~~~~~~~--~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~---g~~~vlv~t~~~~~G  341 (412)
                      ..|...+++.  ...+++||..-.+..+-+.+++...+ ....+.|...-.+|...+.+|+.   ....++++|.+.+.|
T Consensus       618 ~~l~~~~~~l~~~ghrvl~~~q~~~~ldlled~~~~~~-~~~r~dG~~~~~~rq~ai~~~n~~~~~~~cfllstra~g~g  696 (696)
T KOG0383|consen  618 TLLLKMLKKLKSSGHRVLIFSQMIHMLDLLEDYLTYEG-KYERIDGPITGPERQAAIDRFNAPGSNQFCFLLSTRAGGLG  696 (696)
T ss_pred             HHHHHHHHHHHhcchhhHHHHHHHHHHHHhHHHHhccC-cceeccCCccchhhhhhccccCCCCccceEEEeecccccCC
Confidence            3344444443  33689999999999998888888878 88889999999999999999985   356788999988766

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=97.51  E-value=0.00038  Score=54.61  Aligned_cols=41  Identities=17%  Similarity=0.115  Sum_probs=26.1

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHH
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTREL  119 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L  119 (412)
                      ++.+++.+|+|+|||..+...+. .+...  ...++++.+....
T Consensus         2 ~~~~~l~G~~G~GKTtl~~~l~~-~~~~~--~~~~~~~~~~~~~   42 (148)
T smart00382        2 GEVILIVGPPGSGKTTLARALAR-ELGPP--GGGVIYIDGEDIL   42 (148)
T ss_pred             CCEEEEECCCCCcHHHHHHHHHh-ccCCC--CCCEEEECCEEcc
Confidence            46789999999999987644333 32221  1246777766543

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.

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=97.38  E-value=0.0038  Score=58.49  Aligned_cols=127  Identities=19%  Similarity=0.210  Sum_probs=65.8

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhh-ccCCCceeEEEEc-CCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHH
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQL-DYGLVECQALVLA-PTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRI  153 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~-~~~~~~~~~lil~-P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  153 (412)
                      ++.+++.+|||+|||.+....+.... ..  .+.++.++. .+...  ...+++..++...++.+.              
T Consensus       221 ~~~i~~vGptGvGKTTt~~kLA~~~~~~~--~g~~V~li~~D~~r~--~a~eqL~~~a~~~~vp~~--------------  282 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLAKLAARYALLY--GKKKVALITLDTYRI--GAVEQLKTYAKIMGIPVE--------------  282 (424)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhc--CCCeEEEEECCccHH--HHHHHHHHHHHHhCCceE--------------
Confidence            45678899999999977654443332 12  123455544 32111  112334444333343331              


Q ss_pred             hcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhc-cCcHHHHHHHHH-hCCCCceEEEEeecCChHHHHHHH
Q 015158          154 LSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLS-RGFKDQIYDIFQ-LLPPKIQVGVFSATMPPEALEITR  231 (412)
Q Consensus       154 ~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~-~~~~~~~~~i~~-~~~~~~~~i~~SAT~~~~~~~~~~  231 (412)
                             .+.+++.+...+..    ..+.++|+||.+-.... ......+..++. ...+....++++||........+.
T Consensus       283 -------~~~~~~~l~~~l~~----~~~~DlVlIDt~G~~~~d~~~~~~L~~ll~~~~~~~~~~LVl~a~~~~~~l~~~~  351 (424)
T PRK05703        283 -------VVYDPKELAKALEQ----LRDCDVILIDTAGRSQRDKRLIEELKALIEFSGEPIDVYLVLSATTKYEDLKDIY  351 (424)
T ss_pred             -------ccCCHHhHHHHHHH----hCCCCEEEEeCCCCCCCCHHHHHHHHHHHhccCCCCeEEEEEECCCCHHHHHHHH
Confidence                   12333444444432    23579999999865321 112344555555 222345578899998765444433

>PF03354 Terminase_1: Phage Terminase ; InterPro: IPR005021 This entry is represented by Lactococcus phage bIL285, Orf41 (terminase)

Probab=97.37  E-value=0.00074  Score=64.71  Aligned_cols=150  Identities=16%  Similarity=0.097  Sum_probs=82.8

Q ss_pred             HHHHhhhhhhhc-----C----ccEEEECCCCCCchhHhHHHHHHh-hccCCCceeEEEEcCCHHHHHHHHHHHHHhhcc
Q 015158           64 AIQQRGIVPFCK-----G----LDVIQQAQSGTGKTATFCSGILQQ-LDYGLVECQALVLAPTRELAQQIEKVMRALGDY  133 (412)
Q Consensus        64 ~~Q~~a~~~~~~-----~----~~~lv~~~tGsGKT~~~~~~~~~~-~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~  133 (412)
                      |||+-++..++.     |    +.+++..|-|-|||......++.. +..+..+..+++++++..-+...++.+..+...
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            678877777662     2    467889999999996654443333 344455678999999999999999988887543


Q ss_pred             cCcEEEEEEcCcchHHHHHH-hcCCCcEEEeChHHHHHHHHc--CCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCC
Q 015158          134 LGVKVHACVGGTSVREDQRI-LSSGVHVVVGTPGRVFDMLRR--QSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLP  210 (412)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~-~~~~~~iii~T~~~l~~~~~~--~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~  210 (412)
                      ....-... .       .+. ......|.....+.+...+..  ....-.+.+++|+||+|...+......+..-....+
T Consensus        81 ~~~l~~~~-~-------~~~~~~~~~~i~~~~~~s~~~~~s~~~~~~dG~~~~~~i~DE~h~~~~~~~~~~l~~g~~~r~  152 (477)
T PF03354_consen   81 SPELRKRK-K-------PKIIKSNKKEIEFPKTGSFFKALSSDADSLDGLNPSLAIFDELHAHKDDELYDALESGMGARP  152 (477)
T ss_pred             Chhhccch-h-------hhhhhhhceEEEEcCCCcEEEEEecCCCCccCCCCceEEEeCCCCCCCHHHHHHHHhhhccCC
Confidence            21111000 0       000 001122333222222222111  222334668999999998766544444444444433


Q ss_pred             CCceEEEEeec
Q 015158          211 PKIQVGVFSAT  221 (412)
Q Consensus       211 ~~~~~i~~SAT  221 (412)
                      ...-++..||.
T Consensus       153 ~pl~~~ISTag  163 (477)
T PF03354_consen  153 NPLIIIISTAG  163 (477)
T ss_pred             CceEEEEeCCC
Confidence            33333334443

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>KOG0989 consensus Replication factor C, subunit RFC4 [Replication, recombination and repair]

Probab=97.35  E-value=0.0004  Score=59.89  Aligned_cols=44  Identities=16%  Similarity=0.249  Sum_probs=34.1

Q ss_pred             CCCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEeecCC
Q 015158          179 PDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMP  223 (412)
Q Consensus       179 ~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~  223 (412)
                      ...+..||+||||.+.... ...+.+.+...+...++++++.-+.
T Consensus       127 ~~~fKiiIlDEcdsmtsda-q~aLrr~mE~~s~~trFiLIcnyls  170 (346)
T KOG0989|consen  127 CPPFKIIILDECDSMTSDA-QAALRRTMEDFSRTTRFILICNYLS  170 (346)
T ss_pred             CCcceEEEEechhhhhHHH-HHHHHHHHhccccceEEEEEcCChh
Confidence            3567899999999876554 6778888888877888888877653

>PRK10919 ATP-dependent DNA helicase Rep; Provisional

Probab=97.26  E-value=0.00053  Score=68.40  Aligned_cols=69  Identities=16%  Similarity=0.129  Sum_probs=56.2

Q ss_pred             CChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhcc-CCCceeEEEEcCCHHHHHHHHHHHHHhh
Q 015158           61 KPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY-GLVECQALVLAPTRELAQQIEKVMRALG  131 (412)
Q Consensus        61 ~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~-~~~~~~~lil~P~~~L~~q~~~~~~~~~  131 (412)
                      .|++-|++|+.+.  ...++|.|++|||||.+...-+...+.. +....++|+++-|+.-+.++.+.+....
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 RLNPGQQQAVEFV--TGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVAQTL   71 (672)
T ss_pred             CCCHHHHHHHhCC--CCCEEEEecCCCCHHHHHHHHHHHHHHhcCCCHHHeeeEechHHHHHHHHHHHHHHh
Confidence            3789999999764  4578999999999999987777776653 4345689999999999999998887754

>PHA02533 17 large terminase protein; Provisional

Probab=97.26  E-value=0.0023  Score=61.63  Aligned_cols=122  Identities=13%  Similarity=0.071  Sum_probs=73.9

Q ss_pred             ChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCc--EEE
Q 015158           62 PSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGV--KVH  139 (412)
Q Consensus        62 l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~--~~~  139 (412)
                      |+|+|+..+..+..++..++..+-..|||.+....++..... .++..+++++|+..-+...++.++........  ...
T Consensus        60 L~p~Q~~i~~~~~~~R~~ii~~aRq~GKStl~a~~al~~a~~-~~~~~v~i~A~~~~QA~~vF~~ik~~ie~~P~l~~~~  138 (534)
T PHA02533         60 MRDYQKDMLKIMHKNRFNACNLSRQLGKTTVVAIFLLHYVCF-NKDKNVGILAHKASMAAEVLDRTKQAIELLPDFLQPG  138 (534)
T ss_pred             CcHHHHHHHHHHhcCeEEEEEEcCcCChHHHHHHHHHHHHHh-CCCCEEEEEeCCHHHHHHHHHHHHHHHHhCHHHhhcc
Confidence            899999999988767777899999999997776434333222 23458999999999888888877765432211  100


Q ss_pred             EEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhc
Q 015158          140 ACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLS  195 (412)
Q Consensus       140 ~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~  195 (412)
                       +.....   ..-.+.++..|.+.|.+.       ....-.+..++++||+|.+.+
T Consensus       139 -i~~~~~---~~I~l~NGS~I~~lss~~-------~t~rG~~~~~liiDE~a~~~~  183 (534)
T PHA02533        139 -IVEWNK---GSIELENGSKIGAYASSP-------DAVRGNSFAMIYIDECAFIPN  183 (534)
T ss_pred             -eeecCc---cEEEeCCCCEEEEEeCCC-------CccCCCCCceEEEeccccCCC
Confidence             000000   000012344554544221       112234567899999997643

>KOG1513 consensus Nuclear helicase MOP-3/SNO (DEAD-box superfamily) [Transcription; Signal transduction mechanisms]

Probab=97.23  E-value=0.00059  Score=65.90  Aligned_cols=157  Identities=20%  Similarity=0.235  Sum_probs=93.4

Q ss_pred             CChHHHHhhhhhhhc--------Cc--cEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 015158           61 KPSAIQQRGIVPFCK--------GL--DVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRAL  130 (412)
Q Consensus        61 ~l~~~Q~~a~~~~~~--------~~--~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~  130 (412)
                      .+...|.+|+-...+        |.  .++|-...|-||-.+..-.|+.....  ..+++||+.-+..|--+..+.++..
T Consensus       264 ~lSALQLEav~YAcQ~He~llPsG~RaGfLiGDGAGVGKGRTvAgiIfeNyLk--GRKrAlW~SVSsDLKfDAERDL~Di  341 (1300)
T KOG1513|consen  264 HLSALQLEAVTYACQAHEVLLPSGQRAGFLIGDGAGVGKGRTVAGIIFENYLK--GRKRALWFSVSSDLKFDAERDLRDI  341 (1300)
T ss_pred             chhHHHHHHHHHHHhhhhhcCCCCccceeeeccCcccCCCceeEEEEehhhhc--ccceeEEEEeccccccchhhchhhc
Confidence            477889988876554        22  35666666666664443334444333  3368999999999988888888876


Q ss_pred             hcccCcEEEEEEcCcc--hHHHHHHhcCCCcEEEeChHHHHHHHHcCC------------CCCCCc-eEEEEeCCchhhc
Q 015158          131 GDYLGVKVHACVGGTS--VREDQRILSSGVHVVVGTPGRVFDMLRRQS------------LRPDNI-RIFVLDEADEMLS  195 (412)
Q Consensus       131 ~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~iii~T~~~l~~~~~~~~------------~~~~~~-~~iiiDE~h~~~~  195 (412)
                      .. .++.|..+.--.-  +... ....-+-.|+++||..|.-......            +.-..+ ++||+||||...+
T Consensus       342 gA-~~I~V~alnK~KYakIss~-en~n~krGViFaTYtaLIGEs~~~~~kyrtR~rQllqW~Ge~feGvIvfDECHkAKN  419 (1300)
T KOG1513|consen  342 GA-TGIAVHALNKFKYAKISSK-ENTNTKRGVIFATYTALIGESQGKGGKYRTRFRQLLQWCGEDFEGVIVFDECHKAKN  419 (1300)
T ss_pred             CC-CCccceehhhccccccccc-ccCCccceeEEEeeHhhhhhccccCchHHHHHHHHHHHhhhccceeEEehhhhhhcc
Confidence            43 2455544321100  0000 0011224799999977643222100            011122 5899999998654


Q ss_pred             c---------CcHHHHHHHHHhCCCCceEEEEeecC
Q 015158          196 R---------GFKDQIYDIFQLLPPKIQVGVFSATM  222 (412)
Q Consensus       196 ~---------~~~~~~~~i~~~~~~~~~~i~~SAT~  222 (412)
                      .         .....+..+...+| +.+++.-|||-
T Consensus       420 L~p~~~~k~TKtG~tVLdLQk~LP-~ARVVYASATG  454 (1300)
T KOG1513|consen  420 LVPTAGAKSTKTGKTVLDLQKKLP-NARVVYASATG  454 (1300)
T ss_pred             cccccCCCcCcccHhHHHHHHhCC-CceEEEeeccC
Confidence            1         13466667777775 78899999993

>PRK11054 helD DNA helicase IV; Provisional

Probab=97.20  E-value=0.0013  Score=65.24  Aligned_cols=70  Identities=24%  Similarity=0.221  Sum_probs=54.4

Q ss_pred             CCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccC-CCceeEEEEcCCHHHHHHHHHHHHHhh
Q 015158           60 EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYG-LVECQALVLAPTRELAQQIEKVMRALG  131 (412)
Q Consensus        60 ~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~-~~~~~~lil~P~~~L~~q~~~~~~~~~  131 (412)
                      ..|++-|++|+..-  ..+++|.|+.|||||.+...-+...+..+ ....++++++.++..+..+.+++....
T Consensus       195 ~~L~~~Q~~av~~~--~~~~lV~agaGSGKT~vl~~r~ayLl~~~~~~~~~IL~ltft~~AA~em~eRL~~~l  265 (684)
T PRK11054        195 SPLNPSQARAVVNG--EDSLLVLAGAGSGKTSVLVARAGWLLARGQAQPEQILLLAFGRQAAEEMDERIRERL  265 (684)
T ss_pred             CCCCHHHHHHHhCC--CCCeEEEEeCCCCHHHHHHHHHHHHHHhCCCCHHHeEEEeccHHHHHHHHHHHHHhc
Confidence            45999999999643  35689999999999998876665555433 234589999999999999998887644

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=97.16  E-value=0.052  Score=60.66  Aligned_cols=208  Identities=13%  Similarity=0.122  Sum_probs=108.6

Q ss_pred             ChHHHHhhhhhhhcC--ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEE
Q 015158           62 PSAIQQRGIVPFCKG--LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVH  139 (412)
Q Consensus        62 l~~~Q~~a~~~~~~~--~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~  139 (412)
                      +++-|++|+..++..  +-.+|.++.|+|||.+. -.+...+..  .+.+++.++|+..-+..+.+.....       ..
T Consensus       430 Ls~~Q~~Av~~il~s~~~v~ii~G~aGTGKTt~l-~~l~~~~~~--~G~~V~~lAPTgrAA~~L~e~~g~~-------A~  499 (1960)
T TIGR02760       430 LSPSNKDAVSTLFTSTKRFIIINGFGGTGSTEIA-QLLLHLASE--QGYEIQIITAGSLSAQELRQKIPRL-------AS  499 (1960)
T ss_pred             CCHHHHHHHHHHHhCCCCeEEEEECCCCCHHHHH-HHHHHHHHh--cCCeEEEEeCCHHHHHHHHHHhcch-------hh
Confidence            889999999998875  56789999999999764 333333322  3458999999987665555432211       10


Q ss_pred             EEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhC-CCCceEEEE
Q 015158          140 ACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLL-PPKIQVGVF  218 (412)
Q Consensus       140 ~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~-~~~~~~i~~  218 (412)
                            +...+......  ..-..|...|.    .....+..-++|||||+-.+..    ..+..++... +.+.++|++
T Consensus       500 ------Ti~~~l~~l~~--~~~~~tv~~fl----~~~~~l~~~~vlIVDEAsMl~~----~~~~~Ll~~a~~~garvVlv  563 (1960)
T TIGR02760       500 ------TFITWVKNLFN--DDQDHTVQGLL----DKSSPFSNKDIFVVDEANKLSN----NELLKLIDKAEQHNSKLILL  563 (1960)
T ss_pred             ------hHHHHHHhhcc--cccchhHHHhh----cccCCCCCCCEEEEECCCCCCH----HHHHHHHHHHhhcCCEEEEE
Confidence                  01111111111  11122333333    1222234568999999997643    3455555544 467888888


Q ss_pred             eecC--C----hHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhHHHH-HHHHHhc-CCCcEEEEEcchhH
Q 015158          219 SATM--P----PEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETL-CDLYETL-AITQSVIFVNTRRK  290 (412)
Q Consensus       219 SAT~--~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l-~~~~~~~-~~~k~lif~~~~~~  290 (412)
                      .-+-  +    ......+.... -+ .+...........+  ....... ......+ ..++... ...+++|+..+.+.
T Consensus       564 GD~~QL~sV~aG~~f~~L~~~g-v~-t~~l~~i~rq~~~v--~i~~~~~-~~r~~~ia~~y~~L~~~r~~tliv~~t~~d  638 (1960)
T TIGR02760       564 NDSAQRQGMSAGSAIDLLKEGG-VT-TYAWVDTKQQKASV--EISEAVD-KLRVDYIASAWLDLTPDRQNSQVLATTHRE  638 (1960)
T ss_pred             cChhhcCccccchHHHHHHHCC-Cc-EEEeecccccCcce--eeeccCc-hHHHHHHHHHHHhcccccCceEEEcCCcHH
Confidence            7762  1    23333444322 11 12221111111111  1111111 2222223 3333322 23468999999888


Q ss_pred             HHHHHHHHhc
Q 015158          291 VDWLTDKMRS  300 (412)
Q Consensus       291 ~~~~~~~L~~  300 (412)
                      .+.+....+.
T Consensus       639 r~~Ln~~iR~  648 (1960)
T TIGR02760       639 QQDLTQIIRN  648 (1960)
T ss_pred             HHHHHHHHHH
Confidence            8777666653

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.

>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins

Probab=97.14  E-value=0.00069  Score=62.44  Aligned_cols=55  Identities=27%  Similarity=0.273  Sum_probs=40.8

Q ss_pred             ChHHHHhhhhhh------hcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHH
Q 015158           62 PSAIQQRGIVPF------CKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTREL  119 (412)
Q Consensus        62 l~~~Q~~a~~~~------~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L  119 (412)
                      |++-|++++..+      .++.+++|.|+-|+|||..+- ++...+..  .+..+++++||-.-
T Consensus         2 Ln~eQ~~~~~~v~~~~~~~~~~~~fv~G~~GtGKs~l~~-~i~~~~~~--~~~~~~~~a~tg~A   62 (364)
T PF05970_consen    2 LNEEQRRVFDTVIEAIENEEGLNFFVTGPAGTGKSFLIK-AIIDYLRS--RGKKVLVTAPTGIA   62 (364)
T ss_pred             CCHHHHHHHHHHHHHHHccCCcEEEEEcCCCCChhHHHH-HHHHHhcc--ccceEEEecchHHH
Confidence            788899999988      678899999999999997653 33333322  33578888887653

The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].

>PRK05642 DNA replication initiation factor; Validated

Probab=97.12  E-value=0.0016  Score=56.00  Aligned_cols=44  Identities=16%  Similarity=0.404  Sum_probs=29.9

Q ss_pred             CceEEEEeCCchhhcc-CcHHHHHHHHHhCCCCceEEEEeecCCh
Q 015158          181 NIRIFVLDEADEMLSR-GFKDQIYDIFQLLPPKIQVGVFSATMPP  224 (412)
Q Consensus       181 ~~~~iiiDE~h~~~~~-~~~~~~~~i~~~~~~~~~~i~~SAT~~~  224 (412)
                      +.+++|+|++|.+... .+...+..+++.+..+.+.+++|++.++
T Consensus        97 ~~d~LiiDDi~~~~~~~~~~~~Lf~l~n~~~~~g~~ilits~~~p  141 (234)
T PRK05642         97 QYELVCLDDLDVIAGKADWEEALFHLFNRLRDSGRRLLLAASKSP  141 (234)
T ss_pred             hCCEEEEechhhhcCChHHHHHHHHHHHHHHhcCCEEEEeCCCCH
Confidence            5679999999976533 3456677777766554456677777544

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=97.09  E-value=0.0043  Score=59.13  Aligned_cols=106  Identities=12%  Similarity=0.217  Sum_probs=56.2

Q ss_pred             ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcC
Q 015158           77 LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSS  156 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  156 (412)
                      +.+++.||+|+|||..+. ++...+....++.+++++.. ..+..+....+..     +                     
T Consensus       149 ~~l~l~G~~G~GKThL~~-ai~~~~~~~~~~~~v~yi~~-~~~~~~~~~~~~~-----~---------------------  200 (450)
T PRK00149        149 NPLFIYGGVGLGKTHLLH-AIGNYILEKNPNAKVVYVTS-EKFTNDFVNALRN-----N---------------------  200 (450)
T ss_pred             CeEEEECCCCCCHHHHHH-HHHHHHHHhCCCCeEEEEEH-HHHHHHHHHHHHc-----C---------------------
Confidence            458999999999997653 34444443323456666643 3444433322211     0                     


Q ss_pred             CCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccC-cHHHHHHHHHhCCCCceEEEEeecCCh
Q 015158          157 GVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRG-FKDQIYDIFQLLPPKIQVGVFSATMPP  224 (412)
Q Consensus       157 ~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~-~~~~~~~i~~~~~~~~~~i~~SAT~~~  224 (412)
                             +.+.+...+       .+.+++++||+|.+.... ....+..++..+......+++|++.++
T Consensus       201 -------~~~~~~~~~-------~~~dlLiiDDi~~l~~~~~~~~~l~~~~n~l~~~~~~iiits~~~p  255 (450)
T PRK00149        201 -------TMEEFKEKY-------RSVDVLLIDDIQFLAGKERTQEEFFHTFNALHEAGKQIVLTSDRPP  255 (450)
T ss_pred             -------cHHHHHHHH-------hcCCEEEEehhhhhcCCHHHHHHHHHHHHHHHHCCCcEEEECCCCH
Confidence                   112222222       257899999999875432 223444554444333233555555444

>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=97.08  E-value=0.002  Score=54.73  Aligned_cols=107  Identities=18%  Similarity=0.270  Sum_probs=60.3

Q ss_pred             ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcC
Q 015158           77 LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSS  156 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  156 (412)
                      +.+++.||+|+|||-. +.++.+.+....++.+++++... .......+.+..                           
T Consensus        35 ~~l~l~G~~G~GKTHL-L~Ai~~~~~~~~~~~~v~y~~~~-~f~~~~~~~~~~---------------------------   85 (219)
T PF00308_consen   35 NPLFLYGPSGLGKTHL-LQAIANEAQKQHPGKRVVYLSAE-EFIREFADALRD---------------------------   85 (219)
T ss_dssp             SEEEEEESTTSSHHHH-HHHHHHHHHHHCTTS-EEEEEHH-HHHHHHHHHHHT---------------------------
T ss_pred             CceEEECCCCCCHHHH-HHHHHHHHHhccccccceeecHH-HHHHHHHHHHHc---------------------------
Confidence            3589999999999974 45555555443345567776542 333322221111                           


Q ss_pred             CCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccC-cHHHHHHHHHhCC-CCceEEEEeecCChH
Q 015158          157 GVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRG-FKDQIYDIFQLLP-PKIQVGVFSATMPPE  225 (412)
Q Consensus       157 ~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~-~~~~~~~i~~~~~-~~~~~i~~SAT~~~~  225 (412)
                            ...+.+...+       ...+++++|++|.+.... +...+..++..+. .+.++|+.|..+|..
T Consensus        86 ------~~~~~~~~~~-------~~~DlL~iDDi~~l~~~~~~q~~lf~l~n~~~~~~k~li~ts~~~P~~  143 (219)
T PF00308_consen   86 ------GEIEEFKDRL-------RSADLLIIDDIQFLAGKQRTQEELFHLFNRLIESGKQLILTSDRPPSE  143 (219)
T ss_dssp             ------TSHHHHHHHH-------CTSSEEEEETGGGGTTHHHHHHHHHHHHHHHHHTTSEEEEEESS-TTT
T ss_pred             ------ccchhhhhhh-------hcCCEEEEecchhhcCchHHHHHHHHHHHHHHhhCCeEEEEeCCCCcc
Confidence                  1122333322       368999999999876542 3456666665553 355666666566543

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.

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=97.07  E-value=0.0036  Score=59.27  Aligned_cols=108  Identities=12%  Similarity=0.182  Sum_probs=59.5

Q ss_pred             ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcC
Q 015158           77 LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSS  156 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  156 (412)
                      +.+++.|++|+|||..+ .++.+.+....++.+++++.+ ..+..+....+..-     .                    
T Consensus       142 npl~i~G~~G~GKTHLl-~Ai~~~l~~~~~~~~v~yv~~-~~f~~~~~~~l~~~-----~--------------------  194 (450)
T PRK14087        142 NPLFIYGESGMGKTHLL-KAAKNYIESNFSDLKVSYMSG-DEFARKAVDILQKT-----H--------------------  194 (450)
T ss_pred             CceEEECCCCCcHHHHH-HHHHHHHHHhCCCCeEEEEEH-HHHHHHHHHHHHHh-----h--------------------
Confidence            45889999999999654 455555544334557777655 45554444433220     0                    


Q ss_pred             CCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccC-cHHHHHHHHHhCCCCceEEEEeecCCh
Q 015158          157 GVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRG-FKDQIYDIFQLLPPKIQVGVFSATMPP  224 (412)
Q Consensus       157 ~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~-~~~~~~~i~~~~~~~~~~i~~SAT~~~  224 (412)
                            ...+.+...       ....+++|+||+|.+.... ....+..++..+....+.+.+|+..++
T Consensus       195 ------~~~~~~~~~-------~~~~dvLiIDDiq~l~~k~~~~e~lf~l~N~~~~~~k~iIltsd~~P  250 (450)
T PRK14087        195 ------KEIEQFKNE-------ICQNDVLIIDDVQFLSYKEKTNEIFFTIFNNFIENDKQLFFSSDKSP  250 (450)
T ss_pred             ------hHHHHHHHH-------hccCCEEEEeccccccCCHHHHHHHHHHHHHHHHcCCcEEEECCCCH
Confidence                  011112111       1357899999999875332 345566666554433334555544433

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=97.06  E-value=0.004  Score=58.49  Aligned_cols=37  Identities=14%  Similarity=0.111  Sum_probs=24.5

Q ss_pred             ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEc
Q 015158           77 LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLA  114 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~  114 (412)
                      +.+++.||+|+|||..+ .++.+.+....++.+++++.
T Consensus       137 n~l~l~G~~G~GKThL~-~ai~~~l~~~~~~~~v~yi~  173 (405)
T TIGR00362       137 NPLFIYGGVGLGKTHLL-HAIGNEILENNPNAKVVYVS  173 (405)
T ss_pred             CeEEEECCCCCcHHHHH-HHHHHHHHHhCCCCcEEEEE
Confidence            45789999999999765 34444444333345677764

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).

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.03  E-value=0.026  Score=53.68  Aligned_cols=160  Identities=16%  Similarity=0.187  Sum_probs=78.5

Q ss_pred             hhhccccccCCCCHHHHHHHHHCC---C--CCChHHHHhhhhh---------hhcCccEEEECCCCCCchhHhHHHHHHh
Q 015158           35 DEVYDTFDAMGLQENLLRGIYAYG---F--EKPSAIQQRGIVP---------FCKGLDVIQQAQSGTGKTATFCSGILQQ  100 (412)
Q Consensus        35 ~~~~~~f~~~~l~~~~~~~l~~~~---~--~~l~~~Q~~a~~~---------~~~~~~~lv~~~tGsGKT~~~~~~~~~~  100 (412)
                      ...+..+...++++.+.+.|...-   .  ...+.+=...+..         +..|+.+.+.+|+|+|||......+...
T Consensus       295 ~~l~~~L~~~Gvs~~la~~L~~~l~~~~~~~~~~~~l~~~L~~~l~v~~~~~l~~G~vIaLVGPtGvGKTTtaakLAa~l  374 (559)
T PRK12727        295 AQALELMDDYGFDAGLTRDVAMQIPADTELHRGRGLMLGLLSKRLPVAPVDPLERGGVIALVGPTGAGKTTTIAKLAQRF  374 (559)
T ss_pred             HHHHHHHHHCCCCHHHHHHHHHhhhcccchhhHHHHHHHHHHHhcCcCccccccCCCEEEEECCCCCCHHHHHHHHHHHH
Confidence            344567777888888888775421   1  1112121112211         2246778899999999997764433322


Q ss_pred             hccCCCceeEEEEc-CC-HHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCC
Q 015158          101 LDYGLVECQALVLA-PT-RELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLR  178 (412)
Q Consensus       101 ~~~~~~~~~~lil~-P~-~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~  178 (412)
                      .... .+.++.++. .+ +.-.   .+++..+....++.+...                     .+...+...+..    
T Consensus       375 a~~~-~gkkVaLIdtDtyRigA---~EQLk~ya~iLgv~v~~a---------------------~d~~~L~~aL~~----  425 (559)
T PRK12727        375 AAQH-APRDVALVTTDTQRVGG---REQLHSYGRQLGIAVHEA---------------------DSAESLLDLLER----  425 (559)
T ss_pred             HHhc-CCCceEEEecccccccH---HHHHHHhhcccCceeEec---------------------CcHHHHHHHHHH----
Confidence            2221 123454443 22 2211   222333333333322111                     123334444432    


Q ss_pred             CCCceEEEEeCCchhhcc-CcHHHHHHHHHhCCCCceEEEEeecCCh
Q 015158          179 PDNIRIFVLDEADEMLSR-GFKDQIYDIFQLLPPKIQVGVFSATMPP  224 (412)
Q Consensus       179 ~~~~~~iiiDE~h~~~~~-~~~~~~~~i~~~~~~~~~~i~~SAT~~~  224 (412)
                      ..++++|+||.+-..... .....+..+.... ....+++++++...
T Consensus       426 l~~~DLVLIDTaG~s~~D~~l~eeL~~L~aa~-~~a~lLVLpAtss~  471 (559)
T PRK12727        426 LRDYKLVLIDTAGMGQRDRALAAQLNWLRAAR-QVTSLLVLPANAHF  471 (559)
T ss_pred             hccCCEEEecCCCcchhhHHHHHHHHHHHHhh-cCCcEEEEECCCCh
Confidence            235799999999753211 1122333333322 34557888888754

>COG1435 Tdk Thymidine kinase [Nucleotide transport and metabolism]

Probab=97.02  E-value=0.01  Score=48.12  Aligned_cols=104  Identities=21%  Similarity=0.265  Sum_probs=63.2

Q ss_pred             ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCc-EEEEEEcCcchHHHHHHhc
Q 015158           77 LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGV-KVHACVGGTSVREDQRILS  155 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~  155 (412)
                      +-.++.+|+.||||.-.+..+.+....+   .++++..|...-         .+    +. .+....|. .         
T Consensus         5 ~l~~i~gpM~SGKT~eLl~r~~~~~~~g---~~v~vfkp~iD~---------R~----~~~~V~Sr~G~-~---------   58 (201)
T COG1435           5 WLEFIYGPMFSGKTEELLRRARRYKEAG---MKVLVFKPAIDT---------RY----GVGKVSSRIGL-S---------   58 (201)
T ss_pred             EEEEEEccCcCcchHHHHHHHHHHHHcC---CeEEEEeccccc---------cc----ccceeeeccCC-c---------
Confidence            3458899999999998777666665554   488888885431         11    11 12222221 1         


Q ss_pred             CCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhC
Q 015158          156 SGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLL  209 (412)
Q Consensus       156 ~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~  209 (412)
                       ...++|-+...+...+....... ..+.|.+||||.+ +......+.++.+.+
T Consensus        59 -~~A~~i~~~~~i~~~i~~~~~~~-~~~~v~IDEaQF~-~~~~v~~l~~lad~l  109 (201)
T COG1435          59 -SEAVVIPSDTDIFDEIAALHEKP-PVDCVLIDEAQFF-DEELVYVLNELADRL  109 (201)
T ss_pred             -ccceecCChHHHHHHHHhcccCC-CcCEEEEehhHhC-CHHHHHHHHHHHhhc
Confidence             12466666666766666543322 2789999999964 344455666666654

>COG4626 Phage terminase-like protein, large subunit [General function prediction only]

Probab=97.01  E-value=0.0043  Score=58.39  Aligned_cols=152  Identities=13%  Similarity=0.028  Sum_probs=86.1

Q ss_pred             HCCCCCChHHHHhhhhhhhc------C----ccEEEECCCCCCchhHhH-HHHHHhhccCCCceeEEEEcCCHHHHHHHH
Q 015158           56 AYGFEKPSAIQQRGIVPFCK------G----LDVIQQAQSGTGKTATFC-SGILQQLDYGLVECQALVLAPTRELAQQIE  124 (412)
Q Consensus        56 ~~~~~~l~~~Q~~a~~~~~~------~----~~~lv~~~tGsGKT~~~~-~~~~~~~~~~~~~~~~lil~P~~~L~~q~~  124 (412)
                      .+++. +-|||+-++..+..      +    +.++|..|-+-|||..+. +.....+.....+..+.+++|+..-+.+.+
T Consensus        57 ~~p~~-l~PwQkFiia~l~G~~~k~T~~rrf~e~fI~v~RkngKt~l~A~i~~~~~l~~~~~~~~~~i~A~s~~qa~~~F  135 (546)
T COG4626          57 GFPES-LEPWQKFIVAALFGFYDKQTGIRRFKEAFIFIPRKNGKSTLAAGIMMTALLLNWRSGAGIYILAPSVEQAANSF  135 (546)
T ss_pred             CCccc-cchHHHHHHHHHhceeecCCCceEEEEEEEEEecCCchHHHHHHHHHHHHHhhhhcCCcEEEEeccHHHHHHhh
Confidence            33444 89999999999883      1    457999999999996544 333333334456678999999998888888


Q ss_pred             HHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHH--cCCCCCCCceEEEEeCCchhhccCcHHHH
Q 015158          125 KVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLR--RQSLRPDNIRIFVLDEADEMLSRGFKDQI  202 (412)
Q Consensus       125 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~--~~~~~~~~~~~iiiDE~h~~~~~~~~~~~  202 (412)
                      ..++......+          ...........+..|...-.......+.  ....+..+..+.|+||.|.+....  ..+
T Consensus       136 ~~ar~mv~~~~----------~l~~~~~~q~~s~~i~~~~~~s~ik~~aa~~~~~Dg~~~~~~I~DEih~f~~~~--~~~  203 (546)
T COG4626         136 NPARDMVKRDD----------DLRDLCNVQTHSRTITHRKTDSTIKAVAADPNTVDGLNSVGAIIDELHLFGKQE--DMY  203 (546)
T ss_pred             HHHHHHHHhCc----------chhhhhccccceeEEEecccceeeeeeccCCCcccCCCcceEEEehhhhhcCHH--HHH
Confidence            77776543322          0001110001111111111111111111  123334566799999999876542  334


Q ss_pred             HHHHHhC--CCCceEEEEee
Q 015158          203 YDIFQLL--PPKIQVGVFSA  220 (412)
Q Consensus       203 ~~i~~~~--~~~~~~i~~SA  220 (412)
                      ..+..-+  .++.++++.|-
T Consensus       204 ~~~~~g~~ar~~~l~~~ITT  223 (546)
T COG4626         204 SEAKGGLGARPEGLVVYITT  223 (546)
T ss_pred             HHHHhhhccCcCceEEEEec
Confidence            4444333  34566666665

>PRK06921 hypothetical protein; Provisional

Probab=96.99  E-value=0.016  Score=50.82  Aligned_cols=38  Identities=18%  Similarity=0.149  Sum_probs=24.4

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcC
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAP  115 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P  115 (412)
                      +.++++.|++|+|||..+. +++..+... .+..++++..
T Consensus       117 ~~~l~l~G~~G~GKThLa~-aia~~l~~~-~g~~v~y~~~  154 (266)
T PRK06921        117 KNSIALLGQPGSGKTHLLT-AAANELMRK-KGVPVLYFPF  154 (266)
T ss_pred             CCeEEEECCCCCcHHHHHH-HHHHHHhhh-cCceEEEEEH
Confidence            5679999999999997653 344444321 1345666553

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.99  E-value=0.0029  Score=59.39  Aligned_cols=20  Identities=25%  Similarity=0.084  Sum_probs=15.9

Q ss_pred             cEEEECCCCCCchhHhHHHH
Q 015158           78 DVIQQAQSGTGKTATFCSGI   97 (412)
Q Consensus        78 ~~lv~~~tGsGKT~~~~~~~   97 (412)
                      ..++.||.|+|||.++-..+
T Consensus        42 a~Lf~GP~GtGKTTlAriLA   61 (484)
T PRK14956         42 AYIFFGPRGVGKTTIARILA   61 (484)
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            36999999999998875433

>TIGR01075 uvrD DNA helicase II

Probab=96.97  E-value=0.0017  Score=65.58  Aligned_cols=71  Identities=17%  Similarity=0.161  Sum_probs=57.2

Q ss_pred             CCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhcc-CCCceeEEEEcCCHHHHHHHHHHHHHhhc
Q 015158           60 EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY-GLVECQALVLAPTRELAQQIEKVMRALGD  132 (412)
Q Consensus        60 ~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~-~~~~~~~lil~P~~~L~~q~~~~~~~~~~  132 (412)
                      ..|++-|++|+.+-  ...++|.|+.|||||.+...-+...+.. +.+..++|+++-|+..+.++.+.+.++..
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            35899999999764  4579999999999999987777766643 33456899999999999999998887643

Designed to identify uvrD members of the uvrD/rep subfamily.

>TIGR01074 rep ATP-dependent DNA helicase Rep

Probab=96.92  E-value=0.002  Score=64.81  Aligned_cols=68  Identities=16%  Similarity=0.128  Sum_probs=55.2

Q ss_pred             ChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhcc-CCCceeEEEEcCCHHHHHHHHHHHHHhh
Q 015158           62 PSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY-GLVECQALVLAPTRELAQQIEKVMRALG  131 (412)
Q Consensus        62 l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~-~~~~~~~lil~P~~~L~~q~~~~~~~~~  131 (412)
                      |++-|++++.+.  ..+++|.|+.|||||.+.+.-+...+.. +....++++++.|+.-+.++.+.+.+..
T Consensus         2 Ln~~Q~~av~~~--~~~~~V~Ag~GSGKT~~L~~ri~~ll~~~~~~p~~IL~vTFt~~Aa~em~~Rl~~~l   70 (664)
T TIGR01074         2 LNPQQQEAVEYV--TGPCLVLAGAGSGKTRVITNKIAYLIQNCGYKARNIAAVTFTNKAAREMKERVAKTL   70 (664)
T ss_pred             CCHHHHHHHhCC--CCCEEEEecCCCCHHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHHh
Confidence            788999998753  4679999999999999988877777653 3345679999999999999988887654

Designed to identify rep members of the uvrD/rep subfamily.

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=96.91  E-value=0.01  Score=47.78  Aligned_cols=38  Identities=16%  Similarity=0.173  Sum_probs=24.7

Q ss_pred             EEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHH
Q 015158           79 VIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTREL  119 (412)
Q Consensus        79 ~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L  119 (412)
                      +++.+++|+|||..+...+.....   .+..++++......
T Consensus         2 ~~i~G~~G~GKT~l~~~i~~~~~~---~~~~v~~~~~e~~~   39 (165)
T cd01120           2 ILVFGPTGSGKTTLALQLALNIAT---KGGKVVYVDIEEEI   39 (165)
T ss_pred             eeEeCCCCCCHHHHHHHHHHHHHh---cCCEEEEEECCcch
Confidence            578999999999766544443332   23467777665443

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.

>PRK06893 DNA replication initiation factor; Validated

Probab=96.91  E-value=0.0033  Score=53.88  Aligned_cols=45  Identities=18%  Similarity=0.374  Sum_probs=28.6

Q ss_pred             CceEEEEeCCchhhcc-CcHHHHHHHHHhCCC-CceEEEEeecCChH
Q 015158          181 NIRIFVLDEADEMLSR-GFKDQIYDIFQLLPP-KIQVGVFSATMPPE  225 (412)
Q Consensus       181 ~~~~iiiDE~h~~~~~-~~~~~~~~i~~~~~~-~~~~i~~SAT~~~~  225 (412)
                      +.+++++||+|.+... .+...+..++..... +.+++++|++..+.
T Consensus        91 ~~dlLilDDi~~~~~~~~~~~~l~~l~n~~~~~~~~illits~~~p~  137 (229)
T PRK06893         91 QQDLVCLDDLQAVIGNEEWELAIFDLFNRIKEQGKTLLLISADCSPH  137 (229)
T ss_pred             cCCEEEEeChhhhcCChHHHHHHHHHHHHHHHcCCcEEEEeCCCChH
Confidence            5689999999987532 234455565555443 34566777776543

>PRK11773 uvrD DNA-dependent helicase II; Provisional

Probab=96.89  E-value=0.0021  Score=65.03  Aligned_cols=70  Identities=14%  Similarity=0.139  Sum_probs=56.6

Q ss_pred             CChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhcc-CCCceeEEEEcCCHHHHHHHHHHHHHhhc
Q 015158           61 KPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY-GLVECQALVLAPTRELAQQIEKVMRALGD  132 (412)
Q Consensus        61 ~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~-~~~~~~~lil~P~~~L~~q~~~~~~~~~~  132 (412)
                      .|++-|++|+.+.  ...++|.|+.|||||.+...-+...+.. +....++|+++-|+..+.++.+.+.++..
T Consensus         9 ~Ln~~Q~~av~~~--~g~~lV~AgaGSGKT~vl~~Ria~Li~~~~v~p~~IL~lTFT~kAA~Em~~Rl~~~~~   79 (721)
T PRK11773          9 SLNDKQREAVAAP--LGNMLVLAGAGSGKTRVLVHRIAWLMQVENASPYSIMAVTFTNKAAAEMRHRIEQLLG   79 (721)
T ss_pred             hcCHHHHHHHhCC--CCCEEEEecCCCCHHHHHHHHHHHHHHcCCCChhHeEeeeccHHHHHHHHHHHHHHhc
Confidence            4899999999754  4578999999999999887777766542 44456899999999999999998887643

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=96.89  E-value=0.0068  Score=51.94  Aligned_cols=20  Identities=20%  Similarity=0.212  Sum_probs=16.8

Q ss_pred             CccEEEECCCCCCchhHhHH
Q 015158           76 GLDVIQQAQSGTGKTATFCS   95 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~   95 (412)
                      +..+++.||+|+|||..+..
T Consensus        38 ~~~lll~G~~G~GKT~la~~   57 (226)
T TIGR03420        38 DRFLYLWGESGSGKSHLLQA   57 (226)
T ss_pred             CCeEEEECCCCCCHHHHHHH
Confidence            56899999999999977644

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.

>PRK08727 hypothetical protein; Validated

Probab=96.88  E-value=0.0058  Score=52.54  Aligned_cols=45  Identities=13%  Similarity=0.182  Sum_probs=25.6

Q ss_pred             CceEEEEeCCchhhccC-cHHHHHHHHHhCCC-CceEEEEeecCChH
Q 015158          181 NIRIFVLDEADEMLSRG-FKDQIYDIFQLLPP-KIQVGVFSATMPPE  225 (412)
Q Consensus       181 ~~~~iiiDE~h~~~~~~-~~~~~~~i~~~~~~-~~~~i~~SAT~~~~  225 (412)
                      +.+++|+||+|.+.... ....+..++..... ..++|+.|..++..
T Consensus        93 ~~dlLiIDDi~~l~~~~~~~~~lf~l~n~~~~~~~~vI~ts~~~p~~  139 (233)
T PRK08727         93 GRSLVALDGLESIAGQREDEVALFDFHNRARAAGITLLYTARQMPDG  139 (233)
T ss_pred             cCCEEEEeCcccccCChHHHHHHHHHHHHHHHcCCeEEEECCCChhh
Confidence            56799999999876432 23445555554433 33455545444443

>PRK12377 putative replication protein; Provisional

Probab=96.83  E-value=0.012  Score=50.75  Aligned_cols=44  Identities=16%  Similarity=0.243  Sum_probs=26.0

Q ss_pred             ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHH
Q 015158           77 LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIE  124 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~  124 (412)
                      .++++.||+|+|||..+. ++...+...  +..++++ +...|..++.
T Consensus       102 ~~l~l~G~~GtGKThLa~-AIa~~l~~~--g~~v~~i-~~~~l~~~l~  145 (248)
T PRK12377        102 TNFVFSGKPGTGKNHLAA-AIGNRLLAK--GRSVIVV-TVPDVMSRLH  145 (248)
T ss_pred             CeEEEECCCCCCHHHHHH-HHHHHHHHc--CCCeEEE-EHHHHHHHHH
Confidence            578999999999997654 344343322  2344443 4445555443

>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=96.80  E-value=0.00076  Score=54.43  Aligned_cols=124  Identities=19%  Similarity=0.226  Sum_probs=52.3

Q ss_pred             EEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCc
Q 015158           80 IQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVH  159 (412)
Q Consensus        80 lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  159 (412)
                      ++.++-|-|||.+.=+++...+..+  ..+++|.+|+..-++..++.+..-....+.+.....   ...........+..
T Consensus         1 VltA~RGRGKSa~lGl~~a~l~~~~--~~~I~vtAP~~~~~~~lf~~~~~~l~~~~~~~~~~~---~~~~~~~~~~~~~~   75 (177)
T PF05127_consen    1 VLTADRGRGKSAALGLAAAALIQKG--KIRILVTAPSPENVQTLFEFAEKGLKALGYKEEKKK---RIGQIIKLRFNKQR   75 (177)
T ss_dssp             -EEE-TTSSHHHHHHHCCCCSSS-------EEEE-SS--S-HHHHHCC-----------------------------CCC
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHhc--CceEEEecCCHHHHHHHHHHHHhhcccccccccccc---ccccccccccccce
Confidence            4789999999976544443333332  257999999998777777655543332232220000   00000111123456


Q ss_pred             EEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEeecCC
Q 015158          160 VVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMP  223 (412)
Q Consensus       160 iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~  223 (412)
                      |-+..|+.+...       ....|++|||||=.+.    ...+..++...    ..+++|.|..
T Consensus        76 i~f~~Pd~l~~~-------~~~~DlliVDEAAaIp----~p~L~~ll~~~----~~vv~stTi~  124 (177)
T PF05127_consen   76 IEFVAPDELLAE-------KPQADLLIVDEAAAIP----LPLLKQLLRRF----PRVVFSTTIH  124 (177)
T ss_dssp             --B--HHHHCCT-----------SCEEECTGGGS-----HHHHHHHHCCS----SEEEEEEEBS
T ss_pred             EEEECCHHHHhC-------cCCCCEEEEechhcCC----HHHHHHHHhhC----CEEEEEeecc
Confidence            777777766432       1245899999998642    34455554332    3667777764

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.

>PHA03368 DNA packaging terminase subunit 1; Provisional

Probab=96.80  E-value=0.0075  Score=58.24  Aligned_cols=134  Identities=11%  Similarity=0.112  Sum_probs=79.1

Q ss_pred             ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccc--CcEEEEEEcCcchHHHHHHh
Q 015158           77 LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYL--GVKVHACVGGTSVREDQRIL  154 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~  154 (412)
                      +-.++..|--.|||+... +++..+.....+-+++|++|....++..++++.......  +..+....| ...  .....
T Consensus       255 k~tVflVPRR~GKTwivv-~iI~~ll~s~~Gi~IgytAH~~~ts~~vF~eI~~~le~~f~~~~v~~vkG-e~I--~i~f~  330 (738)
T PHA03368        255 RATVFLVPRRHGKTWFLV-PLIALALATFRGIKIGYTAHIRKATEPVFEEIGARLRQWFGASRVDHVKG-ETI--SFSFP  330 (738)
T ss_pred             cceEEEecccCCchhhHH-HHHHHHHHhCCCCEEEEEcCcHHHHHHHHHHHHHHHhhhcchhheeeecC-cEE--EEEec
Confidence            456889999999998765 344333333345689999999999999999888764321  111222222 111  00000


Q ss_pred             cCC-CcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEeecCC
Q 015158          155 SSG-VHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMP  223 (412)
Q Consensus       155 ~~~-~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~  223 (412)
                      .+. ..|.+.|.      .......-..++++|+|||+.+.+..+...+ -.+..  .+.++|++|.|-.
T Consensus       331 nG~kstI~FaSa------rntNsiRGqtfDLLIVDEAqFIk~~al~~il-p~l~~--~n~k~I~ISS~Ns  391 (738)
T PHA03368        331 DGSRSTIVFASS------HNTNGIRGQDFNLLFVDEANFIRPDAVQTIM-GFLNQ--TNCKIIFVSSTNT  391 (738)
T ss_pred             CCCccEEEEEec------cCCCCccCCcccEEEEechhhCCHHHHHHHH-HHHhc--cCccEEEEecCCC
Confidence            111 24555531      1122344568999999999987665433333 22222  3788999998854

>PRK07952 DNA replication protein DnaC; Validated

Probab=96.79  E-value=0.022  Score=48.97  Aligned_cols=42  Identities=19%  Similarity=0.328  Sum_probs=24.8

Q ss_pred             CceEEEEeCCchhhccCcHH-HHHHHHHhCCC-CceEEEEeecC
Q 015158          181 NIRIFVLDEADEMLSRGFKD-QIYDIFQLLPP-KIQVGVFSATM  222 (412)
Q Consensus       181 ~~~~iiiDE~h~~~~~~~~~-~~~~i~~~~~~-~~~~i~~SAT~  222 (412)
                      ..+++|+||++......+.. .+..++..... ..+.+..|--.
T Consensus       162 ~~dlLvIDDig~~~~s~~~~~~l~~Ii~~Ry~~~~~tiitSNl~  205 (244)
T PRK07952        162 NVDLLVIDEIGVQTESRYEKVIINQIVDRRSSSKRPTGMLTNSN  205 (244)
T ss_pred             cCCEEEEeCCCCCCCCHHHHHHHHHHHHHHHhCCCCEEEeCCCC
Confidence            67899999999765443333 44556554332 44455554443

>PRK08084 DNA replication initiation factor; Provisional

Probab=96.79  E-value=0.0045  Score=53.29  Aligned_cols=42  Identities=10%  Similarity=0.259  Sum_probs=24.6

Q ss_pred             ceEEEEeCCchhhcc-CcHHHHHHHHHhCCC-CceEEEEeecCC
Q 015158          182 IRIFVLDEADEMLSR-GFKDQIYDIFQLLPP-KIQVGVFSATMP  223 (412)
Q Consensus       182 ~~~iiiDE~h~~~~~-~~~~~~~~i~~~~~~-~~~~i~~SAT~~  223 (412)
                      .+++++||+|.+... .+...+..++..+.. +...+.+|++.+
T Consensus        98 ~dlliiDdi~~~~~~~~~~~~lf~l~n~~~e~g~~~li~ts~~~  141 (235)
T PRK08084         98 LSLVCIDNIECIAGDELWEMAIFDLYNRILESGRTRLLITGDRP  141 (235)
T ss_pred             CCEEEEeChhhhcCCHHHHHHHHHHHHHHHHcCCCeEEEeCCCC
Confidence            478999999987532 244556666655433 222344455543

>TIGR02785 addA_Gpos recombination helicase AddA, Firmicutes type

Probab=96.79  E-value=0.0056  Score=65.52  Aligned_cols=123  Identities=16%  Similarity=0.185  Sum_probs=78.7

Q ss_pred             ChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEE
Q 015158           62 PSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHAC  141 (412)
Q Consensus        62 l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~  141 (412)
                      +++-|.+++.  ..+++++|.|+.|||||.+..--++..+..+....++++++=|++-+.++.+++.+..... +.    
T Consensus         2 ~t~~Q~~ai~--~~~~~~lv~A~AGsGKT~~lv~r~~~~~~~~~~~~~il~~tFt~~aa~e~~~ri~~~l~~~-~~----   74 (1232)
T TIGR02785         2 WTDEQWQAIY--TRGQNILVSASAGSGKTAVLVERIIKKILRGVDIDRLLVVTFTNAAAREMKERIEEALQKA-LQ----   74 (1232)
T ss_pred             CCHHHHHHHh--CCCCCEEEEecCCCcHHHHHHHHHHHHHhcCCCHhhEEEEeccHHHHHHHHHHHHHHHHHH-Hh----
Confidence            5788999997  4688999999999999999877777766555444579999999999988888877643211 00    


Q ss_pred             EcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCc--eEEEEeCCch
Q 015158          142 VGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNI--RIFVLDEADE  192 (412)
Q Consensus       142 ~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~--~~iiiDE~h~  192 (412)
                       ..............-...-|+|.+.|...+.+.....-++  .+=|.||...
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             0001111222233334678999999865554332211111  2345777664

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.

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.79  E-value=0.025  Score=52.62  Aligned_cols=131  Identities=18%  Similarity=0.121  Sum_probs=64.3

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhc
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILS  155 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  155 (412)
                      +..+.+.||+|+|||.+....+...........-.++.+++--..  ..+++..++...++.+...              
T Consensus       191 g~vi~lvGpnG~GKTTtlakLA~~~~~~~~~~~v~~i~~d~~rig--alEQL~~~a~ilGvp~~~v--------------  254 (420)
T PRK14721        191 GGVYALIGPTGVGKTTTTAKLAARAVIRHGADKVALLTTDSYRIG--GHEQLRIYGKLLGVSVRSI--------------  254 (420)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEecCCcchh--HHHHHHHHHHHcCCceecC--------------
Confidence            566889999999999776433332221111122344445442221  2333444444445444221              


Q ss_pred             CCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhc-cCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHh
Q 015158          156 SGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLS-RGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKF  233 (412)
Q Consensus       156 ~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~-~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~  233 (412)
                             -++..+...+..    +.+.+.+++|.+-+.-. ......+..+.....+...+++++||........+...
T Consensus       255 -------~~~~dl~~al~~----l~~~d~VLIDTaGrsqrd~~~~~~l~~l~~~~~~~~~~LVl~at~~~~~~~~~~~~  322 (420)
T PRK14721        255 -------KDIADLQLMLHE----LRGKHMVLIDTVGMSQRDQMLAEQIAMLSQCGTQVKHLLLLNATSSGDTLDEVISA  322 (420)
T ss_pred             -------CCHHHHHHHHHH----hcCCCEEEecCCCCCcchHHHHHHHHHHhccCCCceEEEEEcCCCCHHHHHHHHHH
Confidence                   122222222221    24668899998643211 11223344433323344567899999876544444333

>PRK08116 hypothetical protein; Validated

Probab=96.75  E-value=0.055  Score=47.52  Aligned_cols=41  Identities=20%  Similarity=0.186  Sum_probs=24.8

Q ss_pred             ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHH
Q 015158           77 LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQ  121 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~  121 (412)
                      ..+++.|++|+|||..+. ++++.+...  +..++++ +...+..
T Consensus       115 ~gl~l~G~~GtGKThLa~-aia~~l~~~--~~~v~~~-~~~~ll~  155 (268)
T PRK08116        115 VGLLLWGSVGTGKTYLAA-CIANELIEK--GVPVIFV-NFPQLLN  155 (268)
T ss_pred             ceEEEECCCCCCHHHHHH-HHHHHHHHc--CCeEEEE-EHHHHHH
Confidence            358999999999997654 444444432  2345554 3344443

>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.74  E-value=0.056  Score=47.26  Aligned_cols=128  Identities=17%  Similarity=0.207  Sum_probs=67.9

Q ss_pred             ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcC-C--HHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHH
Q 015158           77 LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAP-T--RELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRI  153 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P-~--~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  153 (412)
                      ..+.+.+++|+|||..+...+......   +.++.++.. +  .....||..    +....++++..             
T Consensus        76 ~~i~~~G~~g~GKTtl~~~l~~~l~~~---~~~v~~i~~D~~ri~~~~ql~~----~~~~~~~~~~~-------------  135 (270)
T PRK06731         76 QTIALIGPTGVGKTTTLAKMAWQFHGK---KKTVGFITTDHSRIGTVQQLQD----YVKTIGFEVIA-------------  135 (270)
T ss_pred             CEEEEECCCCCcHHHHHHHHHHHHHHc---CCeEEEEecCCCCHHHHHHHHH----HhhhcCceEEe-------------
Confidence            578899999999998765443332221   234444443 2  244455443    32222333211             


Q ss_pred             hcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhh-ccCcHHHHHHHHHhCCCCceEEEEeecCCh-HHHHHHH
Q 015158          154 LSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEML-SRGFKDQIYDIFQLLPPKIQVGVFSATMPP-EALEITR  231 (412)
Q Consensus       154 ~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~-~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~-~~~~~~~  231 (412)
                              ..+++.+...+..-. ...++++|++|-+=+.. +......+..+.....+...++.+|||... +....+.
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                    123444433332111 11357999999886543 222344555555555555568889999765 4444444


Q ss_pred             Hh
Q 015158          232 KF  233 (412)
Q Consensus       232 ~~  233 (412)
                      .+
T Consensus       207 ~f  208 (270)
T PRK06731        207 NF  208 (270)
T ss_pred             Hh
Confidence            44

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=96.73  E-value=0.0074  Score=59.49  Aligned_cols=39  Identities=10%  Similarity=0.371  Sum_probs=25.8

Q ss_pred             CCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEe
Q 015158          180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFS  219 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~S  219 (412)
                      ..++++||||+|.+.... ...+.+.++.-+.+..+|+.|
T Consensus       118 gr~KVIIIDEah~LT~~A-~NALLKtLEEPP~~v~FILaT  156 (830)
T PRK07003        118 ARFKVYMIDEVHMLTNHA-FNAMLKTLEEPPPHVKFILAT  156 (830)
T ss_pred             CCceEEEEeChhhCCHHH-HHHHHHHHHhcCCCeEEEEEE
Confidence            357899999999886554 344555666655566555544

>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=96.73  E-value=0.0062  Score=49.04  Aligned_cols=42  Identities=12%  Similarity=0.320  Sum_probs=31.3

Q ss_pred             CCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEeecC
Q 015158          180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATM  222 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~  222 (412)
                      ..++++|+||+|.+.... ...+.+.++.-+.+..++++|..+
T Consensus       101 ~~~KviiI~~ad~l~~~a-~NaLLK~LEepp~~~~fiL~t~~~  142 (162)
T PF13177_consen  101 GKYKVIIIDEADKLTEEA-QNALLKTLEEPPENTYFILITNNP  142 (162)
T ss_dssp             SSSEEEEEETGGGS-HHH-HHHHHHHHHSTTTTEEEEEEES-G
T ss_pred             CCceEEEeehHhhhhHHH-HHHHHHHhcCCCCCEEEEEEECCh
Confidence            468899999999876553 677888888888788777776655

...

>TIGR01073 pcrA ATP-dependent DNA helicase PcrA

Probab=96.73  E-value=0.0067  Score=61.57  Aligned_cols=71  Identities=15%  Similarity=0.184  Sum_probs=56.9

Q ss_pred             CCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhcc-CCCceeEEEEcCCHHHHHHHHHHHHHhhc
Q 015158           60 EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY-GLVECQALVLAPTRELAQQIEKVMRALGD  132 (412)
Q Consensus        60 ~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~-~~~~~~~lil~P~~~L~~q~~~~~~~~~~  132 (412)
                      ..|++-|++|+.+.  ...++|.|+.|||||.+...-+...+.. +....++|.++-|+.-+.++.+.+.++..
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            35899999999764  4579999999999999887777766653 33445799999999989999988887653

Designed to identify pcrA members of the uvrD/rep subfamily.

>COG2256 MGS1 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]

Probab=96.71  E-value=0.0039  Score=56.10  Aligned_cols=18  Identities=33%  Similarity=0.313  Sum_probs=15.4

Q ss_pred             ccEEEECCCCCCchhHhH
Q 015158           77 LDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~   94 (412)
                      .+.|+++|+|+|||..+-
T Consensus        49 ~SmIl~GPPG~GKTTlA~   66 (436)
T COG2256          49 HSMILWGPPGTGKTTLAR   66 (436)
T ss_pred             ceeEEECCCCCCHHHHHH
Confidence            478999999999998763

>PRK06835 DNA replication protein DnaC; Validated

Probab=96.70  E-value=0.056  Score=48.87  Aligned_cols=44  Identities=20%  Similarity=0.190  Sum_probs=26.6

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHH
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQI  123 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~  123 (412)
                      +.++++.|+||+|||..+.. ++..+...  +..++++. ...+..+.
T Consensus       183 ~~~Lll~G~~GtGKThLa~a-Ia~~l~~~--g~~V~y~t-~~~l~~~l  226 (329)
T PRK06835        183 NENLLFYGNTGTGKTFLSNC-IAKELLDR--GKSVIYRT-ADELIEIL  226 (329)
T ss_pred             CCcEEEECCCCCcHHHHHHH-HHHHHHHC--CCeEEEEE-HHHHHHHH
Confidence            47899999999999976543 33333321  23565544 34444433

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=96.69  E-value=0.011  Score=51.37  Aligned_cols=48  Identities=15%  Similarity=0.197  Sum_probs=30.6

Q ss_pred             cCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHH
Q 015158           75 KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKV  126 (412)
Q Consensus        75 ~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~  126 (412)
                      ++.++++.||+|+|||..+.......+..   +.++ +.+++..++.++...
T Consensus       104 ~~~nl~l~G~~G~GKThLa~Ai~~~l~~~---g~sv-~f~~~~el~~~Lk~~  151 (254)
T COG1484         104 RGENLVLLGPPGVGKTHLAIAIGNELLKA---GISV-LFITAPDLLSKLKAA  151 (254)
T ss_pred             cCCcEEEECCCCCcHHHHHHHHHHHHHHc---CCeE-EEEEHHHHHHHHHHH
Confidence            46799999999999997764434333322   2344 445666776655543

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=96.66  E-value=0.012  Score=50.54  Aligned_cols=42  Identities=7%  Similarity=0.254  Sum_probs=25.6

Q ss_pred             CceEEEEeCCchhhccCcHHHHHHHHHhCCCCce-EEEEeecCC
Q 015158          181 NIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQ-VGVFSATMP  223 (412)
Q Consensus       181 ~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~-~i~~SAT~~  223 (412)
                      +.+++|+||+|.+... ....+..++........ +++++++.+
T Consensus        90 ~~~~liiDdi~~l~~~-~~~~L~~~~~~~~~~~~~~vl~~~~~~  132 (227)
T PRK08903         90 EAELYAVDDVERLDDA-QQIALFNLFNRVRAHGQGALLVAGPAA  132 (227)
T ss_pred             cCCEEEEeChhhcCch-HHHHHHHHHHHHHHcCCcEEEEeCCCC
Confidence            4578999999986543 34455555554433333 466666654

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=96.63  E-value=0.013  Score=54.96  Aligned_cols=131  Identities=15%  Similarity=0.169  Sum_probs=67.6

Q ss_pred             ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcC
Q 015158           77 LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSS  156 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  156 (412)
                      ..+++++++|+|||.++.-.+. .+..  .+.++++++...- -....+++..++...++.+.......           
T Consensus        96 ~vI~lvG~~GsGKTTtaakLA~-~L~~--~g~kV~lV~~D~~-R~aa~eQL~~la~~~gvp~~~~~~~~-----------  160 (437)
T PRK00771         96 QTIMLVGLQGSGKTTTAAKLAR-YFKK--KGLKVGLVAADTY-RPAAYDQLKQLAEKIGVPFYGDPDNK-----------  160 (437)
T ss_pred             eEEEEECCCCCcHHHHHHHHHH-HHHH--cCCeEEEecCCCC-CHHHHHHHHHHHHHcCCcEEecCCcc-----------
Confidence            4578899999999987654443 3322  2235555543211 01123334444333344332111000           


Q ss_pred             CCcEEEeCh-HHHHHHHHcCCCCCCCceEEEEeCCchhh-ccCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHh
Q 015158          157 GVHVVVGTP-GRVFDMLRRQSLRPDNIRIFVLDEADEML-SRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKF  233 (412)
Q Consensus       157 ~~~iii~T~-~~l~~~~~~~~~~~~~~~~iiiDE~h~~~-~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~  233 (412)
                             .+ +.+...+...    ...++||+|.+-+.. +...-..+..+.....+...++.++|+...+.......+
T Consensus       161 -------d~~~i~~~al~~~----~~~DvVIIDTAGr~~~d~~lm~El~~l~~~~~pdevlLVvda~~gq~av~~a~~F  228 (437)
T PRK00771        161 -------DAVEIAKEGLEKF----KKADVIIVDTAGRHALEEDLIEEMKEIKEAVKPDEVLLVIDATIGQQAKNQAKAF  228 (437)
T ss_pred             -------CHHHHHHHHHHHh----hcCCEEEEECCCcccchHHHHHHHHHHHHHhcccceeEEEeccccHHHHHHHHHH
Confidence                   11 1122222221    123899999995432 223445566666666667778889998876655555543

>cd01124 KaiC KaiC is a circadian clock protein primarily found in cyanobacteria KaiC is a RecA-like ATPase, having both Walker A and Walker B motifs

Probab=96.63  E-value=0.0081  Score=49.73  Aligned_cols=48  Identities=21%  Similarity=0.222  Sum_probs=33.2

Q ss_pred             EEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 015158           79 VIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRAL  130 (412)
Q Consensus        79 ~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~  130 (412)
                      ++|.+|+|+|||..++..+...+..+   .+++|++.. .-.++..+.+..+
T Consensus         2 ~li~G~~G~GKT~l~~~~~~~~~~~g---~~v~~~s~e-~~~~~~~~~~~~~   49 (187)
T cd01124           2 TLLSGGPGTGKTTFALQFLYAGLARG---EPGLYVTLE-ESPEELIENAESL   49 (187)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHCC---CcEEEEECC-CCHHHHHHHHHHc
Confidence            68999999999987766666555433   478888654 4455566666554

A related protein is found in archaea.

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=96.62  E-value=0.023  Score=53.77  Aligned_cols=38  Identities=13%  Similarity=0.085  Sum_probs=25.3

Q ss_pred             ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcC
Q 015158           77 LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAP  115 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P  115 (412)
                      +.+++.||+|+|||..+. ++.+.+....++.+++++..
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            468999999999997653 44444443334456777754

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.60  E-value=0.053  Score=54.12  Aligned_cols=126  Identities=18%  Similarity=0.132  Sum_probs=66.4

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhc
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILS  155 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  155 (412)
                      ++-+.+++|||+|||++....+...... ....++.++.--..- .-..++++.+....++.+                 
T Consensus       185 g~Vi~lVGpnGvGKTTTiaKLA~~~~~~-~G~kkV~lit~Dt~R-igA~eQL~~~a~~~gvpv-----------------  245 (767)
T PRK14723        185 GGVLALVGPTGVGKTTTTAKLAARCVAR-EGADQLALLTTDSFR-IGALEQLRIYGRILGVPV-----------------  245 (767)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHhhHHHH-cCCCeEEEecCcccc-hHHHHHHHHHHHhCCCCc-----------------
Confidence            3456889999999997765444332211 112245444432111 001334444443334322                 


Q ss_pred             CCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhc-cCcHHHHHHHHHhCCCCceEEEEeecCChHHHH
Q 015158          156 SGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLS-RGFKDQIYDIFQLLPPKIQVGVFSATMPPEALE  228 (412)
Q Consensus       156 ~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~-~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~  228 (412)
                          .++.+++.+...+..    ..+.++|+||=+=+.-. ......+..+.....+...++.++||...+...
T Consensus       246 ----~~~~~~~~l~~al~~----~~~~D~VLIDTAGRs~~d~~l~eel~~l~~~~~p~e~~LVLsAt~~~~~l~  311 (767)
T PRK14723        246 ----HAVKDAADLRFALAA----LGDKHLVLIDTVGMSQRDRNVSEQIAMLCGVGRPVRRLLLLNAASHGDTLN  311 (767)
T ss_pred             ----cccCCHHHHHHHHHH----hcCCCEEEEeCCCCCccCHHHHHHHHHHhccCCCCeEEEEECCCCcHHHHH
Confidence                122356666555553    23568999998775332 223344444444445566789999998654433

>PLN03025 replication factor C subunit; Provisional

Probab=96.60  E-value=0.025  Score=51.23  Aligned_cols=40  Identities=20%  Similarity=0.379  Sum_probs=26.1

Q ss_pred             CceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEeecC
Q 015158          181 NIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATM  222 (412)
Q Consensus       181 ~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~  222 (412)
                      ..+++|+||+|.+.... ...+.+.+...+....++ ++++.
T Consensus        99 ~~kviiiDE~d~lt~~a-q~aL~~~lE~~~~~t~~i-l~~n~  138 (319)
T PLN03025         99 RHKIVILDEADSMTSGA-QQALRRTMEIYSNTTRFA-LACNT  138 (319)
T ss_pred             CeEEEEEechhhcCHHH-HHHHHHHHhcccCCceEE-EEeCC
Confidence            57899999999876443 556666666555555544 44443

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=96.59  E-value=0.011  Score=51.96  Aligned_cols=18  Identities=39%  Similarity=0.519  Sum_probs=15.6

Q ss_pred             ccEEEECCCCCCchhHhH
Q 015158           77 LDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~   94 (412)
                      .++++.||+|+|||..+-
T Consensus        43 ~~vll~GppGtGKTtlA~   60 (261)
T TIGR02881        43 LHMIFKGNPGTGKTTVAR   60 (261)
T ss_pred             ceEEEEcCCCCCHHHHHH
Confidence            578999999999998763

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.

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=96.59  E-value=0.017  Score=51.87  Aligned_cols=144  Identities=13%  Similarity=0.053  Sum_probs=73.1

Q ss_pred             CCChHHHHhhhhhhhc----C---ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhc
Q 015158           60 EKPSAIQQRGIVPFCK----G---LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGD  132 (412)
Q Consensus        60 ~~l~~~Q~~a~~~~~~----~---~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~  132 (412)
                      +.++|||..++..+..    +   .-.++.+|.|.||+..+...+. .+.......     ++.       ...+..+..
T Consensus         3 ~~~yPW~~~~~~~l~~~~~~~rl~HA~Lf~Gp~G~GK~~lA~~lA~-~LlC~~~~~-----~~~-------c~~c~~~~~   69 (319)
T PRK08769          3 SAFSPWQQRAYDQTVAALDAGRLGHGLLICGPEGLGKRAVALALAE-HVLASGPDP-----AAA-------QRTRQLIAA   69 (319)
T ss_pred             ccccccHHHHHHHHHHHHHcCCcceeEeeECCCCCCHHHHHHHHHH-HHhCCCCCC-----CCc-------chHHHHHhc
Confidence            4689999999988774    3   2478999999999987654333 333221111     110       011111111


Q ss_pred             ccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCCCC
Q 015158          133 YLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPK  212 (412)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~  212 (412)
                      ...-.+..+.........    .....|.|-....+...+..... ....+++||||+|.+.... ...+.++++.-+.+
T Consensus        70 g~HPD~~~i~~~p~~~~~----k~~~~I~idqIR~l~~~~~~~p~-~g~~kV~iI~~ae~m~~~A-aNaLLKtLEEPp~~  143 (319)
T PRK08769         70 GTHPDLQLVSFIPNRTGD----KLRTEIVIEQVREISQKLALTPQ-YGIAQVVIVDPADAINRAA-CNALLKTLEEPSPG  143 (319)
T ss_pred             CCCCCEEEEecCCCcccc----cccccccHHHHHHHHHHHhhCcc-cCCcEEEEeccHhhhCHHH-HHHHHHHhhCCCCC
Confidence            111112222100000000    00112333333333333322222 2457899999999875543 56666777777777


Q ss_pred             ceEEEEeecC
Q 015158          213 IQVGVFSATM  222 (412)
Q Consensus       213 ~~~i~~SAT~  222 (412)
                      ..+|++|..+
T Consensus       144 ~~fiL~~~~~  153 (319)
T PRK08769        144 RYLWLISAQP  153 (319)
T ss_pred             CeEEEEECCh
Confidence            7677776554

>PF13173 AAA_14: AAA domain

Probab=96.57  E-value=0.033  Score=42.84  Aligned_cols=38  Identities=13%  Similarity=0.260  Sum_probs=25.2

Q ss_pred             CceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEeecC
Q 015158          181 NIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATM  222 (412)
Q Consensus       181 ~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~  222 (412)
                      .-.+|++||+|.+.+  +...+..+.+.. ++.+ +.+|++.
T Consensus        61 ~~~~i~iDEiq~~~~--~~~~lk~l~d~~-~~~~-ii~tgS~   98 (128)
T PF13173_consen   61 GKKYIFIDEIQYLPD--WEDALKFLVDNG-PNIK-IILTGSS   98 (128)
T ss_pred             CCcEEEEehhhhhcc--HHHHHHHHHHhc-cCce-EEEEccc
Confidence            446899999998754  457777777755 3454 4445544

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.56  E-value=0.027  Score=51.21  Aligned_cols=122  Identities=16%  Similarity=0.167  Sum_probs=63.0

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEc-CCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHh
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLA-PTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL  154 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~-P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  154 (412)
                      ++.+++.+|+|+|||.+..-.+......+   .++.+++ .+--.+  ..++|+.+....++.+.               
T Consensus       206 ~~ii~lvGptGvGKTTt~akLA~~l~~~g---~~V~lItaDtyR~g--AveQLk~yae~lgvpv~---------------  265 (407)
T PRK12726        206 HRIISLIGQTGVGKTTTLVKLGWQLLKQN---RTVGFITTDTFRSG--AVEQFQGYADKLDVELI---------------  265 (407)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHcC---CeEEEEeCCccCcc--HHHHHHHHhhcCCCCEE---------------
Confidence            45678999999999977655444332322   3455444 322110  12233344333343321               


Q ss_pred             cCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhh-ccCcHHHHHHHHHhCCCCceEEEEeecCCh
Q 015158          155 SSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEML-SRGFKDQIYDIFQLLPPKIQVGVFSATMPP  224 (412)
Q Consensus       155 ~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~-~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~  224 (412)
                            +..+|+.+...+.... ...+.++|++|=+-+.- +......+..+.....+...++.+||+...
T Consensus       266 ------~~~dp~dL~~al~~l~-~~~~~D~VLIDTAGr~~~d~~~l~EL~~l~~~~~p~~~~LVLsag~~~  329 (407)
T PRK12726        266 ------VATSPAELEEAVQYMT-YVNCVDHILIDTVGRNYLAEESVSEISAYTDVVHPDLTCFTFSSGMKS  329 (407)
T ss_pred             ------ecCCHHHHHHHHHHHH-hcCCCCEEEEECCCCCccCHHHHHHHHHHhhccCCceEEEECCCcccH
Confidence                  1234555544443211 11357899999876532 222334455555555555556777887654

>PRK09183 transposase/IS protein; Provisional

Probab=96.56  E-value=0.022  Score=49.82  Aligned_cols=39  Identities=13%  Similarity=0.082  Sum_probs=25.3

Q ss_pred             hhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEc
Q 015158           73 FCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLA  114 (412)
Q Consensus        73 ~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~  114 (412)
                      +..+.++++.||+|+|||..+..........   +.+++++.
T Consensus        99 i~~~~~v~l~Gp~GtGKThLa~al~~~a~~~---G~~v~~~~  137 (259)
T PRK09183         99 IERNENIVLLGPSGVGKTHLAIALGYEAVRA---GIKVRFTT  137 (259)
T ss_pred             hhcCCeEEEEeCCCCCHHHHHHHHHHHHHHc---CCeEEEEe
Confidence            5567899999999999997664433332222   23566553

>PRK14712 conjugal transfer nickase/helicase TraI; Provisional

Probab=96.53  E-value=0.021  Score=61.46  Aligned_cols=62  Identities=19%  Similarity=0.168  Sum_probs=43.9

Q ss_pred             CChHHHHhhhhhhhcC--ccEEEECCCCCCchhHhH--HHHHHhhccCCCceeEEEEcCCHHHHHHH
Q 015158           61 KPSAIQQRGIVPFCKG--LDVIQQAQSGTGKTATFC--SGILQQLDYGLVECQALVLAPTRELAQQI  123 (412)
Q Consensus        61 ~l~~~Q~~a~~~~~~~--~~~lv~~~tGsGKT~~~~--~~~~~~~~~~~~~~~~lil~P~~~L~~q~  123 (412)
                      .|++-|++|+..++..  +.++|.+..|+|||.+.-  +.++..+.. ..+..++.++||-.-+..+
T Consensus       835 ~Lt~~Qr~Av~~iLts~dr~~~IqG~AGTGKTT~l~~i~~~~~~l~e-~~g~~V~glAPTgkAa~~L  900 (1623)
T PRK14712        835 KLTSGQRAATRMILETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPE-SERPRVVGLGPTHRAVGEM  900 (1623)
T ss_pred             ccCHHHHHHHHHHHhCCCceEEEEeCCCCCHHHHHHHHHHHHHHHhh-ccCceEEEEechHHHHHHH
Confidence            4899999999999854  778999999999997642  222222211 1335788899987755544

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional

Probab=96.52  E-value=0.023  Score=52.88  Aligned_cols=33  Identities=21%  Similarity=0.229  Sum_probs=27.3

Q ss_pred             ChHHHHhhhhhhhcCccEEEECCCCCCchhHhH
Q 015158           62 PSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        62 l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~   94 (412)
                      +.......+..+..++++++.+|+|+|||..+-
T Consensus       180 ~e~~le~l~~~L~~~~~iil~GppGtGKT~lA~  212 (459)
T PRK11331        180 PETTIETILKRLTIKKNIILQGPPGVGKTFVAR  212 (459)
T ss_pred             CHHHHHHHHHHHhcCCCEEEECCCCCCHHHHHH
Confidence            455666777778889999999999999997764

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=96.52  E-value=0.029  Score=51.33  Aligned_cols=40  Identities=10%  Similarity=0.209  Sum_probs=25.7

Q ss_pred             CCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEee
Q 015158          180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSA  220 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SA  220 (412)
                      ...++||+||+|.+... ....+..++...+....+|+.+.
T Consensus       124 ~~~~vlilDe~~~l~~~-~~~~L~~~le~~~~~~~~Il~~~  163 (337)
T PRK12402        124 ADYKTILLDNAEALRED-AQQALRRIMEQYSRTCRFIIATR  163 (337)
T ss_pred             CCCcEEEEeCcccCCHH-HHHHHHHHHHhccCCCeEEEEeC
Confidence            34579999999986543 24456666666666666555443

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.52  E-value=0.063  Score=49.68  Aligned_cols=125  Identities=16%  Similarity=0.150  Sum_probs=63.7

Q ss_pred             ccEEEECCCCCCchhHhHHHHHHh-hccCCCceeEEEEc-CC-HHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHH
Q 015158           77 LDVIQQAQSGTGKTATFCSGILQQ-LDYGLVECQALVLA-PT-RELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRI  153 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~~~~~~~-~~~~~~~~~~lil~-P~-~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  153 (412)
                      ..+++.+|+|+|||.++.-.+... ...+   .++.++. .+ +..+.   .++..++...++.+..             
T Consensus       224 ~vi~lvGptGvGKTTtaaKLA~~~~~~~G---~~V~Lit~Dt~R~aA~---eQLk~yAe~lgvp~~~-------------  284 (432)
T PRK12724        224 KVVFFVGPTGSGKTTSIAKLAAKYFLHMG---KSVSLYTTDNYRIAAI---EQLKRYADTMGMPFYP-------------  284 (432)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHhcC---CeEEEecccchhhhHH---HHHHHHHHhcCCCeee-------------
Confidence            347789999999998776555433 2222   2444433 33 22222   2333433333432211             


Q ss_pred             hcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhh-ccCcHHHHHHHHHhCC---CCceEEEEeecCChHHHHH
Q 015158          154 LSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEML-SRGFKDQIYDIFQLLP---PKIQVGVFSATMPPEALEI  229 (412)
Q Consensus       154 ~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~-~~~~~~~~~~i~~~~~---~~~~~i~~SAT~~~~~~~~  229 (412)
                              +.....+...+.     ..+.++|++|=+-+.. +......+..+.....   +...++.+|||...+....
T Consensus       285 --------~~~~~~l~~~l~-----~~~~D~VLIDTaGr~~rd~~~l~eL~~~~~~~~~~~~~e~~LVLsAt~~~~~~~~  351 (432)
T PRK12724        285 --------VKDIKKFKETLA-----RDGSELILIDTAGYSHRNLEQLERMQSFYSCFGEKDSVENLLVLSSTSSYHHTLT  351 (432)
T ss_pred             --------hHHHHHHHHHHH-----hCCCCEEEEeCCCCCccCHHHHHHHHHHHHhhcCCCCCeEEEEEeCCCCHHHHHH
Confidence                    011223333332     1467899999765432 2223344555554432   3356899999998744444


Q ss_pred             HHHh
Q 015158          230 TRKF  233 (412)
Q Consensus       230 ~~~~  233 (412)
                      ....
T Consensus       352 ~~~~  355 (432)
T PRK12724        352 VLKA  355 (432)
T ss_pred             HHHH
Confidence            4433

>KOG2028 consensus ATPase related to the helicase subunit of the Holliday junction resolvase [Replication, recombination and repair]

Probab=96.49  E-value=0.0098  Score=52.81  Aligned_cols=50  Identities=16%  Similarity=0.121  Sum_probs=28.4

Q ss_pred             ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHH
Q 015158           77 LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRA  129 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~  129 (412)
                      .+.++|+|+|+|||..+=+.+-..   ....-+.+=+..+.+-+.+..+.+++
T Consensus       163 pSmIlWGppG~GKTtlArlia~ts---k~~SyrfvelSAt~a~t~dvR~ife~  212 (554)
T KOG2028|consen  163 PSMILWGPPGTGKTTLARLIASTS---KKHSYRFVELSATNAKTNDVRDIFEQ  212 (554)
T ss_pred             CceEEecCCCCchHHHHHHHHhhc---CCCceEEEEEeccccchHHHHHHHHH
Confidence            478999999999997653222211   11122455555665555555444443

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=96.48  E-value=0.015  Score=58.98  Aligned_cols=39  Identities=21%  Similarity=0.405  Sum_probs=28.8

Q ss_pred             CCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEe
Q 015158          180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFS  219 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~S  219 (412)
                      ..++++||||+|.+.... ...+.++++..+.++.+|+++
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            467899999999876554 456667777777777667665

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.46  E-value=0.02  Score=54.34  Aligned_cols=39  Identities=8%  Similarity=0.322  Sum_probs=25.8

Q ss_pred             CCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEe
Q 015158          180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFS  219 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~S  219 (412)
                      ...+++|+||+|.+.... ...+.+.+..-++...+|+.|
T Consensus       115 ~~~KVvIIDEah~Ls~~A-~NaLLK~LEePp~~v~fIlat  153 (491)
T PRK14964        115 SKFKVYIIDEVHMLSNSA-FNALLKTLEEPAPHVKFILAT  153 (491)
T ss_pred             CCceEEEEeChHhCCHHH-HHHHHHHHhCCCCCeEEEEEe
Confidence            467899999999876554 344555556555565555544

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.45  E-value=0.015  Score=56.56  Aligned_cols=41  Identities=10%  Similarity=0.379  Sum_probs=27.0

Q ss_pred             CCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEeec
Q 015158          180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSAT  221 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT  221 (412)
                      ..++++||||+|.+....+ ..+.+.++.-+.++.+|+.|--
T Consensus       123 gr~KViIIDEah~Ls~~Aa-NALLKTLEEPP~~v~FILaTte  163 (700)
T PRK12323        123 GRFKVYMIDEVHMLTNHAF-NAMLKTLEEPPEHVKFILATTD  163 (700)
T ss_pred             CCceEEEEEChHhcCHHHH-HHHHHhhccCCCCceEEEEeCC
Confidence            4678999999998865543 3444555555556666665543

>TIGR01547 phage_term_2 phage terminase, large subunit, PBSX family

Probab=96.45  E-value=0.011  Score=55.55  Aligned_cols=136  Identities=15%  Similarity=0.227  Sum_probs=74.3

Q ss_pred             cEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHH-HHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcC
Q 015158           78 DVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRE-LAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSS  156 (412)
Q Consensus        78 ~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~-L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  156 (412)
                      -.++.++.|||||.+....++..+....++.+++++-++.. +..-+...+.......++....-....+.  .......
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            35789999999998877666655554323467888888876 55556666665544444432221111100  0000111


Q ss_pred             CCcEEEeCh-HHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCC--CCceEEEEeecCCh
Q 015158          157 GVHVVVGTP-GRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLP--PKIQVGVFSATMPP  224 (412)
Q Consensus       157 ~~~iii~T~-~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~--~~~~~i~~SAT~~~  224 (412)
                      +..|++..- +..... .    ....++++.+|||..+...    .+..+...++  .....+.+|.+|..
T Consensus        81 g~~i~f~g~~d~~~~i-k----~~~~~~~~~idEa~~~~~~----~~~~l~~rlr~~~~~~~i~~t~NP~~  142 (396)
T TIGR01547        81 GKKFIFKGLNDKPNKL-K----SGAGIAIIWFEEASQLTFE----DIKELIPRLRETGGKKFIIFSSNPES  142 (396)
T ss_pred             CeEEEeecccCChhHh-h----CcceeeeehhhhhhhcCHH----HHHHHHHHhhccCCccEEEEEcCcCC
Confidence            335666553 222111 1    1234689999999987543    3333333332  22225889999865

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.

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.45  E-value=0.011  Score=59.60  Aligned_cols=38  Identities=8%  Similarity=0.281  Sum_probs=25.5

Q ss_pred             CCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEE
Q 015158          180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVF  218 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~  218 (412)
                      ..+.++||||+|.+.... ...+.+.+..-+.+.++|+.
T Consensus       118 gk~KViIIDEAh~LT~eA-qNALLKtLEEPP~~vrFILa  155 (944)
T PRK14949        118 GRFKVYLIDEVHMLSRSS-FNALLKTLEEPPEHVKFLLA  155 (944)
T ss_pred             CCcEEEEEechHhcCHHH-HHHHHHHHhccCCCeEEEEE
Confidence            357899999999875443 45555666665556655554

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=96.44  E-value=0.0086  Score=54.13  Aligned_cols=37  Identities=16%  Similarity=-0.047  Sum_probs=29.0

Q ss_pred             ChHHHHhhhhhhhcCc----cEEEECCCCCCchhHhHHHHH
Q 015158           62 PSAIQQRGIVPFCKGL----DVIQQAQSGTGKTATFCSGIL   98 (412)
Q Consensus        62 l~~~Q~~a~~~~~~~~----~~lv~~~tGsGKT~~~~~~~~   98 (412)
                      ++|||...+..+...+    ..++.||.|.|||..+...+.
T Consensus         4 ~yPWl~~~~~~~~~~~r~~ha~Lf~G~~G~GK~~~A~~~A~   44 (328)
T PRK05707          4 IYPWQQSLWQQLAGRGRHPHAYLLHGPAGIGKRALAERLAA   44 (328)
T ss_pred             CCCCcHHHHHHHHHCCCcceeeeeECCCCCCHHHHHHHHHH
Confidence            5899999999988653    468899999999977654333

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=96.43  E-value=0.021  Score=53.59  Aligned_cols=19  Identities=42%  Similarity=0.552  Sum_probs=16.0

Q ss_pred             ccEEEECCCCCCchhHhHH
Q 015158           77 LDVIQQAQSGTGKTATFCS   95 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~~   95 (412)
                      .+++|.||+|+|||.+.-.
T Consensus        56 ~~~lI~G~~GtGKT~l~~~   74 (394)
T PRK00411         56 LNVLIYGPPGTGKTTTVKK   74 (394)
T ss_pred             CeEEEECCCCCCHHHHHHH
Confidence            5789999999999987543

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=96.41  E-value=0.089  Score=49.07  Aligned_cols=131  Identities=11%  Similarity=0.137  Sum_probs=67.2

Q ss_pred             cEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcC-C-HHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhc
Q 015158           78 DVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAP-T-RELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILS  155 (412)
Q Consensus        78 ~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P-~-~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  155 (412)
                      -+++++++|+|||+++.-.+......   +.++++++. + +.-+   .++++.+....++++...........      
T Consensus       102 vi~lvG~~GvGKTTtaaKLA~~l~~~---G~kV~lV~~D~~R~aA---~eQLk~~a~~~~vp~~~~~~~~dp~~------  169 (429)
T TIGR01425       102 VIMFVGLQGSGKTTTCTKLAYYYQRK---GFKPCLVCADTFRAGA---FDQLKQNATKARIPFYGSYTESDPVK------  169 (429)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHC---CCCEEEEcCcccchhH---HHHHHHHhhccCCeEEeecCCCCHHH------
Confidence            46789999999997765433322222   336666553 2 2222   23334444334555433222111100      


Q ss_pred             CCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhc-cCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHh
Q 015158          156 SGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLS-RGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKF  233 (412)
Q Consensus       156 ~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~-~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~  233 (412)
                                 ...+.+...  ....+++||+|=+-+.-. ......+..+.....+...++.++||...+.......+
T Consensus       170 -----------i~~~~l~~~--~~~~~DvViIDTaGr~~~d~~lm~El~~i~~~~~p~e~lLVlda~~Gq~a~~~a~~F  235 (429)
T TIGR01425       170 -----------IASEGVEKF--KKENFDIIIVDTSGRHKQEDSLFEEMLQVAEAIQPDNIIFVMDGSIGQAAEAQAKAF  235 (429)
T ss_pred             -----------HHHHHHHHH--HhCCCCEEEEECCCCCcchHHHHHHHHHHhhhcCCcEEEEEeccccChhHHHHHHHH
Confidence                       000111110  113578899998765332 22445666666666666778888998875544444443

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.

>PHA03333 putative ATPase subunit of terminase; Provisional

Probab=96.40  E-value=0.056  Score=52.68  Aligned_cols=58  Identities=10%  Similarity=0.105  Sum_probs=42.0

Q ss_pred             hhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhc
Q 015158           73 FCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGD  132 (412)
Q Consensus        73 ~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~  132 (412)
                      .++.+-.++.+|-|.|||.+.-+.+...+..  .+.+++|.+|...-+++.++.+.....
T Consensus       184 ~fkq~~tV~taPRqrGKS~iVgi~l~~La~f--~Gi~IlvTAH~~~ts~evF~rv~~~le  241 (752)
T PHA03333        184 EYGKCYTAATVPRRCGKTTIMAIILAAMISF--LEIDIVVQAQRKTMCLTLYNRVETVVH  241 (752)
T ss_pred             HHhhcceEEEeccCCCcHHHHHHHHHHHHHh--cCCeEEEECCChhhHHHHHHHHHHHHH
Confidence            3344567889999999997765554433321  235899999999989888888777654

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=96.40  E-value=0.024  Score=55.04  Aligned_cols=106  Identities=15%  Similarity=0.201  Sum_probs=57.3

Q ss_pred             ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcC
Q 015158           77 LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSS  156 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  156 (412)
                      +.++|.|++|+|||..+. ++.+.+.....+.+++++.. ..+..+....+..     +                     
T Consensus       315 NpL~LyG~sGsGKTHLL~-AIa~~a~~~~~g~~V~Yita-eef~~el~~al~~-----~---------------------  366 (617)
T PRK14086        315 NPLFIYGESGLGKTHLLH-AIGHYARRLYPGTRVRYVSS-EEFTNEFINSIRD-----G---------------------  366 (617)
T ss_pred             CcEEEECCCCCCHHHHHH-HHHHHHHHhCCCCeEEEeeH-HHHHHHHHHHHHh-----c---------------------
Confidence            348999999999996543 34444433223446666553 4444433322211     0                     


Q ss_pred             CCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccC-cHHHHHHHHHhCCC-CceEEEEeecCCh
Q 015158          157 GVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRG-FKDQIYDIFQLLPP-KIQVGVFSATMPP  224 (412)
Q Consensus       157 ~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~-~~~~~~~i~~~~~~-~~~~i~~SAT~~~  224 (412)
                             ..+.|.+.+       .++++|||||+|.+.... ....+..+++.+.. +.++|+.|-.++.
T Consensus       367 -------~~~~f~~~y-------~~~DLLlIDDIq~l~gke~tqeeLF~l~N~l~e~gk~IIITSd~~P~  422 (617)
T PRK14086        367 -------KGDSFRRRY-------REMDILLVDDIQFLEDKESTQEEFFHTFNTLHNANKQIVLSSDRPPK  422 (617)
T ss_pred             -------cHHHHHHHh-------hcCCEEEEehhccccCCHHHHHHHHHHHHHHHhcCCCEEEecCCChH
Confidence                   011222221       357899999999876533 34556666665544 4555554444433

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=96.35  E-value=0.027  Score=49.82  Aligned_cols=55  Identities=16%  Similarity=0.134  Sum_probs=34.0

Q ss_pred             hhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHH
Q 015158           72 PFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRA  129 (412)
Q Consensus        72 ~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~  129 (412)
                      -+..|..+++.+++|+|||..+...+......  .+.+++|+.--. -..+..+.+..
T Consensus        26 G~~~g~~~~i~g~~G~GKT~l~~~~~~~~~~~--~g~~vl~iS~E~-~~~~~~~r~~~   80 (271)
T cd01122          26 GLRKGELIILTAGTGVGKTTFLREYALDLITQ--HGVRVGTISLEE-PVVRTARRLLG   80 (271)
T ss_pred             EEcCCcEEEEEcCCCCCHHHHHHHHHHHHHHh--cCceEEEEEccc-CHHHHHHHHHH
Confidence            34456788999999999997766555544333  134788876432 23444444433

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=96.35  E-value=0.033  Score=52.70  Aligned_cols=36  Identities=17%  Similarity=0.176  Sum_probs=23.2

Q ss_pred             ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcC
Q 015158           77 LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAP  115 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P  115 (412)
                      +.+++.||+|+|||..+. ++...+...  +.+++++..
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            458999999999996653 444444321  346776653

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=96.35  E-value=0.017  Score=57.13  Aligned_cols=135  Identities=14%  Similarity=0.083  Sum_probs=73.0

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhc
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILS  155 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  155 (412)
                      .+-+++.+|.|+|||+....+.. ...   .+..+.++.=.. -..+-.+.++.+....+-.+....+...     + ..
T Consensus        37 ~RL~li~APAGfGKttl~aq~~~-~~~---~~~~v~Wlslde-~dndp~rF~~yLi~al~~~~p~~~~~a~-----~-l~  105 (894)
T COG2909          37 YRLILISAPAGFGKTTLLAQWRE-LAA---DGAAVAWLSLDE-SDNDPARFLSYLIAALQQATPTLGDEAQ-----T-LL  105 (894)
T ss_pred             ceEEEEeCCCCCcHHHHHHHHHH-hcC---cccceeEeecCC-ccCCHHHHHHHHHHHHHHhCccccHHHH-----H-HH
Confidence            45678999999999987655543 222   234566665321 1222233333222211111111111111     1 11


Q ss_pred             CCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEeecCC
Q 015158          156 SGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMP  223 (412)
Q Consensus       156 ~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~  223 (412)
                      .+ +..+ .-+.+...+...--.....-++|+|+.|.+.+......+..+++..|++...++.|-+-+
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 112222222221111123358999999999999888999999999999999999998865

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP

Probab=96.34  E-value=0.044  Score=43.55  Aligned_cols=130  Identities=18%  Similarity=0.285  Sum_probs=70.8

Q ss_pred             EEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHH---HHHHHHHHHHHhhcccCcEEEEEEcCcc-----hHHH
Q 015158           79 VIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRE---LAQQIEKVMRALGDYLGVKVHACVGGTS-----VRED  150 (412)
Q Consensus        79 ~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~---L~~q~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~  150 (412)
                      +.|-.++|.|||.+++..++.....+.   +++++-=.+.   -.+  ...++++   .++.......+..     ....
T Consensus         5 i~vy~g~G~Gkt~~a~g~~~ra~~~g~---~v~~vQFlKg~~~~gE--~~~l~~l---~~v~~~~~g~~~~~~~~~~~~~   76 (159)
T cd00561           5 IQVYTGNGKGKTTAALGLALRALGHGY---RVGVVQFLKGGWKYGE--LKALERL---PNIEIHRMGRGFFWTTENDEED   76 (159)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCC---eEEEEEEeCCCCccCH--HHHHHhC---CCcEEEECCCCCccCCCChHHH
Confidence            566788899999999887877776654   6766332221   111  1223333   1333332211110     0000


Q ss_pred             HHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCc--HHHHHHHHHhCCCCceEEEEeecCChHHHH
Q 015158          151 QRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGF--KDQIYDIFQLLPPKIQVGVFSATMPPEALE  228 (412)
Q Consensus       151 ~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~--~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~  228 (412)
                      ....          -+.+ .... .......++++|+||+-.....++  ...+..+++..|....+|+.+-.+++.+.+
T Consensus        77 ~~~a----------~~~~-~~a~-~~~~~~~~dLlVLDEi~~a~~~gli~~~~v~~ll~~rp~~~evIlTGr~~p~~l~e  144 (159)
T cd00561          77 IAAA----------AEGW-AFAK-EAIASGEYDLVILDEINYALGYGLLDVEEVVDLLKAKPEDLELVLTGRNAPKELIE  144 (159)
T ss_pred             HHHH----------HHHH-HHHH-HHHhcCCCCEEEEechHhHhhCCCCCHHHHHHHHHcCCCCCEEEEECCCCCHHHHH
Confidence            0000          0111 1111 112235789999999998766653  456777888888787777777777665544

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.

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=96.33  E-value=0.061  Score=54.09  Aligned_cols=27  Identities=22%  Similarity=0.687  Sum_probs=18.1

Q ss_pred             CCceEEEEeCCchhhccCcHHHHHHHHH
Q 015158          180 DNIRIFVLDEADEMLSRGFKDQIYDIFQ  207 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~~~~~~~~~i~~  207 (412)
                      ....+||+||+|.+.... ...+..++.
T Consensus       868 r~v~IIILDEID~L~kK~-QDVLYnLFR  894 (1164)
T PTZ00112        868 RNVSILIIDEIDYLITKT-QKVLFTLFD  894 (1164)
T ss_pred             ccceEEEeehHhhhCccH-HHHHHHHHH
Confidence            456789999999987542 344554444

>PTZ00293 thymidine kinase; Provisional

Probab=96.33  E-value=0.024  Score=47.22  Aligned_cols=40  Identities=13%  Similarity=0.069  Sum_probs=29.1

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHH
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRE  118 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  118 (412)
                      |.--++.+|++||||.-.+..+......+   .+++++-|...
T Consensus         4 G~i~vi~GpMfSGKTteLLr~i~~y~~ag---~kv~~~kp~~D   43 (211)
T PTZ00293          4 GTISVIIGPMFSGKTTELMRLVKRFTYSE---KKCVVIKYSKD   43 (211)
T ss_pred             eEEEEEECCCCChHHHHHHHHHHHHHHcC---CceEEEEeccc
Confidence            44568899999999987776666554443   47888888643

>PRK13709 conjugal transfer nickase/helicase TraI; Provisional

Probab=96.31  E-value=0.037  Score=60.36  Aligned_cols=124  Identities=16%  Similarity=0.175  Sum_probs=72.6

Q ss_pred             CChHHHHhhhhhhhcC--ccEEEECCCCCCchhHhHHHHHHhhc--cCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCc
Q 015158           61 KPSAIQQRGIVPFCKG--LDVIQQAQSGTGKTATFCSGILQQLD--YGLVECQALVLAPTRELAQQIEKVMRALGDYLGV  136 (412)
Q Consensus        61 ~l~~~Q~~a~~~~~~~--~~~lv~~~tGsGKT~~~~~~~~~~~~--~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~  136 (412)
                      .+++-|++|+..++.+  +-.+|.+..|+|||.+. -.+...+.  ....+.+++.++||-.-+..+.    +.    |+
T Consensus       967 ~Lt~~Q~~Av~~il~s~dr~~~I~G~AGTGKTT~l-~~v~~~~~~l~~~~~~~V~glAPTgrAAk~L~----e~----Gi 1037 (1747)
T PRK13709        967 GLTSGQRAATRMILESTDRFTVVQGYAGVGKTTQF-RAVMSAVNTLPESERPRVVGLGPTHRAVGEMR----SA----GV 1037 (1747)
T ss_pred             CCCHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHHH-HHHHHHHHHhhcccCceEEEECCcHHHHHHHH----hc----Cc
Confidence            4899999999999875  57889999999999764 22322221  1122346888999977555433    21    32


Q ss_pred             EEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHH----HcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCCC-
Q 015158          137 KVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDML----RRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPP-  211 (412)
Q Consensus       137 ~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~----~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~-  211 (412)
                      ..                        .|..+|+...    ..........++|||||+-.+...    .+..++...+. 
T Consensus      1038 ~A------------------------~TI~s~L~~~~~~~~~~~~~~~~~~llIVDEaSMv~~~----~m~~Ll~~~~~~ 1089 (1747)
T PRK13709       1038 DA------------------------QTLASFLHDTQLQQRSGETPDFSNTLFLLDESSMVGNT----DMARAYALIAAG 1089 (1747)
T ss_pred             ch------------------------hhHHHHhcccccccccccCCCCCCcEEEEEccccccHH----HHHHHHHhhhcC
Confidence            21                        1222221110    000111123479999999976443    34455555543 


Q ss_pred             CceEEEEeec
Q 015158          212 KIQVGVFSAT  221 (412)
Q Consensus       212 ~~~~i~~SAT  221 (412)
                      +.++|++.-+
T Consensus      1090 garvVLVGD~ 1099 (1747)
T PRK13709       1090 GGRAVSSGDT 1099 (1747)
T ss_pred             CCEEEEecch
Confidence            6777777766

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.31  E-value=0.02  Score=55.06  Aligned_cols=39  Identities=8%  Similarity=0.306  Sum_probs=27.6

Q ss_pred             CCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEe
Q 015158          180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFS  219 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~S  219 (412)
                      ..++++|+||+|.+.... ...+.+.+...++.+.+|+.|
T Consensus       118 ~~~kV~iIDE~~~ls~~a-~naLLk~LEepp~~~~fIlat  156 (509)
T PRK14958        118 GRFKVYLIDEVHMLSGHS-FNALLKTLEEPPSHVKFILAT  156 (509)
T ss_pred             CCcEEEEEEChHhcCHHH-HHHHHHHHhccCCCeEEEEEE
Confidence            467899999999876554 345556666666677666655

>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA

Probab=96.25  E-value=0.0071  Score=58.87  Aligned_cols=125  Identities=15%  Similarity=0.121  Sum_probs=76.1

Q ss_pred             CChHHHHhhhhhhhcC--ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHH-HHHHHhhcccCcE
Q 015158           61 KPSAIQQRGIVPFCKG--LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIE-KVMRALGDYLGVK  137 (412)
Q Consensus        61 ~l~~~Q~~a~~~~~~~--~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~-~~~~~~~~~~~~~  137 (412)
                      ..+|||.+.+..+...  +.+.+..++-+|||.+.+.++...+... + ..++++.||..++.++. +.+..+......-
T Consensus        16 ~~~Py~~eimd~~~~~~v~~Vv~~k~aQ~GkT~~~~n~~g~~i~~~-P-~~~l~v~Pt~~~a~~~~~~rl~Pmi~~sp~l   93 (557)
T PF05876_consen   16 DRTPYLREIMDALSDPSVREVVVMKSAQVGKTELLLNWIGYSIDQD-P-GPMLYVQPTDDAAKDFSKERLDPMIRASPVL   93 (557)
T ss_pred             CCChhHHHHHHhcCCcCccEEEEEEcchhhHhHHHHhhceEEEEeC-C-CCEEEEEEcHHHHHHHHHHHHHHHHHhCHHH
Confidence            4789999999988876  5788999999999997766666555443 3 46999999999998876 4454443222110


Q ss_pred             EEEEEc---C-cchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhh
Q 015158          138 VHACVG---G-TSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEML  194 (412)
Q Consensus       138 ~~~~~~---~-~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~  194 (412)
                      -..+..   . .......+.+. +..+.++...+-      ..+....++++++||++.+.
T Consensus        94 ~~~~~~~~~~~~~~t~~~k~f~-gg~l~~~ga~S~------~~l~s~~~r~~~~DEvD~~p  147 (557)
T PF05876_consen   94 RRKLSPSKSRDSGNTILYKRFP-GGFLYLVGANSP------SNLRSRPARYLLLDEVDRYP  147 (557)
T ss_pred             HHHhCchhhcccCCchhheecC-CCEEEEEeCCCC------cccccCCcCEEEEechhhcc
Confidence            011111   0 00011112222 234554442221      12334568899999999874

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 [].

>COG2805 PilT Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=96.22  E-value=0.0082  Score=51.96  Aligned_cols=58  Identities=12%  Similarity=0.186  Sum_probs=36.5

Q ss_pred             CCCChhhhccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCC
Q 015158           30 FFTSYDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLV  106 (412)
Q Consensus        30 ~~~~~~~~~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~  106 (412)
                      .++.......+|+++++++-+.+.+..                  ...-++|.+|||||||.+. .++.+.++....
T Consensus        97 vlR~Ip~~i~~~e~LglP~i~~~~~~~------------------~~GLILVTGpTGSGKSTTl-AamId~iN~~~~  154 (353)
T COG2805          97 VLRLIPSKIPTLEELGLPPIVRELAES------------------PRGLILVTGPTGSGKSTTL-AAMIDYINKHKA  154 (353)
T ss_pred             EEeccCccCCCHHHcCCCHHHHHHHhC------------------CCceEEEeCCCCCcHHHHH-HHHHHHHhccCC
Confidence            344444555566666666655553321                  1234788999999999774 677777776543

>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=96.19  E-value=0.069  Score=48.92  Aligned_cols=45  Identities=13%  Similarity=0.143  Sum_probs=29.8

Q ss_pred             CceEEEEeCCchhhccCcHHHHHHHHHh-CCCCceEEEEeecCChHH
Q 015158          181 NIRIFVLDEADEMLSRGFKDQIYDIFQL-LPPKIQVGVFSATMPPEA  226 (412)
Q Consensus       181 ~~~~iiiDE~h~~~~~~~~~~~~~i~~~-~~~~~~~i~~SAT~~~~~  226 (412)
                      ...++++||.|. .+-+-...+.+++.. +..+..+|..|-++|.++
T Consensus       127 ~~~lLcfDEF~V-~DiaDAmil~rLf~~l~~~gvvlVaTSN~~P~~L  172 (362)
T PF03969_consen  127 ESRLLCFDEFQV-TDIADAMILKRLFEALFKRGVVLVATSNRPPEDL  172 (362)
T ss_pred             cCCEEEEeeeec-cchhHHHHHHHHHHHHHHCCCEEEecCCCChHHH
Confidence            457999999994 444434555555544 345777888888887553

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

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.15  E-value=0.023  Score=55.41  Aligned_cols=39  Identities=8%  Similarity=0.294  Sum_probs=26.0

Q ss_pred             CCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEe
Q 015158          180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFS  219 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~S  219 (412)
                      ..++++||||+|.+.... ...+.+.+...+....+|+.+
T Consensus       117 gk~KV~IIDEVh~LS~~A-~NALLKtLEEPP~~v~FILaT  155 (702)
T PRK14960        117 GRFKVYLIDEVHMLSTHS-FNALLKTLEEPPEHVKFLFAT  155 (702)
T ss_pred             CCcEEEEEechHhcCHHH-HHHHHHHHhcCCCCcEEEEEE
Confidence            357899999999876554 445566666656566555544

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=96.14  E-value=0.13  Score=45.34  Aligned_cols=131  Identities=24%  Similarity=0.311  Sum_probs=66.9

Q ss_pred             ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEc-CC-HHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHh
Q 015158           77 LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLA-PT-RELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL  154 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~-P~-~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  154 (412)
                      +-+++.+++|+|||.+..-.+......   +.+++++. .+ +.-+   .+++..+....++.+.  ......       
T Consensus        73 ~vi~l~G~~G~GKTTt~akLA~~l~~~---g~~V~li~~D~~r~~a---~~ql~~~~~~~~i~~~--~~~~~~-------  137 (272)
T TIGR00064        73 NVILFVGVNGVGKTTTIAKLANKLKKQ---GKSVLLAAGDTFRAAA---IEQLEEWAKRLGVDVI--KQKEGA-------  137 (272)
T ss_pred             eEEEEECCCCCcHHHHHHHHHHHHHhc---CCEEEEEeCCCCCHHH---HHHHHHHHHhCCeEEE--eCCCCC-------
Confidence            456778999999998765444433222   34666655 32 2222   2233333333343332  211110       


Q ss_pred             cCCCcEEEeChHH-HHHHHHcCCCCCCCceEEEEeCCchhh-ccCcHHHHHHHHHhCC------CCceEEEEeecCChHH
Q 015158          155 SSGVHVVVGTPGR-VFDMLRRQSLRPDNIRIFVLDEADEML-SRGFKDQIYDIFQLLP------PKIQVGVFSATMPPEA  226 (412)
Q Consensus       155 ~~~~~iii~T~~~-l~~~~~~~~~~~~~~~~iiiDE~h~~~-~~~~~~~~~~i~~~~~------~~~~~i~~SAT~~~~~  226 (412)
                               .|.. ....+..  ....++++|++|=+-+.. +......+..+....+      +...++.++||...+.
T Consensus       138 ---------dp~~~~~~~l~~--~~~~~~D~ViIDT~G~~~~d~~~~~el~~~~~~~~~~~~~~~~~~~LVl~a~~~~~~  206 (272)
T TIGR00064       138 ---------DPAAVAFDAIQK--AKARNIDVVLIDTAGRLQNKVNLMDELKKIKRVIKKVDKDAPDEVLLVLDATTGQNA  206 (272)
T ss_pred             ---------CHHHHHHHHHHH--HHHCCCCEEEEeCCCCCcchHHHHHHHHHHHHHHhcccCCCCceEEEEEECCCCHHH
Confidence                     0111 1111111  012467999999876543 2223345666655554      5667899999976654


Q ss_pred             HHHHHHh
Q 015158          227 LEITRKF  233 (412)
Q Consensus       227 ~~~~~~~  233 (412)
                      ......+
T Consensus       207 ~~~~~~f  213 (272)
T TIGR00064       207 LEQAKVF  213 (272)
T ss_pred             HHHHHHH
Confidence            4444444

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.

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.14  E-value=0.026  Score=54.23  Aligned_cols=24  Identities=25%  Similarity=0.281  Sum_probs=17.4

Q ss_pred             cEEEECCCCCCchhHhHHHHHHhhc
Q 015158           78 DVIQQAQSGTGKTATFCSGILQQLD  102 (412)
Q Consensus        78 ~~lv~~~tGsGKT~~~~~~~~~~~~  102 (412)
                      ..++.||+|+|||.++.. ++..+.
T Consensus        38 a~Lf~GppGtGKTTlA~~-lA~~l~   61 (504)
T PRK14963         38 AYLFSGPRGVGKTTTARL-IAMAVN   61 (504)
T ss_pred             EEEEECCCCCCHHHHHHH-HHHHHh
Confidence            349999999999988754 333443

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=96.13  E-value=0.078  Score=45.45  Aligned_cols=53  Identities=17%  Similarity=0.118  Sum_probs=34.0

Q ss_pred             hcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 015158           74 CKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRAL  130 (412)
Q Consensus        74 ~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~  130 (412)
                      -.+..+++.+++|+|||..++..+...+..+   .++++++... -..+..+.+..+
T Consensus        22 ~~g~~~~i~G~~G~GKTtl~~~~~~~~~~~g---~~~~yi~~e~-~~~~~~~~~~~~   74 (230)
T PRK08533         22 PAGSLILIEGDESTGKSILSQRLAYGFLQNG---YSVSYVSTQL-TTTEFIKQMMSL   74 (230)
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHHHhCC---CcEEEEeCCC-CHHHHHHHHHHh
Confidence            3467789999999999987655555443333   4788888543 334455555443

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=96.13  E-value=0.041  Score=50.05  Aligned_cols=40  Identities=13%  Similarity=0.322  Sum_probs=28.1

Q ss_pred             CCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEee
Q 015158          180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSA  220 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SA  220 (412)
                      ..+.+||+|||+.+... ....+.+.+..-+.+..+++.+-
T Consensus       108 ~~~kviiidead~mt~~-A~nallk~lEep~~~~~~il~~n  147 (325)
T COG0470         108 GGYKVVIIDEADKLTED-AANALLKTLEEPPKNTRFILITN  147 (325)
T ss_pred             CCceEEEeCcHHHHhHH-HHHHHHHHhccCCCCeEEEEEcC
Confidence            56789999999987654 35666667666666665555554

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=96.12  E-value=0.026  Score=55.51  Aligned_cols=38  Identities=8%  Similarity=0.288  Sum_probs=25.9

Q ss_pred             CCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEE
Q 015158          180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVF  218 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~  218 (412)
                      ..+.++||||+|.+.... ...+.+.+..-+.+..+|+.
T Consensus       118 g~~KV~IIDEah~Ls~~a-~NALLKtLEEPp~~v~FIL~  155 (647)
T PRK07994        118 GRFKVYLIDEVHMLSRHS-FNALLKTLEEPPEHVKFLLA  155 (647)
T ss_pred             CCCEEEEEechHhCCHHH-HHHHHHHHHcCCCCeEEEEe
Confidence            467899999999876554 44555566665556655555

>COG1444 Predicted P-loop ATPase fused to an acetyltransferase [General function prediction only]

Probab=96.09  E-value=0.065  Score=53.05  Aligned_cols=157  Identities=18%  Similarity=0.238  Sum_probs=90.3

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHhhhhhhhcCc--cEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHH
Q 015158           46 LQENLLRGIYAYGFEKPSAIQQRGIVPFCKGL--DVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQI  123 (412)
Q Consensus        46 l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~--~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~  123 (412)
                      .++.....+.....++....|.+.+..+++.+  -+++.|+-|=|||.+.=+++....... ...+++|.+|+.+-++..
T Consensus       199 ~~~~~~~~l~~l~~T~dQ~~~l~~~~~l~~~~~~~~vlTAdRGRGKSA~lGi~~~~~~~~~-~~~~iiVTAP~~~nv~~L  277 (758)
T COG1444         199 LDPVFPRELYELCLTEDQAEALEILERLLDAPKRALVLTADRGRGKSAALGIALAAAARLA-GSVRIIVTAPTPANVQTL  277 (758)
T ss_pred             CCCCCCHHHhhhhcChhHHHHHHHHHHHHcCCCceEEEEcCCCCcHhHHHhHHHHHHHHhc-CCceEEEeCCCHHHHHHH
Confidence            33334444555555566666777777777653  578899999999966543332222211 135899999999988888


Q ss_pred             HHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHH
Q 015158          124 EKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIY  203 (412)
Q Consensus       124 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~  203 (412)
                      ++.+.+-....|.+.........  .......+...|-+.+|....          ..-+++|+|||=-+    -...+.
T Consensus       278 f~fa~~~l~~lg~~~~v~~d~~g--~~~~~~~~~~~i~y~~P~~a~----------~~~DllvVDEAAaI----plplL~  341 (758)
T COG1444         278 FEFAGKGLEFLGYKRKVAPDALG--EIREVSGDGFRIEYVPPDDAQ----------EEADLLVVDEAAAI----PLPLLH  341 (758)
T ss_pred             HHHHHHhHHHhCCcccccccccc--ceeeecCCceeEEeeCcchhc----------ccCCEEEEehhhcC----ChHHHH
Confidence            87766644444443222111100  000011122235555555432          11579999999754    234555


Q ss_pred             HHHHhCCCCceEEEEeecCC
Q 015158          204 DIFQLLPPKIQVGVFSATMP  223 (412)
Q Consensus       204 ~i~~~~~~~~~~i~~SAT~~  223 (412)
                      ++....+    .+++|.|..
T Consensus       342 ~l~~~~~----rv~~sTTIh  357 (758)
T COG1444         342 KLLRRFP----RVLFSTTIH  357 (758)
T ss_pred             HHHhhcC----ceEEEeeec
Confidence            6655443    788999975

>CHL00181 cbbX CbbX; Provisional

Probab=96.08  E-value=0.043  Score=48.73  Aligned_cols=21  Identities=33%  Similarity=0.384  Sum_probs=16.9

Q ss_pred             CccEEEECCCCCCchhHhHHH
Q 015158           76 GLDVIQQAQSGTGKTATFCSG   96 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~   96 (412)
                      +.++++.||+|+|||..+-..
T Consensus        59 ~~~ill~G~pGtGKT~lAr~l   79 (287)
T CHL00181         59 GLHMSFTGSPGTGKTTVALKM   79 (287)
T ss_pred             CceEEEECCCCCCHHHHHHHH
Confidence            456899999999999877443

>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=96.07  E-value=0.22  Score=40.51  Aligned_cols=54  Identities=17%  Similarity=0.354  Sum_probs=29.7

Q ss_pred             CCceEEEEeCCchhh-ccCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHh
Q 015158          180 DNIRIFVLDEADEML-SRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKF  233 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~-~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~  233 (412)
                      .+.+++|+|...... +......+..+.........++.+++.-..+..+....+
T Consensus        81 ~~~d~viiDt~g~~~~~~~~l~~l~~l~~~~~~~~~~lVv~~~~~~~~~~~~~~~  135 (173)
T cd03115          81 ENFDVVIVDTAGRLQIDENLMEELKKIKRVVKPDEVLLVVDAMTGQDAVNQAKAF  135 (173)
T ss_pred             CCCCEEEEECcccchhhHHHHHHHHHHHhhcCCCeEEEEEECCCChHHHHHHHHH
Confidence            356889999988642 222234444444444455556777776554444444333

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.

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.05  E-value=0.021  Score=55.97  Aligned_cols=39  Identities=13%  Similarity=0.387  Sum_probs=25.1

Q ss_pred             CCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEe
Q 015158          180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFS  219 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~S  219 (412)
                      ..++++||||+|.+....+ ..+.+.+..-+....+|+.|
T Consensus       123 g~~KV~IIDEvh~Ls~~a~-NaLLKtLEEPP~~~~fIL~T  161 (618)
T PRK14951        123 GRFKVFMIDEVHMLTNTAF-NAMLKTLEEPPEYLKFVLAT  161 (618)
T ss_pred             CCceEEEEEChhhCCHHHH-HHHHHhcccCCCCeEEEEEE
Confidence            4678999999998765543 34445555545555555544

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.02  E-value=0.038  Score=51.67  Aligned_cols=39  Identities=13%  Similarity=0.261  Sum_probs=23.6

Q ss_pred             CCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEe
Q 015158          180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFS  219 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~S  219 (412)
                      ....++|+||+|.+.... ...+.+.+...++...+|+.+
T Consensus       126 ~~~kvvIIdea~~l~~~~-~~~LLk~LEep~~~t~~Il~t  164 (397)
T PRK14955        126 GRYRVYIIDEVHMLSIAA-FNAFLKTLEEPPPHAIFIFAT  164 (397)
T ss_pred             CCeEEEEEeChhhCCHHH-HHHHHHHHhcCCCCeEEEEEe
Confidence            456899999999876543 234444455444455445444

>PRK05986 cob(I)alamin adenolsyltransferase/cobinamide ATP-dependent adenolsyltransferase; Validated

Probab=96.01  E-value=0.045  Score=44.81  Aligned_cols=141  Identities=17%  Similarity=0.219  Sum_probs=73.2

Q ss_pred             cCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHH-HHHHHHHhhcccCcEEEEEEcCcchHHHHHH
Q 015158           75 KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQ-IEKVMRALGDYLGVKVHACVGGTSVREDQRI  153 (412)
Q Consensus        75 ~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  153 (412)
                      ....+.+..++|.|||.+++..++..+..+.   +++++-=.+.-... -...++.+   .++.....  +......   
T Consensus        21 ~~g~v~v~~g~GkGKtt~a~g~a~ra~g~G~---~V~ivQFlKg~~~~GE~~~l~~l---~~v~~~~~--g~~~~~~---   89 (191)
T PRK05986         21 EKGLLIVHTGNGKGKSTAAFGMALRAVGHGK---KVGVVQFIKGAWSTGERNLLEFG---GGVEFHVM--GTGFTWE---   89 (191)
T ss_pred             cCCeEEEECCCCCChHHHHHHHHHHHHHCCC---eEEEEEEecCCCccCHHHHHhcC---CCcEEEEC--CCCCccc---
Confidence            4568899999999999999888888777664   66666533321000 01122222   12322221  1110000   


Q ss_pred             hcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCc--HHHHHHHHHhCCCCceEEEEeecCChHHHH
Q 015158          154 LSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGF--KDQIYDIFQLLPPKIQVGVFSATMPPEALE  228 (412)
Q Consensus       154 ~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~--~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~  228 (412)
                       .....--............ ..+....+++||+||+-...+.++  ...+..++...|+..-+|+..-.+++.+.+
T Consensus        90 -~~~~~e~~~~~~~~~~~a~-~~l~~~~ydlvVLDEi~~Al~~gli~~eevi~~L~~rp~~~evVlTGR~~p~~Lie  164 (191)
T PRK05986         90 -TQDRERDIAAAREGWEEAK-RMLADESYDLVVLDELTYALKYGYLDVEEVLEALNARPGMQHVVITGRGAPRELIE  164 (191)
T ss_pred             -CCCcHHHHHHHHHHHHHHH-HHHhCCCCCEEEEehhhHHHHCCCccHHHHHHHHHcCCCCCEEEEECCCCCHHHHH
Confidence             0000000001111111111 112235789999999998887774  456677777777776655555555554433

>PF05496 RuvB_N: Holliday junction DNA helicase ruvB N-terminus; InterPro: IPR008824 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair

Probab=96.01  E-value=0.019  Score=48.04  Aligned_cols=17  Identities=24%  Similarity=0.233  Sum_probs=14.5

Q ss_pred             ccEEEECCCCCCchhHh
Q 015158           77 LDVIQQAQSGTGKTATF   93 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~   93 (412)
                      .+++++||+|.|||..+
T Consensus        51 ~h~lf~GPPG~GKTTLA   67 (233)
T PF05496_consen   51 DHMLFYGPPGLGKTTLA   67 (233)
T ss_dssp             -EEEEESSTTSSHHHHH
T ss_pred             ceEEEECCCccchhHHH
Confidence            37899999999999765

Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the N-terminal region of the proteins.; GO: 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1IQP_B 3PFI_B 1IXR_C 1HQC_B 1IXS_B.

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.01  E-value=0.027  Score=54.84  Aligned_cols=39  Identities=23%  Similarity=0.376  Sum_probs=27.3

Q ss_pred             CCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEe
Q 015158          180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFS  219 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~S  219 (412)
                      ....++||||+|.+.... ...+.+.+...+.+..+|+.|
T Consensus       117 ~~~KVvIIDEah~Lt~~A-~NALLK~LEEpp~~~~fIL~t  155 (584)
T PRK14952        117 SRYRIFIVDEAHMVTTAG-FNALLKIVEEPPEHLIFIFAT  155 (584)
T ss_pred             CCceEEEEECCCcCCHHH-HHHHHHHHhcCCCCeEEEEEe
Confidence            467899999999876554 445566666666666666666

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.99  E-value=0.033  Score=54.65  Aligned_cols=39  Identities=15%  Similarity=0.384  Sum_probs=27.0

Q ss_pred             CCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEe
Q 015158          180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFS  219 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~S  219 (412)
                      ..++++||||+|.+.... ...+.+.+...+.+..+|+.|
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            467899999999876543 445666666666666666555

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.97  E-value=0.027  Score=52.04  Aligned_cols=39  Identities=10%  Similarity=0.307  Sum_probs=24.2

Q ss_pred             CCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEe
Q 015158          180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFS  219 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~S  219 (412)
                      ....++|+||+|.+.... ...+.+.+...+....+|+.|
T Consensus       118 ~~~kviIIDEa~~l~~~a-~naLLk~lEe~~~~~~fIl~t  156 (363)
T PRK14961        118 SRFKVYLIDEVHMLSRHS-FNALLKTLEEPPQHIKFILAT  156 (363)
T ss_pred             CCceEEEEEChhhcCHHH-HHHHHHHHhcCCCCeEEEEEc
Confidence            356899999999876443 233444555555555555544

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.97  E-value=0.051  Score=51.76  Aligned_cols=19  Identities=32%  Similarity=0.198  Sum_probs=15.5

Q ss_pred             cEEEECCCCCCchhHhHHH
Q 015158           78 DVIQQAQSGTGKTATFCSG   96 (412)
Q Consensus        78 ~~lv~~~tGsGKT~~~~~~   96 (412)
                      ..++.||+|+|||..+-..
T Consensus        38 ~~Lf~GPpGtGKTTlA~~l   56 (472)
T PRK14962         38 AYIFAGPRGTGKTTVARIL   56 (472)
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            3689999999999877543

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=95.97  E-value=0.055  Score=49.03  Aligned_cols=39  Identities=8%  Similarity=0.152  Sum_probs=26.8

Q ss_pred             CceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEe
Q 015158          181 NIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFS  219 (412)
Q Consensus       181 ~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~S  219 (412)
                      ..++||+||+|.+........+..++...+.+.++|+.|
T Consensus       100 ~~~vliiDe~d~l~~~~~~~~L~~~le~~~~~~~~Ilt~  138 (316)
T PHA02544        100 GGKVIIIDEFDRLGLADAQRHLRSFMEAYSKNCSFIITA  138 (316)
T ss_pred             CCeEEEEECcccccCHHHHHHHHHHHHhcCCCceEEEEc
Confidence            457999999998733334556677777766677666544

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

Probab=95.96  E-value=0.026  Score=48.39  Aligned_cols=86  Identities=26%  Similarity=0.382  Sum_probs=63.5

Q ss_pred             CceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCc-chHHHHHHhc-CCCcEEEeChHHHHHHHHcCCCCCCCce
Q 015158          106 VECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGT-SVREDQRILS-SGVHVVVGTPGRVFDMLRRQSLRPDNIR  183 (412)
Q Consensus       106 ~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~-~~~~iii~T~~~l~~~~~~~~~~~~~~~  183 (412)
                      ..+.+||||.+.--+.++.+.++.+... +..+.-+.... ..+++...+. ...+|.|+||+++..+++...+.++++.
T Consensus       125 gsP~~lvvs~SalRa~dl~R~l~~~~~k-~~~v~KLFaKH~Kl~eqv~~L~~~~~~i~vGTP~Rl~kLle~~~L~l~~l~  203 (252)
T PF14617_consen  125 GSPHVLVVSSSALRAADLIRALRSFKGK-DCKVAKLFAKHIKLEEQVKLLKKTRVHIAVGTPGRLSKLLENGALSLSNLK  203 (252)
T ss_pred             CCCEEEEEcchHHHHHHHHHHHHhhccC-CchHHHHHHhhccHHHHHHHHHhCCceEEEeChHHHHHHHHcCCCCcccCe
Confidence            3567999999887888888888887321 22333333333 4444444444 4679999999999999999999999999


Q ss_pred             EEEEeCCch
Q 015158          184 IFVLDEADE  192 (412)
Q Consensus       184 ~iiiDE~h~  192 (412)
                      +||+|--|.
T Consensus       204 ~ivlD~s~~  212 (252)
T PF14617_consen  204 RIVLDWSYL  212 (252)
T ss_pred             EEEEcCCcc
Confidence            999998774

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=95.94  E-value=0.042  Score=52.65  Aligned_cols=20  Identities=20%  Similarity=0.076  Sum_probs=16.3

Q ss_pred             ccEEEECCCCCCchhHhHHH
Q 015158           77 LDVIQQAQSGTGKTATFCSG   96 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~~~   96 (412)
                      +..++.||.|+|||.++-..
T Consensus        44 ~a~Lf~Gp~G~GKTT~Aril   63 (507)
T PRK06645         44 GGYLLTGIRGVGKTTSARII   63 (507)
T ss_pred             ceEEEECCCCCCHHHHHHHH
Confidence            36899999999999887443

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=95.94  E-value=0.1  Score=47.36  Aligned_cols=38  Identities=18%  Similarity=0.327  Sum_probs=25.0

Q ss_pred             CceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEe
Q 015158          181 NIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFS  219 (412)
Q Consensus       181 ~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~S  219 (412)
                      ..++|++||+|.+.... ...+..++...+....+|+.+
T Consensus       102 ~~~vviiDe~~~l~~~~-~~~L~~~le~~~~~~~lIl~~  139 (319)
T PRK00440        102 PFKIIFLDEADNLTSDA-QQALRRTMEMYSQNTRFILSC  139 (319)
T ss_pred             CceEEEEeCcccCCHHH-HHHHHHHHhcCCCCCeEEEEe
Confidence            45799999999875432 345666666666666655544

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=95.93  E-value=0.055  Score=46.87  Aligned_cols=40  Identities=20%  Similarity=0.022  Sum_probs=28.4

Q ss_pred             hcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcC
Q 015158           74 CKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAP  115 (412)
Q Consensus        74 ~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P  115 (412)
                      ..|.-++|.|++|+|||..++..+.......  +.++++++.
T Consensus        11 ~~G~l~lI~G~~G~GKT~~~~~~~~~~~~~~--g~~vly~s~   50 (242)
T cd00984          11 QPGDLIIIAARPSMGKTAFALNIAENIAKKQ--GKPVLFFSL   50 (242)
T ss_pred             CCCeEEEEEeCCCCCHHHHHHHHHHHHHHhC--CCceEEEeC
Confidence            3467789999999999977665555554431  347888874

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.

>COG3972 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=95.91  E-value=0.048  Score=50.55  Aligned_cols=68  Identities=15%  Similarity=0.081  Sum_probs=50.4

Q ss_pred             ChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhh
Q 015158           62 PSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALG  131 (412)
Q Consensus        62 l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~  131 (412)
                      +-..|++|.-..-.|.- .+.+=.|||||...++-+. .+....+..++++.+-|+.|..++.+...+++
T Consensus       163 fD~~Q~kaa~~~~~G~q-rIrGLAGSGKT~~La~Kaa-~lh~knPd~~I~~Tfftk~L~s~~r~lv~~F~  230 (660)
T COG3972         163 FDTDQTKAAFQSGFGKQ-RIRGLAGSGKTELLAHKAA-ELHSKNPDSRIAFTFFTKILASTMRTLVPEFF  230 (660)
T ss_pred             ccchhheeeeecCCchh-hhhcccCCCchhHHHHHHH-HHhcCCCCceEEEEeehHHHHHHHHHHHHHHH
Confidence            44567777766666654 6788999999977544333 45555677899999999999998888777664

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=95.90  E-value=0.015  Score=52.26  Aligned_cols=64  Identities=17%  Similarity=0.273  Sum_probs=40.5

Q ss_pred             HHHHCCCCCChHHHHhhhhh-hhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHH
Q 015158           53 GIYAYGFEKPSAIQQRGIVP-FCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTREL  119 (412)
Q Consensus        53 ~l~~~~~~~l~~~Q~~a~~~-~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L  119 (412)
                      .+...|.  +.+.|.+.+.. +..++++++.++||||||..+ .+++..+....+..+++++-.+.++
T Consensus       126 ~l~~~g~--~~~~~~~~L~~~v~~~~~ilI~G~tGSGKTTll-~aL~~~~~~~~~~~rivtIEd~~El  190 (319)
T PRK13894        126 QYVERGI--MTAAQREAIIAAVRAHRNILVIGGTGSGKTTLV-NAIINEMVIQDPTERVFIIEDTGEI  190 (319)
T ss_pred             HHHhcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHHH-HHHHHhhhhcCCCceEEEEcCCCcc
Confidence            3434444  35667777775 445689999999999999543 4455443222234577777776654

>PF02572 CobA_CobO_BtuR: ATP:corrinoid adenosyltransferase BtuR/CobO/CobP; InterPro: IPR003724 ATP:cob(I)alamin (or ATP:corrinoid) adenosyltransferases (2

Probab=95.89  E-value=0.15  Score=41.02  Aligned_cols=137  Identities=15%  Similarity=0.255  Sum_probs=63.1

Q ss_pred             EEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCC
Q 015158           79 VIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGV  158 (412)
Q Consensus        79 ~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  158 (412)
                      +.|-...|-|||.+++-.++..+.++.   +|+++-=.+.-.  ..-+...+....++.....-.+......    ....
T Consensus         6 i~vytG~GKGKTTAAlGlalRA~G~G~---rV~ivQFlKg~~--~~GE~~~l~~l~~~~~~~~g~~f~~~~~----~~~~   76 (172)
T PF02572_consen    6 IQVYTGDGKGKTTAALGLALRAAGHGM---RVLIVQFLKGGR--YSGELKALKKLPNVEIERFGKGFVWRMN----EEEE   76 (172)
T ss_dssp             EEEEESSSS-HHHHHHHHHHHHHCTT-----EEEEESS--SS----HHHHHHGGGT--EEEE--TT----GG----GHHH
T ss_pred             EEEEeCCCCCchHHHHHHHHHHHhCCC---EEEEEEEecCCC--CcCHHHHHHhCCeEEEEEcCCcccccCC----CcHH
Confidence            556778999999999988888877664   788877555411  1222333322223333222111000000    0000


Q ss_pred             cEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCc--HHHHHHHHHhCCCCceEEEEeecCChHHH
Q 015158          159 HVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGF--KDQIYDIFQLLPPKIQVGVFSATMPPEAL  227 (412)
Q Consensus       159 ~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~--~~~~~~i~~~~~~~~~~i~~SAT~~~~~~  227 (412)
                      +  ....+...+... ..+....+++||+||+-...+.++  ...+..++...|...-+|+..-.+++.+.
T Consensus        77 ~--~~~~~~~~~~a~-~~i~~~~~dlvILDEi~~a~~~gll~~~~v~~~l~~rp~~~evVlTGR~~~~~l~  144 (172)
T PF02572_consen   77 D--RAAAREGLEEAK-EAISSGEYDLVILDEINYAVDYGLLSEEEVLDLLENRPESLEVVLTGRNAPEELI  144 (172)
T ss_dssp             H--HHHHHHHHHHHH-HHTT-TT-SEEEEETHHHHHHTTSS-HHHHHHHHHTS-TT-EEEEE-SS--HHHH
T ss_pred             H--HHHHHHHHHHHH-HHHhCCCCCEEEEcchHHHhHCCCccHHHHHHHHHcCCCCeEEEEECCCCCHHHH
Confidence            1  111111111111 122345789999999998877764  35667777777767765555555554433

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.

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.89  E-value=0.074  Score=51.41  Aligned_cols=39  Identities=8%  Similarity=0.266  Sum_probs=26.9

Q ss_pred             CCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEe
Q 015158          180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFS  219 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~S  219 (412)
                      ....++|+||+|.+.... ...+.+.+...+....+|+.|
T Consensus       118 g~~kViIIDEa~~ls~~a-~naLLK~LEepp~~v~fIL~T  156 (546)
T PRK14957        118 GRYKVYLIDEVHMLSKQS-FNALLKTLEEPPEYVKFILAT  156 (546)
T ss_pred             CCcEEEEEechhhccHHH-HHHHHHHHhcCCCCceEEEEE
Confidence            456899999999876543 445566666666666666655

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=95.88  E-value=0.075  Score=48.98  Aligned_cols=46  Identities=15%  Similarity=0.324  Sum_probs=31.0

Q ss_pred             CceEEEEeCCchhhcc-CcHHHHHHHHHhCCCCc-eEEEEeecCChHH
Q 015158          181 NIRIFVLDEADEMLSR-GFKDQIYDIFQLLPPKI-QVGVFSATMPPEA  226 (412)
Q Consensus       181 ~~~~iiiDE~h~~~~~-~~~~~~~~i~~~~~~~~-~~i~~SAT~~~~~  226 (412)
                      +.+++++|+++.+... .....+..++..+.... ++++.|..+|.++
T Consensus       175 ~~dlllIDDiq~l~gk~~~qeefFh~FN~l~~~~kqIvltsdr~P~~l  222 (408)
T COG0593         175 SLDLLLIDDIQFLAGKERTQEEFFHTFNALLENGKQIVLTSDRPPKEL  222 (408)
T ss_pred             ccCeeeechHhHhcCChhHHHHHHHHHHHHHhcCCEEEEEcCCCchhh
Confidence            5789999999987755 34566777776665544 5666665555443

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=95.82  E-value=0.035  Score=54.41  Aligned_cols=39  Identities=10%  Similarity=0.346  Sum_probs=26.9

Q ss_pred             CCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEe
Q 015158          180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFS  219 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~S  219 (412)
                      ...+++||||+|.+.... ...+.+.+...+..+.+|+.+
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            457899999999876543 345555566666667666655

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=95.80  E-value=0.095  Score=49.72  Aligned_cols=23  Identities=26%  Similarity=0.173  Sum_probs=17.7

Q ss_pred             CccEEEECCCCCCchhHhHHHHH
Q 015158           76 GLDVIQQAQSGTGKTATFCSGIL   98 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~   98 (412)
                      ++-+.+.||||+|||++....+.
T Consensus       256 g~Vi~LvGpnGvGKTTTiaKLA~  278 (484)
T PRK06995        256 GGVFALMGPTGVGKTTTTAKLAA  278 (484)
T ss_pred             CcEEEEECCCCccHHHHHHHHHH
Confidence            45678899999999987755443

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=95.79  E-value=0.034  Score=54.66  Aligned_cols=39  Identities=8%  Similarity=0.288  Sum_probs=26.0

Q ss_pred             CCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEe
Q 015158          180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFS  219 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~S  219 (412)
                      ...+++||||+|.+.... ...+.+.+...+..+.+|+.|
T Consensus       118 gk~KVIIIDEad~Ls~~A-~NALLKtLEEPp~~v~fILaT  156 (709)
T PRK08691        118 GKYKVYIIDEVHMLSKSA-FNAMLKTLEEPPEHVKFILAT  156 (709)
T ss_pred             CCcEEEEEECccccCHHH-HHHHHHHHHhCCCCcEEEEEe
Confidence            357899999999865433 344555666556666666655

>COG4962 CpaF Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]

Probab=95.78  E-value=0.022  Score=50.56  Aligned_cols=58  Identities=16%  Similarity=0.177  Sum_probs=42.0

Q ss_pred             CCCCChHHHHhhhhhhhcCc-cEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHH
Q 015158           58 GFEKPSAIQQRGIVPFCKGL-DVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTREL  119 (412)
Q Consensus        58 ~~~~l~~~Q~~a~~~~~~~~-~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L  119 (412)
                      .|..+++.|...+..+...+ ++++++.||||||+.. -++...+..   ..+++.+-.+.+|
T Consensus       154 ~~gt~~~~~a~~L~~av~~r~NILisGGTGSGKTTlL-Nal~~~i~~---~eRvItiEDtaEL  212 (355)
T COG4962         154 IFGTMIRRAAKFLRRAVGIRCNILISGGTGSGKTTLL-NALSGFIDS---DERVITIEDTAEL  212 (355)
T ss_pred             HcCCcCHHHHHHHHHHHhhceeEEEeCCCCCCHHHHH-HHHHhcCCC---cccEEEEeehhhh
Confidence            45557888888888877765 9999999999999754 333333332   2388888887666

>PRK08939 primosomal protein DnaI; Reviewed

Probab=95.77  E-value=0.11  Score=46.52  Aligned_cols=48  Identities=13%  Similarity=0.040  Sum_probs=27.0

Q ss_pred             CCceEEEEeCCchhhccCcH--HHHHHHHHhC-CCCceEEEEeecCChHHH
Q 015158          180 DNIRIFVLDEADEMLSRGFK--DQIYDIFQLL-PPKIQVGVFSATMPPEAL  227 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~~~~--~~~~~i~~~~-~~~~~~i~~SAT~~~~~~  227 (412)
                      .+.+++|+||...-....+.  ..+..++... ....+.++.|--...++.
T Consensus       216 ~~~dlLiIDDiG~e~~s~~~~~~ll~~Il~~R~~~~~~ti~TSNl~~~el~  266 (306)
T PRK08939        216 KEAPVLMLDDIGAEQMSSWVRDEVLGVILQYRMQEELPTFFTSNFDFDELE  266 (306)
T ss_pred             cCCCEEEEecCCCccccHHHHHHHHHHHHHHHHHCCCeEEEECCCCHHHHH
Confidence            36899999999854322233  2345555433 345556666655544433

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=95.77  E-value=0.021  Score=51.26  Aligned_cols=57  Identities=19%  Similarity=0.268  Sum_probs=38.0

Q ss_pred             ChHHHHhhhhhhh-cCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHH
Q 015158           62 PSAIQQRGIVPFC-KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTREL  119 (412)
Q Consensus        62 l~~~Q~~a~~~~~-~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L  119 (412)
                      +.+.|...+..+. .+.++++.|+||||||... -+++..+....+..+++.+=...+|
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            4566776666644 4678999999999999764 4455554332334577776666665

>PHA00729 NTP-binding motif containing protein

Probab=95.74  E-value=0.13  Score=43.39  Aligned_cols=74  Identities=15%  Similarity=0.269  Sum_probs=36.0

Q ss_pred             cEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhcc-CcH----HHHHHHHHhCCCCceEEEEeecCChHHHHHHHH
Q 015158          159 HVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSR-GFK----DQIYDIFQLLPPKIQVGVFSATMPPEALEITRK  232 (412)
Q Consensus       159 ~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~-~~~----~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~  232 (412)
                      ..++.+.+.+...+..........+++|+||+---... .|.    .....+...+...+.++.++..-+.+....+..
T Consensus        60 ~~~fid~~~Ll~~L~~a~~~~~~~dlLIIDd~G~~~~~~~wh~~~~~~yf~L~~aLrSR~~l~il~~ls~edL~~~Lr~  138 (226)
T PHA00729         60 NSYFFELPDALEKIQDAIDNDYRIPLIIFDDAGIWLSKYVWYEDYMKTFYKIYALIRTRVSAVIFTTPSPEDLAFYLRE  138 (226)
T ss_pred             cEEEEEHHHHHHHHHHHHhcCCCCCEEEEeCCchhhcccchhhhccchHHHHHHHHHhhCcEEEEecCCHHHHHHHHHh
Confidence            46666666665555432111234578999994322211 111    222234444444455666666544455454443

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=95.73  E-value=0.045  Score=49.27  Aligned_cols=138  Identities=8%  Similarity=-0.004  Sum_probs=68.2

Q ss_pred             ChHHHHhhhhhhhc----C---ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccc
Q 015158           62 PSAIQQRGIVPFCK----G---LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYL  134 (412)
Q Consensus        62 l~~~Q~~a~~~~~~----~---~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~  134 (412)
                      ++|||...+..+..    |   .-.++.||.|.||+..+...+...+........   -|..       .+.++.+....
T Consensus         3 ~yPW~~~~~~~l~~~~~~~rl~HA~Lf~G~~G~GK~~lA~~~A~~llC~~~~~~~---~Cg~-------C~sC~~~~~g~   72 (325)
T PRK06871          3 LYPWLQPTYQQITQAFQQGLGHHALLFKADSGLGTEQLIRALAQWLMCQTPQGDQ---PCGQ-------CHSCHLFQAGN   72 (325)
T ss_pred             CCcchHHHHHHHHHHHHcCCcceeEEeECCCCCCHHHHHHHHHHHHcCCCCCCCC---CCCC-------CHHHHHHhcCC
Confidence            46777777777653    3   346789999999998765444333322211100   1111       12233332222


Q ss_pred             CcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCCCCce
Q 015158          135 GVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQ  214 (412)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~  214 (412)
                      .-.+..+....           +..|-|-....+.+.+.... .....+++|+|++|.+.... ...+.+.+..-|++..
T Consensus        73 HPD~~~i~p~~-----------~~~I~id~iR~l~~~~~~~~-~~g~~KV~iI~~a~~m~~~A-aNaLLKtLEEPp~~~~  139 (325)
T PRK06871         73 HPDFHILEPID-----------NKDIGVDQVREINEKVSQHA-QQGGNKVVYIQGAERLTEAA-ANALLKTLEEPRPNTY  139 (325)
T ss_pred             CCCEEEEcccc-----------CCCCCHHHHHHHHHHHhhcc-ccCCceEEEEechhhhCHHH-HHHHHHHhcCCCCCeE
Confidence            22222222110           01121222222222222222 22467899999999876554 5666677776666665


Q ss_pred             EEEEeecC
Q 015158          215 VGVFSATM  222 (412)
Q Consensus       215 ~i~~SAT~  222 (412)
                      ++++|..+
T Consensus       140 fiL~t~~~  147 (325)
T PRK06871        140 FLLQADLS  147 (325)
T ss_pred             EEEEECCh
Confidence            55555443

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=95.69  E-value=0.031  Score=50.99  Aligned_cols=30  Identities=23%  Similarity=0.262  Sum_probs=22.0

Q ss_pred             hhcCccEEEECCCCCCchhHhHHHHHHhhcc
Q 015158           73 FCKGLDVIQQAQSGTGKTATFCSGILQQLDY  103 (412)
Q Consensus        73 ~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~  103 (412)
                      +-+|+..+|.+|.|+|||..+ ..+++.+..
T Consensus       166 IGkGQR~lIvgppGvGKTTLa-K~Ian~I~~  195 (416)
T PRK09376        166 IGKGQRGLIVAPPKAGKTVLL-QNIANSITT  195 (416)
T ss_pred             cccCceEEEeCCCCCChhHHH-HHHHHHHHh
Confidence            336899999999999999654 345555544

>TIGR00767 rho transcription termination factor Rho

Probab=95.69  E-value=0.034  Score=50.99  Aligned_cols=31  Identities=29%  Similarity=0.309  Sum_probs=22.6

Q ss_pred             hhhcCccEEEECCCCCCchhHhHHHHHHhhcc
Q 015158           72 PFCKGLDVIQQAQSGTGKTATFCSGILQQLDY  103 (412)
Q Consensus        72 ~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~  103 (412)
                      .+-.|+.++|.+|+|+|||..+. .+...+..
T Consensus       164 pig~Gq~~~IvG~~g~GKTtL~~-~i~~~I~~  194 (415)
T TIGR00767       164 PIGKGQRGLIVAPPKAGKTVLLQ-KIAQAITR  194 (415)
T ss_pred             EeCCCCEEEEECCCCCChhHHHH-HHHHhhcc
Confidence            35578999999999999997543 35544443

Members of this family differ in the specificity of RNA binding.

>TIGR00708 cobA cob(I)alamin adenosyltransferase

Probab=95.65  E-value=0.15  Score=41.16  Aligned_cols=135  Identities=18%  Similarity=0.247  Sum_probs=68.9

Q ss_pred             cEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHH---HHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHh
Q 015158           78 DVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTREL---AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL  154 (412)
Q Consensus        78 ~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L---~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  154 (412)
                      -+.+..++|.|||.+++..++.....+.   +++++-=.+.-   .+  ...+..+    ++.+.....+.....     
T Consensus         7 li~v~~g~GkGKtt~a~g~a~ra~~~g~---~v~ivQFlKg~~~~GE--~~~l~~~----~~~~~~~g~g~~~~~-----   72 (173)
T TIGR00708         7 IIIVHTGNGKGKTTAAFGMALRALGHGK---KVGVIQFIKGAWPNGE--RAAFEPH----GVEFQVMGTGFTWET-----   72 (173)
T ss_pred             EEEEECCCCCChHHHHHHHHHHHHHCCC---eEEEEEEecCCcccCh--HHHHHhc----CcEEEECCCCCeecC-----
Confidence            4677889999999999888887776654   66665322211   11  1112221    222222211100000     


Q ss_pred             cCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCc--HHHHHHHHHhCCCCceEEEEeecCChHHHH
Q 015158          155 SSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGF--KDQIYDIFQLLPPKIQVGVFSATMPPEALE  228 (412)
Q Consensus       155 ~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~--~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~  228 (412)
                       .+..--............ ..+....+++||+||+-...+.++  ...+..++...|+...+|+..-.+++.+.+
T Consensus        73 -~~~~~~~~~~~~~~~~a~-~~l~~~~~DlvVLDEi~~A~~~gli~~~~v~~lL~~rp~~~evVlTGR~~p~~l~e  146 (173)
T TIGR00708        73 -QNREADTAIAKAAWQHAK-EMLADPELDLVLLDELTYALKYGYLDVEEVVEALQERPGHQHVIITGRGCPQDLLE  146 (173)
T ss_pred             -CCcHHHHHHHHHHHHHHH-HHHhcCCCCEEEehhhHHHHHCCCcCHHHHHHHHHhCCCCCEEEEECCCCCHHHHH
Confidence             000000000111111111 112235789999999998777663  356667777777777666665556554443

Alternate name: corrinoid adenosyltransferase.

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.65  E-value=0.054  Score=52.52  Aligned_cols=39  Identities=8%  Similarity=0.298  Sum_probs=26.4

Q ss_pred             CCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEe
Q 015158          180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFS  219 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~S  219 (412)
                      ..++++||||+|.+.... ...+.+.+...+....+|+.|
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            457899999999876544 334555555555666666655

>PRK13342 recombination factor protein RarA; Reviewed

Probab=95.64  E-value=0.061  Score=50.70  Aligned_cols=18  Identities=33%  Similarity=0.309  Sum_probs=15.3

Q ss_pred             ccEEEECCCCCCchhHhH
Q 015158           77 LDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~   94 (412)
                      .++++.||+|+|||..+-
T Consensus        37 ~~ilL~GppGtGKTtLA~   54 (413)
T PRK13342         37 SSMILWGPPGTGKTTLAR   54 (413)
T ss_pred             ceEEEECCCCCCHHHHHH
Confidence            378999999999997764

>PF00004 AAA: ATPase family associated with various cellular activities (AAA); InterPro: IPR003959 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport

Probab=95.63  E-value=0.01  Score=45.78  Aligned_cols=16  Identities=31%  Similarity=0.468  Sum_probs=13.5

Q ss_pred             EEEECCCCCCchhHhH
Q 015158           79 VIQQAQSGTGKTATFC   94 (412)
Q Consensus        79 ~lv~~~tGsGKT~~~~   94 (412)
                      +++.||+|+|||..+-
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            5789999999997653

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 ....

>PRK05580 primosome assembly protein PriA; Validated

Probab=95.62  E-value=0.15  Score=51.26  Aligned_cols=77  Identities=17%  Similarity=0.223  Sum_probs=64.2

Q ss_pred             CCcEEEEEcchhHHHHHHHHHhcC-CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccC
Q 015158          278 ITQSVIFVNTRRKVDWLTDKMRSR-DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDL  355 (412)
Q Consensus       278 ~~k~lif~~~~~~~~~~~~~L~~~-~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~  355 (412)
                      +.++||.+++++.+.++.+.|++. +..+..+||+++..+|.+.+....+|+.+|+|+|.... -..+.++..+|+.+.
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            468999999999999999999874 67899999999999999999999999999999997332 245667888876653

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=95.61  E-value=0.047  Score=50.62  Aligned_cols=18  Identities=39%  Similarity=0.431  Sum_probs=15.5

Q ss_pred             ccEEEECCCCCCchhHhH
Q 015158           77 LDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~   94 (412)
                      .+++|.||+|+|||.+.-
T Consensus        41 ~~i~I~G~~GtGKT~l~~   58 (365)
T TIGR02928        41 SNVFIYGKTGTGKTAVTK   58 (365)
T ss_pred             CcEEEECCCCCCHHHHHH
Confidence            579999999999997653

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.

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=95.59  E-value=0.036  Score=53.78  Aligned_cols=38  Identities=11%  Similarity=0.286  Sum_probs=24.4

Q ss_pred             CceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEe
Q 015158          181 NIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFS  219 (412)
Q Consensus       181 ~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~S  219 (412)
                      ..+++|+||+|.+.... ...+.+.+...+....+|++|
T Consensus       119 ~~KVIIIDEad~Lt~~A-~NaLLKtLEEPp~~tvfIL~T  156 (605)
T PRK05896        119 KYKVYIIDEAHMLSTSA-WNALLKTLEEPPKHVVFIFAT  156 (605)
T ss_pred             CcEEEEEechHhCCHHH-HHHHHHHHHhCCCcEEEEEEC
Confidence            46799999999875433 345555556555555555555

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=95.57  E-value=0.1  Score=52.48  Aligned_cols=79  Identities=19%  Similarity=0.287  Sum_probs=66.5

Q ss_pred             CCCcEEEEEcchhHHHHHHHHHhc----CCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcC-CCcCCCCCCCCCEEE
Q 015158          277 AITQSVIFVNTRRKVDWLTDKMRS----RDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTD-LLARGIDVQQVSLVI  351 (412)
Q Consensus       277 ~~~k~lif~~~~~~~~~~~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~-~~~~G~d~~~~~~vi  351 (412)
                      .+.++++.+|++.-|.+.++.+++    .+..+..++|+++..+|..++....+|+.+|+|+|. .+...+.++++..||
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            346899999999988877777654    468999999999999999999999999999999997 556677888888888


Q ss_pred             EccC
Q 015158          352 NYDL  355 (412)
Q Consensus       352 ~~~~  355 (412)
                      +.+.
T Consensus       389 IDE~  392 (681)
T PRK10917        389 IDEQ  392 (681)
T ss_pred             Eech
Confidence            6543

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.57  E-value=0.06  Score=52.95  Aligned_cols=39  Identities=13%  Similarity=0.289  Sum_probs=25.1

Q ss_pred             CCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEe
Q 015158          180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFS  219 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~S  219 (412)
                      ...+++||||+|.+.... ...+.+.+...+....+|+++
T Consensus       126 ~~~KVvIIdEad~Lt~~a-~naLLK~LEePp~~tv~IL~t  164 (620)
T PRK14954        126 GRYRVYIIDEVHMLSTAA-FNAFLKTLEEPPPHAIFIFAT  164 (620)
T ss_pred             CCCEEEEEeChhhcCHHH-HHHHHHHHhCCCCCeEEEEEe
Confidence            457899999999876543 344555555555555555555

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=95.56  E-value=0.057  Score=48.22  Aligned_cols=56  Identities=20%  Similarity=0.284  Sum_probs=36.6

Q ss_pred             hHHHHhhhhh-hhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHH
Q 015158           63 SAIQQRGIVP-FCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTREL  119 (412)
Q Consensus        63 ~~~Q~~a~~~-~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L  119 (412)
                      .+.|...+.. +..++++++.++||||||..+ .+++..+....+..+++.+-...++
T Consensus       118 ~~~~~~~L~~~v~~~~~ilI~G~tGSGKTTll-~al~~~i~~~~~~~ri~tiEd~~El  174 (299)
T TIGR02782       118 TAAQRDVLREAVLARKNILVVGGTGSGKTTLA-NALLAEIAKNDPTDRVVIIEDTREL  174 (299)
T ss_pred             CHHHHHHHHHHHHcCCeEEEECCCCCCHHHHH-HHHHHHhhccCCCceEEEECCchhh
Confidence            3445555555 444679999999999999765 4455555432234578777776665

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.

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily

Probab=95.56  E-value=0.04  Score=48.58  Aligned_cols=33  Identities=21%  Similarity=0.261  Sum_probs=22.9

Q ss_pred             ChHHHHhhhhhhh----cC-ccEEEECCCCCCchhHhH
Q 015158           62 PSAIQQRGIVPFC----KG-LDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        62 l~~~Q~~a~~~~~----~~-~~~lv~~~tGsGKT~~~~   94 (412)
                      +.+.+++++..+.    .+ ..+++.||+|+|||+.+-
T Consensus        24 ~~~~~~~~~~~l~~~~~~~~~~~~l~G~~G~GKTtl~~   61 (269)
T TIGR03015        24 PSKGHKRAMAYLEYGLSQREGFILITGEVGAGKTTLIR   61 (269)
T ss_pred             CCHHHHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHHH
Confidence            4555666666553    22 357899999999997764

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.

>PRK10867 signal recognition particle protein; Provisional

Probab=95.55  E-value=0.28  Score=46.09  Aligned_cols=35  Identities=20%  Similarity=0.114  Sum_probs=21.8

Q ss_pred             cEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEc
Q 015158           78 DVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLA  114 (412)
Q Consensus        78 ~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~  114 (412)
                      -+++++++|+|||+++.-.+......  .+.+++++.
T Consensus       102 vI~~vG~~GsGKTTtaakLA~~l~~~--~G~kV~lV~  136 (433)
T PRK10867        102 VIMMVGLQGAGKTTTAGKLAKYLKKK--KKKKVLLVA  136 (433)
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHh--cCCcEEEEE
Confidence            46789999999998765544433222  123555544

>PRK04195 replication factor C large subunit; Provisional

Probab=95.51  E-value=0.11  Score=50.17  Aligned_cols=19  Identities=21%  Similarity=0.240  Sum_probs=16.0

Q ss_pred             CccEEEECCCCCCchhHhH
Q 015158           76 GLDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~   94 (412)
                      .+.+++.||+|+|||..+-
T Consensus        39 ~~~lLL~GppG~GKTtla~   57 (482)
T PRK04195         39 KKALLLYGPPGVGKTSLAH   57 (482)
T ss_pred             CCeEEEECCCCCCHHHHHH
Confidence            4578999999999997763

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.50  E-value=0.05  Score=53.13  Aligned_cols=22  Identities=18%  Similarity=0.025  Sum_probs=17.0

Q ss_pred             ccEEEECCCCCCchhHhHHHHH
Q 015158           77 LDVIQQAQSGTGKTATFCSGIL   98 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~~~~~   98 (412)
                      ...|+.+|.|+|||.++...+.
T Consensus        39 ha~Lf~GPpG~GKTtiArilAk   60 (624)
T PRK14959         39 PAYLFSGTRGVGKTTIARIFAK   60 (624)
T ss_pred             ceEEEECCCCCCHHHHHHHHHH
Confidence            3578899999999988754443

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=95.46  E-value=0.072  Score=52.09  Aligned_cols=37  Identities=8%  Similarity=0.292  Sum_probs=22.1

Q ss_pred             CCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEE
Q 015158          180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGV  217 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~  217 (412)
                      ....++|+||+|.+.... ...+.+.+...+.+..+|+
T Consensus       118 ~~~kViIIDE~~~Lt~~a-~naLLKtLEepp~~~ifIl  154 (559)
T PRK05563        118 AKYKVYIIDEVHMLSTGA-FNALLKTLEEPPAHVIFIL  154 (559)
T ss_pred             CCeEEEEEECcccCCHHH-HHHHHHHhcCCCCCeEEEE
Confidence            457899999999876543 3344444444444443333

>PRK11823 DNA repair protein RadA; Provisional

Probab=95.45  E-value=0.092  Score=49.82  Aligned_cols=51  Identities=20%  Similarity=0.169  Sum_probs=33.7

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRAL  130 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~  130 (412)
                      |.-+++.+++|+|||...+..+......   +.+++|+.-.. -..|.......+
T Consensus        80 Gs~~lI~G~pG~GKTtL~lq~a~~~a~~---g~~vlYvs~Ee-s~~qi~~ra~rl  130 (446)
T PRK11823         80 GSVVLIGGDPGIGKSTLLLQVAARLAAA---GGKVLYVSGEE-SASQIKLRAERL  130 (446)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHhc---CCeEEEEEccc-cHHHHHHHHHHc
Confidence            4567899999999998766555544322   34788887543 345555555554

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=95.45  E-value=0.44  Score=42.99  Aligned_cols=54  Identities=20%  Similarity=0.407  Sum_probs=32.4

Q ss_pred             CCceEEEEeCCchhhcc-CcHHHHHHHHHhC------CCCceEEEEeecCChHHHHHHHHh
Q 015158          180 DNIRIFVLDEADEMLSR-GFKDQIYDIFQLL------PPKIQVGVFSATMPPEALEITRKF  233 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~-~~~~~~~~i~~~~------~~~~~~i~~SAT~~~~~~~~~~~~  233 (412)
                      +++++||+|=+-+.... .....+..+...+      .+...++.++||...+.......+
T Consensus       195 ~~~D~ViIDTaGr~~~~~~l~~eL~~~~~v~~~~~~~~p~~~~LVl~a~~g~~~~~~a~~f  255 (318)
T PRK10416        195 RGIDVLIIDTAGRLHNKTNLMEELKKIKRVIKKADPDAPHEVLLVLDATTGQNALSQAKAF  255 (318)
T ss_pred             CCCCEEEEeCCCCCcCCHHHHHHHHHHHHHHhhhcCCCCceEEEEEECCCChHHHHHHHHH
Confidence            46899999988764322 2234455544322      244568999999766544444443

>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed

Probab=95.43  E-value=0.077  Score=53.29  Aligned_cols=18  Identities=28%  Similarity=0.242  Sum_probs=15.4

Q ss_pred             ccEEEECCCCCCchhHhH
Q 015158           77 LDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~   94 (412)
                      .++++.||+|+|||..+-
T Consensus        53 ~slLL~GPpGtGKTTLA~   70 (725)
T PRK13341         53 GSLILYGPPGVGKTTLAR   70 (725)
T ss_pred             ceEEEECCCCCCHHHHHH
Confidence            478999999999997763

>cd01128 rho_factor Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase

Probab=95.38  E-value=0.039  Score=47.68  Aligned_cols=32  Identities=25%  Similarity=0.324  Sum_probs=23.1

Q ss_pred             hhhhcCccEEEECCCCCCchhHhHHHHHHhhcc
Q 015158           71 VPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY  103 (412)
Q Consensus        71 ~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~  103 (412)
                      -.+..|+.+++.+|.|+|||..+ -.+++.+..
T Consensus        11 ~~i~~Gqr~~I~G~~G~GKTTLl-r~I~n~l~~   42 (249)
T cd01128          11 APIGKGQRGLIVAPPKAGKTTLL-QSIANAITK   42 (249)
T ss_pred             cccCCCCEEEEECCCCCCHHHHH-HHHHhcccc
Confidence            34567899999999999999643 445544443

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.

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=95.37  E-value=0.066  Score=59.86  Aligned_cols=61  Identities=26%  Similarity=0.280  Sum_probs=43.0

Q ss_pred             CChHHHHhhhhhhhcC--ccEEEECCCCCCchhHhH---HHHHHhhccCCCceeEEEEcCCHHHHHHH
Q 015158           61 KPSAIQQRGIVPFCKG--LDVIQQAQSGTGKTATFC---SGILQQLDYGLVECQALVLAPTRELAQQI  123 (412)
Q Consensus        61 ~l~~~Q~~a~~~~~~~--~~~lv~~~tGsGKT~~~~---~~~~~~~~~~~~~~~~lil~P~~~L~~q~  123 (412)
                      .+++.|+.|+..++.+  +-++|.++.|+|||...-   -++......  .+.+++.++||..-+.++
T Consensus      1019 ~Lt~~Q~~Ai~~il~~~~~~~~i~G~AGtGKTt~l~~~~~~i~~~~~~--~g~~v~glApT~~Aa~~L 1084 (1960)
T TIGR02760      1019 RLTHGQKQAIHLIISTKDRFVAVQGLAGVGKTTMLESRYKPVLQAFES--EQLQVIGLAPTHEAVGEL 1084 (1960)
T ss_pred             CCCHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHhHHHHHHHHHHHHHh--cCCeEEEEeChHHHHHHH
Confidence            4899999999998865  556889999999997652   222222221  235788899987655444

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.

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=95.35  E-value=0.11  Score=45.70  Aligned_cols=17  Identities=24%  Similarity=0.347  Sum_probs=15.1

Q ss_pred             ccEEEECCCCCCchhHh
Q 015158           77 LDVIQQAQSGTGKTATF   93 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~   93 (412)
                      .+.+++|++|-|||...
T Consensus        62 p~lLivG~snnGKT~Ii   78 (302)
T PF05621_consen   62 PNLLIVGDSNNGKTMII   78 (302)
T ss_pred             CceEEecCCCCcHHHHH
Confidence            47999999999999865

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>COG3973 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=95.33  E-value=0.054  Score=51.55  Aligned_cols=82  Identities=26%  Similarity=0.161  Sum_probs=52.9

Q ss_pred             HHHHHHHHHCCCCCC-------hHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCC---CceeEEEEcCCH
Q 015158           48 ENLLRGIYAYGFEKP-------SAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGL---VECQALVLAPTR  117 (412)
Q Consensus        48 ~~~~~~l~~~~~~~l-------~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~---~~~~~lil~P~~  117 (412)
                      +-+...|+...-..+       .+-|-+++.. -.++-.+|+|..|||||.+++--++..+...+   .++.++++.|++
T Consensus       192 EvL~~~Lek~ss~~mrdIV~TIQkEQneIIR~-ek~~ilVVQGaAGSGKTtiALHRvAyLlY~~R~~l~~k~vlvl~PN~  270 (747)
T COG3973         192 EVLQRVLEKNSSAKMRDIVETIQKEQNEIIRF-EKNKILVVQGAAGSGKTTIALHRVAYLLYGYRGPLQAKPVLVLGPNR  270 (747)
T ss_pred             HHHHHHHHhccchhHHHHHHHhhHhHHHHHhc-cCCCeEEEecCCCCCchhHHHHHHHHHHhccccccccCceEEEcCcH
Confidence            344556665443333       3345554422 23456789999999999998776665554322   234599999999


Q ss_pred             HHHHHHHHHHHHh
Q 015158          118 ELAQQIEKVMRAL  130 (412)
Q Consensus       118 ~L~~q~~~~~~~~  130 (412)
                      .+.+-..+.+=++
T Consensus       271 vFleYis~VLPeL  283 (747)
T COG3973         271 VFLEYISRVLPEL  283 (747)
T ss_pred             HHHHHHHHhchhh
Confidence            9887777766555

>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif

Probab=95.30  E-value=0.029  Score=45.92  Aligned_cols=47  Identities=21%  Similarity=0.270  Sum_probs=27.0

Q ss_pred             hhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHH
Q 015158           72 PFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQ  122 (412)
Q Consensus        72 ~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q  122 (412)
                      .+.+++++++.|++|+|||..+...+...+..+   ..++++ +...|...
T Consensus        43 ~~~~~~~l~l~G~~G~GKThLa~ai~~~~~~~g---~~v~f~-~~~~L~~~   89 (178)
T PF01695_consen   43 FIENGENLILYGPPGTGKTHLAVAIANEAIRKG---YSVLFI-TASDLLDE   89 (178)
T ss_dssp             S-SC--EEEEEESTTSSHHHHHHHHHHHHHHTT-----EEEE-EHHHHHHH
T ss_pred             CcccCeEEEEEhhHhHHHHHHHHHHHHHhccCC---cceeEe-ecCceecc
Confidence            344578999999999999987655444444433   356554 43444443

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.

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=95.30  E-value=0.11  Score=49.99  Aligned_cols=39  Identities=13%  Similarity=0.318  Sum_probs=27.2

Q ss_pred             CCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEe
Q 015158          180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFS  219 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~S  219 (412)
                      ..+.++|+||+|.+.... ...+.+.+...++...+|+.+
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            467899999999876543 445566666666677666655

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=95.29  E-value=0.28  Score=42.21  Aligned_cols=51  Identities=16%  Similarity=0.175  Sum_probs=34.7

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRAL  130 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~  130 (412)
                      |.-+++.+++|+|||..+...+...+..   +.+++|+.-... .++..+.+..+
T Consensus        25 g~~~~i~G~~GsGKt~l~~~~~~~~~~~---g~~~~y~~~e~~-~~~~~~~~~~~   75 (234)
T PRK06067         25 PSLILIEGDHGTGKSVLSQQFVYGALKQ---GKKVYVITTENT-SKSYLKQMESV   75 (234)
T ss_pred             CcEEEEECCCCCChHHHHHHHHHHHHhC---CCEEEEEEcCCC-HHHHHHHHHHC
Confidence            5678899999999997776666555443   347888776433 34566666555

>PF05729 NACHT: NACHT domain

Probab=95.29  E-value=0.13  Score=41.32  Aligned_cols=21  Identities=14%  Similarity=0.158  Sum_probs=15.9

Q ss_pred             cEEEECCCCCCchhHhHHHHH
Q 015158           78 DVIQQAQSGTGKTATFCSGIL   98 (412)
Q Consensus        78 ~~lv~~~tGsGKT~~~~~~~~   98 (412)
                      -++|.|++|+|||..+...+.
T Consensus         2 ~l~I~G~~G~GKStll~~~~~   22 (166)
T PF05729_consen    2 VLWISGEPGSGKSTLLRKLAQ   22 (166)
T ss_pred             EEEEECCCCCChHHHHHHHHH
Confidence            468999999999977644333

>PRK12608 transcription termination factor Rho; Provisional

Probab=95.27  E-value=0.13  Score=46.81  Aligned_cols=36  Identities=22%  Similarity=0.166  Sum_probs=24.8

Q ss_pred             Hhhhhhhh---cCccEEEECCCCCCchhHhHHHHHHhhcc
Q 015158           67 QRGIVPFC---KGLDVIQQAQSGTGKTATFCSGILQQLDY  103 (412)
Q Consensus        67 ~~a~~~~~---~~~~~lv~~~tGsGKT~~~~~~~~~~~~~  103 (412)
                      .+++..+.   +|++.+|.+|.|+|||...-. +++.+..
T Consensus       121 ~RvID~l~PiGkGQR~LIvG~pGtGKTTLl~~-la~~i~~  159 (380)
T PRK12608        121 MRVVDLVAPIGKGQRGLIVAPPRAGKTVLLQQ-IAAAVAA  159 (380)
T ss_pred             HhhhhheeecCCCceEEEECCCCCCHHHHHHH-HHHHHHh
Confidence            34555544   689999999999999977543 4444433

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=95.25  E-value=0.074  Score=44.05  Aligned_cols=39  Identities=13%  Similarity=0.353  Sum_probs=24.2

Q ss_pred             CCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEe
Q 015158          180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFS  219 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~S  219 (412)
                      ....+||+||+|.+.... ...+...+...++...+|+++
T Consensus        95 ~~~kviiide~~~l~~~~-~~~Ll~~le~~~~~~~~il~~  133 (188)
T TIGR00678        95 SGRRVVIIEDAERMNEAA-ANALLKTLEEPPPNTLFILIT  133 (188)
T ss_pred             CCeEEEEEechhhhCHHH-HHHHHHHhcCCCCCeEEEEEE
Confidence            456899999999876543 344555555544445444443

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.

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=95.24  E-value=0.13  Score=47.34  Aligned_cols=51  Identities=16%  Similarity=0.182  Sum_probs=32.8

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRAL  130 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~  130 (412)
                      |.-+++.+++|+|||..++..+......   +.+++|+.-... ..|.......+
T Consensus        82 GslvLI~G~pG~GKStLllq~a~~~a~~---g~~VlYvs~EEs-~~qi~~Ra~rl  132 (372)
T cd01121          82 GSVILIGGDPGIGKSTLLLQVAARLAKR---GGKVLYVSGEES-PEQIKLRADRL  132 (372)
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHhc---CCeEEEEECCcC-HHHHHHHHHHc
Confidence            4667899999999998776555444332   247888876433 34555444444

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.

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=95.24  E-value=0.084  Score=47.40  Aligned_cols=138  Identities=11%  Similarity=0.058  Sum_probs=69.7

Q ss_pred             ChHHHHhhhhhhhc----C---ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccc
Q 015158           62 PSAIQQRGIVPFCK----G---LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYL  134 (412)
Q Consensus        62 l~~~Q~~a~~~~~~----~---~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~  134 (412)
                      ++|||...+..+.+    +   .-.++.||.|.||+..+...+...+... ....   -|..       ...+..+....
T Consensus         4 ~yPWl~~~~~~l~~~~~~~rl~hA~L~~G~~G~Gk~~lA~~~a~~llC~~-~~~~---~Cg~-------C~sC~~~~~g~   72 (319)
T PRK06090          4 DYPWLVPVWQNWKAGLDAGRIPGALLLQSDEGLGVESLVELFSRALLCQN-YQSE---ACGF-------CHSCELMQSGN   72 (319)
T ss_pred             CcccHHHHHHHHHHHHHcCCcceeEeeECCCCCCHHHHHHHHHHHHcCCC-CCCC---CCCC-------CHHHHHHHcCC
Confidence            67888888777663    3   3578999999999977644333333222 1111   1111       12222222222


Q ss_pred             CcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCCCCce
Q 015158          135 GVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQ  214 (412)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~  214 (412)
                      .-.+..+.....          +..|-|-....+...+... ......+++|||+||.+.... ...+.+.++.-|++..
T Consensus        73 HPD~~~i~p~~~----------~~~I~vdqiR~l~~~~~~~-~~~~~~kV~iI~~ae~m~~~A-aNaLLKtLEEPp~~t~  140 (319)
T PRK06090         73 HPDLHVIKPEKE----------GKSITVEQIRQCNRLAQES-SQLNGYRLFVIEPADAMNESA-SNALLKTLEEPAPNCL  140 (319)
T ss_pred             CCCEEEEecCcC----------CCcCCHHHHHHHHHHHhhC-cccCCceEEEecchhhhCHHH-HHHHHHHhcCCCCCeE
Confidence            222222221100          0112222222222222211 123567899999999876443 5666677776666666


Q ss_pred             EEEEeecC
Q 015158          215 VGVFSATM  222 (412)
Q Consensus       215 ~i~~SAT~  222 (412)
                      +|++|..+
T Consensus       141 fiL~t~~~  148 (319)
T PRK06090        141 FLLVTHNQ  148 (319)
T ss_pred             EEEEECCh
Confidence            66666554

>TIGR00595 priA primosomal protein N'

Probab=95.23  E-value=0.15  Score=49.21  Aligned_cols=77  Identities=14%  Similarity=0.192  Sum_probs=63.4

Q ss_pred             CCcEEEEEcchhHHHHHHHHHhcC-CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccC
Q 015158          278 ITQSVIFVNTRRKVDWLTDKMRSR-DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDL  355 (412)
Q Consensus       278 ~~k~lif~~~~~~~~~~~~~L~~~-~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~  355 (412)
                      ++++|+.+|++.-+.++.+.|++. +..+..+||+++..+|.+.+.+..+|+.+|+|+|...- =..++++..||+.+.
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            468999999999999999999864 66789999999999999999999999999999997322 134667787876553

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).

>PRK06620 hypothetical protein; Validated

Probab=95.23  E-value=0.041  Score=46.51  Aligned_cols=39  Identities=10%  Similarity=0.336  Sum_probs=23.5

Q ss_pred             CceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEeecCC
Q 015158          181 NIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMP  223 (412)
Q Consensus       181 ~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~  223 (412)
                      ..+++++||+|.+.    ...+..+++.+......+++|+|-+
T Consensus        85 ~~d~lliDdi~~~~----~~~lf~l~N~~~e~g~~ilits~~~  123 (214)
T PRK06620         85 KYNAFIIEDIENWQ----EPALLHIFNIINEKQKYLLLTSSDK  123 (214)
T ss_pred             cCCEEEEeccccch----HHHHHHHHHHHHhcCCEEEEEcCCC
Confidence            34789999999542    1355566555544444566666543

>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]

Probab=95.22  E-value=0.036  Score=57.01  Aligned_cols=99  Identities=15%  Similarity=0.131  Sum_probs=74.0

Q ss_pred             CCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCc-EEEEcCCCcCCCCCCCCCEEEEccC
Q 015158          277 AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSR-VLITTDLLARGIDVQQVSLVINYDL  355 (412)
Q Consensus       277 ~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~-vlv~t~~~~~G~d~~~~~~vi~~~~  355 (412)
                      ...++|+|.........+...+.-.++......+.-   +...-+..|++  ++ .++-++..+.|+|+-.+.||+..++
T Consensus      1220 ~qekvIvfsqws~~ldV~e~~~~~N~I~~~~~~~t~---d~~dc~~~fk~--I~clll~~~~~~~GLNL~eA~Hvfl~eP 1294 (1394)
T KOG0298|consen 1220 EQEKVIVFSQWSVVLDVKELRYLMNLIKKQLDGETE---DFDDCIICFKS--IDCLLLFVSKGSKGLNLIEATHVFLVEP 1294 (1394)
T ss_pred             cCceEEEEEehHHHHHHHHHHHHhhhhHhhhccCCc---chhhhhhhccc--ceEEEEEeccCcccccHHhhhhhheecc
Confidence            447899999988777777777766665554443322   22334444544  54 4566889999999999999999999


Q ss_pred             CCChhhHHHhhhhcccCCCCceEEE
Q 015158          356 PTQPENYLHRIGRSGRFGRKGVAIN  380 (412)
Q Consensus       356 ~~s~~~~~Q~~GR~~R~g~~g~~~~  380 (412)
                      -.++..-.|++||+.|.|+.-...+
T Consensus      1295 iLN~~~E~QAigRvhRiGQ~~pT~V 1319 (1394)
T KOG0298|consen 1295 ILNPGDEAQAIGRVHRIGQKRPTFV 1319 (1394)
T ss_pred             ccCchHHHhhhhhhhhcccccchhh
Confidence            9999999999999999998755443

>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=95.19  E-value=0.079  Score=46.19  Aligned_cols=41  Identities=10%  Similarity=0.202  Sum_probs=25.2

Q ss_pred             cEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHH
Q 015158           78 DVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTREL  119 (412)
Q Consensus        78 ~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L  119 (412)
                      -++|-||||+||+-.. -.++..-.-......|++|+|.+.-
T Consensus        89 I~~VYGPTG~GKSqLl-RNLis~~lI~P~PETVfFItP~~~m  129 (369)
T PF02456_consen   89 IGVVYGPTGSGKSQLL-RNLISCQLIQPPPETVFFITPQKDM  129 (369)
T ss_pred             EEEEECCCCCCHHHHH-HHhhhcCcccCCCCceEEECCCCCC
Confidence            3578999999999432 2222221112234479999998754

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

>TIGR00959 ffh signal recognition particle protein

Probab=95.16  E-value=0.25  Score=46.36  Aligned_cols=22  Identities=23%  Similarity=0.206  Sum_probs=16.9

Q ss_pred             cEEEECCCCCCchhHhHHHHHH
Q 015158           78 DVIQQAQSGTGKTATFCSGILQ   99 (412)
Q Consensus        78 ~~lv~~~tGsGKT~~~~~~~~~   99 (412)
                      .+++++++|+|||+++.-.+..
T Consensus       101 vi~~vG~~GsGKTTtaakLA~~  122 (428)
T TIGR00959       101 VILMVGLQGSGKTTTCGKLAYY  122 (428)
T ss_pred             EEEEECCCCCcHHHHHHHHHHH
Confidence            4678999999999886554443

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.

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=95.16  E-value=0.08  Score=48.69  Aligned_cols=43  Identities=19%  Similarity=0.315  Sum_probs=28.8

Q ss_pred             CCCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEeecC
Q 015158          179 PDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATM  222 (412)
Q Consensus       179 ~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~  222 (412)
                      .....++||||+|.+.... ...+.+.+...+.+..+|++|..+
T Consensus       139 ~~~~kVviIDead~m~~~a-anaLLK~LEepp~~~~~IL~t~~~  181 (365)
T PRK07471        139 EGGWRVVIVDTADEMNANA-ANALLKVLEEPPARSLFLLVSHAP  181 (365)
T ss_pred             cCCCEEEEEechHhcCHHH-HHHHHHHHhcCCCCeEEEEEECCc
Confidence            3567899999999865443 455666666665566666666555

>PHA00012 I assembly protein

Probab=95.15  E-value=0.43  Score=42.43  Aligned_cols=26  Identities=31%  Similarity=0.360  Sum_probs=21.9

Q ss_pred             EEEECCCCCCchhHhHHHHHHhhccC
Q 015158           79 VIQQAQSGTGKTATFCSGILQQLDYG  104 (412)
Q Consensus        79 ~lv~~~tGsGKT~~~~~~~~~~~~~~  104 (412)
                      .++.+-.|+|||+.+...+...+..+
T Consensus         4 ylITGkPGSGKSl~aV~~I~~~L~~G   29 (361)
T PHA00012          4 YVVTGKLGAGKTLVAVSRIQDKLVKG   29 (361)
T ss_pred             EEEecCCCCCchHHHHHHHHHHHHcC
Confidence            47899999999998888788777765

>KOG0742 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=95.11  E-value=0.072  Score=48.28  Aligned_cols=17  Identities=29%  Similarity=0.364  Sum_probs=15.3

Q ss_pred             ccEEEECCCCCCchhHh
Q 015158           77 LDVIQQAQSGTGKTATF   93 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~   93 (412)
                      +|+++-+|+|+|||+.+
T Consensus       385 RNilfyGPPGTGKTm~A  401 (630)
T KOG0742|consen  385 RNILFYGPPGTGKTMFA  401 (630)
T ss_pred             hheeeeCCCCCCchHHH
Confidence            68999999999999765

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=95.10  E-value=0.064  Score=48.70  Aligned_cols=139  Identities=9%  Similarity=-0.017  Sum_probs=70.1

Q ss_pred             ChHHHHhhhhhhhc----C---ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccc
Q 015158           62 PSAIQQRGIVPFCK----G---LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYL  134 (412)
Q Consensus        62 l~~~Q~~a~~~~~~----~---~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~  134 (412)
                      ++|||...+..+.+    +   .-.++.||.|.||+..+...+...+-.......   -|..       ...++.+....
T Consensus         3 ~yPWl~~~~~~l~~~~~~~rl~HA~Lf~G~~G~Gk~~lA~~~A~~LlC~~~~~~~---~Cg~-------C~sC~~~~~g~   72 (334)
T PRK07993          3 WYPWLRPDYEQLVGSYQAGRGHHALLIQALPGMGDDALIYALSRWLMCQQPQGHK---SCGH-------CRGCQLMQAGT   72 (334)
T ss_pred             CCCCChHHHHHHHHHHHcCCcceEEeeECCCCCCHHHHHHHHHHHHcCCCCCCCC---CCCC-------CHHHHHHHcCC
Confidence            67888888877663    3   346789999999998765443333222111111   1111       12222322222


Q ss_pred             CcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCCCCce
Q 015158          135 GVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQ  214 (412)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~  214 (412)
                      .-.+..+.....          +..|-|-....+.+.+.... .....+++|||++|.+.... ...+.+.++.-|.+..
T Consensus        73 HPD~~~i~p~~~----------~~~I~idqiR~l~~~~~~~~-~~g~~kV~iI~~ae~m~~~A-aNaLLKtLEEPp~~t~  140 (334)
T PRK07993         73 HPDYYTLTPEKG----------KSSLGVDAVREVTEKLYEHA-RLGGAKVVWLPDAALLTDAA-ANALLKTLEEPPENTW  140 (334)
T ss_pred             CCCEEEEecccc----------cccCCHHHHHHHHHHHhhcc-ccCCceEEEEcchHhhCHHH-HHHHHHHhcCCCCCeE
Confidence            222222322110          01122222222333332222 23467899999999876553 5566666666566665


Q ss_pred             EEEEeecC
Q 015158          215 VGVFSATM  222 (412)
Q Consensus       215 ~i~~SAT~  222 (412)
                      ++++|.-+
T Consensus       141 fiL~t~~~  148 (334)
T PRK07993        141 FFLACREP  148 (334)
T ss_pred             EEEEECCh
Confidence            56655544

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=95.10  E-value=0.23  Score=42.62  Aligned_cols=51  Identities=20%  Similarity=0.169  Sum_probs=31.5

Q ss_pred             cCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHH
Q 015158           75 KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRA  129 (412)
Q Consensus        75 ~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~  129 (412)
                      .|..+++.+++|+|||..+...+...+..   +..++++..- ...++..+....
T Consensus        19 ~G~~~~i~G~~G~GKT~l~~~~~~~~~~~---g~~~~~is~e-~~~~~i~~~~~~   69 (229)
T TIGR03881        19 RGFFVAVTGEPGTGKTIFCLHFAYKGLRD---GDPVIYVTTE-ESRESIIRQAAQ   69 (229)
T ss_pred             CCeEEEEECCCCCChHHHHHHHHHHHHhc---CCeEEEEEcc-CCHHHHHHHHHH
Confidence            36788999999999997765545444433   3467777642 233444444443

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.

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=95.09  E-value=0.064  Score=48.66  Aligned_cols=42  Identities=19%  Similarity=0.279  Sum_probs=29.2

Q ss_pred             CCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEeecC
Q 015158          180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATM  222 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~  222 (412)
                      ...+++|||+||.+.... ...+.+.++.-+++..+|++|..+
T Consensus       131 ~~~kV~iI~~ae~m~~~A-aNaLLKtLEEPp~~t~fiL~t~~~  172 (342)
T PRK06964        131 GGARVVVLYPAEALNVAA-ANALLKTLEEPPPGTVFLLVSARI  172 (342)
T ss_pred             CCceEEEEechhhcCHHH-HHHHHHHhcCCCcCcEEEEEECCh
Confidence            467899999999876554 455666666666666666666554

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=95.08  E-value=0.058  Score=47.82  Aligned_cols=67  Identities=13%  Similarity=0.094  Sum_probs=35.9

Q ss_pred             hhhhccccccCCCCHHHHHHHHHC--CCCCChHHHHhhhhhh---h-----------cCccEEEECCCCCCchhHhHHHH
Q 015158           34 YDEVYDTFDAMGLQENLLRGIYAY--GFEKPSAIQQRGIVPF---C-----------KGLDVIQQAQSGTGKTATFCSGI   97 (412)
Q Consensus        34 ~~~~~~~f~~~~l~~~~~~~l~~~--~~~~l~~~Q~~a~~~~---~-----------~~~~~lv~~~tGsGKT~~~~~~~   97 (412)
                      ....+..+...++++.+.+.+...  ........+......+   +           .++.+++.+|||+|||.+....+
T Consensus       136 l~~l~~~L~~~gv~~~la~~L~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~vi~~vGptGvGKTTt~~kLa  215 (282)
T TIGR03499       136 GAKLLERLLRAGVSPELARELLEKLPERADAEDAWRWLREALEKMLPVKPEEDEILEQGGVIALVGPTGVGKTTTLAKLA  215 (282)
T ss_pred             HHHHHHHHHHCCCCHHHHHHHHHHhhccCCHHHHHHHHHHHHHHHhccCCccccccCCCeEEEEECCCCCCHHHHHHHHH
Confidence            344455666677777776666442  1111111222111111   1           23467889999999998765444


Q ss_pred             HHh
Q 015158           98 LQQ  100 (412)
Q Consensus        98 ~~~  100 (412)
                      ...
T Consensus       216 ~~~  218 (282)
T TIGR03499       216 ARF  218 (282)
T ss_pred             HHH
Confidence            433

>COG2109 BtuR ATP:corrinoid adenosyltransferase [Coenzyme metabolism]

Probab=95.05  E-value=0.2  Score=40.46  Aligned_cols=138  Identities=20%  Similarity=0.344  Sum_probs=70.1

Q ss_pred             cEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHH---HHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHh
Q 015158           78 DVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRE---LAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL  154 (412)
Q Consensus        78 ~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~---L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  154 (412)
                      -++|.-..|-|||++++-.++..+.++.   +++|+-=.+.   -.+.  ..+..+.  .++....+..+...+...   
T Consensus        30 li~V~TG~GKGKTTAAlG~alRa~GhG~---rv~vvQFiKg~~~~GE~--~~~~~~~--~~v~~~~~~~g~tw~~~~---   99 (198)
T COG2109          30 LIIVFTGNGKGKTTAALGLALRALGHGL---RVGVVQFIKGGWKYGEE--AALEKFG--LGVEFHGMGEGFTWETQD---   99 (198)
T ss_pred             eEEEEecCCCChhHHHHHHHHHHhcCCC---EEEEEEEeecCcchhHH--HHHHhhc--cceeEEecCCceeCCCcC---
Confidence            3677888999999999999998887765   6666542221   1111  1122221  112211111111100000   


Q ss_pred             cCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCc--HHHHHHHHHhCCCCceEEEEeecCChHHHHH
Q 015158          155 SSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGF--KDQIYDIFQLLPPKIQVGVFSATMPPEALEI  229 (412)
Q Consensus       155 ~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~--~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~  229 (412)
                       ...++  ............ -+....+++||+||.-..+..++  ...+..++...|....+|+..-..++.+.+.
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             00022  111111111111 12224689999999998776663  3566677777776776665555555554443

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

Probab=95.02  E-value=0.085  Score=53.35  Aligned_cols=73  Identities=21%  Similarity=0.256  Sum_probs=59.1

Q ss_pred             hHHHHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcCC-----CeeEE-ecCCCCHHHHHHHHHHHhcCCCcEEEEcCC
Q 015158          265 KLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRD-----HTVSA-THGDMDQNTRDIIMREFRSGSSRVLITTDL  337 (412)
Q Consensus       265 ~~~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~-----~~~~~-~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~  337 (412)
                      ..-.+..+.-...+++.++.+|+..-+.++++.|.+..     ..+.. +|+.++..+++..+++|.+|..+|+|+|..
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            34455555556666899999999999999998887642     33333 999999999999999999999999999874

>KOG1132 consensus Helicase of the DEAD superfamily [Replication, recombination and repair]

Probab=95.01  E-value=0.81  Score=45.86  Aligned_cols=74  Identities=15%  Similarity=0.139  Sum_probs=51.7

Q ss_pred             HCCCCCChHHHHhhhhhhhc----CccEEEECCCCCCchhHhHHHHHHhh---c---------cCC--------------
Q 015158           56 AYGFEKPSAIQQRGIVPFCK----GLDVIQQAQSGTGKTATFCSGILQQL---D---------YGL--------------  105 (412)
Q Consensus        56 ~~~~~~l~~~Q~~a~~~~~~----~~~~lv~~~tGsGKT~~~~~~~~~~~---~---------~~~--------------  105 (412)
                      .++|. ||+.|..-+..++.    .+++++..|||+|||++.+-..+...   .         ...              
T Consensus        17 ~fP~q-pY~~Q~a~M~rvl~~L~~~q~~llESPTGTGKSLsLLCS~LAW~q~~k~~~~~~~~s~~~~~~~p~~~s~~~g~   95 (945)
T KOG1132|consen   17 EFPFQ-PYPTQLAFMTRVLSCLDRKQNGLLESPTGTGKSLSLLCSTLAWQQHLKSRKPKGKISERKAGFIPTQPSDSGGE   95 (945)
T ss_pred             eccCC-cchHHHHHHHHHHHHHHHhhhhhccCCCCCCccHHHHHHHHHHHHHhhccccccchhhhhccccCCCCccCCCC
Confidence            45666 89999987777665    57899999999999987654444322   1         000              


Q ss_pred             -------------CceeEEEEcCCHHHHHHHHHHHHHh
Q 015158          106 -------------VECQALVLAPTRELAQQIEKVMRAL  130 (412)
Q Consensus       106 -------------~~~~~lil~P~~~L~~q~~~~~~~~  130 (412)
                                   ..++++|-.-|-.-..|..+++++.
T Consensus        96 ~s~e~~e~~~~~~~ipkIyyaSRTHsQltQvvrElrrT  133 (945)
T KOG1132|consen   96 KSEEAGEPIACYTGIPKIYYASRTHSQLTQVVRELRRT  133 (945)
T ss_pred             chhhhcCccccccCCceEEEecchHHHHHHHHHHHhhc
Confidence                         1346777777777788888888774

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=94.99  E-value=0.14  Score=46.88  Aligned_cols=42  Identities=24%  Similarity=0.358  Sum_probs=28.7

Q ss_pred             CCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEeecC
Q 015158          180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATM  222 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~  222 (412)
                      ..+.++||||+|.+.... ...+.+.+...+.+..++++|..+
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            467899999999875443 455666666666666666666443

>COG0552 FtsY Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=94.97  E-value=0.71  Score=41.12  Aligned_cols=132  Identities=21%  Similarity=0.300  Sum_probs=71.1

Q ss_pred             cEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEE-cCcchHHHHHHhcC
Q 015158           78 DVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACV-GGTSVREDQRILSS  156 (412)
Q Consensus        78 ~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~  156 (412)
                      .+++++-.|+|||++.-=.+......+   .++++.+- ...-.-..++++.|....|..+.... |..+          
T Consensus       141 Vil~vGVNG~GKTTTIaKLA~~l~~~g---~~VllaA~-DTFRAaAiEQL~~w~er~gv~vI~~~~G~Dp----------  206 (340)
T COG0552         141 VILFVGVNGVGKTTTIAKLAKYLKQQG---KSVLLAAG-DTFRAAAIEQLEVWGERLGVPVISGKEGADP----------  206 (340)
T ss_pred             EEEEEecCCCchHhHHHHHHHHHHHCC---CeEEEEec-chHHHHHHHHHHHHHHHhCCeEEccCCCCCc----------
Confidence            467899999999988644333333333   35555443 22222233344444444465554321 2221          


Q ss_pred             CCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhcc-CcHHHHHHHHHhCCCCc------eEEEEeecCChHHHHH
Q 015158          157 GVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSR-GFKDQIYDIFQLLPPKI------QVGVFSATMPPEALEI  229 (412)
Q Consensus       157 ~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~-~~~~~~~~i~~~~~~~~------~~i~~SAT~~~~~~~~  229 (412)
                       +.|+       +..+.+..  .+++|+|++|=|-++=+. +.-..+.++.+-+.+..      .++.+-||.+.+....
T Consensus       207 -AaVa-------fDAi~~Ak--ar~~DvvliDTAGRLhnk~nLM~EL~KI~rV~~k~~~~ap~e~llvlDAttGqnal~Q  276 (340)
T COG0552         207 -AAVA-------FDAIQAAK--ARGIDVVLIDTAGRLHNKKNLMDELKKIVRVIKKDDPDAPHEILLVLDATTGQNALSQ  276 (340)
T ss_pred             -HHHH-------HHHHHHHH--HcCCCEEEEeCcccccCchhHHHHHHHHHHHhccccCCCCceEEEEEEcccChhHHHH
Confidence             1111       12222211  257899999998876533 24466666666665433      4566689988765555


Q ss_pred             HHHh
Q 015158          230 TRKF  233 (412)
Q Consensus       230 ~~~~  233 (412)
                      .+.+
T Consensus       277 Ak~F  280 (340)
T COG0552         277 AKIF  280 (340)
T ss_pred             HHHH
Confidence            5443

>COG1485 Predicted ATPase [General function prediction only]

Probab=94.97  E-value=0.34  Score=43.34  Aligned_cols=110  Identities=15%  Similarity=0.152  Sum_probs=61.7

Q ss_pred             ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcC
Q 015158           77 LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSS  156 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  156 (412)
                      +.+.++|+.|.|||..+  ..+........+.    -++.-.-+.++.+++..+.           |..           
T Consensus        66 ~GlYl~GgVGrGKT~LM--D~Fy~~lp~~~k~----R~HFh~FM~~vH~~l~~l~-----------g~~-----------  117 (367)
T COG1485          66 RGLYLWGGVGRGKTMLM--DLFYESLPGERKR----RLHFHRFMARVHQRLHTLQ-----------GQT-----------  117 (367)
T ss_pred             ceEEEECCCCccHHHHH--HHHHhhCCccccc----cccHHHHHHHHHHHHHHHc-----------CCC-----------
Confidence            56899999999999543  3333322221111    1344455566666655542           111           


Q ss_pred             CCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHh-CCCCceEEEEeecCChHHH
Q 015158          157 GVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQL-LPPKIQVGVFSATMPPEAL  227 (412)
Q Consensus       157 ~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~-~~~~~~~i~~SAT~~~~~~  227 (412)
                        +.+-    .+...+.      .+..++++||.| +.+-+-...+.+++.. +..++.++..|-|.|.++.
T Consensus       118 --dpl~----~iA~~~~------~~~~vLCfDEF~-VtDI~DAMiL~rL~~~Lf~~GV~lvaTSN~~P~~LY  176 (367)
T COG1485         118 --DPLP----PIADELA------AETRVLCFDEFE-VTDIADAMILGRLLEALFARGVVLVATSNTAPDNLY  176 (367)
T ss_pred             --CccH----HHHHHHH------hcCCEEEeeeee-ecChHHHHHHHHHHHHHHHCCcEEEEeCCCChHHhc
Confidence              1110    1111111      356899999999 4554444455555543 4568888999999886543

>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]

Probab=94.97  E-value=0.45  Score=43.79  Aligned_cols=29  Identities=21%  Similarity=0.446  Sum_probs=20.1

Q ss_pred             CceEEEEeCCchhhccCcHHHHHHHHHhCC
Q 015158          181 NIRIFVLDEADEMLSRGFKDQIYDIFQLLP  210 (412)
Q Consensus       181 ~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~  210 (412)
                      ..-+||+||++.+..... ..+..+.....
T Consensus       123 ~~~IvvLDEid~L~~~~~-~~LY~L~r~~~  151 (366)
T COG1474         123 KTVIVILDEVDALVDKDG-EVLYSLLRAPG  151 (366)
T ss_pred             CeEEEEEcchhhhccccc-hHHHHHHhhcc
Confidence            455899999999887753 55555555443

>PRK05973 replicative DNA helicase; Provisional

Probab=94.92  E-value=0.072  Score=45.55  Aligned_cols=58  Identities=19%  Similarity=0.156  Sum_probs=39.1

Q ss_pred             hhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 015158           69 GIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRAL  130 (412)
Q Consensus        69 a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~  130 (412)
                      ...-+..|.-++|.|++|+|||..++..+......   +.+++|++--.. .+|..+.+..+
T Consensus        57 l~GGl~~Gsl~LIaG~PG~GKT~lalqfa~~~a~~---Ge~vlyfSlEes-~~~i~~R~~s~  114 (237)
T PRK05973         57 LFSQLKPGDLVLLGARPGHGKTLLGLELAVEAMKS---GRTGVFFTLEYT-EQDVRDRLRAL  114 (237)
T ss_pred             hcCCCCCCCEEEEEeCCCCCHHHHHHHHHHHHHhc---CCeEEEEEEeCC-HHHHHHHHHHc
Confidence            33445567788999999999998877666655543   346777764332 45666666665

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=94.91  E-value=0.17  Score=46.77  Aligned_cols=18  Identities=28%  Similarity=0.272  Sum_probs=14.7

Q ss_pred             ccEEEECCCCCCchhHhH
Q 015158           77 LDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~   94 (412)
                      +..++.||+|+|||..+.
T Consensus        37 ~~~Ll~G~~G~GKt~~a~   54 (355)
T TIGR02397        37 HAYLFSGPRGTGKTSIAR   54 (355)
T ss_pred             eEEEEECCCCCCHHHHHH
Confidence            346889999999997663

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.

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=94.87  E-value=0.18  Score=45.59  Aligned_cols=147  Identities=12%  Similarity=0.056  Sum_probs=69.6

Q ss_pred             ChHHHHhhhhhhhcC-----ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCc
Q 015158           62 PSAIQQRGIVPFCKG-----LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGV  136 (412)
Q Consensus        62 l~~~Q~~a~~~~~~~-----~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~  136 (412)
                      ++|||...+..+...     ...++.||.|.|||..+...+. .+....+... -.-|.       ....++.+.....-
T Consensus         2 ~yPW~~~~w~~l~~~~~r~~hA~Lf~G~~G~GK~~la~~~a~-~llC~~~~~~-~~~Cg-------~C~~C~~~~~~~Hp   72 (325)
T PRK08699          2 IYPWHQEQWRQIAEHWERRPNAWLFAGKKGIGKTAFARFAAQ-ALLCETPAPG-HKPCG-------ECMSCHLFGQGSHP   72 (325)
T ss_pred             CCCccHHHHHHHHHhcCCcceEEEeECCCCCCHHHHHHHHHH-HHcCCCCCCC-CCCCC-------cCHHHHHHhcCCCC
Confidence            367888888777632     3578999999999987654433 3332111000 00011       11222333222222


Q ss_pred             EEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEE
Q 015158          137 KVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVG  216 (412)
Q Consensus       137 ~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i  216 (412)
                      .+..+..........   .....|-|-....+...+..... ....+++|+|++|.+... ....+.+.+...+.+..+|
T Consensus        73 D~~~~~p~~~~~~~g---~~~~~I~id~iR~l~~~~~~~p~-~~~~kV~iiEp~~~Ld~~-a~naLLk~LEep~~~~~~I  147 (325)
T PRK08699         73 DFYEITPLSDEPENG---RKLLQIKIDAVREIIDNVYLTSV-RGGLRVILIHPAESMNLQ-AANSLLKVLEEPPPQVVFL  147 (325)
T ss_pred             CEEEEeccccccccc---ccCCCcCHHHHHHHHHHHhhCcc-cCCceEEEEechhhCCHH-HHHHHHHHHHhCcCCCEEE
Confidence            333333211000000   00012322222233333322222 245788999999986544 4556666666666566555


Q ss_pred             EEeecC
Q 015158          217 VFSATM  222 (412)
Q Consensus       217 ~~SAT~  222 (412)
                      ++|-.+
T Consensus       148 lvth~~  153 (325)
T PRK08699        148 LVSHAA  153 (325)
T ss_pred             EEeCCh
Confidence            554443

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.82  E-value=0.16  Score=50.07  Aligned_cols=38  Identities=11%  Similarity=0.293  Sum_probs=22.7

Q ss_pred             CCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEE
Q 015158          180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVF  218 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~  218 (412)
                      ....+|||||+|.+.... ...+.+.+...+....+|+.
T Consensus       119 ~~~kVvIIDEa~~L~~~a-~naLLk~LEepp~~tv~Il~  156 (585)
T PRK14950        119 ARYKVYIIDEVHMLSTAA-FNALLKTLEEPPPHAIFILA  156 (585)
T ss_pred             CCeEEEEEeChHhCCHHH-HHHHHHHHhcCCCCeEEEEE
Confidence            457899999999875443 33444444444444444443

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.81  E-value=0.11  Score=51.30  Aligned_cols=38  Identities=13%  Similarity=0.356  Sum_probs=22.7

Q ss_pred             CCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEE
Q 015158          180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVF  218 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~  218 (412)
                      ....++||||+|.+.... ...+.+.+..-+....+|+.
T Consensus       120 ~~~KViIIDEad~Lt~~a-~naLLK~LEePp~~tvfIL~  157 (620)
T PRK14948        120 ARWKVYVIDECHMLSTAA-FNALLKTLEEPPPRVVFVLA  157 (620)
T ss_pred             CCceEEEEECccccCHHH-HHHHHHHHhcCCcCeEEEEE
Confidence            456899999999875433 33444555544444434443

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

Probab=94.79  E-value=0.12  Score=51.55  Aligned_cols=101  Identities=19%  Similarity=0.223  Sum_probs=77.2

Q ss_pred             ceEEEEEeccchhhHHHHHHHHHhc--CCCcEEEEEcchhHHHHHHHHHhcC-CCeeEEecCCCCHHHHHHHHHHHhcCC
Q 015158          252 IKQFHVNVEKEEWKLETLCDLYETL--AITQSVIFVNTRRKVDWLTDKMRSR-DHTVSATHGDMDQNTRDIIMREFRSGS  328 (412)
Q Consensus       252 ~~~~~~~~~~~~~~~~~l~~~~~~~--~~~k~lif~~~~~~~~~~~~~L~~~-~~~~~~~~~~~~~~~r~~~~~~f~~g~  328 (412)
                      ...+...-...+.|.+.+.+++...  .++.+||.++.+....++.+.|+.+ |..+.++|+++++.+|...+.+..+|+
T Consensus       217 ~~~~Ll~GvTGSGKTEvYl~~i~~~L~~GkqvLvLVPEI~Ltpq~~~rf~~rFg~~v~vlHS~Ls~~er~~~W~~~~~G~  296 (730)
T COG1198         217 FAPFLLDGVTGSGKTEVYLEAIAKVLAQGKQVLVLVPEIALTPQLLARFKARFGAKVAVLHSGLSPGERYRVWRRARRGE  296 (730)
T ss_pred             ccceeEeCCCCCcHHHHHHHHHHHHHHcCCEEEEEeccccchHHHHHHHHHHhCCChhhhcccCChHHHHHHHHHHhcCC
Confidence            3444455555566777777777664  4468999999999988888888765 778999999999999999999999999


Q ss_pred             CcEEEEcCCCcCCCCCCCCCEEEEc
Q 015158          329 SRVLITTDLLARGIDVQQVSLVINY  353 (412)
Q Consensus       329 ~~vlv~t~~~~~G~d~~~~~~vi~~  353 (412)
                      .+|+|+|...- =.-+++.-.+|..
T Consensus       297 ~~vVIGtRSAl-F~Pf~~LGLIIvD  320 (730)
T COG1198         297 ARVVIGTRSAL-FLPFKNLGLIIVD  320 (730)
T ss_pred             ceEEEEechhh-cCchhhccEEEEe
Confidence            99999997421 2244566666643

>PRK07414 cob(I)yrinic acid a,c-diamide adenosyltransferase; Validated

Probab=94.77  E-value=0.65  Score=37.59  Aligned_cols=137  Identities=12%  Similarity=0.110  Sum_probs=72.1

Q ss_pred             cEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHH---HHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHh
Q 015158           78 DVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTREL---AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL  154 (412)
Q Consensus        78 ~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L---~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  154 (412)
                      -+.|-...|-|||.+++-.++....++.   +++++-=.+.-   .+..  .++.+ .  ++.......+.....     
T Consensus        23 li~VYtGdGKGKTTAAlGlalRAaG~G~---rV~iiQFlKg~~~~GE~~--~l~~~-~--~v~~~~~g~~~~~~~-----   89 (178)
T PRK07414         23 LVQVFTSSQRNFFTSVMAQALRIAGQGT---PVLIVQFLKGGIQQGPDR--PIQLG-Q--NLDWVRCDLPRCLDT-----   89 (178)
T ss_pred             EEEEEeCCCCCchHHHHHHHHHHhcCCC---EEEEEEEecCCCcchHHH--HHHhC-C--CcEEEECCCCCeeeC-----
Confidence            4667788999999999988888877664   77776533322   1211  12222 1  333322111000000     


Q ss_pred             cCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCc--HHHHHHHHHhCCCCceEEEEeecCChHHHH
Q 015158          155 SSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGF--KDQIYDIFQLLPPKIQVGVFSATMPPEALE  228 (412)
Q Consensus       155 ~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~--~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~  228 (412)
                      ......-....+....... ..+....+++||+||+-...+.++  ...+..+++..|+...+|+..-.+++.+.+
T Consensus        90 ~~~~~~~~~~~~~~~~~a~-~~l~~~~~dlvVLDEi~~Al~~gli~~eeVl~~L~~rp~~~evILTGR~~p~~Lie  164 (178)
T PRK07414         90 PHLDESEKKALQELWQYTQ-AVVDEGRYSLVVLDELSLAIQFGLIPETEVLEFLEKRPSHVDVILTGPEMPESLLA  164 (178)
T ss_pred             CCcCHHHHHHHHHHHHHHH-HHHhCCCCCEEEEehhHHHHHCCCccHHHHHHHHHhCCCCCEEEEECCCCCHHHHH
Confidence            0000000000111111111 112235789999999998887774  356777777777777666666666655443

>KOG0991 consensus Replication factor C, subunit RFC2 [Replication, recombination and repair]

Probab=94.75  E-value=0.088  Score=43.99  Aligned_cols=36  Identities=19%  Similarity=0.362  Sum_probs=24.0

Q ss_pred             CCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEE
Q 015158          180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVG  216 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i  216 (412)
                      .....||+|||+.+.+. ....+++......+..++.
T Consensus       112 grhKIiILDEADSMT~g-AQQAlRRtMEiyS~ttRFa  147 (333)
T KOG0991|consen  112 GRHKIIILDEADSMTAG-AQQALRRTMEIYSNTTRFA  147 (333)
T ss_pred             CceeEEEeeccchhhhH-HHHHHHHHHHHHcccchhh
Confidence            46689999999986654 3566666666555444443

>PRK14873 primosome assembly protein PriA; Provisional

Probab=94.70  E-value=0.19  Score=50.01  Aligned_cols=92  Identities=21%  Similarity=0.159  Sum_probs=72.1

Q ss_pred             hhhHHHHHHHHHhc--CCCcEEEEEcchhHHHHHHHHHhcCC--CeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCC
Q 015158          263 EWKLETLCDLYETL--AITQSVIFVNTRRKVDWLTDKMRSRD--HTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLL  338 (412)
Q Consensus       263 ~~~~~~l~~~~~~~--~~~k~lif~~~~~~~~~~~~~L~~~~--~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~  338 (412)
                      +.|.+.+.+++...  .++.+||.++.+..+.++.+.|+++.  ..+..+|+++++.+|.+.+.+..+|+.+|+|+|...
T Consensus       171 SGKTevyl~~i~~~l~~Gk~vLvLvPEi~lt~q~~~rl~~~f~~~~v~~lhS~l~~~~R~~~w~~~~~G~~~IViGtRSA  250 (665)
T PRK14873        171 EDWARRLAAAAAATLRAGRGALVVVPDQRDVDRLEAALRALLGAGDVAVLSAGLGPADRYRRWLAVLRGQARVVVGTRSA  250 (665)
T ss_pred             CcHHHHHHHHHHHHHHcCCeEEEEecchhhHHHHHHHHHHHcCCCcEEEECCCCCHHHHHHHHHHHhCCCCcEEEEccee
Confidence            35666666666553  35679999999999999999998764  579999999999999999999999999999999742


Q ss_pred             cCCCCCCCCCEEEEccC
Q 015158          339 ARGIDVQQVSLVINYDL  355 (412)
Q Consensus       339 ~~G~d~~~~~~vi~~~~  355 (412)
                      - =.-+++...||+.+-
T Consensus       251 v-FaP~~~LgLIIvdEE  266 (665)
T PRK14873        251 V-FAPVEDLGLVAIWDD  266 (665)
T ss_pred             E-EeccCCCCEEEEEcC
Confidence            1 234556667765543

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=94.65  E-value=0.23  Score=49.67  Aligned_cols=79  Identities=18%  Similarity=0.271  Sum_probs=66.1

Q ss_pred             CCCcEEEEEcchhHHHHHHHHHhc----CCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcC-CCcCCCCCCCCCEEE
Q 015158          277 AITQSVIFVNTRRKVDWLTDKMRS----RDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTD-LLARGIDVQQVSLVI  351 (412)
Q Consensus       277 ~~~k~lif~~~~~~~~~~~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~-~~~~G~d~~~~~~vi  351 (412)
                      .+.++++.+|++.-|.+.++.+++    .+..+..++|+++..+|..+++...+|+.+|+|+|. .+...+++.++..||
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            346899999999988887776654    478999999999999999999999999999999998 555677788888888


Q ss_pred             EccC
Q 015158          352 NYDL  355 (412)
Q Consensus       352 ~~~~  355 (412)
                      +.+.
T Consensus       363 IDEa  366 (630)
T TIGR00643       363 IDEQ  366 (630)
T ss_pred             Eech
Confidence            6543

>PF01443 Viral_helicase1: Viral (Superfamily 1) RNA helicase; InterPro: IPR000606 This entry includes RNA and DNA helicases

Probab=94.61  E-value=0.045  Score=47.14  Aligned_cols=15  Identities=20%  Similarity=0.556  Sum_probs=12.7

Q ss_pred             EEEECCCCCCchhHh
Q 015158           79 VIQQAQSGTGKTATF   93 (412)
Q Consensus        79 ~lv~~~tGsGKT~~~   93 (412)
                      ++|.|++|+|||...
T Consensus         1 ~vv~G~pGsGKSt~i   15 (234)
T PF01443_consen    1 IVVHGVPGSGKSTLI   15 (234)
T ss_pred             CEEEcCCCCCHHHHH
Confidence            378999999999754

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

>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=94.57  E-value=0.048  Score=51.06  Aligned_cols=42  Identities=21%  Similarity=0.290  Sum_probs=29.9

Q ss_pred             ChHHHHhhhhhhhcCc--cEEEECCCCCCchhHhHHHHHHhhccC
Q 015158           62 PSAIQQRGIVPFCKGL--DVIQQAQSGTGKTATFCSGILQQLDYG  104 (412)
Q Consensus        62 l~~~Q~~a~~~~~~~~--~~lv~~~tGsGKT~~~~~~~~~~~~~~  104 (412)
                      ..+.|...+..+++..  -+++.||||||||.+. .+++..+...
T Consensus       242 ~~~~~~~~~~~~~~~p~GliLvTGPTGSGKTTTL-Y~~L~~ln~~  285 (500)
T COG2804         242 MSPFQLARLLRLLNRPQGLILVTGPTGSGKTTTL-YAALSELNTP  285 (500)
T ss_pred             CCHHHHHHHHHHHhCCCeEEEEeCCCCCCHHHHH-HHHHHHhcCC
Confidence            3677777787777653  4678999999999874 4555555443

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=94.56  E-value=0.069  Score=46.09  Aligned_cols=51  Identities=22%  Similarity=0.212  Sum_probs=36.1

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRAL  130 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~  130 (412)
                      |..++|.+++|+|||..++..+...+..+   .+++|++- ..-..+..+.+..+
T Consensus        21 gs~~lI~G~pGsGKT~la~~~l~~~~~~g---e~~lyvs~-ee~~~~i~~~~~~~   71 (237)
T TIGR03877        21 RNVVLLSGGPGTGKSIFSQQFLWNGLQMG---EPGIYVAL-EEHPVQVRRNMAQF   71 (237)
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHHHHcC---CcEEEEEe-eCCHHHHHHHHHHh
Confidence            56789999999999987776666655433   47888874 34455666666654

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.

>PRK04841 transcriptional regulator MalT; Provisional

Probab=94.54  E-value=0.12  Score=54.38  Aligned_cols=41  Identities=15%  Similarity=0.301  Sum_probs=33.2

Q ss_pred             eEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEeecCC
Q 015158          183 RIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMP  223 (412)
Q Consensus       183 ~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~  223 (412)
                      -+||+|++|.+.+......+..++...+.+..+|+.|-+.+
T Consensus       123 ~~lvlDD~h~~~~~~~~~~l~~l~~~~~~~~~lv~~sR~~~  163 (903)
T PRK04841        123 LYLVIDDYHLITNPEIHEAMRFFLRHQPENLTLVVLSRNLP  163 (903)
T ss_pred             EEEEEeCcCcCCChHHHHHHHHHHHhCCCCeEEEEEeCCCC
Confidence            48999999988666556688888888888898888887743

>PRK06904 replicative DNA helicase; Validated

Probab=94.54  E-value=0.29  Score=46.78  Aligned_cols=117  Identities=18%  Similarity=0.091  Sum_probs=58.4

Q ss_pred             hhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEE-Ec-CcchHHH
Q 015158           73 FCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHAC-VG-GTSVRED  150 (412)
Q Consensus        73 ~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~-~~-~~~~~~~  150 (412)
                      +..|.-++|.|.||.|||..++-.+.+....  .+..++|++.- .-.+|+..++-....  ++....+ .| ..+...+
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 LQPSDLIIVAARPSMGKTTFAMNLCENAAMA--SEKPVLVFSLE-MPAEQIMMRMLASLS--RVDQTKIRTGQNLDQQDW  292 (472)
T ss_pred             cCCCcEEEEEeCCCCChHHHHHHHHHHHHHh--cCCeEEEEecc-CCHHHHHHHHHHhhC--CCCHHHhccCCCCCHHHH
Confidence            4445667889999999997664444433222  13467776653 335555555443221  2222222 22 1222222


Q ss_pred             HH------HhcCCCcEEE-----eChHHHHHHHHcCCCCCCCceEEEEeCCchhh
Q 015158          151 QR------ILSSGVHVVV-----GTPGRVFDMLRRQSLRPDNIRIFVLDEADEML  194 (412)
Q Consensus       151 ~~------~~~~~~~iii-----~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~  194 (412)
                      ..      .+.....+.|     .|...+.....+.......+++||||=.|.+.
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            11      1222334665     34455543332211112357899999998765

>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=94.52  E-value=0.1  Score=45.74  Aligned_cols=143  Identities=20%  Similarity=0.161  Sum_probs=70.4

Q ss_pred             cCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEE-cCcchHHHHHH
Q 015158           75 KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACV-GGTSVREDQRI  153 (412)
Q Consensus        75 ~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~  153 (412)
                      .|.-+++.|.+|.|||..++-.+.+.....  +..++|++.--. .+++..++-...  .++....+. +..........
T Consensus        18 ~g~L~vi~a~pg~GKT~~~l~ia~~~a~~~--~~~vly~SlEm~-~~~l~~R~la~~--s~v~~~~i~~g~l~~~e~~~~   92 (259)
T PF03796_consen   18 PGELTVIAARPGVGKTAFALQIALNAALNG--GYPVLYFSLEMS-EEELAARLLARL--SGVPYNKIRSGDLSDEEFERL   92 (259)
T ss_dssp             TT-EEEEEESTTSSHHHHHHHHHHHHHHTT--SSEEEEEESSS--HHHHHHHHHHHH--HTSTHHHHHCCGCHHHHHHHH
T ss_pred             cCcEEEEEecccCCchHHHHHHHHHHHHhc--CCeEEEEcCCCC-HHHHHHHHHHHh--hcchhhhhhccccCHHHHHHH
Confidence            355678999999999988777776665542  247888886433 222333322211  122111111 11111111111


Q ss_pred             -----hcCCCcEEE-e----ChHHHHHHHHcCCCCCCCceEEEEeCCchhhcc----CcHHHHHHHHHhCC-----CCce
Q 015158          154 -----LSSGVHVVV-G----TPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSR----GFKDQIYDIFQLLP-----PKIQ  214 (412)
Q Consensus       154 -----~~~~~~iii-~----T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~----~~~~~~~~i~~~~~-----~~~~  214 (412)
                           ......+++ .    |.+.+...+.........+++||||=.|.+...    +....+..+...+.     .++.
T Consensus        93 ~~~~~~l~~~~l~i~~~~~~~~~~i~~~i~~~~~~~~~~~~v~IDyl~ll~~~~~~~~~~~~~~~i~~~Lk~lA~~~~i~  172 (259)
T PF03796_consen   93 QAAAEKLSDLPLYIEDTPSLTIDDIESKIRRLKREGKKVDVVFIDYLQLLKSEDSSDNRRQEIGEISRELKALAKELNIP  172 (259)
T ss_dssp             HHHHHHHHTSEEEEEESSS-BHHHHHHHHHHHHHHSTTEEEEEEEEGGGSBTSCSSSCCHHHHHHHHHHHHHHHHHHTSE
T ss_pred             HHHHHHHhhCcEEEECCCCCCHHHHHHHHHHHHhhccCCCEEEechHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHcCCe
Confidence                 012223443 2    334444444322222257899999999987653    22333333322221     2677


Q ss_pred             EEEEeecC
Q 015158          215 VGVFSATM  222 (412)
Q Consensus       215 ~i~~SAT~  222 (412)
                      ++++|...
T Consensus       173 vi~~sQln  180 (259)
T PF03796_consen  173 VIALSQLN  180 (259)
T ss_dssp             EEEEEEBS
T ss_pred             EEEccccC
Confidence            77777764

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 ....

>KOG0733 consensus Nuclear AAA ATPase (VCP subfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=94.50  E-value=0.11  Score=49.59  Aligned_cols=98  Identities=16%  Similarity=0.214  Sum_probs=51.7

Q ss_pred             CceEEEEeCCchhhcc-------CcHHHHHHHHHh---CCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccC
Q 015158          181 NIRIFVLDEADEMLSR-------GFKDQIYDIFQL---LPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLE  250 (412)
Q Consensus       181 ~~~~iiiDE~h~~~~~-------~~~~~~~~i~~~---~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  250 (412)
                      .-.+|++||++.+...       ...+.+..++-.   +.....+..+-||-.+++.+-.-               ..+.
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            4578999999987521       122334444333   33455678888887665322111               0111


Q ss_pred             Cc-eEEEEEeccchhhHHHHHHHHHhcCCCcEEEEEcchhHHHHHHHHH
Q 015158          251 GI-KQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKM  298 (412)
Q Consensus       251 ~~-~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L  298 (412)
                      -+ +..++.++...++...|..+.+.++ .+    +.+.-..++++...
T Consensus       669 RlDk~LyV~lPn~~eR~~ILK~~tkn~k-~p----l~~dVdl~eia~~~  712 (802)
T KOG0733|consen  669 RLDKLLYVGLPNAEERVAILKTITKNTK-PP----LSSDVDLDEIARNT  712 (802)
T ss_pred             ccCceeeecCCCHHHHHHHHHHHhccCC-CC----CCcccCHHHHhhcc
Confidence            12 3345556666667777776666522 11    33334455555544

>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily

Probab=94.48  E-value=0.37  Score=45.62  Aligned_cols=118  Identities=17%  Similarity=0.124  Sum_probs=58.0

Q ss_pred             hhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEE-EcCcchHHH
Q 015158           72 PFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHAC-VGGTSVRED  150 (412)
Q Consensus        72 ~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~-~~~~~~~~~  150 (412)
                      -+..|.-++|.|++|+|||..++..+.+....  .+.+++|++.- .-..|+..++-...  .++....+ .|......+
T Consensus       190 G~~~g~liviag~pg~GKT~~al~ia~~~a~~--~g~~v~~fSlE-m~~~~l~~Rl~~~~--~~v~~~~~~~~~l~~~~~  264 (421)
T TIGR03600       190 GLVKGDLIVIGARPSMGKTTLALNIAENVALR--EGKPVLFFSLE-MSAEQLGERLLASK--SGINTGNIRTGRFNDSDF  264 (421)
T ss_pred             CCCCCceEEEEeCCCCCHHHHHHHHHHHHHHh--CCCcEEEEECC-CCHHHHHHHHHHHH--cCCCHHHHhcCCCCHHHH
Confidence            34456678899999999997766555444311  23467777632 23444444433321  12222211 122221111


Q ss_pred             H------HHhcCCCcEEEe-----ChHHHHHHHHcCCCCCCCceEEEEeCCchhhc
Q 015158          151 Q------RILSSGVHVVVG-----TPGRVFDMLRRQSLRPDNIRIFVLDEADEMLS  195 (412)
Q Consensus       151 ~------~~~~~~~~iii~-----T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~  195 (412)
                      .      .... +..+.|.     |.+.+.....+.......+++||||=.|.+..
T Consensus       265 ~~~~~~~~~l~-~~~l~i~d~~~~t~~~i~~~~r~~~~~~~~~~lvvIDyLql~~~  319 (421)
T TIGR03600       265 NRLLNAVDRLS-EKDLYIDDTGGLTVAQIRSIARRIKRKKGGLDLIVVDYIQLMAP  319 (421)
T ss_pred             HHHHHHHHHHh-cCCEEEECCCCCCHHHHHHHHHHHHHhcCCCCEEEEecccccCC
Confidence            1      1111 2345553     33444443332211122588999999987653

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.

>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=94.46  E-value=1.1  Score=41.48  Aligned_cols=145  Identities=15%  Similarity=0.103  Sum_probs=61.8

Q ss_pred             EEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHH-HHHHHH---HHHHHhhcc-cCcEEEEEEcCcchHHHHHHh
Q 015158           80 IQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRE-LAQQIE---KVMRALGDY-LGVKVHACVGGTSVREDQRIL  154 (412)
Q Consensus        80 lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~-L~~q~~---~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~  154 (412)
                      ++.++.|+|||.+....++...........++++ ++.. +.....   .....+... ............-.      +
T Consensus         1 ~i~~~r~~GKT~~~~~~~~~~~~~~~~~~~vi~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~   73 (384)
T PF03237_consen    1 LINGGRGSGKTTLIAIWFLWWALTRPPGRRVIIA-STYRQARDIFGRFWKGIIELLPSWFEIKFNEWNDRKII------L   73 (384)
T ss_dssp             -EEE-SSS-HHHHHHHHHHHHHHSSSS--EEEEE-ESSHHHHHHHHHHHHHHHHTS-TTTS--EEEE-SSEEE------E
T ss_pred             CCcCCccccHHHHHHHHHHHHHhhCCCCcEEEEe-cCHHHHHHHHHHhHHHHHHHHHHhcCcccccCCCCcEE------e
Confidence            4678999999988777666665544333455555 5554 444322   223333222 12222111111110      1


Q ss_pred             cCCCcEEEeChHHH--HHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEeecCC--hHHHHHH
Q 015158          155 SSGVHVVVGTPGRV--FDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMP--PEALEIT  230 (412)
Q Consensus       155 ~~~~~iii~T~~~l--~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~--~~~~~~~  230 (412)
                      .++..|.+.+...=  ..-+.     -..++++++||+-...+..+...+........... .+..|.|+.  .......
T Consensus        74 ~nG~~i~~~~~~~~~~~~~~~-----G~~~~~i~iDE~~~~~~~~~~~~~~~~~~~~~~~~-~~~~s~p~~~~~~~~~~~  147 (384)
T PF03237_consen   74 PNGSRIQFRGADSPDSGDNIR-----GFEYDLIIIDEAAKVPDDAFSELIRRLRATWGGSI-RMYISTPPNPGGWFYEIF  147 (384)
T ss_dssp             TTS-EEEEES-----SHHHHH-----TS--SEEEEESGGGSTTHHHHHHHHHHHHCSTT---EEEEEE---SSSHHHHHH
T ss_pred             cCceEEEEecccccccccccc-----ccccceeeeeecccCchHHHHHHHHhhhhcccCcc-eEEeecCCCCCCceeeee
Confidence            23445666663321  11111     14678999999887655544444444444333222 224454443  3444455


Q ss_pred             HHhcCCC
Q 015158          231 RKFMNKP  237 (412)
Q Consensus       231 ~~~~~~~  237 (412)
                      .......
T Consensus       148 ~~~~~~~  154 (384)
T PF03237_consen  148 QRNLDDD  154 (384)
T ss_dssp             HHHHCTS
T ss_pred             ehhhcCC
Confidence            5444444

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.

>PRK13851 type IV secretion system protein VirB11; Provisional

Probab=94.44  E-value=0.064  Score=48.72  Aligned_cols=43  Identities=19%  Similarity=0.290  Sum_probs=29.8

Q ss_pred             hhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHH
Q 015158           73 FCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTREL  119 (412)
Q Consensus        73 ~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L  119 (412)
                      +..+++++|.||||||||... -+++..+..   ..+++.+-++.++
T Consensus       159 v~~~~nilI~G~tGSGKTTll-~aLl~~i~~---~~rivtiEd~~El  201 (344)
T PRK13851        159 VVGRLTMLLCGPTGSGKTTMS-KTLISAIPP---QERLITIEDTLEL  201 (344)
T ss_pred             HHcCCeEEEECCCCccHHHHH-HHHHcccCC---CCCEEEECCCccc
Confidence            445789999999999999764 445554443   2467776676654

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=94.41  E-value=0.18  Score=46.86  Aligned_cols=41  Identities=20%  Similarity=0.383  Sum_probs=25.5

Q ss_pred             CCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEeec
Q 015158          180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSAT  221 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT  221 (412)
                      .+..++||||+|.+.... ...+.+.+..-+++..+|+.|.+
T Consensus       116 ~~~kViiIDead~m~~~a-anaLLk~LEep~~~~~fIL~a~~  156 (394)
T PRK07940        116 GRWRIVVIEDADRLTERA-ANALLKAVEEPPPRTVWLLCAPS  156 (394)
T ss_pred             CCcEEEEEechhhcCHHH-HHHHHHHhhcCCCCCeEEEEECC
Confidence            467899999999976543 34455555555555544444444

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.31  E-value=0.27  Score=48.70  Aligned_cols=39  Identities=10%  Similarity=0.203  Sum_probs=26.0

Q ss_pred             CCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEe
Q 015158          180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFS  219 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~S  219 (412)
                      ...+++|+||+|.+.... ...+.+.+...+....+|+.|
T Consensus       120 ~~~KVvIIdea~~Ls~~a-~naLLK~LEepp~~tifIL~t  158 (614)
T PRK14971        120 GKYKIYIIDEVHMLSQAA-FNAFLKTLEEPPSYAIFILAT  158 (614)
T ss_pred             CCcEEEEEECcccCCHHH-HHHHHHHHhCCCCCeEEEEEe
Confidence            467899999999876543 445666666655555544444

>KOG0738 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=94.31  E-value=0.25  Score=44.72  Aligned_cols=62  Identities=23%  Similarity=0.335  Sum_probs=35.9

Q ss_pred             CChhhhccccccCCCCHHHHHHHHHCCCC-----------CChH---HHHhhh------hhhhcC-----ccEEEECCCC
Q 015158           32 TSYDEVYDTFDAMGLQENLLRGIYAYGFE-----------KPSA---IQQRGI------VPFCKG-----LDVIQQAQSG   86 (412)
Q Consensus        32 ~~~~~~~~~f~~~~l~~~~~~~l~~~~~~-----------~l~~---~Q~~a~------~~~~~~-----~~~lv~~~tG   86 (412)
                      ...+.....|+.++....+...+..--..           .+..   .=++|+      +...+|     +.++.++|+|
T Consensus       176 ~~~~~~~~~f~~~~~d~~Lve~lerdIl~~np~ikW~DIagl~~AK~lL~EAVvlPi~mPe~F~GirrPWkgvLm~GPPG  255 (491)
T KOG0738|consen  176 ASLKGEDKKFDSLGYDADLVEALERDILQRNPNIKWDDIAGLHEAKKLLKEAVVLPIWMPEFFKGIRRPWKGVLMVGPPG  255 (491)
T ss_pred             cccccccCCCCcccchHHHHHHHHHHHhccCCCcChHhhcchHHHHHHHHHHHhhhhhhHHHHhhcccccceeeeeCCCC
Confidence            34455667888888887887777532110           1111   111111      122233     6789999999


Q ss_pred             CCchhHh
Q 015158           87 TGKTATF   93 (412)
Q Consensus        87 sGKT~~~   93 (412)
                      +|||+.+
T Consensus       256 TGKTlLA  262 (491)
T KOG0738|consen  256 TGKTLLA  262 (491)
T ss_pred             CcHHHHH
Confidence            9999765

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical

Probab=94.29  E-value=0.058  Score=46.19  Aligned_cols=51  Identities=22%  Similarity=0.293  Sum_probs=35.3

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhcc-CCCceeEEEEcCCHHHHHHHHHHHHHh
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDY-GLVECQALVLAPTRELAQQIEKVMRAL  130 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~-~~~~~~~lil~P~~~L~~q~~~~~~~~  130 (412)
                      |..++|.+++|+|||..++..+.+.+.+ +   .++++++-. .-.+++.+.+..+
T Consensus        19 gs~~li~G~~GsGKT~l~~q~l~~~~~~~g---e~vlyvs~e-e~~~~l~~~~~s~   70 (226)
T PF06745_consen   19 GSVVLISGPPGSGKTTLALQFLYNGLKNFG---EKVLYVSFE-EPPEELIENMKSF   70 (226)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHHHHHHT-----EEEEESS-S-HHHHHHHHHTT
T ss_pred             CcEEEEEeCCCCCcHHHHHHHHHHhhhhcC---CcEEEEEec-CCHHHHHHHHHHc
Confidence            5678999999999998877777766655 4   378888753 3345566666655

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 ....

>PHA00350 putative assembly protein

Probab=94.29  E-value=0.37  Score=44.48  Aligned_cols=26  Identities=19%  Similarity=0.176  Sum_probs=19.3

Q ss_pred             EEEECCCCCCchhHhHH-HHHHhhccC
Q 015158           79 VIQQAQSGTGKTATFCS-GILQQLDYG  104 (412)
Q Consensus        79 ~lv~~~tGsGKT~~~~~-~~~~~~~~~  104 (412)
                      .++.+..|||||..++- .++..+..+
T Consensus         4 ~l~tG~pGSGKT~~aV~~~i~palk~G   30 (399)
T PHA00350          4 YAIVGRPGSYKSYEAVVYHIIPALKDG   30 (399)
T ss_pred             EEEecCCCCchhHHHHHHHHHHHHHCC
Confidence            47899999999987765 455555554

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=94.25  E-value=0.1  Score=47.91  Aligned_cols=40  Identities=13%  Similarity=0.100  Sum_probs=25.3

Q ss_pred             cCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcC
Q 015158           75 KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAP  115 (412)
Q Consensus        75 ~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P  115 (412)
                      .+..+++.+|||||||... .+++..+....+..+++.+=.
T Consensus       148 ~~GlilI~G~TGSGKTT~l-~al~~~i~~~~~~~~IvtiEd  187 (372)
T TIGR02525       148 AAGLGLICGETGSGKSTLA-ASIYQHCGETYPDRKIVTYED  187 (372)
T ss_pred             cCCEEEEECCCCCCHHHHH-HHHHHHHHhcCCCceEEEEec
Confidence            3456899999999999765 455555543323345555533

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).

>KOG0739 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=94.17  E-value=1.1  Score=39.22  Aligned_cols=129  Identities=18%  Similarity=0.185  Sum_probs=70.7

Q ss_pred             hhhhcCc-----cEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCc
Q 015158           71 VPFCKGL-----DVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGT  145 (412)
Q Consensus        71 ~~~~~~~-----~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~  145 (412)
                      +++..|+     .+++.+|+|+||+..+=..+.   .    .....+-+.+..|+..|.-+-.++..             
T Consensus       156 PqlFtGkR~PwrgiLLyGPPGTGKSYLAKAVAT---E----AnSTFFSvSSSDLvSKWmGESEkLVk-------------  215 (439)
T KOG0739|consen  156 PQLFTGKRKPWRGILLYGPPGTGKSYLAKAVAT---E----ANSTFFSVSSSDLVSKWMGESEKLVK-------------  215 (439)
T ss_pred             hhhhcCCCCcceeEEEeCCCCCcHHHHHHHHHh---h----cCCceEEeehHHHHHHHhccHHHHHH-------------
Confidence            4455553     478999999999955421111   1    12577777778887776654444310             


Q ss_pred             chHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccC---cHHHHHHH----HHhC----CCCce
Q 015158          146 SVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRG---FKDQIYDI----FQLL----PPKIQ  214 (412)
Q Consensus       146 ~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~---~~~~~~~i----~~~~----~~~~~  214 (412)
                                           .|+.+.+.     +.-+.|++||++.+....   -....++|    +-.+    ..+-.
T Consensus       216 ---------------------nLFemARe-----~kPSIIFiDEiDslcg~r~enEseasRRIKTEfLVQMqGVG~d~~g  269 (439)
T KOG0739|consen  216 ---------------------NLFEMARE-----NKPSIIFIDEIDSLCGSRSENESEASRRIKTEFLVQMQGVGNDNDG  269 (439)
T ss_pred             ---------------------HHHHHHHh-----cCCcEEEeehhhhhccCCCCCchHHHHHHHHHHHHhhhccccCCCc
Confidence                                 12222221     245789999999754221   11222222    2222    23456


Q ss_pred             EEEEeecCChH-HHHHHHHhcCCCeEEEecCC
Q 015158          215 VGVFSATMPPE-ALEITRKFMNKPVRILVKRD  245 (412)
Q Consensus       215 ~i~~SAT~~~~-~~~~~~~~~~~~~~~~~~~~  245 (412)
                      ++.+.||-.+- +...+++-+.+.+++.....
T Consensus       270 vLVLgATNiPw~LDsAIRRRFekRIYIPLPe~  301 (439)
T KOG0739|consen  270 VLVLGATNIPWVLDSAIRRRFEKRIYIPLPEA  301 (439)
T ss_pred             eEEEecCCCchhHHHHHHHHhhcceeccCCcH
Confidence            88888886553 34456666666555554433

>COG5008 PilU Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=94.14  E-value=0.069  Score=45.50  Aligned_cols=27  Identities=22%  Similarity=0.281  Sum_probs=18.2

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhcc
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDY  103 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~  103 (412)
                      ..-++++++||||||.+. .++..+-.+
T Consensus       127 RGLviiVGaTGSGKSTtm-AaMi~yRN~  153 (375)
T COG5008         127 RGLVIIVGATGSGKSTTM-AAMIGYRNK  153 (375)
T ss_pred             CceEEEECCCCCCchhhH-HHHhccccc
Confidence            345688999999999775 344444333

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=94.10  E-value=0.18  Score=49.33  Aligned_cols=39  Identities=15%  Similarity=0.318  Sum_probs=23.2

Q ss_pred             CCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEe
Q 015158          180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFS  219 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~S  219 (412)
                      ...+++|+||+|.+.... ...+.+.+...+....+|+.+
T Consensus       118 ~~~KVvIIDEa~~Ls~~a-~naLLK~LEepp~~~vfI~~t  156 (563)
T PRK06647        118 SRYRVYIIDEVHMLSNSA-FNALLKTIEEPPPYIVFIFAT  156 (563)
T ss_pred             CCCEEEEEEChhhcCHHH-HHHHHHhhccCCCCEEEEEec
Confidence            467899999999875443 334444444444444444433

>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=94.04  E-value=0.025  Score=46.18  Aligned_cols=43  Identities=26%  Similarity=0.305  Sum_probs=28.2

Q ss_pred             hcCCCcEEEeChHHHHHHHHcCCCC--CCCceEEEEeCCchhhcc
Q 015158          154 LSSGVHVVVGTPGRVFDMLRRQSLR--PDNIRIFVLDEADEMLSR  196 (412)
Q Consensus       154 ~~~~~~iii~T~~~l~~~~~~~~~~--~~~~~~iiiDE~h~~~~~  196 (412)
                      ....++|||+++..|+.......+.  ...-.+||+||||.+.+.
T Consensus       116 ~~~~adivi~~y~yl~~~~~~~~~~~~~~~~~ivI~DEAHNL~~~  160 (174)
T PF06733_consen  116 LAKNADIVICNYNYLFDPSIRKSLFGIDLKDNIVIFDEAHNLEDA  160 (174)
T ss_dssp             CGGG-SEEEEETHHHHSHHHHHHHCT--CCCEEEEETTGGGCGGG
T ss_pred             hcccCCEEEeCHHHHhhHHHHhhhccccccCcEEEEecccchHHH
Confidence            3456899999999887654332221  123468999999997643

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.

>COG0210 UvrD Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]

Probab=94.01  E-value=0.14  Score=51.57  Aligned_cols=70  Identities=20%  Similarity=0.193  Sum_probs=55.7

Q ss_pred             CChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccC-CCceeEEEEcCCHHHHHHHHHHHHHhhc
Q 015158           61 KPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYG-LVECQALVLAPTRELAQQIEKVMRALGD  132 (412)
Q Consensus        61 ~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~-~~~~~~lil~P~~~L~~q~~~~~~~~~~  132 (412)
                      .|++-|++|+...  ...++|.++.|||||.+..--+...+... -....++.++=|+.-+.++.+++..+..
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            4889999999887  55689999999999998877777776653 3334688888888888889888888764

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=93.97  E-value=0.09  Score=48.18  Aligned_cols=27  Identities=22%  Similarity=0.406  Sum_probs=20.2

Q ss_pred             cCccEEEECCCCCCchhHhHHHHHHhhc
Q 015158           75 KGLDVIQQAQSGTGKTATFCSGILQQLD  102 (412)
Q Consensus        75 ~~~~~lv~~~tGsGKT~~~~~~~~~~~~  102 (412)
                      .+..++|.+|||||||... .+++..+.
T Consensus       133 ~~glilI~GpTGSGKTTtL-~aLl~~i~  159 (358)
T TIGR02524       133 QEGIVFITGATGSGKSTLL-AAIIRELA  159 (358)
T ss_pred             cCCEEEEECCCCCCHHHHH-HHHHHHHh
Confidence            4567899999999999765 45555553

Members of this protein family are the DotB component of Dot/Icm secretion systems, as found in obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii. While this system resembles type IV secretion systems and has been called a form of type IV, the liturature now seems to favor calling this the Dot/Icm system. This family is most closely related to TraJ proteins of plasmid transfer, rather than to proteins of other type IV secretion systems.

>KOG0732 consensus AAA+-type ATPase containing the bromodomain [Posttranslational modification, protein turnover, chaperones]

Probab=93.92  E-value=0.12  Score=53.04  Aligned_cols=57  Identities=19%  Similarity=0.140  Sum_probs=39.9

Q ss_pred             hhccccccCCCCHHHHHHHHHCCCCCC-hHHHHhhhhhhhcCccEEEECCCCCCchhHh
Q 015158           36 EVYDTFDAMGLQENLLRGIYAYGFEKP-SAIQQRGIVPFCKGLDVIQQAQSGTGKTATF   93 (412)
Q Consensus        36 ~~~~~f~~~~l~~~~~~~l~~~~~~~l-~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~   93 (412)
                      .....|++.+....++..|+++-+..+ ||-+..-+ .+.-.+.++..+|.|+|||+.+
T Consensus       259 ~~~v~fd~vggl~~~i~~LKEmVl~PLlyPE~f~~~-~itpPrgvL~~GppGTGkTl~a  316 (1080)
T KOG0732|consen  259 DSSVGFDSVGGLENYINQLKEMVLLPLLYPEFFDNF-NITPPRGVLFHGPPGTGKTLMA  316 (1080)
T ss_pred             hcccCccccccHHHHHHHHHHHHHhHhhhhhHhhhc-ccCCCcceeecCCCCCchhHHH
Confidence            445689999988999999988755432 33222222 3444577999999999999775

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=93.90  E-value=0.23  Score=51.42  Aligned_cols=78  Identities=21%  Similarity=0.276  Sum_probs=65.2

Q ss_pred             CCCcEEEEEcchhHHHHHHHHHhcC----CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcC-CCcCCCCCCCCCEEE
Q 015158          277 AITQSVIFVNTRRKVDWLTDKMRSR----DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTD-LLARGIDVQQVSLVI  351 (412)
Q Consensus       277 ~~~k~lif~~~~~~~~~~~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~-~~~~G~d~~~~~~vi  351 (412)
                      .+.+++|.+|+..-|.+.++.+++.    +..+..++|..+..++.++++.+.+|+.+|+|+|. .+...+.+.++..+|
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            3468999999999999888877653    56788899999999999999999999999999998 555667888888888


Q ss_pred             Ecc
Q 015158          352 NYD  354 (412)
Q Consensus       352 ~~~  354 (412)
                      +-+
T Consensus       579 IDE  581 (926)
T TIGR00580       579 IDE  581 (926)
T ss_pred             eec
Confidence            544

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.

>PRK09087 hypothetical protein; Validated

Probab=93.90  E-value=0.24  Score=42.30  Aligned_cols=38  Identities=3%  Similarity=0.044  Sum_probs=23.8

Q ss_pred             eEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEeecC
Q 015158          183 RIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATM  222 (412)
Q Consensus       183 ~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~  222 (412)
                      +++++|++|.+. . ....+..+++.+......+++|++.
T Consensus        89 ~~l~iDDi~~~~-~-~~~~lf~l~n~~~~~g~~ilits~~  126 (226)
T PRK09087         89 GPVLIEDIDAGG-F-DETGLFHLINSVRQAGTSLLMTSRL  126 (226)
T ss_pred             CeEEEECCCCCC-C-CHHHHHHHHHHHHhCCCeEEEECCC
Confidence            489999999763 2 2456777776665533445555553

>PRK08506 replicative DNA helicase; Provisional

Probab=93.89  E-value=0.76  Score=44.09  Aligned_cols=115  Identities=22%  Similarity=0.167  Sum_probs=59.2

Q ss_pred             hhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEE-EcCcchHHHH
Q 015158           73 FCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHAC-VGGTSVREDQ  151 (412)
Q Consensus        73 ~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~  151 (412)
                      +..|.-+++.|.||.|||..++-.+.+....   +.++++++.- .-..|+..++-....  +++...+ .|..+...+.
T Consensus       189 ~~~G~LivIaarpg~GKT~fal~ia~~~~~~---g~~V~~fSlE-Ms~~ql~~Rlla~~s--~v~~~~i~~~~l~~~e~~  262 (472)
T PRK08506        189 FNKGDLIIIAARPSMGKTTLCLNMALKALNQ---DKGVAFFSLE-MPAEQLMLRMLSAKT--SIPLQNLRTGDLDDDEWE  262 (472)
T ss_pred             CCCCceEEEEcCCCCChHHHHHHHHHHHHhc---CCcEEEEeCc-CCHHHHHHHHHHHhc--CCCHHHHhcCCCCHHHHH
Confidence            3345667889999999998776666555432   3467777543 335555555433211  2222111 1222222221


Q ss_pred             ------HHhcCCCcEEEe-----ChHHHHHHHHcCCCCCCCceEEEEeCCchhh
Q 015158          152 ------RILSSGVHVVVG-----TPGRVFDMLRRQSLRPDNIRIFVLDEADEML  194 (412)
Q Consensus       152 ------~~~~~~~~iii~-----T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~  194 (412)
                            ..+.. ..+.|-     |.+.+...+++.......+++||||=.+.+.
T Consensus       263 ~~~~a~~~l~~-~~l~I~d~~~~ti~~I~~~~r~l~~~~~~~~lvvIDyLql~~  315 (472)
T PRK08506        263 RLSDACDELSK-KKLFVYDSGYVNIHQVRAQLRKLKSQHPEIGLAVIDYLQLMS  315 (472)
T ss_pred             HHHHHHHHHHc-CCeEEECCCCCCHHHHHHHHHHHHHhCCCCCEEEEcChhhcc
Confidence                  11122 235442     4444444333211112357899999999765

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=93.71  E-value=0.087  Score=47.75  Aligned_cols=42  Identities=19%  Similarity=0.255  Sum_probs=28.1

Q ss_pred             hcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHH
Q 015158           74 CKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTREL  119 (412)
Q Consensus        74 ~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L  119 (412)
                      ..+++++|+|+||||||... -+++..+...   .+++.+=.+.++
T Consensus       158 ~~~~nili~G~tgSGKTTll-~aL~~~ip~~---~ri~tiEd~~El  199 (332)
T PRK13900        158 ISKKNIIISGGTSTGKTTFT-NAALREIPAI---ERLITVEDAREI  199 (332)
T ss_pred             HcCCcEEEECCCCCCHHHHH-HHHHhhCCCC---CeEEEecCCCcc
Confidence            35789999999999999764 4555555433   366665444443

>cd01393 recA_like RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=93.58  E-value=0.3  Score=41.78  Aligned_cols=42  Identities=17%  Similarity=0.069  Sum_probs=28.1

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhccC---CCceeEEEEcCCH
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDYG---LVECQALVLAPTR  117 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~~---~~~~~~lil~P~~  117 (412)
                      |.-+.|.+++|+|||..++..+......+   .....++++....
T Consensus        19 g~v~~I~G~~GsGKT~l~~~ia~~~~~~~~~~g~~~~v~yi~~e~   63 (226)
T cd01393          19 GRITEIFGEFGSGKTQLCLQLAVEAQLPGELGGLEGKVVYIDTEG   63 (226)
T ss_pred             CcEEEEeCCCCCChhHHHHHHHHHhhcccccCCCcceEEEEecCC
Confidence            56788999999999987766555543322   0124678877654

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.

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=93.55  E-value=0.28  Score=44.60  Aligned_cols=41  Identities=10%  Similarity=0.312  Sum_probs=28.1

Q ss_pred             CCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEeec
Q 015158          180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSAT  221 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT  221 (412)
                      ...+++||||+|.+.... ...+.+.+..-|.+..+|++|..
T Consensus       109 ~~~kvviI~~a~~~~~~a-~NaLLK~LEEPp~~~~~Il~t~~  149 (329)
T PRK08058        109 SNKKVYIIEHADKMTASA-ANSLLKFLEEPSGGTTAILLTEN  149 (329)
T ss_pred             cCceEEEeehHhhhCHHH-HHHHHHHhcCCCCCceEEEEeCC
Confidence            457899999999876543 45666666666666666665443

>KOG0737 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=93.54  E-value=0.73  Score=41.49  Aligned_cols=59  Identities=17%  Similarity=0.056  Sum_probs=36.4

Q ss_pred             hhccccccCCCCHHHHHHHHHCCCCCC-hHHHHhhhhhhhcCccEEEECCCCCCchhHhH
Q 015158           36 EVYDTFDAMGLQENLLRGIYAYGFEKP-SAIQQRGIVPFCKGLDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        36 ~~~~~f~~~~l~~~~~~~l~~~~~~~l-~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~   94 (412)
                      ....+|.+.+--+.+.+.|++.-.-.+ +|-.-.-...+...+.+++.+|+|+|||+++-
T Consensus        86 ~I~v~f~DIggLe~v~~~L~e~VilPlr~pelF~~g~Ll~p~kGiLL~GPpG~GKTmlAK  145 (386)
T KOG0737|consen   86 EIGVSFDDIGGLEEVKDALQELVILPLRRPELFAKGKLLRPPKGILLYGPPGTGKTMLAK  145 (386)
T ss_pred             hceeehhhccchHHHHHHHHHHHhhcccchhhhcccccccCCccceecCCCCchHHHHHH
Confidence            344577777777777777765433222 22222222223334788999999999998873

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.43  E-value=0.76  Score=44.17  Aligned_cols=37  Identities=14%  Similarity=0.374  Sum_probs=21.8

Q ss_pred             CCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEE
Q 015158          180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGV  217 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~  217 (412)
                      ....++|+||+|.+.... ...+...+...++...+|+
T Consensus       118 ~~~KVvIIDEad~Lt~~a-~naLLk~LEepp~~~v~Il  154 (486)
T PRK14953        118 GKYKVYIIDEAHMLTKEA-FNALLKTLEEPPPRTIFIL  154 (486)
T ss_pred             CCeeEEEEEChhhcCHHH-HHHHHHHHhcCCCCeEEEE
Confidence            456899999999875443 2344444444444443333

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=93.37  E-value=0.41  Score=48.87  Aligned_cols=19  Identities=32%  Similarity=0.282  Sum_probs=16.1

Q ss_pred             cCccEEEECCCCCCchhHh
Q 015158           75 KGLDVIQQAQSGTGKTATF   93 (412)
Q Consensus        75 ~~~~~lv~~~tGsGKT~~~   93 (412)
                      .++.+++.||+|+|||..+
T Consensus       211 ~~~giLL~GppGtGKT~la  229 (733)
T TIGR01243       211 PPKGVLLYGPPGTGKTLLA  229 (733)
T ss_pred             CCceEEEECCCCCChHHHH
Confidence            4578999999999999664

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.

>PRK10689 transcription-repair coupling factor; Provisional

Probab=93.34  E-value=0.34  Score=51.48  Aligned_cols=78  Identities=21%  Similarity=0.230  Sum_probs=63.9

Q ss_pred             CCCcEEEEEcchhHHHHHHHHHhcC----CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcC-CCcCCCCCCCCCEEE
Q 015158          277 AITQSVIFVNTRRKVDWLTDKMRSR----DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTD-LLARGIDVQQVSLVI  351 (412)
Q Consensus       277 ~~~k~lif~~~~~~~~~~~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~-~~~~G~d~~~~~~vi  351 (412)
                      .+.+++|.+|++.-|.+.++.+++.    +..+..+++..+..++.++++...+|+.+|+|+|. .+...+++.++..+|
T Consensus       648 ~g~qvlvLvPT~eLA~Q~~~~f~~~~~~~~v~i~~l~g~~s~~e~~~il~~l~~g~~dIVVgTp~lL~~~v~~~~L~lLV  727 (1147)
T PRK10689        648 NHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLLQSDVKWKDLGLLI  727 (1147)
T ss_pred             cCCeEEEEeCcHHHHHHHHHHHHHhhccCCceEEEEECCCCHHHHHHHHHHHHhCCCCEEEECHHHHhCCCCHhhCCEEE
Confidence            4568999999999999988888753    45778899999999999999999999999999997 445556777788877


Q ss_pred             Ecc
Q 015158          352 NYD  354 (412)
Q Consensus       352 ~~~  354 (412)
                      +-+
T Consensus       728 IDE  730 (1147)
T PRK10689        728 VDE  730 (1147)
T ss_pred             Eec
Confidence            543

>KOG1513 consensus Nuclear helicase MOP-3/SNO (DEAD-box superfamily) [Transcription; Signal transduction mechanisms]

Probab=93.32  E-value=0.068  Score=52.38  Aligned_cols=55  Identities=25%  Similarity=0.418  Sum_probs=47.1

Q ss_pred             HHHHHhcCCCcEEEEcCCCcCCCCCCCCCEE--------EEccCCCChhhHHHhhhhcccCCC
Q 015158          320 IMREFRSGSSRVLITTDLLARGIDVQQVSLV--------INYDLPTQPENYLHRIGRSGRFGR  374 (412)
Q Consensus       320 ~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~v--------i~~~~~~s~~~~~Q~~GR~~R~g~  374 (412)
                      -.++|..|+..|-|.+.+.+.||.+..-+.|        |-+++|||....+|..||..|.++
T Consensus       849 EKqrFM~GeK~vAIISEAaSSGiSLQsDrRv~NqRRRvHiTLELPWSADrAIQQFGRTHRSNQ  911 (1300)
T KOG1513|consen  849 EKQRFMDGEKLVAIISEAASSGISLQSDRRVQNQRRRVHITLELPWSADRAIQQFGRTHRSNQ  911 (1300)
T ss_pred             HHhhhccccceeeeeehhhccCceeecchhhhhhhheEEEEEECCcchhHHHHHhcccccccc
Confidence            4578999999999999999999998754443        457899999999999999999865

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=93.30  E-value=1.7  Score=41.76  Aligned_cols=77  Identities=5%  Similarity=0.113  Sum_probs=63.1

Q ss_pred             CCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcC-CCcCCC-------CCCCCCE
Q 015158          278 ITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTD-LLARGI-------DVQQVSL  349 (412)
Q Consensus       278 ~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~-~~~~G~-------d~~~~~~  349 (412)
                      .+.+||.+|+++-++...+.|+..++.+..+++..+..++..++....+++.+++++|+ .+....       ....+..
T Consensus        51 ~~~~lVi~P~~~L~~dq~~~l~~~gi~~~~l~~~~~~~~~~~i~~~~~~~~~~il~~TPe~l~~~~~~~~~l~~~~~i~~  130 (470)
T TIGR00614        51 DGITLVISPLISLMEDQVLQLKASGIPATFLNSSQSKEQQKNVLTDLKDGKIKLLYVTPEKCSASNRLLQTLEERKGITL  130 (470)
T ss_pred             CCcEEEEecHHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHcCchhHHHHHHhcCCcCE
Confidence            46799999999999999999999999999999999999999999999999999999998 222222       3456777


Q ss_pred             EEEcc
Q 015158          350 VINYD  354 (412)
Q Consensus       350 vi~~~  354 (412)
                      +|+.+
T Consensus       131 iViDE  135 (470)
T TIGR00614       131 IAVDE  135 (470)
T ss_pred             EEEeC
Confidence            76544

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

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=93.27  E-value=0.77  Score=43.72  Aligned_cols=39  Identities=10%  Similarity=0.309  Sum_probs=24.5

Q ss_pred             CCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEe
Q 015158          180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFS  219 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~S  219 (412)
                      ....+||+||+|.+.... ...+.+.+...+....+|+.+
T Consensus       120 ~~~kvvIIdead~lt~~~-~n~LLk~lEep~~~~~~Il~t  158 (451)
T PRK06305        120 SRYKIYIIDEVHMLTKEA-FNSLLKTLEEPPQHVKFFLAT  158 (451)
T ss_pred             CCCEEEEEecHHhhCHHH-HHHHHHHhhcCCCCceEEEEe
Confidence            356899999999875443 344555555555555555544

>COG0541 Ffh Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=93.11  E-value=1.6  Score=40.40  Aligned_cols=133  Identities=16%  Similarity=0.243  Sum_probs=75.7

Q ss_pred             cEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCC
Q 015158           78 DVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSG  157 (412)
Q Consensus        78 ~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  157 (412)
                      .++.++=-|||||+++-=.+.. +..  .+.++++++.-.- -.-..++++.++...++.+.....+..  ..       
T Consensus       102 vImmvGLQGsGKTTt~~KLA~~-lkk--~~~kvllVaaD~~-RpAA~eQL~~La~q~~v~~f~~~~~~~--Pv-------  168 (451)
T COG0541         102 VILMVGLQGSGKTTTAGKLAKY-LKK--KGKKVLLVAADTY-RPAAIEQLKQLAEQVGVPFFGSGTEKD--PV-------  168 (451)
T ss_pred             EEEEEeccCCChHhHHHHHHHH-HHH--cCCceEEEecccC-ChHHHHHHHHHHHHcCCceecCCCCCC--HH-------
Confidence            3677899999999876433332 222  3345666553211 111344555555555665544411111  11       


Q ss_pred             CcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhh-ccCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHh
Q 015158          158 VHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEML-SRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKF  233 (412)
Q Consensus       158 ~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~-~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~  233 (412)
                       +  |+     .+.+...  ....++++|+|=|-++- +...-..+..+...+.++-.++.+-|+...+.......|
T Consensus       169 -~--Ia-----k~al~~a--k~~~~DvvIvDTAGRl~ide~Lm~El~~Ik~~~~P~E~llVvDam~GQdA~~~A~aF  235 (451)
T COG0541         169 -E--IA-----KAALEKA--KEEGYDVVIVDTAGRLHIDEELMDELKEIKEVINPDETLLVVDAMIGQDAVNTAKAF  235 (451)
T ss_pred             -H--HH-----HHHHHHH--HHcCCCEEEEeCCCcccccHHHHHHHHHHHhhcCCCeEEEEEecccchHHHHHHHHH
Confidence             0  11     1222211  12457899999887643 445667888888888888888999999876655444433

>PRK08840 replicative DNA helicase; Provisional

Probab=93.07  E-value=1  Score=43.01  Aligned_cols=120  Identities=18%  Similarity=0.094  Sum_probs=57.7

Q ss_pred             hhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEE-EcCcchH
Q 015158           70 IVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHAC-VGGTSVR  148 (412)
Q Consensus        70 ~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~-~~~~~~~  148 (412)
                      +.-+..|.-++|.|.||.|||..++-.+.+....  .+..++|...- .-.+|+..++-....  ++....+ .|..+..
T Consensus       211 ~~G~~~g~LiviaarPg~GKTafalnia~~~a~~--~~~~v~~fSlE-Ms~~ql~~Rlla~~s--~v~~~~i~~~~l~~~  285 (464)
T PRK08840        211 TAGLQGSDLIIVAARPSMGKTTFAMNLCENAAMD--QDKPVLIFSLE-MPAEQLMMRMLASLS--RVDQTKIRTGQLDDE  285 (464)
T ss_pred             hcCCCCCceEEEEeCCCCchHHHHHHHHHHHHHh--CCCeEEEEecc-CCHHHHHHHHHHhhC--CCCHHHHhcCCCCHH
Confidence            3334456677889999999997665444443222  13457776543 334555544433211  2222111 1222222


Q ss_pred             HHHH------HhcCCCcEEEe-----ChHHHHHHHHcCCCCCCCceEEEEeCCchhh
Q 015158          149 EDQR------ILSSGVHVVVG-----TPGRVFDMLRRQSLRPDNIRIFVLDEADEML  194 (412)
Q Consensus       149 ~~~~------~~~~~~~iii~-----T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~  194 (412)
                      .+..      .+.....+.|-     |...+.....+.......+++||||=.|.+.
T Consensus       286 e~~~~~~a~~~l~~~~~l~I~d~~~~ti~~i~~~~r~~~~~~~~~~lvvIDYLql~~  342 (464)
T PRK08840        286 DWARISSTMGILMEKKNMYIDDSSGLTPTEVRSRARRIAREHGGLSMIMVDYLQLMR  342 (464)
T ss_pred             HHHHHHHHHHHHHhcCCEEEECCCCCCHHHHHHHHHHHHHhcCCCCEEEEccHHhcC
Confidence            2211      11122345553     3334433222211111257899999999774

>PHA03372 DNA packaging terminase subunit 1; Provisional

Probab=93.02  E-value=0.99  Score=43.66  Aligned_cols=133  Identities=17%  Similarity=0.154  Sum_probs=71.8

Q ss_pred             ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHh-hcccCcEEEEEEcCcchHHHHHHhc
Q 015158           77 LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRAL-GDYLGVKVHACVGGTSVREDQRILS  155 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~  155 (412)
                      +-.+.-.|---|||+.. .+++..+.....+-++.|++.-+.-++-..+++... ..+++-......-+........  .
T Consensus       203 kaTVFLVPRRHGKTWf~-VpiIsllL~s~~gI~IGYvAHqKhvs~~Vf~EI~~~lrrwF~~~~vi~~k~~tI~~s~p--g  279 (668)
T PHA03372        203 KATVFLVPRRHGKTWFI-IPIISFLLKNIIGISIGYVAHQKHVSQFVLKEVEFRCRRMFPRKHTIENKDNVISIDHR--G  279 (668)
T ss_pred             cceEEEecccCCceehH-HHHHHHHHHhhcCceEEEEeeHHHHHHHHHHHHHHHHhhhcCccceeeecCcEEEEecC--C
Confidence            44577789999999764 344444444445668999999887766666655432 1222211111100000000000  0


Q ss_pred             CCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhC-CCCceEEEEeecC
Q 015158          156 SGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLL-PPKIQVGVFSATM  222 (412)
Q Consensus       156 ~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~-~~~~~~i~~SAT~  222 (412)
                      .+..++.+|      ......+..++++++++||||.+..    ..+..++..+ .++.++|++|.|-
T Consensus       280 ~Kst~~fas------c~n~NsiRGQ~fnll~VDEA~FI~~----~a~~tilgfm~q~~~KiIfISS~N  337 (668)
T PHA03372        280 AKSTALFAS------CYNTNSIRGQNFHLLLVDEAHFIKK----DAFNTILGFLAQNTTKIIFISSTN  337 (668)
T ss_pred             Ccceeeehh------hccCccccCCCCCEEEEehhhccCH----HHHHHhhhhhcccCceEEEEeCCC
Confidence            011122222      1223345567899999999996543    3344444443 3578899999884

>KOG0780 consensus Signal recognition particle, subunit Srp54 [Intracellular trafficking, secretion, and vesicular transport]

Probab=92.99  E-value=0.53  Score=42.59  Aligned_cols=133  Identities=12%  Similarity=0.150  Sum_probs=75.4

Q ss_pred             cEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCC
Q 015158           78 DVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSG  157 (412)
Q Consensus        78 ~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  157 (412)
                      -+++++=.|+|||.+..-.++..-..   +.++.++|.-.= -.-.+++++..+...++++..-+  +..+.        
T Consensus       103 VimfVGLqG~GKTTtc~KlA~y~kkk---G~K~~LvcaDTF-RagAfDQLkqnA~k~~iP~ygsy--te~dp--------  168 (483)
T KOG0780|consen  103 VIMFVGLQGSGKTTTCTKLAYYYKKK---GYKVALVCADTF-RAGAFDQLKQNATKARVPFYGSY--TEADP--------  168 (483)
T ss_pred             EEEEEeccCCCcceeHHHHHHHHHhc---CCceeEEeeccc-ccchHHHHHHHhHhhCCeeEecc--cccch--------
Confidence            45779999999997765444444333   345666664321 11134444444433355443321  11111        


Q ss_pred             CcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhh-ccCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHh
Q 015158          158 VHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEML-SRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKF  233 (412)
Q Consensus       158 ~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~-~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~  233 (412)
                        +.|+.     .-+.  .+...++++||+|=.-+.- +.+....+..+.+...++.-++.+-|+...........+
T Consensus       169 --v~ia~-----egv~--~fKke~fdvIIvDTSGRh~qe~sLfeEM~~v~~ai~Pd~vi~VmDasiGQaae~Qa~aF  236 (483)
T KOG0780|consen  169 --VKIAS-----EGVD--RFKKENFDVIIVDTSGRHKQEASLFEEMKQVSKAIKPDEIIFVMDASIGQAAEAQARAF  236 (483)
T ss_pred             --HHHHH-----HHHH--HHHhcCCcEEEEeCCCchhhhHHHHHHHHHHHhhcCCCeEEEEEeccccHhHHHHHHHH
Confidence              11111     1111  2233578999999876543 333567788888888888889999999876655544443

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=92.99  E-value=0.59  Score=42.11  Aligned_cols=60  Identities=10%  Similarity=0.177  Sum_probs=35.8

Q ss_pred             EEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEeecC
Q 015158          160 VVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATM  222 (412)
Q Consensus       160 iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~  222 (412)
                      |-|-....+.+.+...... ...+++|+|++|.+.... ...+.+.+..-+ +..+|++|..+
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            3344444455545444333 467899999999875443 455666666665 66555555443

>PF12846 AAA_10: AAA-like domain

Probab=92.98  E-value=0.12  Score=46.36  Aligned_cols=38  Identities=18%  Similarity=0.334  Sum_probs=26.6

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCC
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPT  116 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~  116 (412)
                      +.+++|.|+||+|||..+...+...+..+   ..++++=|.
T Consensus         1 n~h~~i~G~tGsGKT~~~~~l~~~~~~~g---~~~~i~D~~   38 (304)
T PF12846_consen    1 NPHTLILGKTGSGKTTLLKNLLEQLIRRG---PRVVIFDPK   38 (304)
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHHHHcC---CCEEEEcCC
Confidence            35789999999999988765554444444   456666454

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=92.98  E-value=0.44  Score=47.56  Aligned_cols=39  Identities=10%  Similarity=0.272  Sum_probs=24.2

Q ss_pred             CCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEe
Q 015158          180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFS  219 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~S  219 (412)
                      ....++|+||+|.+.... ...+.+.+...+....+|+.|
T Consensus       117 g~~KV~IIDEa~~LT~~A-~NALLKtLEEPP~~tifILaT  155 (725)
T PRK07133        117 SKYKIYIIDEVHMLSKSA-FNALLKTLEEPPKHVIFILAT  155 (725)
T ss_pred             CCCEEEEEEChhhCCHHH-HHHHHHHhhcCCCceEEEEEc
Confidence            467899999999876443 334455555545455445444

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=92.98  E-value=0.77  Score=46.83  Aligned_cols=19  Identities=26%  Similarity=0.274  Sum_probs=16.2

Q ss_pred             ccEEEECCCCCCchhHhHH
Q 015158           77 LDVIQQAQSGTGKTATFCS   95 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~~   95 (412)
                      .+.++.||+|+|||..+-.
T Consensus       204 ~n~lL~G~pG~GKT~l~~~  222 (731)
T TIGR02639       204 NNPLLVGEPGVGKTAIAEG  222 (731)
T ss_pred             CceEEECCCCCCHHHHHHH
Confidence            5899999999999977643

>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=92.97  E-value=0.12  Score=45.58  Aligned_cols=43  Identities=16%  Similarity=0.328  Sum_probs=29.3

Q ss_pred             hcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHH
Q 015158           74 CKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTREL  119 (412)
Q Consensus        74 ~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L  119 (412)
                      ..++++++.|+||||||..+ .+++..+...  ..+++.+-...++
T Consensus       125 ~~~~~ili~G~tGSGKTT~l-~all~~i~~~--~~~iv~iEd~~E~  167 (270)
T PF00437_consen  125 RGRGNILISGPTGSGKTTLL-NALLEEIPPE--DERIVTIEDPPEL  167 (270)
T ss_dssp             HTTEEEEEEESTTSSHHHHH-HHHHHHCHTT--TSEEEEEESSS-S
T ss_pred             ccceEEEEECCCccccchHH-HHHhhhcccc--ccceEEeccccce
Confidence            45688999999999999776 4455555443  2467777665553

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 ....

>COG1132 MdlB ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]

Probab=92.92  E-value=0.82  Score=45.24  Aligned_cols=37  Identities=24%  Similarity=0.272  Sum_probs=23.8

Q ss_pred             hhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEE
Q 015158           73 FCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALV  112 (412)
Q Consensus        73 ~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~li  112 (412)
                      +..|..+.+++|+|||||+..-  ++..+... ..+++++
T Consensus       352 i~~Ge~vaiVG~sGsGKSTl~~--LL~r~~~~-~~G~I~i  388 (567)
T COG1132         352 IEPGEKVAIVGPSGSGKSTLIK--LLLRLYDP-TSGEILI  388 (567)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH--HHhccCCC-CCCeEEE
Confidence            5567888899999999986543  23333332 2345666

>TIGR02868 CydC thiol reductant ABC exporter, CydC subunit

Probab=92.92  E-value=0.92  Score=44.45  Aligned_cols=21  Identities=29%  Similarity=0.384  Sum_probs=17.5

Q ss_pred             hhcCccEEEECCCCCCchhHh
Q 015158           73 FCKGLDVIQQAQSGTGKTATF   93 (412)
Q Consensus        73 ~~~~~~~lv~~~tGsGKT~~~   93 (412)
                      +..|+.+.++||+|+|||+..
T Consensus       358 i~~G~~vaIvG~SGsGKSTLl  378 (529)
T TIGR02868       358 LPPGERVAILGPSGSGKSTLL  378 (529)
T ss_pred             EcCCCEEEEECCCCCCHHHHH
Confidence            446889999999999999654

The gene pair cydCD encodes an ABC-family transporter in which each gene contains an N-terminal membrane-spanning domain (pfam00664) and a C-terminal ATP-binding domain (pfam00005). In E. coli these genes were discovered as mutants which caused the terminal heme-copper oxidase complex cytochrome bd to fail to assemble. Recent work has shown that the transporter is involved in export of redox-active thiol compounds such as cysteine and glutathione. The linkage to assembly of the cytochrome bd complex is further supported by the conserved operon structure found outside the gammaproteobacteria (cydABCD) containing both the transporter and oxidase genes components. The genes used as the seed members for this model are all either found in the gammproteobacterial context or the CydABCD context. All members of this family scoring above trusted at the time of its creation were from genomes which encode a cytochrome bd complex.

>PRK09165 replicative DNA helicase; Provisional

Probab=92.92  E-value=0.47  Score=45.81  Aligned_cols=117  Identities=11%  Similarity=0.058  Sum_probs=57.8

Q ss_pred             hcCccEEEECCCCCCchhHhHHHHHHhhccC------------CCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEE
Q 015158           74 CKGLDVIQQAQSGTGKTATFCSGILQQLDYG------------LVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHAC  141 (412)
Q Consensus        74 ~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~------------~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~  141 (412)
                      ..|.-++|.|.||.|||..++-.+.+.....            ..+.+++|++.- .-..|+..++.....  +++...+
T Consensus       215 ~~g~livIaarpg~GKT~~al~ia~~~a~~~~~~~~~~~~~~~~~g~~vl~fSlE-Ms~~ql~~R~la~~s--~v~~~~i  291 (497)
T PRK09165        215 HPSDLIILAGRPSMGKTALATNIAFNAAKAYRREAQPDGSKKAVNGGVVGFFSLE-MSAEQLATRILSEQS--EISSSKI  291 (497)
T ss_pred             CCCceEEEEeCCCCChHHHHHHHHHHHHHhhcccccccccccccCCCeEEEEeCc-CCHHHHHHHHHHHhc--CCCHHHH
Confidence            3455678899999999977655444433211            113467776543 334556555443321  2222211


Q ss_pred             -EcCcchHHHHHHh-----cCCCcEEEe-----ChHHHHHHHHcCCCCCCCceEEEEeCCchhh
Q 015158          142 -VGGTSVREDQRIL-----SSGVHVVVG-----TPGRVFDMLRRQSLRPDNIRIFVLDEADEML  194 (412)
Q Consensus       142 -~~~~~~~~~~~~~-----~~~~~iii~-----T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~  194 (412)
                       .|......+....     .....+.|-     |.+.+.....+... ...+++||||=.|.+.
T Consensus       292 ~~~~l~~~e~~~l~~a~~~l~~~~l~I~d~~~~ti~~i~~~ir~l~~-~~~~~lvvIDyLqli~  354 (497)
T PRK09165        292 RRGKISEEDFEKLVDASQELQKLPLYIDDTPALSISQLRARARRLKR-QHGLDLLVVDYLQLIR  354 (497)
T ss_pred             hcCCCCHHHHHHHHHHHHHHhcCCeEEeCCCCCCHHHHHHHHHHHHH-hcCCCEEEEcchHhcc
Confidence             2222222221110     122345543     34455443332211 1358999999999765

>PRK04328 hypothetical protein; Provisional

Probab=92.90  E-value=0.2  Score=43.53  Aligned_cols=51  Identities=24%  Similarity=0.240  Sum_probs=34.2

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRAL  130 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~  130 (412)
                      |..++|.+++|+|||..++..+...+..+   .+++|+.- ..-..+..+.+..+
T Consensus        23 gs~ili~G~pGsGKT~l~~~fl~~~~~~g---e~~lyis~-ee~~~~i~~~~~~~   73 (249)
T PRK04328         23 RNVVLLSGGPGTGKSIFSQQFLWNGLQMG---EPGVYVAL-EEHPVQVRRNMRQF   73 (249)
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHHHhcC---CcEEEEEe-eCCHHHHHHHHHHc
Confidence            56789999999999987766666655443   36777763 33344455555554

>TIGR00416 sms DNA repair protein RadA

Probab=92.90  E-value=0.56  Score=44.66  Aligned_cols=51  Identities=20%  Similarity=0.179  Sum_probs=34.0

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRAL  130 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~  130 (412)
                      |.-+++.+++|+|||..++..+......   +.+++|+..-. -..|+......+
T Consensus        94 GsvilI~G~pGsGKTTL~lq~a~~~a~~---g~kvlYvs~EE-s~~qi~~ra~rl  144 (454)
T TIGR00416        94 GSLILIGGDPGIGKSTLLLQVACQLAKN---QMKVLYVSGEE-SLQQIKMRAIRL  144 (454)
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHHHhc---CCcEEEEECcC-CHHHHHHHHHHc
Confidence            5678899999999998776655544333   24788887643 345555555544

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)).

>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=92.87  E-value=0.079  Score=46.45  Aligned_cols=18  Identities=22%  Similarity=0.350  Sum_probs=15.6

Q ss_pred             CccEEEECCCCCCchhHh
Q 015158           76 GLDVIQQAQSGTGKTATF   93 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~   93 (412)
                      ..|+++.+|||||||+.+
T Consensus        97 KSNILLiGPTGsGKTlLA  114 (408)
T COG1219          97 KSNILLIGPTGSGKTLLA  114 (408)
T ss_pred             eccEEEECCCCCcHHHHH
Confidence            358999999999999766

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

Probab=92.83  E-value=1  Score=44.10  Aligned_cols=78  Identities=19%  Similarity=0.311  Sum_probs=66.3

Q ss_pred             CCCcEEEEEcch----hHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcC-CCcCCCCCCCCCEEE
Q 015158          277 AITQSVIFVNTR----RKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTD-LLARGIDVQQVSLVI  351 (412)
Q Consensus       277 ~~~k~lif~~~~----~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~-~~~~G~d~~~~~~vi  351 (412)
                      .+..+.+-+|+.    .+...+.+.|...|+.+.++.|.+....|.+++++..+|+.+++|+|- .+...+++.+.-.||
T Consensus       310 ~G~Q~ALMAPTEILA~QH~~~~~~~l~~~~i~V~lLtG~~kgk~r~~~l~~l~~G~~~ivVGTHALiQd~V~F~~LgLVI  389 (677)
T COG1200         310 AGYQAALMAPTEILAEQHYESLRKWLEPLGIRVALLTGSLKGKARKEILEQLASGEIDIVVGTHALIQDKVEFHNLGLVI  389 (677)
T ss_pred             cCCeeEEeccHHHHHHHHHHHHHHHhhhcCCeEEEeecccchhHHHHHHHHHhCCCCCEEEEcchhhhcceeecceeEEE
Confidence            445678888884    566777888888899999999999999999999999999999999997 558899998888887


Q ss_pred             Ecc
Q 015158          352 NYD  354 (412)
Q Consensus       352 ~~~  354 (412)
                      +.+
T Consensus       390 iDE  392 (677)
T COG1200         390 IDE  392 (677)
T ss_pred             Eec
Confidence            544

>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases

Probab=92.75  E-value=0.12  Score=42.71  Aligned_cols=39  Identities=18%  Similarity=0.248  Sum_probs=26.8

Q ss_pred             ChHHHHhhhhhhh-cCccEEEECCCCCCchhHhHHHHHHhh
Q 015158           62 PSAIQQRGIVPFC-KGLDVIQQAQSGTGKTATFCSGILQQL  101 (412)
Q Consensus        62 l~~~Q~~a~~~~~-~~~~~lv~~~tGsGKT~~~~~~~~~~~  101 (412)
                      +.+.|.+.+.... .+..+++.+|||||||..+ -+++..+
T Consensus        10 ~~~~~~~~l~~~v~~g~~i~I~G~tGSGKTTll-~aL~~~i   49 (186)
T cd01130          10 FSPLQAAYLWLAVEARKNILISGGTGSGKTTLL-NALLAFI   49 (186)
T ss_pred             CCHHHHHHHHHHHhCCCEEEEECCCCCCHHHHH-HHHHhhc
Confidence            3555666666644 5788999999999999764 3344443

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.

>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP)

Probab=92.74  E-value=0.25  Score=43.36  Aligned_cols=51  Identities=16%  Similarity=0.170  Sum_probs=30.6

Q ss_pred             hHHHHhhhhhhhc--CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCC
Q 015158           63 SAIQQRGIVPFCK--GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPT  116 (412)
Q Consensus        63 ~~~Q~~a~~~~~~--~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~  116 (412)
                      .+.|.+.+..+..  +..+++.++||||||... .+++..+..  ...+++.+-..
T Consensus        65 ~~~~~~~l~~~~~~~~GlilisG~tGSGKTT~l-~all~~i~~--~~~~iitiEdp  117 (264)
T cd01129          65 KPENLEIFRKLLEKPHGIILVTGPTGSGKTTTL-YSALSELNT--PEKNIITVEDP  117 (264)
T ss_pred             CHHHHHHHHHHHhcCCCEEEEECCCCCcHHHHH-HHHHhhhCC--CCCeEEEECCC
Confidence            4456666665543  346889999999999765 334444432  22345555433

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.

>KOG0058 consensus Peptide exporter, ABC superfamily [Intracellular trafficking, secretion, and vesicular transport]

Probab=92.56  E-value=0.17  Score=49.56  Aligned_cols=41  Identities=22%  Similarity=0.244  Sum_probs=29.4

Q ss_pred             CCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEeec
Q 015158          180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSAT  221 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT  221 (412)
                      ++-.++|+|||-..+|......+++.+..+..+ +.+.+=|.
T Consensus       621 r~P~VLILDEATSALDaeSE~lVq~aL~~~~~~-rTVlvIAH  661 (716)
T KOG0058|consen  621 RNPRVLILDEATSALDAESEYLVQEALDRLMQG-RTVLVIAH  661 (716)
T ss_pred             cCCCEEEEechhhhcchhhHHHHHHHHHHhhcC-CeEEEEeh
Confidence            466789999999888877777777777766655 34444444

>PRK07004 replicative DNA helicase; Provisional

Probab=92.54  E-value=0.6  Score=44.57  Aligned_cols=143  Identities=15%  Similarity=0.072  Sum_probs=67.2

Q ss_pred             hhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEE-EcCcchHHHH
Q 015158           73 FCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHAC-VGGTSVREDQ  151 (412)
Q Consensus        73 ~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~  151 (412)
                      +..|.-++|.|.+|+|||..++-.+......  .+..+++++.- .-..|+..++-...  .++....+ .|......+.
T Consensus       210 ~~~g~liviaarpg~GKT~~al~ia~~~a~~--~~~~v~~fSlE-M~~~ql~~R~la~~--~~v~~~~i~~g~l~~~e~~  284 (460)
T PRK07004        210 MHGGELIIVAGRPSMGKTAFSMNIGEYVAVE--YGLPVAVFSME-MPGTQLAMRMLGSV--GRLDQHRMRTGRLTDEDWP  284 (460)
T ss_pred             CCCCceEEEEeCCCCCccHHHHHHHHHHHHH--cCCeEEEEeCC-CCHHHHHHHHHHhh--cCCCHHHHhcCCCCHHHHH
Confidence            4445677889999999997765544433221  12356666542 23444444442211  12222211 2222222221


Q ss_pred             ------HHhcCCCcEEEe-----ChHHHHHHHHcCCCCCCCceEEEEeCCchhhccC----cHHHHHHHHHhCC-----C
Q 015158          152 ------RILSSGVHVVVG-----TPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRG----FKDQIYDIFQLLP-----P  211 (412)
Q Consensus       152 ------~~~~~~~~iii~-----T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~----~~~~~~~i~~~~~-----~  211 (412)
                            ..+ ....+.|.     |+..+.....+-......+++||+|=.|.+....    ....+..+...++     -
T Consensus       285 ~~~~a~~~l-~~~~l~I~d~~~~~~~~i~~~~r~l~~~~~~~~lviIDYLql~~~~~~~~~r~~ei~~Isr~LK~lAkel  363 (460)
T PRK07004        285 KLTHAVQKM-SEAQLFIDETGGLNPMELRSRARRLARQCGKLGLIIIDYLQLMSGSSQGENRATEISEISRSLKSLAKEL  363 (460)
T ss_pred             HHHHHHHHH-hcCCEEEECCCCCCHHHHHHHHHHHHHhCCCCCEEEEChhhhccCCCCCCcHHHHHHHHHHHHHHHHHHh
Confidence                  112 22356553     3444433322211112357899999999775321    2223333333332     2


Q ss_pred             CceEEEEeec
Q 015158          212 KIQVGVFSAT  221 (412)
Q Consensus       212 ~~~~i~~SAT  221 (412)
                      +++++++|--
T Consensus       364 ~ipVi~lsQL  373 (460)
T PRK07004        364 DVPVIALSQL  373 (460)
T ss_pred             CCeEEEEecc
Confidence            5666666643

>CHL00176 ftsH cell division protein; Validated

Probab=92.54  E-value=0.66  Score=46.09  Aligned_cols=17  Identities=35%  Similarity=0.362  Sum_probs=15.0

Q ss_pred             ccEEEECCCCCCchhHh
Q 015158           77 LDVIQQAQSGTGKTATF   93 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~   93 (412)
                      +.+++.+|+|+|||..+
T Consensus       217 ~gVLL~GPpGTGKT~LA  233 (638)
T CHL00176        217 KGVLLVGPPGTGKTLLA  233 (638)
T ss_pred             ceEEEECCCCCCHHHHH
Confidence            46899999999999765

>PRK05748 replicative DNA helicase; Provisional

Probab=92.48  E-value=0.76  Score=43.90  Aligned_cols=145  Identities=13%  Similarity=0.097  Sum_probs=68.9

Q ss_pred             hhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEE-EcCcchHHHH
Q 015158           73 FCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHAC-VGGTSVREDQ  151 (412)
Q Consensus        73 ~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~  151 (412)
                      +..|.-++|.|.||.|||..++-.+......  .+..+++++.- .-..|+..++.....  ++....+ .|......+.
T Consensus       200 ~~~G~livIaarpg~GKT~~al~ia~~~a~~--~g~~v~~fSlE-ms~~~l~~R~l~~~~--~v~~~~i~~~~l~~~e~~  274 (448)
T PRK05748        200 LQPNDLIIVAARPSVGKTAFALNIAQNVATK--TDKNVAIFSLE-MGAESLVMRMLCAEG--NIDAQRLRTGQLTDDDWP  274 (448)
T ss_pred             CCCCceEEEEeCCCCCchHHHHHHHHHHHHh--CCCeEEEEeCC-CCHHHHHHHHHHHhc--CCCHHHhhcCCCCHHHHH
Confidence            3345678889999999997766555543322  12357776543 334455555432111  2222111 1222222221


Q ss_pred             HH-----hcCCCcEEEe-----ChHHHHHHHHcCCCCCCCceEEEEeCCchhhccC-----cHHHHHHHHHhCC-----C
Q 015158          152 RI-----LSSGVHVVVG-----TPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRG-----FKDQIYDIFQLLP-----P  211 (412)
Q Consensus       152 ~~-----~~~~~~iii~-----T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~-----~~~~~~~i~~~~~-----~  211 (412)
                      ..     ...+..+.|.     |++.+...+.+......++++||||=.|.+....     ....+..+...+.     .
T Consensus       275 ~~~~a~~~l~~~~~~i~d~~~~ti~~i~~~~r~~~~~~~~~~~vvIDyL~li~~~~~~~~~r~~~i~~i~~~LK~lAke~  354 (448)
T PRK05748        275 KLTIAMGSLSDAPIYIDDTPGIKVTEIRARCRRLAQEHGGLGLILIDYLQLIQGSGRSGENRQQEVSEISRSLKALAKEL  354 (448)
T ss_pred             HHHHHHHHHhcCCEEEECCCCCCHHHHHHHHHHHHHhcCCCCEEEEccchhcCCCCCCCcCHHHHHHHHHHHHHHHHHHh
Confidence            11     1122345543     3444444333211111257899999999874221     1223333333331     2


Q ss_pred             CceEEEEeecC
Q 015158          212 KIQVGVFSATM  222 (412)
Q Consensus       212 ~~~~i~~SAT~  222 (412)
                      ++.++++|-..
T Consensus       355 ~i~vi~lsQln  365 (448)
T PRK05748        355 KVPVIALSQLS  365 (448)
T ss_pred             CCeEEEecccC
Confidence            56667766654

>COG1074 RecB ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]

Probab=92.31  E-value=0.23  Score=52.98  Aligned_cols=55  Identities=31%  Similarity=0.409  Sum_probs=44.8

Q ss_pred             cCccEEEECCCCCCchhHhHHHHHHhhccC--CCceeEEEEcCCHHHHHHHHHHHHH
Q 015158           75 KGLDVIQQAQSGTGKTATFCSGILQQLDYG--LVECQALVLAPTRELAQQIEKVMRA  129 (412)
Q Consensus        75 ~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~--~~~~~~lil~P~~~L~~q~~~~~~~  129 (412)
                      .+++++|.|..|||||.+....++..+..+  ..-..+|+++-|++-+.++..++..
T Consensus        15 ~~~~~lveASAGSGKT~vL~~r~lrlLl~~~~~~v~~ILvvTFT~aAa~Emk~RI~~   71 (1139)
T COG1074          15 PGQSVLVEASAGTGKTFVLAERVLRLLLEGGPLDVDEILVVTFTKAAAAEMKERIRD   71 (1139)
T ss_pred             CCCcEEEEEcCCCCchhHHHHHHHHHHhhcCCCChhHeeeeeccHHHHHHHHHHHHH
Confidence            357899999999999999887777777663  3456899999999988888777655

>cd01126 TraG_VirD4 The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion

Probab=92.31  E-value=0.19  Score=46.98  Aligned_cols=56  Identities=29%  Similarity=0.266  Sum_probs=37.6

Q ss_pred             cEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEE
Q 015158           78 DVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACV  142 (412)
Q Consensus        78 ~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~  142 (412)
                      ++++.||||+|||.+++++-+...     ...++++=|--++........+..    |.+|.++.
T Consensus         1 H~lv~g~tGsGKt~~~viP~ll~~-----~~s~vv~D~Kge~~~~t~~~r~~~----G~~V~v~n   56 (384)
T cd01126           1 HVLVFAPTRSGKGVGFVIPNLLTW-----PGSVVVLDPKGENFELTSEHRRAL----GRKVFVFD   56 (384)
T ss_pred             CeeEecCCCCCCccEEEccchhcC-----CCCEEEEccchhHHHHHHHHHHHc----CCeEEEEc
Confidence            478999999999988765544332     236777778777877666555443    45555554

These proteins aid the transfer of DNA from the plasmid into the host bacterial chromosome. They contain an ATP binding domain. VirD4 is involved in DNA transfer to plant cells and is required for virulence.

>PF01637 Arch_ATPase: Archaeal ATPase; InterPro: IPR011579 This domain has been found in a number of bacterial and archaeal proteins, all of which contain a conserved P-loop motif that is involved in binding ATP

Probab=92.27  E-value=0.16  Score=43.40  Aligned_cols=56  Identities=16%  Similarity=0.285  Sum_probs=29.6

Q ss_pred             eChHHHHHHHHcCCCCCCCceEEEEeCCchhh-c----cCcHHHHHHHHHhCCC-CceEEEEeecC
Q 015158          163 GTPGRVFDMLRRQSLRPDNIRIFVLDEADEML-S----RGFKDQIYDIFQLLPP-KIQVGVFSATM  222 (412)
Q Consensus       163 ~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~-~----~~~~~~~~~i~~~~~~-~~~~i~~SAT~  222 (412)
                      .+...+...+.....   . -+||+||+|.+. .    ..+...+..++..... ....+.++++.
T Consensus       104 ~~l~~~~~~l~~~~~---~-~iiviDe~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~v~~~S~  165 (234)
T PF01637_consen  104 SALERLLEKLKKKGK---K-VIIVIDEFQYLAIASEEDKDFLKSLRSLLDSLLSQQNVSIVITGSS  165 (234)
T ss_dssp             --HHHHHHHHHHCHC---C-EEEEEETGGGGGBCTTTTHHHHHHHHHHHHH----TTEEEEEEESS
T ss_pred             HHHHHHHHHHHhcCC---c-EEEEEecHHHHhhcccchHHHHHHHHHHHhhccccCCceEEEECCc
Confidence            334445555544322   2 589999999988 2    2244566666655322 23345566665

; GO: 0005524 ATP binding; PDB: 2FNA_A 2QEN_A.

>KOG2227 consensus Pre-initiation complex, subunit CDC6, AAA+ superfamily ATPase [Replication, recombination and repair; Cell cycle control, cell division, chromosome partitioning]

Probab=92.26  E-value=1.1  Score=41.72  Aligned_cols=49  Identities=24%  Similarity=0.206  Sum_probs=27.7

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhccCCCcee-EEEEcCCHHHHHHHHH
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQ-ALVLAPTRELAQQIEK  125 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~-~lil~P~~~L~~q~~~  125 (412)
                      +.+..|.+.+|+|||.+.-. ++........... +-+=|-+...+...+.
T Consensus       175 ~gSlYVsG~PGtgkt~~l~r-vl~~~~~~~~~~~~v~inc~sl~~~~aiF~  224 (529)
T KOG2227|consen  175 SGSLYVSGQPGTGKTALLSR-VLDSLSKSSKSPVTVYINCTSLTEASAIFK  224 (529)
T ss_pred             CcceEeeCCCCcchHHHHHH-HHHhhhhhcccceeEEEeeccccchHHHHH
Confidence            35789999999999977533 3334433333323 3333443345444444

>TIGR00665 DnaB replicative DNA helicase

Probab=92.25  E-value=0.86  Score=43.37  Aligned_cols=143  Identities=17%  Similarity=0.085  Sum_probs=68.6

Q ss_pred             hhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEE-EcCcchHHHH
Q 015158           73 FCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHAC-VGGTSVREDQ  151 (412)
Q Consensus        73 ~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~  151 (412)
                      +..|.-++|.|++|+|||..++-.+......  .+..+++++.-. -..++.+++.....  ++....+ .|......+.
T Consensus       192 ~~~G~l~vi~g~pg~GKT~~~l~~a~~~a~~--~g~~vl~~SlEm-~~~~i~~R~~~~~~--~v~~~~~~~g~l~~~~~~  266 (434)
T TIGR00665       192 LQPSDLIILAARPSMGKTAFALNIAENAAIK--EGKPVAFFSLEM-SAEQLAMRMLSSES--RVDSQKLRTGKLSDEDWE  266 (434)
T ss_pred             CCCCeEEEEEeCCCCChHHHHHHHHHHHHHh--CCCeEEEEeCcC-CHHHHHHHHHHHhc--CCCHHHhccCCCCHHHHH
Confidence            3345667889999999997766555544322  123677776432 34444444433221  2222111 1221211111


Q ss_pred             ------HHhcCCCcEEEe-----ChHHHHHHHHcCCCCCCCceEEEEeCCchhhccC----cHHHHHHHHHhCC-----C
Q 015158          152 ------RILSSGVHVVVG-----TPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRG----FKDQIYDIFQLLP-----P  211 (412)
Q Consensus       152 ------~~~~~~~~iii~-----T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~----~~~~~~~i~~~~~-----~  211 (412)
                            ..... ..+.|.     |.+.+...+.+.... ..+++||||=.+.+....    ....+..+...+.     .
T Consensus       267 ~~~~a~~~l~~-~~l~i~d~~~~~~~~i~~~i~~~~~~-~~~~~vvID~l~~i~~~~~~~~r~~~i~~i~~~Lk~lA~e~  344 (434)
T TIGR00665       267 KLTSAAGKLSE-APLYIDDTPGLTITELRAKARRLKRE-HGLGLIVIDYLQLMSGSGRSENRQQEVSEISRSLKALAKEL  344 (434)
T ss_pred             HHHHHHHHHhc-CCEEEECCCCCCHHHHHHHHHHHHHh-cCCCEEEEcchHhcCCCCCCCCHHHHHHHHHHHHHHHHHHh
Confidence                  11122 234442     344444333321111 247899999988764322    2223333333332     3


Q ss_pred             CceEEEEeecC
Q 015158          212 KIQVGVFSATM  222 (412)
Q Consensus       212 ~~~~i~~SAT~  222 (412)
                      ++.++++|-..
T Consensus       345 ~i~vi~lsqln  355 (434)
T TIGR00665       345 NVPVIALSQLS  355 (434)
T ss_pred             CCeEEEEeccC
Confidence            66667766543

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=92.25  E-value=1.6  Score=44.45  Aligned_cols=20  Identities=30%  Similarity=0.272  Sum_probs=16.6

Q ss_pred             CccEEEECCCCCCchhHhHH
Q 015158           76 GLDVIQQAQSGTGKTATFCS   95 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~   95 (412)
                      ..+.++.||+|+|||..+-.
T Consensus       207 ~~n~LLvGppGvGKT~lae~  226 (758)
T PRK11034        207 KNNPLLVGESGVGKTAIAEG  226 (758)
T ss_pred             CCCeEEECCCCCCHHHHHHH
Confidence            36899999999999977643

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.24  E-value=1.2  Score=41.27  Aligned_cols=19  Identities=21%  Similarity=0.186  Sum_probs=15.4

Q ss_pred             ccEEEECCCCCCchhHhHH
Q 015158           77 LDVIQQAQSGTGKTATFCS   95 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~~   95 (412)
                      +..++.||+|+|||..+..
T Consensus        40 ~~~L~~G~~G~GKt~~a~~   58 (367)
T PRK14970         40 QALLFCGPRGVGKTTCARI   58 (367)
T ss_pred             eEEEEECCCCCCHHHHHHH
Confidence            3678999999999976643

>KOG0701 consensus dsRNA-specific nuclease Dicer and related ribonucleases [RNA processing and modification]

Probab=92.21  E-value=0.067  Score=57.25  Aligned_cols=94  Identities=26%  Similarity=0.381  Sum_probs=76.3

Q ss_pred             CcEEEEEcchhHHHHHHHHHhcCCC-eeEEecCCC-----------CHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCC
Q 015158          279 TQSVIFVNTRRKVDWLTDKMRSRDH-TVSATHGDM-----------DQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQ  346 (412)
Q Consensus       279 ~k~lif~~~~~~~~~~~~~L~~~~~-~~~~~~~~~-----------~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~  346 (412)
                      =..++|++....+....+.+++.+. ++..+.|.+           ....+.+++..|...++++|++|.++.+|+|++.
T Consensus       293 l~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~k~~~~~~~~~~~~vl~~~~~~~ln~L~~~~~~~e~~d~~~  372 (1606)
T KOG0701|consen  293 LSGIIFVDQRYTAYVLLELLREIFSNDPLFVTGASGANLWKSFKNELELRQAEVLRRFHFHELNLLIATSVLEEGVDVPK  372 (1606)
T ss_pred             hhheeecccchHHHHHHHHHHHhhccCcceeeccccCccchhhHHHHHhhhHHHHHHHhhhhhhHHHHHHHHHhhcchhh
Confidence            3579999999999888888876422 233344432           1223678899999999999999999999999999


Q ss_pred             CCEEEEccCCCChhhHHHhhhhcccC
Q 015158          347 VSLVINYDLPTQPENYLHRIGRSGRF  372 (412)
Q Consensus       347 ~~~vi~~~~~~s~~~~~Q~~GR~~R~  372 (412)
                      ++.++.+..|...+.|+|..||+.+.
T Consensus       373 ~~~~~~~~~~~~~~~~vq~~~r~~~~  398 (1606)
T KOG0701|consen  373 CNLVVLFDAPTYYRSYVQKKGRARAA  398 (1606)
T ss_pred             hhhheeccCcchHHHHHHhhcccccc
Confidence            99999999999999999999999765

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=92.20  E-value=0.13  Score=46.27  Aligned_cols=18  Identities=22%  Similarity=0.219  Sum_probs=15.2

Q ss_pred             ccEEEECCCCCCchhHhH
Q 015158           77 LDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~   94 (412)
                      +++++.||+|+|||..+.
T Consensus        31 ~~~ll~Gp~G~GKT~la~   48 (305)
T TIGR00635        31 DHLLLYGPPGLGKTTLAH   48 (305)
T ss_pred             CeEEEECCCCCCHHHHHH
Confidence            468999999999997653

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.

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

Probab=92.10  E-value=3.1  Score=39.86  Aligned_cols=99  Identities=15%  Similarity=0.190  Sum_probs=74.7

Q ss_pred             CCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHH----hcCCCc
Q 015158           84 QSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRI----LSSGVH  159 (412)
Q Consensus        84 ~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~  159 (412)
                      -.+.||+..-++++.+.+..+ -.+.++|.+-+..-+.|+++.+..+   .++++..++|..........    ..+...
T Consensus       365 lvF~gse~~K~lA~rq~v~~g-~~PP~lIfVQs~eRak~L~~~L~~~---~~i~v~vIh~e~~~~qrde~~~~FR~g~Iw  440 (593)
T KOG0344|consen  365 LVFCGSEKGKLLALRQLVASG-FKPPVLIFVQSKERAKQLFEELEIY---DNINVDVIHGERSQKQRDETMERFRIGKIW  440 (593)
T ss_pred             heeeecchhHHHHHHHHHhcc-CCCCeEEEEecHHHHHHHHHHhhhc---cCcceeeEecccchhHHHHHHHHHhccCee
Confidence            357888888888888777776 4556888899999999999888733   37889999998665444322    246678


Q ss_pred             EEEeChHHHHHHHHcCCCCCCCceEEEEeCCch
Q 015158          160 VVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADE  192 (412)
Q Consensus       160 iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~  192 (412)
                      ++|||     ..+.++ +++.++.+||-++.-.
T Consensus       441 vLicT-----dll~RG-iDf~gvn~VInyD~p~  467 (593)
T KOG0344|consen  441 VLICT-----DLLARG-IDFKGVNLVINYDFPQ  467 (593)
T ss_pred             EEEeh-----hhhhcc-ccccCcceEEecCCCc
Confidence            99999     666654 7888999999977664

>KOG1806 consensus DEAD box containing helicases [Replication, recombination and repair]

Probab=92.04  E-value=0.3  Score=49.49  Aligned_cols=70  Identities=21%  Similarity=0.159  Sum_probs=55.9

Q ss_pred             CCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 015158           60 EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRAL  130 (412)
Q Consensus        60 ~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~  130 (412)
                      -..+|-|.+++..-...+.+.+++|+|+|||-.+.- ++.-+.+..+.++++|++.+..-..|.++...+.
T Consensus       737 v~ft~~qveai~sg~qpgltmvvgppgtgktd~avq-il~~lyhn~p~qrTlivthsnqaln~lfeKi~~~  806 (1320)
T KOG1806|consen  737 VKFTPTQVEAILSGMQPGLTMVVGPPGTGKTDVAVQ-ILSVLYHNSPNQRTLIVTHSNQALNQLFEKIMAL  806 (1320)
T ss_pred             hccCHHHHHHHHhcCCCCceeeecCCCCCCcchhhh-hhhhhhhcCCCcceEEEEecccchhHHHHHHHhc
Confidence            346788999998888888999999999999977643 4445555667889999999988888888877654

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=92.02  E-value=0.2  Score=43.81  Aligned_cols=37  Identities=16%  Similarity=-0.015  Sum_probs=27.3

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcC
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAP  115 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P  115 (412)
                      |.-++|.+++|+|||..++..+...+..   +.+++|++-
T Consensus        36 gs~~lI~G~pGtGKT~l~~qf~~~~a~~---Ge~vlyis~   72 (259)
T TIGR03878        36 YSVINITGVSDTGKSLMVEQFAVTQASR---GNPVLFVTV   72 (259)
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHHHhC---CCcEEEEEe
Confidence            5678999999999998777666655443   347888773

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=91.94  E-value=0.57  Score=40.28  Aligned_cols=42  Identities=17%  Similarity=-0.022  Sum_probs=27.4

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhccC---CCceeEEEEcCCH
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDYG---LVECQALVLAPTR  117 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~~---~~~~~~lil~P~~  117 (412)
                      |.-+.+.+++|+|||..++..++......   ..+..++++....
T Consensus        19 g~i~~i~G~~GsGKT~l~~~l~~~~~~~~~~~g~~~~viyi~~e~   63 (235)
T cd01123          19 GSITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYIDTEG   63 (235)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHeeCccccCCCCccEEEEeCCC
Confidence            56678999999999987766555433221   0124688877543

This group of recombinases includes the eukaryotic proteins RAD51, RAD55/57 and the meiosis-specific protein DMC1, and the archaeal proteins radA and radB. They are closely related to the bacterial RecA group. Rad51 proteins catalyze a similiar recombination reaction as RecA, using ATP-dependent DNA binding activity and a DNA-dependent ATPase. However, this reaction is less efficient and requires accessory proteins such as RAD55/57 .

>KOG0734 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=91.93  E-value=1.1  Score=42.49  Aligned_cols=45  Identities=22%  Similarity=0.229  Sum_probs=29.3

Q ss_pred             CceEEEEeCCchhhccC-------cHHHHHHHHHh---CCCCceEEEEeecCChH
Q 015158          181 NIRIFVLDEADEMLSRG-------FKDQIYDIFQL---LPPKIQVGVFSATMPPE  225 (412)
Q Consensus       181 ~~~~iiiDE~h~~~~~~-------~~~~~~~i~~~---~~~~~~~i~~SAT~~~~  225 (412)
                      .-.+|+|||++.+....       ....+..++..   +..+.-+|.+.||--++
T Consensus       396 APcIIFIDEiDavG~kR~~~~~~y~kqTlNQLLvEmDGF~qNeGiIvigATNfpe  450 (752)
T KOG0734|consen  396 APCIIFIDEIDAVGGKRNPSDQHYAKQTLNQLLVEMDGFKQNEGIIVIGATNFPE  450 (752)
T ss_pred             CCeEEEEechhhhcccCCccHHHHHHHHHHHHHHHhcCcCcCCceEEEeccCChh
Confidence            45789999999865322       12334444433   45677799999997654

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

Probab=91.90  E-value=2.1  Score=41.65  Aligned_cols=113  Identities=13%  Similarity=0.208  Sum_probs=71.8

Q ss_pred             EEEEEcchhHHHHHHHHHhcC-----CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcC-----CCcCC-CCCCCCCE
Q 015158          281 SVIFVNTRRKVDWLTDKMRSR-----DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTD-----LLARG-IDVQQVSL  349 (412)
Q Consensus       281 ~lif~~~~~~~~~~~~~L~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~-----~~~~G-~d~~~~~~  349 (412)
                      +||++++++.|.++++.+...     +..+..++|+.+...+...++   .| .+|||+|+     .+..+ +++..+.+
T Consensus       102 aLil~PTRELA~Qi~~~~~~~~~~~~~~~~~~i~GG~~~~~q~~~l~---~~-~~ivVaTPGRllD~i~~~~l~l~~v~~  177 (513)
T COG0513         102 ALILAPTRELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQIEALK---RG-VDIVVATPGRLLDLIKRGKLDLSGVET  177 (513)
T ss_pred             eEEECCCHHHHHHHHHHHHHHHhhcCCccEEEEECCCCHHHHHHHHh---cC-CCEEEECccHHHHHHHcCCcchhhcCE
Confidence            899999999999998888643     567889999988766654444   45 99999998     34444 88888999


Q ss_pred             EEEccC--CCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHHhc
Q 015158          350 VINYDL--PTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYN  398 (412)
Q Consensus       350 vi~~~~--~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~  398 (412)
                      +|+.+-  -.++ -|..-+-+..+.-+.....++++..-...+..+.+-+.
T Consensus       178 lVlDEADrmLd~-Gf~~~i~~I~~~~p~~~qtllfSAT~~~~i~~l~~~~l  227 (513)
T COG0513         178 LVLDEADRMLDM-GFIDDIEKILKALPPDRQTLLFSATMPDDIRELARRYL  227 (513)
T ss_pred             EEeccHhhhhcC-CCHHHHHHHHHhCCcccEEEEEecCCCHHHHHHHHHHc
Confidence            886432  1222 23333333333322345556666543334555544443

>PRK08006 replicative DNA helicase; Provisional

Probab=91.88  E-value=1.5  Score=42.06  Aligned_cols=145  Identities=19%  Similarity=0.081  Sum_probs=70.1

Q ss_pred             hhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEE-cCcchHHH
Q 015158           72 PFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACV-GGTSVRED  150 (412)
Q Consensus        72 ~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~-~~~~~~~~  150 (412)
                      -+..|.-++|.|.+|.|||..++-.+.+....  .+..++|...- .-..|+..++-...  .++....+. |..+...+
T Consensus       220 Gl~~G~LiiIaarPgmGKTafalnia~~~a~~--~g~~V~~fSlE-M~~~ql~~Rlla~~--~~v~~~~i~~~~l~~~e~  294 (471)
T PRK08006        220 GLQPSDLIIVAARPSMGKTTFAMNLCENAAML--QDKPVLIFSLE-MPGEQIMMRMLASL--SRVDQTRIRTGQLDDEDW  294 (471)
T ss_pred             CCCCCcEEEEEeCCCCCHHHHHHHHHHHHHHh--cCCeEEEEecc-CCHHHHHHHHHHHh--cCCCHHHhhcCCCCHHHH
Confidence            34445667889999999997765544443322  12357766543 33455555444321  122222222 22222222


Q ss_pred             HH------HhcCCCcEEEe-----ChHHHHHHHHcCCCCCCCceEEEEeCCchhhcc----CcHHHHHHHHHhCC-----
Q 015158          151 QR------ILSSGVHVVVG-----TPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSR----GFKDQIYDIFQLLP-----  210 (412)
Q Consensus       151 ~~------~~~~~~~iii~-----T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~----~~~~~~~~i~~~~~-----  210 (412)
                      ..      .......+.|-     |...+.....+.......+++||||=.|.+...    +....+..+...++     
T Consensus       295 ~~~~~a~~~~~~~~~l~I~d~~~~t~~~i~~~~r~~~~~~~~~~lvvIDYLqli~~~~~~~~r~~ei~~isr~LK~lAke  374 (471)
T PRK08006        295 ARISGTMGILLEKRNMYIDDSSGLTPTEVRSRARRIFREHGGLSLIMIDYLQLMRVPSLSDNRTLEIAEISRSLKALAKE  374 (471)
T ss_pred             HHHHHHHHHHHhcCCEEEECCCCCCHHHHHHHHHHHHHhcCCCCEEEEccHHHccCCCCCCCcHHHHHHHHHHHHHHHHH
Confidence            11      11123345553     344443333221111235899999999976422    12223444333332     


Q ss_pred             CCceEEEEeec
Q 015158          211 PKIQVGVFSAT  221 (412)
Q Consensus       211 ~~~~~i~~SAT  221 (412)
                      -++.++++|-.
T Consensus       375 l~ipVi~LsQL  385 (471)
T PRK08006        375 LQVPVVALSQL  385 (471)
T ss_pred             hCCeEEEEEec
Confidence            26667777744

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=91.79  E-value=0.17  Score=44.35  Aligned_cols=28  Identities=29%  Similarity=0.338  Sum_probs=22.0

Q ss_pred             HhhhhhhhcCccEEEECCCCCCchhHhH
Q 015158           67 QRGIVPFCKGLDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        67 ~~a~~~~~~~~~~lv~~~tGsGKT~~~~   94 (412)
                      ++++..+..+.++++.||+|+|||..+.
T Consensus        12 ~~~l~~l~~g~~vLL~G~~GtGKT~lA~   39 (262)
T TIGR02640        12 SRALRYLKSGYPVHLRGPAGTGKTTLAM   39 (262)
T ss_pred             HHHHHHHhcCCeEEEEcCCCCCHHHHHH
Confidence            3444556678899999999999998764

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).

>KOG0730 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=91.78  E-value=0.99  Score=43.85  Aligned_cols=57  Identities=23%  Similarity=0.316  Sum_probs=39.9

Q ss_pred             hhhhccccccCCCCHHHHHHHHH---CCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHh
Q 015158           34 YDEVYDTFDAMGLQENLLRGIYA---YGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATF   93 (412)
Q Consensus        34 ~~~~~~~f~~~~l~~~~~~~l~~---~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~   93 (412)
                      .+.+-.+|++.+=-+++.+.|+.   ++...|-.+.+..+   ...+.+++-+|+|+|||+++
T Consensus       426 ve~p~v~W~dIGGlE~lK~elq~~V~~p~~~pe~F~r~Gi---~ppkGVLlyGPPGC~KT~lA  485 (693)
T KOG0730|consen  426 VEMPNVSWDDIGGLEELKRELQQAVEWPLKHPEKFARFGI---SPPKGVLLYGPPGCGKTLLA  485 (693)
T ss_pred             ccCCCCChhhccCHHHHHHHHHHHHhhhhhchHHHHHhcC---CCCceEEEECCCCcchHHHH
Confidence            55556788888877777777763   45555555555542   23467999999999999876

>PRK10436 hypothetical protein; Provisional

Probab=91.77  E-value=0.31  Score=46.32  Aligned_cols=40  Identities=23%  Similarity=0.227  Sum_probs=26.7

Q ss_pred             ChHHHHhhhhhhhc--CccEEEECCCCCCchhHhHHHHHHhhc
Q 015158           62 PSAIQQRGIVPFCK--GLDVIQQAQSGTGKTATFCSGILQQLD  102 (412)
Q Consensus        62 l~~~Q~~a~~~~~~--~~~~lv~~~tGsGKT~~~~~~~~~~~~  102 (412)
                      +.+.|.+.+..+..  +.-+++.+|||||||.+. .+++..+.
T Consensus       202 ~~~~~~~~l~~~~~~~~GliLvtGpTGSGKTTtL-~a~l~~~~  243 (462)
T PRK10436        202 MTPAQLAQFRQALQQPQGLILVTGPTGSGKTVTL-YSALQTLN  243 (462)
T ss_pred             cCHHHHHHHHHHHHhcCCeEEEECCCCCChHHHH-HHHHHhhC
Confidence            34556666666543  356789999999999875 34555543

>cd00544 CobU Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU)

Probab=91.76  E-value=1.2  Score=36.02  Aligned_cols=45  Identities=7%  Similarity=0.105  Sum_probs=32.2

Q ss_pred             EEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHH
Q 015158           79 VIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRA  129 (412)
Q Consensus        79 ~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~  129 (412)
                      ++|.+++|||||..+...+..      .+.+++|+........++.+.+..
T Consensus         2 ~li~G~~~sGKS~~a~~~~~~------~~~~~~y~at~~~~d~em~~rI~~   46 (169)
T cd00544           2 ILVTGGARSGKSRFAERLAAE------LGGPVTYIATAEAFDDEMAERIAR   46 (169)
T ss_pred             EEEECCCCCCHHHHHHHHHHh------cCCCeEEEEccCcCCHHHHHHHHH
Confidence            578999999999877655433      224788888777776666666554

CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is a homotrimer with a propeller-like shape.

>KOG1807 consensus Helicases [Replication, recombination and repair]

Probab=91.74  E-value=0.61  Score=45.96  Aligned_cols=67  Identities=19%  Similarity=-0.019  Sum_probs=50.7

Q ss_pred             ChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccC---CCceeEEEEcCCHHHHHHHHHHHH
Q 015158           62 PSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYG---LVECQALVLAPTRELAQQIEKVMR  128 (412)
Q Consensus        62 l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~---~~~~~~lil~P~~~L~~q~~~~~~  128 (412)
                      +-.-|..|+...+..+-.++.+|+|+|||.+.+.++-..+.+.   ...-.++++|-|..-++|....+.
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            4556999999888888889999999999988776655444332   223469999999988888766544

>PRK08760 replicative DNA helicase; Provisional

Probab=91.72  E-value=0.88  Score=43.67  Aligned_cols=115  Identities=14%  Similarity=0.094  Sum_probs=57.7

Q ss_pred             hhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEE-EcCcchHHHH
Q 015158           73 FCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHAC-VGGTSVREDQ  151 (412)
Q Consensus        73 ~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~  151 (412)
                      +..|.-++|.|.+|.|||..++-.+......  .+..++|.+.- .-..|+..++.....  ++....+ .|......+.
T Consensus       226 ~~~G~LivIaarPg~GKTafal~iA~~~a~~--~g~~V~~fSlE-Ms~~ql~~Rl~a~~s--~i~~~~i~~g~l~~~e~~  300 (476)
T PRK08760        226 LQPTDLIILAARPAMGKTTFALNIAEYAAIK--SKKGVAVFSME-MSASQLAMRLISSNG--RINAQRLRTGALEDEDWA  300 (476)
T ss_pred             CCCCceEEEEeCCCCChhHHHHHHHHHHHHh--cCCceEEEecc-CCHHHHHHHHHHhhC--CCcHHHHhcCCCCHHHHH
Confidence            3445667889999999997766555444322  12357776543 234556655544321  1211111 1222222221


Q ss_pred             ------HHhcCCCcEEEe-----ChHHHHHHHHcCCCCCCCceEEEEeCCchhh
Q 015158          152 ------RILSSGVHVVVG-----TPGRVFDMLRRQSLRPDNIRIFVLDEADEML  194 (412)
Q Consensus       152 ------~~~~~~~~iii~-----T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~  194 (412)
                            ..+ ....+.|.     |++.+.....+... ...+++||||=.+.+.
T Consensus       301 ~~~~a~~~l-~~~~l~I~d~~~~t~~~I~~~~r~l~~-~~~~~lVvIDyLql~~  352 (476)
T PRK08760        301 RVTGAIKML-KETKIFIDDTPGVSPEVLRSKCRRLKR-EHDLGLIVIDYLQLMS  352 (476)
T ss_pred             HHHHHHHHH-hcCCEEEeCCCCCCHHHHHHHHHHHHH-hcCCCEEEEecHHhcC
Confidence                  111 12345443     34454443332111 1357899999998764

>PF02534 T4SS-DNA_transf: Type IV secretory system Conjugative DNA transfer; InterPro: IPR003688 This entry represents TraG proteins and their homologues

Probab=91.59  E-value=0.34  Score=46.62  Aligned_cols=49  Identities=24%  Similarity=0.337  Sum_probs=35.5

Q ss_pred             ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 015158           77 LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRAL  130 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~  130 (412)
                      .++++.||||||||..++++.+-.  ..   ..++|.=|--+|...+...+++.
T Consensus        45 ~h~lvig~tgSGKt~~~viP~ll~--~~---~s~iV~D~KgEl~~~t~~~r~~~   93 (469)
T PF02534_consen   45 THVLVIGPTGSGKTTSFVIPNLLN--YP---GSMIVTDPKGELYEKTAGYRKKR   93 (469)
T ss_pred             eEEEEEeCCCCCccceeeHhHHHh--cc---CCEEEEECCCcHHHHHHHHHHHC
Confidence            479999999999999887765532  21   25777778778877777666554

These proteins contain a P-loop and walker-B site for nucleotide binding. TraG is essential for DNA transfer in bacterial conjugation. These proteins are thought to mediate interactions between the DNA-processing (Dtr) and the mating pair formation (Mpf) systems [, ].; GO: 0009291 unidirectional conjugation, 0016020 membrane

>TIGR02784 addA_alphas double-strand break repair helicase AddA, alphaproteobacterial type

Probab=91.59  E-value=0.39  Score=51.68  Aligned_cols=55  Identities=20%  Similarity=0.263  Sum_probs=44.9

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRAL  130 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~  130 (412)
                      .++++|.++.|||||.+...-++..+..+....++++++-|+.-+.++.+++...
T Consensus        10 ~~~~~~~a~agsgkt~~l~~~~~~~~~~~~~~~~i~~~t~t~~aa~em~~Ri~~~   64 (1141)
T TIGR02784        10 KTSAWVSANAGSGKTHVLTQRVIRLLLNGVPPSKILCLTYTKAAAAEMQNRVFDR   64 (1141)
T ss_pred             CCCEEEEEECCCCHHHHHHHHHHHHHHcCCCCCeEEEEecCHHHHHHHHHHHHHH
Confidence            4688999999999998887777777666555668999999999888887776654

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.

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=91.43  E-value=0.3  Score=41.21  Aligned_cols=38  Identities=13%  Similarity=0.071  Sum_probs=27.5

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCC
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPT  116 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~  116 (412)
                      |.-+.+.+|+|+|||..++..+......   +.+++|+.-.
T Consensus        12 g~i~~i~G~~GsGKT~l~~~~~~~~~~~---g~~v~yi~~e   49 (209)
T TIGR02237        12 GTITQIYGPPGSGKTNICMILAVNAARQ---GKKVVYIDTE   49 (209)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhC---CCeEEEEECC
Confidence            5678899999999998776655554433   3467777764

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=91.43  E-value=0.38  Score=42.74  Aligned_cols=19  Identities=32%  Similarity=0.358  Sum_probs=16.2

Q ss_pred             CccEEEECCCCCCchhHhH
Q 015158           76 GLDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~   94 (412)
                      +.++++.||+|+|||.++-
T Consensus        58 ~~~vll~G~pGTGKT~lA~   76 (284)
T TIGR02880        58 TLHMSFTGNPGTGKTTVAL   76 (284)
T ss_pred             CceEEEEcCCCCCHHHHHH
Confidence            4579999999999998763

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.

>PF13555 AAA_29: P-loop containing region of AAA domain

Probab=91.41  E-value=0.16  Score=33.04  Aligned_cols=18  Identities=22%  Similarity=0.418  Sum_probs=15.1

Q ss_pred             CccEEEECCCCCCchhHh
Q 015158           76 GLDVIQQAQSGTGKTATF   93 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~   93 (412)
                      |...++.+++|+|||..+
T Consensus        23 g~~tli~G~nGsGKSTll   40 (62)
T PF13555_consen   23 GDVTLITGPNGSGKSTLL   40 (62)
T ss_pred             CcEEEEECCCCCCHHHHH
Confidence            446899999999999764

>PF01580 FtsK_SpoIIIE: FtsK/SpoIIIE family; InterPro: IPR002543 The FtsK/SpoIIIE domain is found extensively in a wide variety of proteins from prokaryotes and plasmids [] some of which contain up to three copies

Probab=91.41  E-value=0.3  Score=41.07  Aligned_cols=45  Identities=13%  Similarity=0.121  Sum_probs=23.7

Q ss_pred             hhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCH
Q 015158           73 FCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTR  117 (412)
Q Consensus        73 ~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~  117 (412)
                      +.+..+++|.++||||||.+....+...+....+..--++++..+
T Consensus        35 l~~~~h~li~G~tgsGKS~~l~~ll~~l~~~~~p~~~~l~iiD~k   79 (205)
T PF01580_consen   35 LKKNPHLLIAGATGSGKSTLLRTLLLSLALTYSPDDVQLYIIDPK   79 (205)
T ss_dssp             GGGS-SEEEE--TTSSHHHHHHHHHHHHHTT--TTTEEEEEE-TT
T ss_pred             cCCCceEEEEcCCCCCccHHHHHHHHHHHHHhcCCccEEEEEcCC
Confidence            334558999999999999776544444444222223345555443

The domain contains a putative ATP binding P-loop motif. A mutation in FtsK causes a temperature sensitive block in cell division and it is involved in peptidoglycan synthesis or modification []. The SpoIIIE protein is implicated in intercellular chromosomal DNA transfer []. ; GO: 0000166 nucleotide binding, 0003677 DNA binding, 0005524 ATP binding, 0007049 cell cycle, 0007059 chromosome segregation, 0051301 cell division, 0016021 integral to membrane; PDB: 2IUS_E 2IUU_A 2IUT_A.

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family

Probab=91.38  E-value=0.48  Score=40.43  Aligned_cols=51  Identities=22%  Similarity=0.231  Sum_probs=35.3

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRAL  130 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~  130 (412)
                      |..+++.+++|+|||..++..+...+..+   .+++|++-.. -.++..+.+..+
T Consensus        16 g~~~li~G~~G~GKt~~~~~~~~~~~~~g---~~~~y~s~e~-~~~~l~~~~~~~   66 (224)
T TIGR03880        16 GHVIVVIGEYGTGKTTFSLQFLYQGLKNG---EKAMYISLEE-REERILGYAKSK   66 (224)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhCC---CeEEEEECCC-CHHHHHHHHHHc
Confidence            56788999999999977666565555433   4788877644 456666666665

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.

>PF08423 Rad51: Rad51; InterPro: IPR013632 This domain is found at the C terminus of the DNA repair and recombination protein Rad51

Probab=91.27  E-value=0.4  Score=41.82  Aligned_cols=42  Identities=17%  Similarity=0.118  Sum_probs=26.5

Q ss_pred             cEEEECCCCCCchhHhHHHHHHh-hcc--CCCceeEEEEcCCHHH
Q 015158           78 DVIQQAQSGTGKTATFCSGILQQ-LDY--GLVECQALVLAPTREL  119 (412)
Q Consensus        78 ~~lv~~~tGsGKT~~~~~~~~~~-~~~--~~~~~~~lil~P~~~L  119 (412)
                      -+=++++.|+|||...+..++.. +..  +..+.+++|+.-....
T Consensus        40 itEi~G~~gsGKTql~l~l~~~~~l~~~~~g~~~~vvyidTe~~f   84 (256)
T PF08423_consen   40 ITEIVGESGSGKTQLCLQLAVNVQLPEEIGGLGGKVVYIDTEGTF   84 (256)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHTTSGGCTTSSSSEEEEEESSSSS
T ss_pred             EEEEEEecccccchHHHHHHHHhhcccccccCCCceEEEeCCCCC
Confidence            34579999999996555444433 322  2345679998765543

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 ....

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=91.15  E-value=0.29  Score=42.87  Aligned_cols=52  Identities=21%  Similarity=0.250  Sum_probs=37.0

Q ss_pred             cCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 015158           75 KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRAL  130 (412)
Q Consensus        75 ~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~  130 (412)
                      .|+.++|.+++|+|||.-.+..+...+..+   .++++++-. +...+..+.+..+
T Consensus        22 ~g~~~lI~G~pGsGKT~f~~qfl~~~~~~g---e~vlyvs~~-e~~~~l~~~~~~~   73 (260)
T COG0467          22 RGSVVLITGPPGTGKTIFALQFLYEGAREG---EPVLYVSTE-ESPEELLENARSF   73 (260)
T ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHHHhcC---CcEEEEEec-CCHHHHHHHHHHc
Confidence            367899999999999988777777766653   478887754 4445555555554

>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C

Probab=91.15  E-value=0.56  Score=38.89  Aligned_cols=57  Identities=19%  Similarity=0.135  Sum_probs=35.2

Q ss_pred             cCccEEEECCCCCCchhHhHHHHHHhhccC-------CCceeEEEEcCCHHHHHHHHHHHHHhhc
Q 015158           75 KGLDVIQQAQSGTGKTATFCSGILQQLDYG-------LVECQALVLAPTRELAQQIEKVMRALGD  132 (412)
Q Consensus        75 ~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~-------~~~~~~lil~P~~~L~~q~~~~~~~~~~  132 (412)
                      .|.-+++.|++|+|||...+..+.......       ....+++|+..-.. ..++.+.+.....
T Consensus        31 ~g~l~~i~g~~g~GKT~~~~~l~~~~~~g~~~~g~~~~~~~~Vl~i~~E~~-~~~~~~rl~~~~~   94 (193)
T PF13481_consen   31 RGELTLIAGPPGSGKTTLALQLAAALATGRPFLGELPPRPGRVLYISLEDS-ESQIARRLRALLQ   94 (193)
T ss_dssp             TTSEEEEEECSTSSHHHHHHHHHHHHHT---TT---------EEEEESSS--HHHHHHHHHHHHT
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHhCCccCCcccccCceEEEEeccCC-HHHHHHHHHHHhc
Confidence            567789999999999977665555444311       13457888876555 5567777776543

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=91.06  E-value=0.37  Score=46.29  Aligned_cols=40  Identities=20%  Similarity=0.227  Sum_probs=27.1

Q ss_pred             ChHHHHhhhhhhhcC--ccEEEECCCCCCchhHhHHHHHHhhc
Q 015158           62 PSAIQQRGIVPFCKG--LDVIQQAQSGTGKTATFCSGILQQLD  102 (412)
Q Consensus        62 l~~~Q~~a~~~~~~~--~~~lv~~~tGsGKT~~~~~~~~~~~~  102 (412)
                      +.+.|.+.+..+...  .-+++.+|||||||.+. .+++..+.
T Consensus       226 ~~~~~~~~l~~~~~~~~GlilitGptGSGKTTtL-~a~L~~l~  267 (486)
T TIGR02533       226 MSPELLSRFERLIRRPHGIILVTGPTGSGKTTTL-YAALSRLN  267 (486)
T ss_pred             CCHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHH-HHHHhccC
Confidence            356677777766553  34689999999999775 33455543

This family describes GspE, the E protein of the type II secretion system, also called the main terminal branch of the general secretion pathway. This model separates GspE from the PilB protein of type IV pilin biosynthesis.

>COG5410 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=91.06  E-value=0.79  Score=38.06  Aligned_cols=66  Identities=15%  Similarity=0.032  Sum_probs=47.2

Q ss_pred             HhhhhhhhcC--ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhc
Q 015158           67 QRGIVPFCKG--LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGD  132 (412)
Q Consensus        67 ~~a~~~~~~~--~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~  132 (412)
                      ..-+.++..|  +++++..|+|+-|+.+.....-..+....+.++++.+.-+..|+.+..+.++...+
T Consensus        48 ~~~L~~Vi~G~~k~~Iin~PP~~skS~~Vs~~~PaY~L~~NP~KR~~~~SYSd~La~~~s~~~r~ii~  115 (305)
T COG5410          48 AGVLDDVIAGRRKDVIINVPPGSSKSELVAINVPAYGLALNPYKRFLHISYSDDLALLNSETAREIVQ  115 (305)
T ss_pred             HHHHHHHhccccceEEEecCCccccceEEEeechhhhhhcCccceEEEeeHhHHHHHHhchHHHHHHh
Confidence            3445556666  68899999999999765443333433344667899999999999988887776543

>KOG2543 consensus Origin recognition complex, subunit 5 [Replication, recombination and repair]

Probab=90.91  E-value=1.8  Score=39.35  Aligned_cols=142  Identities=16%  Similarity=0.135  Sum_probs=73.8

Q ss_pred             ChHHHHhhhhhhhcCcc------EEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccC
Q 015158           62 PSAIQQRGIVPFCKGLD------VIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLG  135 (412)
Q Consensus        62 l~~~Q~~a~~~~~~~~~------~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~  135 (412)
                      -+..|..-+..++.+++      +++.|.+|+|||.+.. .++...     +...+++++..-  -.+..-+.++....+
T Consensus        10 ~Re~qi~~L~~Llg~~~~~~PS~~~iyG~sgTGKT~~~r-~~l~~~-----n~~~vw~n~~ec--ft~~~lle~IL~~~~   81 (438)
T KOG2543|consen   10 CRESQIRRLKSLLGNNSCTIPSIVHIYGHSGTGKTYLVR-QLLRKL-----NLENVWLNCVEC--FTYAILLEKILNKSQ   81 (438)
T ss_pred             chHHHHHHHHHHhCCCCcccceeEEEeccCCCchhHHHH-HHHhhc-----CCcceeeehHHh--ccHHHHHHHHHHHhc
Confidence            57888888888887643      3889999999997643 333332     235677766321  111112222211111


Q ss_pred             cEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCC--CCCceEEEEeCCchhhccC--cHHHHHHHHHhCCC
Q 015158          136 VKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLR--PDNIRIFVLDEADEMLSRG--FKDQIYDIFQLLPP  211 (412)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~--~~~~~~iiiDE~h~~~~~~--~~~~~~~i~~~~~~  211 (412)
                           ..........         +..-+...+.+.+.++...  .+.--++|+|-++.+.+.+  ....+.++...++.
T Consensus        82 -----~~d~dg~~~~---------~~~en~~d~i~~l~q~~~~t~~d~~~~liLDnad~lrD~~a~ll~~l~~L~el~~~  147 (438)
T KOG2543|consen   82 -----LADKDGDKVE---------GDAENFSDFIYLLVQWPAATNRDQKVFLILDNADALRDMDAILLQCLFRLYELLNE  147 (438)
T ss_pred             -----cCCCchhhhh---------hHHHHHHHHHHHHHhhHHhhccCceEEEEEcCHHhhhccchHHHHHHHHHHHHhCC
Confidence                 0000000000         0001111223333321111  1223489999999988766  23444555566666


Q ss_pred             CceEEEEeecCChH
Q 015158          212 KIQVGVFSATMPPE  225 (412)
Q Consensus       212 ~~~~i~~SAT~~~~  225 (412)
                      +.-.+.+|+++.+.
T Consensus       148 ~~i~iils~~~~e~  161 (438)
T KOG2543|consen  148 PTIVIILSAPSCEK  161 (438)
T ss_pred             CceEEEEeccccHH
Confidence            77789999998764

>PRK13897 type IV secretion system component VirD4; Provisional

Probab=90.88  E-value=0.52  Score=46.40  Aligned_cols=57  Identities=19%  Similarity=0.089  Sum_probs=41.0

Q ss_pred             ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEE
Q 015158           77 LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACV  142 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~  142 (412)
                      +++++.||||||||..++++-+-...     ..++|+=|--++...+....++.    |..|..+.
T Consensus       159 ~hvLviapTgSGKg~g~VIPnLL~~~-----~S~VV~DpKGEl~~~Ta~~R~~~----G~~V~vfd  215 (606)
T PRK13897        159 QHALLFAPTGSGKGVGFVIPNLLFWE-----DSVVVHDIKLENYELTSGWREKQ----GQKVFVWE  215 (606)
T ss_pred             ceEEEEcCCCCCcceEEehhhHHhCC-----CCEEEEeCcHHHHHHHHHHHHHC----CCeEEEEe
Confidence            57899999999999988777765431     35777778778887777666554    55555554

>PRK14701 reverse gyrase; Provisional

Probab=90.81  E-value=2.1  Score=47.44  Aligned_cols=61  Identities=18%  Similarity=0.257  Sum_probs=53.3

Q ss_pred             CCCcEEEEEcchhHHHHHHHHHhcC------CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCC
Q 015158          277 AITQSVIFVNTRRKVDWLTDKMRSR------DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDL  337 (412)
Q Consensus       277 ~~~k~lif~~~~~~~~~~~~~L~~~------~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~  337 (412)
                      .+.+++|.+|+++-+.++++.++..      +..+..+||+++..++..+++.+.+|+.+|||+|+.
T Consensus       121 ~g~~aLVl~PTreLa~Qi~~~l~~l~~~~~~~v~v~~~~g~~s~~e~~~~~~~l~~g~~dILV~TPg  187 (1638)
T PRK14701        121 KGKKCYIILPTTLLVKQTVEKIESFCEKANLDVRLVYYHSNLRKKEKEEFLERIENGDFDILVTTAQ  187 (1638)
T ss_pred             cCCeEEEEECHHHHHHHHHHHHHHHHhhcCCceeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECCc
Confidence            4458999999999999999888762      456788999999999999999999999999999983

>PRK05636 replicative DNA helicase; Provisional

Probab=90.75  E-value=1.5  Score=42.36  Aligned_cols=114  Identities=13%  Similarity=0.115  Sum_probs=52.8

Q ss_pred             cCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEE-cCcchHHHHHH
Q 015158           75 KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACV-GGTSVREDQRI  153 (412)
Q Consensus        75 ~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~  153 (412)
                      .|.-++|.|.||.|||..++-.+......  .+..+++.+. ..-..|+..++-...  .++....+. |..+...+...
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 GGQMIIVAARPGVGKSTLALDFMRSASIK--HNKASVIFSL-EMSKSEIVMRLLSAE--AEVRLSDMRGGKMDEDAWEKL  338 (505)
T ss_pred             CCceEEEEeCCCCCHHHHHHHHHHHHHHh--CCCeEEEEEe-eCCHHHHHHHHHHHh--cCCCHHHHhcCCCCHHHHHHH
Confidence            34566889999999997665444333221  1235666643 222344444332211  122221111 22222222111


Q ss_pred             -----hcCCCcEEEe-----ChHHHHHHHHcCCCCCCCceEEEEeCCchhh
Q 015158          154 -----LSSGVHVVVG-----TPGRVFDMLRRQSLRPDNIRIFVLDEADEML  194 (412)
Q Consensus       154 -----~~~~~~iii~-----T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~  194 (412)
                           ......+.|-     |.+.+....++... ...+++||||=.|.+.
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                 0122345553     33334333322111 1358899999999875

>PRK06321 replicative DNA helicase; Provisional

Probab=90.67  E-value=1.7  Score=41.59  Aligned_cols=112  Identities=15%  Similarity=0.048  Sum_probs=55.3

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEE-EcCcchHHHH---
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHAC-VGGTSVREDQ---  151 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~---  151 (412)
                      |.-++|.|.+|.|||..++-.+......  .+..+++++.- .-..|+.+++....  .++....+ .+......+.   
T Consensus       226 G~LiiiaarPgmGKTafal~ia~~~a~~--~g~~v~~fSLE-Ms~~ql~~Rlla~~--s~v~~~~i~~~~l~~~e~~~~~  300 (472)
T PRK06321        226 SNLMILAARPAMGKTALALNIAENFCFQ--NRLPVGIFSLE-MTVDQLIHRIICSR--SEVESKKISVGDLSGRDFQRIV  300 (472)
T ss_pred             CcEEEEEeCCCCChHHHHHHHHHHHHHh--cCCeEEEEecc-CCHHHHHHHHHHhh--cCCCHHHhhcCCCCHHHHHHHH
Confidence            4556889999999997665533332211  12356666542 23444555443321  12222222 2222222221   


Q ss_pred             ---HHhcCCCcEEEe-----ChHHHHHHHHcCCCCCCCceEEEEeCCchhh
Q 015158          152 ---RILSSGVHVVVG-----TPGRVFDMLRRQSLRPDNIRIFVLDEADEML  194 (412)
Q Consensus       152 ---~~~~~~~~iii~-----T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~  194 (412)
                         ..+ ....+.|-     |.+.+.....+... ...+++||||=.|.+.
T Consensus       301 ~a~~~l-~~~~~~idd~~~~ti~~i~~~~r~~~~-~~~~~lvvIDyLql~~  349 (472)
T PRK06321        301 SVVNEM-QEHTLLIDDQPGLKITDLRARARRMKE-SYDIQFLIIDYLQLLS  349 (472)
T ss_pred             HHHHHH-HcCCEEEeCCCCCCHHHHHHHHHHHHH-hcCCCEEEEcchHHcC
Confidence               111 22345554     44445443332211 1358899999999875

>TIGR00763 lon ATP-dependent protease La

Probab=90.63  E-value=1.7  Score=44.77  Aligned_cols=18  Identities=28%  Similarity=0.230  Sum_probs=15.2

Q ss_pred             CccEEEECCCCCCchhHh
Q 015158           76 GLDVIQQAQSGTGKTATF   93 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~   93 (412)
                      +..+++.+|+|+|||..+
T Consensus       347 ~~~lll~GppG~GKT~lA  364 (775)
T TIGR00763       347 GPILCLVGPPGVGKTSLG  364 (775)
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            356889999999999765

This protein is induced by heat shock and other stresses in E. coli, B. subtilis, and other species. The yeast member, designated PIM1, is located in the mitochondrial matrix, required for mitochondrial function, and also induced by heat shock.

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

Probab=90.60  E-value=1.3  Score=46.11  Aligned_cols=76  Identities=14%  Similarity=0.194  Sum_probs=62.5

Q ss_pred             CCCcEEEEEcchhHHHHHHHHH----hcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcC-CCcCCCCCCCCCEEE
Q 015158          277 AITQSVIFVNTRRKVDWLTDKM----RSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTD-LLARGIDVQQVSLVI  351 (412)
Q Consensus       277 ~~~k~lif~~~~~~~~~~~~~L----~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~-~~~~G~d~~~~~~vi  351 (412)
                      .++.+.|.+|+-=-|++=++.+    ....+++..++.-.+.++...+++...+|+++|||+|= .++.++-+++.-.+|
T Consensus       642 ~GKQVAvLVPTTlLA~QHy~tFkeRF~~fPV~I~~LSRF~s~kE~~~il~~la~G~vDIvIGTHrLL~kdv~FkdLGLlI  721 (1139)
T COG1197         642 DGKQVAVLVPTTLLAQQHYETFKERFAGFPVRIEVLSRFRSAKEQKEILKGLAEGKVDIVIGTHRLLSKDVKFKDLGLLI  721 (1139)
T ss_pred             CCCeEEEEcccHHhHHHHHHHHHHHhcCCCeeEEEecccCCHHHHHHHHHHHhcCCccEEEechHhhCCCcEEecCCeEE
Confidence            4467899999975555555555    44577888898888999999999999999999999985 889999999988888


Q ss_pred             E
Q 015158          352 N  352 (412)
Q Consensus       352 ~  352 (412)
                      +
T Consensus       722 I  722 (1139)
T COG1197         722 I  722 (1139)
T ss_pred             E
Confidence            4

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=90.59  E-value=0.45  Score=45.90  Aligned_cols=51  Identities=18%  Similarity=0.139  Sum_probs=37.5

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRAL  130 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~  130 (412)
                      |..++|.+|+|+|||...+..+...+..+   .+++|++- .+-.+|..+.+..+
T Consensus       263 gs~~li~G~~G~GKt~l~~~f~~~~~~~g---e~~~y~s~-eEs~~~i~~~~~~l  313 (484)
T TIGR02655       263 DSIILATGATGTGKTLLVSKFLENACANK---ERAILFAY-EESRAQLLRNAYSW  313 (484)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHCC---CeEEEEEe-eCCHHHHHHHHHHc
Confidence            45789999999999988877777665543   47888774 45566777777665

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.

>COG2812 DnaX DNA polymerase III, gamma/tau subunits [DNA replication, recombination, and repair]

Probab=90.54  E-value=0.39  Score=45.87  Aligned_cols=41  Identities=10%  Similarity=0.353  Sum_probs=24.8

Q ss_pred             CCCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEee
Q 015158          179 PDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSA  220 (412)
Q Consensus       179 ~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SA  220 (412)
                      ..++++.|+||+|.+....|...+ +.+..-|.++.+|+.|-
T Consensus       117 ~~ryKVyiIDEvHMLS~~afNALL-KTLEEPP~hV~FIlATT  157 (515)
T COG2812         117 EGRYKVYIIDEVHMLSKQAFNALL-KTLEEPPSHVKFILATT  157 (515)
T ss_pred             cccceEEEEecHHhhhHHHHHHHh-cccccCccCeEEEEecC
Confidence            357899999999987766544333 33343444554444443

>PF01935 DUF87: Domain of unknown function DUF87; InterPro: IPR002789 The function of this domain is unknown

Probab=90.34  E-value=0.37  Score=41.32  Aligned_cols=41  Identities=17%  Similarity=0.217  Sum_probs=27.1

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHH
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRE  118 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  118 (412)
                      ++++.|.|.||||||.+.-..+. .+.. ..+..++|+=|.-+
T Consensus        23 ~~H~~I~G~TGsGKS~~~~~ll~-~l~~-~~~~~~ii~D~~GE   63 (229)
T PF01935_consen   23 NRHIAIFGTTGSGKSNTVKVLLE-ELLK-KKGAKVIIFDPHGE   63 (229)
T ss_pred             cceEEEECCCCCCHHHHHHHHHH-HHHh-cCCCCEEEEcCCCc
Confidence            46899999999999987644333 3331 23346777767544

It contains several conserved aspartates and histidines that could be metal ligands.

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=90.29  E-value=1.7  Score=45.28  Aligned_cols=19  Identities=26%  Similarity=0.314  Sum_probs=16.2

Q ss_pred             ccEEEECCCCCCchhHhHH
Q 015158           77 LDVIQQAQSGTGKTATFCS   95 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~~   95 (412)
                      ++.++.||+|+|||..+-.
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.

>cd01394 radB RadB

Probab=90.27  E-value=0.44  Score=40.48  Aligned_cols=36  Identities=17%  Similarity=0.086  Sum_probs=26.1

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEc
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLA  114 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~  114 (412)
                      |.-+.|.+++|+|||..++..+......   +.+++++.
T Consensus        19 g~i~~i~G~~GsGKT~l~~~~a~~~~~~---g~~v~yi~   54 (218)
T cd01394          19 GTVTQVYGPPGTGKTNIAIQLAVETAGQ---GKKVAYID   54 (218)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhc---CCeEEEEE
Confidence            4568899999999998776666555433   34788874

The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=90.23  E-value=0.85  Score=47.15  Aligned_cols=132  Identities=18%  Similarity=0.199  Sum_probs=0.0

Q ss_pred             HhhhhhhhcC--ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcC
Q 015158           67 QRGIVPFCKG--LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGG  144 (412)
Q Consensus        67 ~~a~~~~~~~--~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~  144 (412)
                      .+.+..+..+  .+.+++||+|+|||                           ++++..++.+..     +.....+.+.
T Consensus       197 ~~~i~~l~r~~~~n~lLvG~pGvGKT---------------------------al~~~La~~i~~-----~~v~~~l~~~  244 (852)
T TIGR03345       197 RQMIDILLRRRQNNPILTGEAGVGKT---------------------------AVVEGLALRIAA-----GDVPPALRNV  244 (852)
T ss_pred             HHHHHHHhcCCcCceeEECCCCCCHH---------------------------HHHHHHHHHHhh-----CCCCccccCC


Q ss_pred             cchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccC---cHHHHHHHHHhCCCCceEEEEeec
Q 015158          145 TSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRG---FKDQIYDIFQLLPPKIQVGVFSAT  221 (412)
Q Consensus       145 ~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~---~~~~~~~i~~~~~~~~~~i~~SAT  221 (412)
                      .-.......+..+....--..+.+...+....-...+. ++++||+|.+...+   -......++...-....+.++.||
T Consensus       245 ~i~~l~l~~l~ag~~~~ge~e~~lk~ii~e~~~~~~~~-ILfIDEih~l~~~g~~~~~~d~~n~Lkp~l~~G~l~~IgaT  323 (852)
T TIGR03345       245 RLLSLDLGLLQAGASVKGEFENRLKSVIDEVKASPQPI-ILFIDEAHTLIGAGGQAGQGDAANLLKPALARGELRTIAAT  323 (852)
T ss_pred             eEEEeehhhhhcccccchHHHHHHHHHHHHHHhcCCCe-EEEEeChHHhccCCCccccccHHHHhhHHhhCCCeEEEEec


Q ss_pred             CChHHHHHHH
Q 015158          222 MPPEALEITR  231 (412)
Q Consensus       222 ~~~~~~~~~~  231 (412)
                      -..+....+.
T Consensus       324 T~~e~~~~~~  333 (852)
T TIGR03345       324 TWAEYKKYFE  333 (852)
T ss_pred             CHHHHhhhhh

Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=90.19  E-value=2  Score=38.87  Aligned_cols=39  Identities=5%  Similarity=0.276  Sum_probs=26.0

Q ss_pred             CCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEe
Q 015158          180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFS  219 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~S  219 (412)
                      ...+++|+||+|.+.... ...+.+.+...|++..++++|
T Consensus        92 ~~~kv~iI~~ad~m~~~a-~naLLK~LEepp~~t~~il~~  130 (313)
T PRK05564         92 GDKKVIIIYNSEKMTEQA-QNAFLKTIEEPPKGVFIILLC  130 (313)
T ss_pred             CCceEEEEechhhcCHHH-HHHHHHHhcCCCCCeEEEEEe
Confidence            467899999999875443 445556666656566555554

>PF10593 Z1: Z1 domain; InterPro: IPR018310 This entry represents the Z1 domain of unknown function that is found in a group of putative endonucleases

Probab=90.18  E-value=1.4  Score=37.88  Aligned_cols=93  Identities=11%  Similarity=0.185  Sum_probs=63.9

Q ss_pred             HHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCC----CcEEEEcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhh
Q 015158          292 DWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGS----SRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIG  367 (412)
Q Consensus       292 ~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~----~~vlv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~G  367 (412)
                      ..+.+.+.. +..+..++++.+...     -.+.+++    ..|+|+-+.+++|+.+++..+.++...+.....+.||.-
T Consensus       101 ~~l~~~~~~-~~~v~~vNS~~~~~~-----ldy~~~~~~~~~~I~VGGn~LsRGlTleGL~vsYf~R~s~~~DTL~QmgR  174 (239)
T PF10593_consen  101 PELPKAISD-GIEVVVVNSGSSDDS-----LDYDDGENLGLNVIAVGGNKLSRGLTLEGLTVSYFLRNSKQYDTLMQMGR  174 (239)
T ss_pred             HHHHHHHhc-CceEEEEeCCCcccc-----ccccccccCCceEEEECCccccCceeECCcEEEEecCCCchHHHHHHHhh
Confidence            344444444 678888887654432     3344443    678888999999999999999999998888888888754


Q ss_pred             hcc-cCCCCceEEEEeccCcHHHH
Q 015158          368 RSG-RFGRKGVAINFVTRDDERML  390 (412)
Q Consensus       368 R~~-R~g~~g~~~~~~~~~~~~~~  390 (412)
                      -.| |.|-...|=++.++.-.+.+
T Consensus       175 wFGYR~gY~dl~Ri~~~~~l~~~f  198 (239)
T PF10593_consen  175 WFGYRPGYEDLCRIYMPEELYDWF  198 (239)
T ss_pred             cccCCcccccceEEecCHHHHHHH
Confidence            443 44445678878777544333

This domain is found associated with a helicase domain of superfamily type II [].

>TIGR02012 tigrfam_recA protein RecA

Probab=90.17  E-value=0.61  Score=41.93  Aligned_cols=43  Identities=16%  Similarity=0.112  Sum_probs=31.0

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHH
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQ  121 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~  121 (412)
                      |+-+.|.+|+|+|||..++..+......   +.+++|+-.-..+..
T Consensus        55 G~iteI~G~~GsGKTtLaL~~~~~~~~~---g~~v~yId~E~~~~~   97 (321)
T TIGR02012        55 GRIIEIYGPESSGKTTLALHAIAEAQKA---GGTAAFIDAEHALDP   97 (321)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHc---CCcEEEEcccchhHH
Confidence            5678899999999998877666665543   357888766555444

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.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	412
2zu6_A	388	Crystal Structure Of The Eif4a-Pdcd4 Complex Length		1e-157
3eiq_A	414	Crystal Structure Of Pdcd4-eif4a Length = 414		1e-156
2xb2_A	411	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		1e-151
2j0q_A	410	The Crystal Structure Of The Exon Junction Complex		1e-151
2hyi_C	413	Structure Of The Human Exon Junction Complex With A		1e-151
2hxy_A	391	Crystal Structure Of Human Apo-Eif4aiii Length = 39		1e-150
2j0u_B	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		1e-149
2j0u_A	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		1e-149
2vso_A	395	Crystal Structure Of A Translation Initiation Compl		1e-133
1fuu_A	394	Yeast Initiation Factor 4a Length = 394		1e-127
1s2m_A	400	Crystal Structure Of The Dead Box Protein Dhh1p Len		2e-81
3bor_A	237	Crystal Structure Of The Deadc Domain Of Human Tran		1e-80
2g9n_A	221	Structure Of The Dead Domain Of Human Eukaryotic In		2e-73
1qde_A	224	Crystal Structure Of The Atpase Domain Of Translati		2e-73
3pew_A	395	S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3		7e-73
3pey_A	395	S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length		9e-73
3fmp_B	479	Crystal Structure Of The Nucleoporin Nup214 In Comp		1e-69
3g0h_A	424	Human Dead-box Rna Helicase Ddx19, In Complex With		1e-69
3ews_A	445	Human Dead-Box Rna-Helicase Ddx19 In Complex With A		1e-69
3fht_A	412	Crystal Structure Of Human Dbp5 In Complex With Amp		2e-69
1qva_A	223	Yeast Initiation Factor 4a N-Terminal Domain Length		2e-67
1xtk_A	390	Structure Of Decd To Dead Mutation Of Human Uap56 L		5e-67
1xtj_A	386	Structure Of Human Uap56 In Complex With Adp Length		1e-66
1xti_A	391	Structure Of Wildtype Human Uap56 Length = 391		1e-66
3fho_B	508	Structure Of S. Pombe Dbp5 Length = 508		2e-66
1hv8_A	367	Crystal Structure Of A Dead Box Protein From The Hy		1e-57
1fuk_A	165	Crystal Structure Of The Carboxy Terminal Domain Of		1e-52
2db3_A	434	Structural Basis For Rna Unwinding By The Dead-Box		2e-50
2i4i_A	417	Crystal Structure Of Human Dead-Box Rna Helicase Dd		4e-50
2z0m_A	337	Crystal Structure Of Hypothetical Atp-Dependent Rna		3e-41
3i5x_A	563	Structure Of Mss116p Bound To Ssrna And Amp-Pnp Len		7e-36
3sqx_A	512	Structure Of Mss116p (Nte And C-Tail Double Deletio		8e-36
3sqw_A	579	Structure Of Mss116p (Nte Deletion) Bound To Ssrna		9e-36
1t6n_A	220	Crystal Structure Of The N-Terminal Domain Of Human		2e-35
2rb4_A	175	Crystal Structure Of The Helicase Domain Of Human D		2e-35
2kbf_A	187	Solution Structure Of Carboxyl-Terminal Domain Of D		3e-35
1vec_A	206	Crystal Structure Of The N-Terminal Domain Of RckP5		7e-35
3peu_A	188	S. Cerevisiae Dbp5 L327v C-Terminal Domain Bound To		2e-34
3gfp_A	189	Structure Of The C-Terminal Domain Of The Dead-Box		2e-34
2oxc_A	230	Human Dead-Box Rna Helicase Ddx20, Dead Domain In C		3e-33
2wax_A	193	Structure Of The Human Ddx6 C-Terminal Domain In Co		7e-33
2kbe_A	226	Solution Structure Of Amino-Terminal Domain Of Dbp5		2e-30
2gxq_A	207	Hera N-Terminal Domain In Complex With Amp, Crystal		1e-29
3mwj_A	207	Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Ap		4e-29
3fhc_B	235	Crystal Structure Of Human Dbp5 In Complex With Nup		3e-28
2hjv_A	163	Structure Of The Second Domain (Residues 207-368) O		3e-28
3fmo_B	300	Crystal Structure Of The Nucleoporin Nup214 In Comp		5e-28
3ber_A	249	Human Dead-Box Rna-Helicase Ddx47, Conserved Domain		3e-25
1t5i_A	172	Crystal Structure Of The C-Terminal Domain Of Uap56		1e-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		5e-24
3fe2_A	242	Human Dead-Box Rna Helicase Ddx5 (P68), Conserved D		3e-21
4a4d_A	253	Crystal Structure Of The N-Terminal Domain Of The H		5e-21
3ly5_A	262	Ddx18 Dead-Domain Length = 262		5e-21
2jgn_A	185	Ddx3 Helicase Domain Length = 185		2e-20
2yjt_D	170	Crystal Structure Of E. Coli Dead-Box Protein Srmb		5e-20
3iuy_A	228	Crystal Structure Of Ddx53 Dead-Box Domain Length =		3e-19
2pl3_A	236	Human Dead-Box Rna Helicase Ddx10, Dead Domain In C		1e-18
2p6n_A	191	Human Dead-box Rna Helicase Ddx41, Helicase Domain		2e-18
3i32_A	300	Dimeric Structure Of A Hera Helicase Fragment Inclu		5e-16
3eaq_A	212	Novel Dimerization Motif In The Dead Box Rna Helica		4e-15
3dkp_A	245	Human Dead-Box Rna-Helicase Ddx52, Conserved Domain		6e-15
4db4_A	256	Mss116p Dead-Box Helicase Domain 2 Bound To A Chima		8e-15
4db2_C	257	Mss116p Dead-Box Helicase Domain 2 Bound To An Rna		8e-15
4db2_A	257	Mss116p Dead-Box Helicase Domain 2 Bound To An Rna		8e-15
1oyy_A	523	Structure Of The Recq Catalytic Core Bound To Atp-G		5e-09
1oyw_A	523	Structure Of The Recq Catalytic Core Length = 523		6e-09
4gl2_A	699	Structural Basis For Dsrna Duplex Backbone Recognit		1e-04
1gm5_A	780	Structure Of Recg Bound To Three-Way Dna Junction L		2e-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		3e-04
4i1s_A	243	Melanoma Differentiation Associated Protein-5 Helic		6e-04
1wp9_A	494	Crystal Structure Of Pyrococcus Furiosus Hef Helica		8e-04

>pdb|2ZU6|A Chain A, Crystal Structure Of The Eif4a-Pdcd4 Complex Length = 388

Iteration: 1
 Score =  550 bits (1417), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 276/382 (72%), Positives = 321/382 (84%), Gaps = 1/382 (0%)
Query: 32  TSYDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTA 91
           ++++E+ D+FD M L E+LLRGIYAYGFEKPSAIQQR I+P  KG DVI QAQSGTGKTA
Sbjct: 7   SNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTA 66
Query: 92  TFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVR-ED 150
           TF   ILQQ++  L   QALVLAPTRELAQQI+KV+ ALGDY+G   HAC+GGT+VR E 
Sbjct: 67  TFAISILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEV 126
Query: 151 QRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLP 210
           Q++     H++VGTPGRVFDML R+ L P  I++FVLDEADEMLSRGFKDQIYDIFQ L 
Sbjct: 127 QKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLN 186
Query: 211 PKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLC 270
              QV + SATMP + LE+T+KFM  P+RILVK++ELTLEGI+QF++NVE+EEWKL+TLC
Sbjct: 187 SNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLC 246
Query: 271 DLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSR 330
           DLYETL ITQ+VIF+NTRRKVDWLT+KM +RD TVSA HGDMDQ  RD+IMREFRSGSSR
Sbjct: 247 DLYETLTITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSR 306
Query: 331 VLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERML 390
           VLITTDLLARGIDVQQVSLVINYDLPT  ENY+HRIGR GRFGRKGVAIN VT +D+R L
Sbjct: 307 VLITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTEEDKRTL 366
Query: 391 FDIQKFYNVVIEELPANVADLL 412
            DI+ FYN  IEE+P NVADL+
Sbjct: 367 RDIETFYNTSIEEMPLNVADLI 388

>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a Length = 414

Iteration: 1
 Score =  549 bits (1414), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 283/409 (69%), Positives = 332/409 (81%), Gaps = 6/409 (1%)
Query: 9   QFDARQFDARMNDLLGSDGQD----FFTSYDEVYDTFDAMGLQENLLRGIYAYGFEKPSA 64
           +F +   D+R  D  G DG +      ++++E+ D+FD M L E+LLRGIYAYGFEKPSA
Sbjct: 7   EFMSASQDSRSRDN-GPDGMEPEGVIESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSA 65
Query: 65  IQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIE 124
           IQQR I+P  KG DVI QAQSGTGKTATF   ILQQ++  L   QALVLAPTRELAQQI+
Sbjct: 66  IQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQQIQ 125
Query: 125 KVMRALGDYLGVKVHACVGGTSVR-EDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIR 183
           KV+ ALGDY+G   HAC+GGT+VR E Q++     H++VGTPGRVFDML R+ L P  I+
Sbjct: 126 KVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIK 185
Query: 184 IFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVK 243
           +FVLDEADEMLSRGFKDQIYDIFQ L    QV + SATMP + LE+T+KFM  P+RILVK
Sbjct: 186 MFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVK 245
Query: 244 RDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDH 303
           ++ELTLEGI+QF++NVE+EEWKL+TLCDLYETL ITQ+VIF+NTRRKVDWLT+KM +RD 
Sbjct: 246 KEELTLEGIRQFYINVEREEWKLDTLCDLYETLTITQAVIFINTRRKVDWLTEKMHARDF 305
Query: 304 TVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYL 363
           TVSA HGDMDQ  RD+IMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPT  ENY+
Sbjct: 306 TVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENYI 365
Query: 364 HRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVADLL 412
           HRIGR GRFGRKGVAIN VT +D+R L DI+ FYN  IEE+P NVADL+
Sbjct: 366 HRIGRGGRFGRKGVAINMVTEEDKRTLRDIETFYNTSIEEMPLNVADLI 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 =  530 bits (1364), Expect = e-151,   Method: Compositional matrix adjust.
 Identities = 258/385 (67%), Positives = 312/385 (81%), Gaps = 1/385 (0%)
Query: 29  DFFTSYD-EVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGT 87
           +F TS + +V  TFD MGL+E+LLRGIYAYGFEKPSAIQQR I    KG DVI Q+QSGT
Sbjct: 27  EFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGT 86
Query: 88  GKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSV 147
           GKTATF   +LQ LD  + E QAL+LAPTRELA QI+K + ALGDY+ V+ HAC+GGT+V
Sbjct: 87  GKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNV 146
Query: 148 REDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQ 207
            ED R L  G HVV GTPGRVFDM+RR+SLR   I++ VLDEADEML++GFK+QIYD+++
Sbjct: 147 GEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYR 206
Query: 208 LLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLE 267
            LPP  QV + SAT+P E LE+T KFM  P+RILVKRDELTLEGIKQF V VE+EEWK +
Sbjct: 207 YLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFD 266
Query: 268 TLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSG 327
           TLCDLY+TL ITQ+VIF NT+RKVDWLT+KMR  + TVS+ HGDM Q  R+ IM+EFRSG
Sbjct: 267 TLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSG 326
Query: 328 SSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDE 387
           +SRVLI+TD+ ARG+DV QVSL+INYDLP   E Y+HRIGRSGR+GRKGVAINFV  DD 
Sbjct: 327 ASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDI 386
Query: 388 RMLFDIQKFYNVVIEELPANVADLL 412
           R+L DI+++Y+  I+E+P NVADL+
Sbjct: 387 RILRDIEQYYSTQIDEMPMNVADLI 411

>pdb|2J0Q|A Chain A, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 410

Iteration: 1
 Score =  530 bits (1364), Expect = e-151,   Method: Compositional matrix adjust.
 Identities = 258/385 (67%), Positives = 312/385 (81%), Gaps = 1/385 (0%)
Query: 29  DFFTSYD-EVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGT 87
           +F TS + +V  TFD MGL+E+LLRGIYAYGFEKPSAIQQR I    KG DVI Q+QSGT
Sbjct: 26  EFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGT 85
Query: 88  GKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSV 147
           GKTATF   +LQ LD  + E QAL+LAPTRELA QI+K + ALGDY+ V+ HAC+GGT+V
Sbjct: 86  GKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNV 145
Query: 148 REDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQ 207
            ED R L  G HVV GTPGRVFDM+RR+SLR   I++ VLDEADEML++GFK+QIYD+++
Sbjct: 146 GEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYR 205
Query: 208 LLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLE 267
            LPP  QV + SAT+P E LE+T KFM  P+RILVKRDELTLEGIKQF V VE+EEWK +
Sbjct: 206 YLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFD 265
Query: 268 TLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSG 327
           TLCDLY+TL ITQ+VIF NT+RKVDWLT+KMR  + TVS+ HGDM Q  R+ IM+EFRSG
Sbjct: 266 TLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSG 325
Query: 328 SSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDE 387
           +SRVLI+TD+ ARG+DV QVSL+INYDLP   E Y+HRIGRSGR+GRKGVAINFV  DD 
Sbjct: 326 ASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDI 385
Query: 388 RMLFDIQKFYNVVIEELPANVADLL 412
           R+L DI+++Y+  I+E+P NVADL+
Sbjct: 386 RILRDIEQYYSTQIDEMPMNVADLI 410

>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 =  530 bits (1364), Expect = e-151,   Method: Compositional matrix adjust.
 Identities = 258/385 (67%), Positives = 312/385 (81%), Gaps = 1/385 (0%)
Query: 29  DFFTSYD-EVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGT 87
           +F TS + +V  TFD MGL+E+LLRGIYAYGFEKPSAIQQR I    KG DVI Q+QSGT
Sbjct: 27  EFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGT 86
Query: 88  GKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSV 147
           GKTATF   +LQ LD  + E QAL+LAPTRELA QI+K + ALGDY+ V+ HAC+GGT+V
Sbjct: 87  GKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNV 146
Query: 148 REDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQ 207
            ED R L  G HVV GTPGRVFDM+RR+SLR   I++ VLDEADEML++GFK+QIYD+++
Sbjct: 147 GEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYR 206
Query: 208 LLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLE 267
            LPP  QV + SAT+P E LE+T KFM  P+RILVKRDELTLEGIKQF V VE+EEWK +
Sbjct: 207 YLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFD 266
Query: 268 TLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSG 327
           TLCDLY+TL ITQ+VIF NT+RKVDWLT+KMR  + TVS+ HGDM Q  R+ IM+EFRSG
Sbjct: 267 TLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSG 326
Query: 328 SSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDE 387
           +SRVLI+TD+ ARG+DV QVSL+INYDLP   E Y+HRIGRSGR+GRKGVAINFV  DD 
Sbjct: 327 ASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDI 386
Query: 388 RMLFDIQKFYNVVIEELPANVADLL 412
           R+L DI+++Y+  I+E+P NVADL+
Sbjct: 387 RILRDIEQYYSTQIDEMPMNVADLI 411

>pdb|2HXY|A Chain A, Crystal Structure Of Human Apo-Eif4aiii Length = 391

Iteration: 1
 Score =  528 bits (1360), Expect = e-150,   Method: Compositional matrix adjust.
 Identities = 258/385 (67%), Positives = 312/385 (81%), Gaps = 1/385 (0%)
Query: 29  DFFTSYD-EVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGT 87
           +F TS + +V  TFD MGL+E+LLRGIYAYGFEKPSAIQQR I    KG DVI Q+QSGT
Sbjct: 5   EFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGT 64
Query: 88  GKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSV 147
           GKTATF   +LQ LD  + E QAL+LAPTRELA QI+K + ALGDY+ V+ HAC+GGT+V
Sbjct: 65  GKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNV 124
Query: 148 REDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQ 207
            ED R L  G HVV GTPGRVFDM+RR+SLR   I++ VLDEADEML++GFK+QIYD+++
Sbjct: 125 GEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYR 184
Query: 208 LLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLE 267
            LPP  QV + SAT+P E LE+T KFM  P+RILVKRDELTLEGIKQF V VE+EEWK +
Sbjct: 185 YLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFD 244
Query: 268 TLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSG 327
           TLCDLY+TL ITQ+VIF NT+RKVDWLT+KMR  + TVS+ HGDM Q  R+ IM+EFRSG
Sbjct: 245 TLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSG 304
Query: 328 SSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDE 387
           +SRVLI+TD+ ARG+DV QVSL+INYDLP   E Y+HRIGRSGR+GRKGVAINFV  DD 
Sbjct: 305 ASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDI 364
Query: 388 RMLFDIQKFYNVVIEELPANVADLL 412
           R+L DI+++Y+  I+E+P NVADL+
Sbjct: 365 RILRDIEQYYSTQIDEMPMNVADLI 389

>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score =  526 bits (1354), Expect = e-149,   Method: Compositional matrix adjust.
 Identities = 252/373 (67%), Positives = 305/373 (81%)
Query: 40  TFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQ 99
           TFD MGL+E+LLRGIYAYGFEKPSAIQQR I    KG DVI Q+QSGTGKTATF   +LQ
Sbjct: 2   TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSVSVLQ 61
Query: 100 QLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVH 159
            LD  + E QAL+LAPTRELA Q++K + ALGDY+ V+ HAC+GGT+V ED R L  G H
Sbjct: 62  CLDIQVRETQALILAPTRELAVQVQKGLLALGDYMNVQSHACIGGTNVGEDIRKLDYGQH 121
Query: 160 VVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFS 219
           VV GTPGRVFDM+RR+SLR   I++ VLDEADEML++GFK+QIYD+++ LPP  QV + S
Sbjct: 122 VVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLIS 181
Query: 220 ATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAIT 279
           AT+P E LE+T KFM  P+RILVKRDELTLEGIKQF V VE+EEWK +TLCDLY+TL IT
Sbjct: 182 ATLPHEVLEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTIT 241
Query: 280 QSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLA 339
           Q+VIF NT+RKVDWLT+KMR  + TVS+ HGDM Q  R+ IM+EFRSG+SRVLI+TD+ A
Sbjct: 242 QAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWA 301
Query: 340 RGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNV 399
           RG+DV QVSL+INYDLP   E Y+HRIGRSGR+GRKGVA+NFV  DD R+L DI+++Y+ 
Sbjct: 302 RGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAVNFVKNDDIRVLRDIEQYYST 361
Query: 400 VIEELPANVADLL 412
            I+E+P NVADL+
Sbjct: 362 QIDEMPMNVADLI 374

>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score =  525 bits (1352), Expect = e-149,   Method: Compositional matrix adjust.
 Identities = 252/373 (67%), Positives = 305/373 (81%)
Query: 40  TFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQ 99
           TFD MGL+E+LLRGIYAYGFEKPSAIQQR I    KG DVI Q+QSGTGKTATF   +LQ
Sbjct: 2   TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSVSVLQ 61
Query: 100 QLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVH 159
            LD  + E QAL+LAPTRELA Q++K + ALGDY+ V+ HAC+GGT+V ED R L  G H
Sbjct: 62  CLDIQVRETQALILAPTRELAVQVQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQH 121
Query: 160 VVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFS 219
           VV GTPGRVFDM+RR+SLR   I++ VLDEADEML++GFK+QIYD+++ LPP  QV + S
Sbjct: 122 VVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLIS 181
Query: 220 ATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAIT 279
           AT+P E LE+T KFM  P+RILVKRDELTLEGIKQF V VE+EEWK +TLCDLY+TL IT
Sbjct: 182 ATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTIT 241
Query: 280 QSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLA 339
           Q+VIF NT+RKVDWLT+KMR  + TVS+ HGDM Q  R+ IM+EFRSG+SRVLI+TD+ A
Sbjct: 242 QAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWA 301
Query: 340 RGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNV 399
           RG+DV QVSL+INYDLP   E Y+HRIGRSGR+GRKGVA+NFV  DD R+L DI+++Y+ 
Sbjct: 302 RGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAVNFVKNDDIRVLRDIEQYYST 361
Query: 400 VIEELPANVADLL 412
            I+E+P NVADL+
Sbjct: 362 QIDEMPMNVADLI 374

>pdb|2VSO|A Chain A, Crystal Structure Of A Translation Initiation Complex Length = 395

Iteration: 1
 Score =  470 bits (1209), Expect = e-133,   Method: Compositional matrix adjust.
 Identities = 243/381 (63%), Positives = 300/381 (78%), Gaps = 1/381 (0%)
Query: 32  TSYDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTA 91
           T+YD+V   FD M L ENLLRG++ YGFE+PSAIQQR I+P  +G DV+ QAQSGTGKT 
Sbjct: 15  TNYDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTG 74
Query: 92  TFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQ 151
           TF    LQ++D  +   QAL+LAPTRELA QI+KV+ AL  ++ +KVHAC+GGTS  ED 
Sbjct: 75  TFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDA 134
Query: 152 RILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPP 211
             L     +VVGTPGRVFD ++R+  R D I++F+LDEADEMLS GFK+QIY IF LLPP
Sbjct: 135 EGLRDA-QIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLPP 193
Query: 212 KIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCD 271
             QV + SATMP + LE+T KFM  PVRILVK+DELTLEGIKQF+VNVE+EE+K E L D
Sbjct: 194 TTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKDELTLEGIKQFYVNVEEEEYKYECLTD 253
Query: 272 LYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRV 331
           LY+++++TQ+VIF NTRRKV+ LT K+R+   TVSA + D+ Q  RD IM+EFRSGSSR+
Sbjct: 254 LYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRI 313
Query: 332 LITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLF 391
           LI+TDLLARGIDVQQVSLVINYDLP   ENY+HRIGR GRFGRKGVAINFVT +D   + 
Sbjct: 314 LISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMR 373
Query: 392 DIQKFYNVVIEELPANVADLL 412
           +++KFY+  IEELP+++A LL
Sbjct: 374 ELEKFYSTQIEELPSDIATLL 394

>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a Length = 394

Iteration: 1
 Score =  452 bits (1162), Expect = e-127,   Method: Compositional matrix adjust.
 Identities = 238/381 (62%), Positives = 290/381 (76%), Gaps = 1/381 (0%)
Query: 32  TSYDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTA 91
           T+YD+V   FD   L ENLLRG++ YGFE+PSAIQQR I P  +G DV+ QAQSGTGKT 
Sbjct: 14  TNYDKVVYKFDDXELDENLLRGVFGYGFEEPSAIQQRAIXPIIEGHDVLAQAQSGTGKTG 73
Query: 92  TFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQ 151
           TF    LQ++D  +   QAL LAPTRELA QI+KV+ AL  +  +KVHAC+GGTS  ED 
Sbjct: 74  TFSIAALQRIDTSVKAPQALXLAPTRELALQIQKVVXALAFHXDIKVHACIGGTSFVEDA 133
Query: 152 RILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPP 211
             L     +VVGTPGRVFD ++R+  R D I+ F+LDEADE LS GFK+QIY IF LLPP
Sbjct: 134 EGLRDA-QIVVGTPGRVFDNIQRRRFRTDKIKXFILDEADEXLSSGFKEQIYQIFTLLPP 192
Query: 212 KIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCD 271
             QV + SAT P + LE+T KF   PVRILVK+DELTLEGIKQF+VNVE+EE+K E L D
Sbjct: 193 TTQVVLLSATXPNDVLEVTTKFXRNPVRILVKKDELTLEGIKQFYVNVEEEEYKYECLTD 252
Query: 272 LYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRV 331
           LY+++++TQ+VIF NTRRKV+ LT K+R+   TVSA + D+ Q  RD I +EFRSGSSR+
Sbjct: 253 LYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIXKEFRSGSSRI 312
Query: 332 LITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLF 391
           LI+TDLLARGIDVQQVSLVINYDLP   ENY+HRIGR GRFGRKGVAINFVT +D     
Sbjct: 313 LISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAXR 372
Query: 392 DIQKFYNVVIEELPANVADLL 412
           +++KFY+  IEELP+++A LL
Sbjct: 373 ELEKFYSTQIEELPSDIATLL 393

>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p Length = 400

Iteration: 1
 Score =  299 bits (766), Expect = 2e-81,   Method: Compositional matrix adjust.
 Identities = 157/370 (42%), Positives = 224/370 (60%), Gaps = 2/370 (0%)
Query: 39  DTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGIL 98
           +TF+   L+  LL GI+  GFEKPS IQ+  I     G D++ +A++GTGKTA F    L
Sbjct: 21  NTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTL 80
Query: 99  QQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGV 158
           +++   L + QAL++ PTRELA Q  +V+R LG + G+      GGT++R+D   L+  V
Sbjct: 81  EKVKPKLNKIQALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLNETV 140
Query: 159 HVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVF 218
           H++VGTPGRV D+  R+     +  +F++DEAD+MLSR FK  I  I   LPP  Q  +F
Sbjct: 141 HILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSRDFKTIIEQILSFLPPTHQSLLF 200
Query: 219 SATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAI 278
           SAT P    E   K ++KP  I +  +ELTL+GI Q++  VE E  KL  L  L+  L I
Sbjct: 201 SATFPLTVKEFMVKHLHKPYEINL-MEELTLKGITQYYAFVE-ERQKLHCLNTLFSKLQI 258
Query: 279 TQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLL 338
            Q++IF N+  +V+ L  K+    ++   +H  M Q  R+ +  EFR G  R L+ +DLL
Sbjct: 259 NQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLL 318
Query: 339 ARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYN 398
            RGID+Q V++VIN+D P   E YLHRIGRSGRFG  G+AIN +  +D   L+ I++   
Sbjct: 319 TRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWNDRFNLYKIEQELG 378
Query: 399 VVIEELPANV 408
             I  +PA +
Sbjct: 379 TEIAAIPATI 388

>pdb|3BOR|A Chain A, Crystal Structure Of The Deadc Domain Of Human Translation Initiation Factor 4a-2 Length = 237

Iteration: 1
 Score =  296 bits (759), Expect = 1e-80,   Method: Compositional matrix adjust.
 Identities = 144/215 (66%), Positives = 173/215 (80%), Gaps = 1/215 (0%)
Query: 32  TSYDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTA 91
           ++++E+ D FD M L+E+LLRGIYAYGFEKPSAIQQR I+P  KG DVI QAQSGTGKTA
Sbjct: 23  SNWNEIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTA 82
Query: 92  TFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVR-ED 150
           TF   ILQQL+    E QALVLAPTRELAQQI+KV+ ALGDY+G   HAC+GGT+VR E 
Sbjct: 83  TFAISILQQLEIEFKETQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRNEM 142
Query: 151 QRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLP 210
           Q++ +   H+VVGTPGRVFDML R+ L P  I++FVLDEADEMLSRGFKDQIY+IFQ L 
Sbjct: 143 QKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSRGFKDQIYEIFQKLN 202
Query: 211 PKIQVGVFSATMPPEALEITRKFMNKPVRILVKRD 245
             IQV + SATMP + LE+T+KFM  P+RILVK++
Sbjct: 203 TSIQVVLLSATMPTDVLEVTKKFMRDPIRILVKKE 237

>pdb|2G9N|A Chain A, Structure Of The Dead Domain Of Human Eukaryotic Initiation Factor 4a, Eif4a Length = 221

Iteration: 1
 Score =  273 bits (697), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 135/212 (63%), Positives = 159/212 (75%), Gaps = 1/212 (0%)
Query: 32  TSYDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTA 91
           ++++E+ D+FD M L E+LLRGIYAYGFE PSAIQQR I+P   G DVI QAQSGTG TA
Sbjct: 8   SNWNEIVDSFDDMNLSESLLRGIYAYGFEXPSAIQQRAILPCIXGYDVIAQAQSGTGXTA 67
Query: 92  TFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVR-ED 150
           TF   ILQQ++  L   QALVLAPTRELAQQI+ V+ ALGDY+G   HAC+GGT+VR E 
Sbjct: 68  TFAISILQQIELDLXATQALVLAPTRELAQQIQXVVMALGDYMGASCHACIGGTNVRAEV 127
Query: 151 QRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLP 210
           Q +     H++VGTPGRVFDML R+ L P  I +FVLDEADEMLSRGF DQIYDIFQ L 
Sbjct: 128 QXLQMEAPHIIVGTPGRVFDMLNRRYLSPXYIXMFVLDEADEMLSRGFXDQIYDIFQXLN 187
Query: 211 PKIQVGVFSATMPPEALEITRKFMNKPVRILV 242
              QV + SATMP + LE+T  FM  P+RILV
Sbjct: 188 SNTQVVLLSATMPSDVLEVTXXFMRDPIRILV 219

>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 =  272 bits (696), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 135/219 (61%), Positives = 165/219 (75%), Gaps = 1/219 (0%)
Query: 32  TSYDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTA 91
           T+YD+V   FD M L ENLLRG++ YGFE+PSAIQQR I+P  +G DV+ QAQSGTGKT 
Sbjct: 7   TNYDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTG 66
Query: 92  TFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQ 151
           TF    LQ++D  +   QAL+LAPTRELA QI+KV+ AL  ++ +KVHAC+GGTS  ED 
Sbjct: 67  TFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDA 126
Query: 152 RILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPP 211
             L     +VVGTPGRVFD ++R+  R D I++F+LDEADEMLS GFK+QIY IF LLPP
Sbjct: 127 EGLRDA-QIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLPP 185
Query: 212 KIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLE 250
             QV + SATMP + LE+T KFM  PVRILVK+DELTLE
Sbjct: 186 TTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKDELTLE 224

>pdb|3PEW|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score =  271 bits (692), Expect = 7e-73,   Method: Compositional matrix adjust.
 Identities = 149/368 (40%), Positives = 228/368 (61%), Gaps = 14/368 (3%)
Query: 40  TFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGL--DVIQQAQSGTGKTATFCSGI 97
           +FD +GL   LL+GIYA  F+KPS IQ+R +         ++I Q+QSGTGKTA F   +
Sbjct: 6   SFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTM 65
Query: 98  LQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSG 157
           L +++      QA+ LAP+RELA+Q  +V++ +G +  +     V   S  ++++I    
Sbjct: 66  LTRVNPEDASPQAICLAPSRELARQTLEVVQEMGKFTKITSQLIVPD-SFEKNKQI---N 121
Query: 158 VHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEML-SRGFKDQIYDIFQLLPPKIQVG 216
             V+VGTPG V D++RR+ ++   I+IFVLDEAD ML  +G  DQ   + + LP   Q+ 
Sbjct: 122 AQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVKRFLPKDTQLV 181
Query: 217 VFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETL 276
           +FSAT      +  +K +     + ++ +E+ ++ IKQ +++ + E  K + L +LY  +
Sbjct: 182 LFSATFADAVRQYAKKIVPNANTLELQTNEVNVDAIKQLYMDCKNEADKFDVLTELYGVM 241
Query: 277 AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTD 336
            I  S+IFV T++  + L  K++S  H VS  HGD+    RD ++ +FR G S+VLITT+
Sbjct: 242 TIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTN 301
Query: 337 LLARGIDVQQVSLVINYDLPT------QPENYLHRIGRSGRFGRKGVAINFV-TRDDERM 389
           +LARGID+  VS+V+NYDLPT       P  Y+HRIGR+GRFGRKGVAI+FV  ++   +
Sbjct: 302 VLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDKNSFNI 361
Query: 390 LFDIQKFY 397
           L  IQK++
Sbjct: 362 LSAIQKYF 369

>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score =  270 bits (691), Expect = 9e-73,   Method: Compositional matrix adjust.
 Identities = 149/368 (40%), Positives = 228/368 (61%), Gaps = 14/368 (3%)
Query: 40  TFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGL--DVIQQAQSGTGKTATFCSGI 97
           +FD +GL   LL+GIYA  F+KPS IQ+R +         ++I Q+QSGTGKTA F   +
Sbjct: 6   SFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTM 65
Query: 98  LQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSG 157
           L +++      QA+ LAP+RELA+Q  +V++ +G +  +     V   S  ++++I    
Sbjct: 66  LTRVNPEDASPQAICLAPSRELARQTLEVVQEMGKFTKITSQLIVPD-SFEKNKQI---N 121
Query: 158 VHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEML-SRGFKDQIYDIFQLLPPKIQVG 216
             V+VGTPG V D++RR+ ++   I+IFVLDEAD ML  +G  DQ   + + LP   Q+ 
Sbjct: 122 AQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVKRFLPKDTQLV 181
Query: 217 VFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETL 276
           +FSAT      +  +K +     + ++ +E+ ++ IKQ +++ + E  K + L +LY  +
Sbjct: 182 LFSATFADAVRQYAKKIVPNANTLELQTNEVNVDAIKQLYMDCKNEADKFDVLTELYGLM 241
Query: 277 AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTD 336
            I  S+IFV T++  + L  K++S  H VS  HGD+    RD ++ +FR G S+VLITT+
Sbjct: 242 TIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTN 301
Query: 337 LLARGIDVQQVSLVINYDLPT------QPENYLHRIGRSGRFGRKGVAINFV-TRDDERM 389
           +LARGID+  VS+V+NYDLPT       P  Y+HRIGR+GRFGRKGVAI+FV  ++   +
Sbjct: 302 VLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDKNSFNI 361
Query: 390 LFDIQKFY 397
           L  IQK++
Sbjct: 362 LSAIQKYF 369

>pdb|3FMP|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex With The Dead- Box Helicase Ddx19 Length = 479

Iteration: 1
 Score =  260 bits (664), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 149/378 (39%), Positives = 226/378 (59%), Gaps = 17/378 (4%)
Query: 40  TFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKG---LDVIQQAQSGTGKTATFCSG 96
           +F+ + L+  LL+G+YA GF +PS IQ+  + P        ++I Q+QSGTGKTA F   
Sbjct: 93  SFEELRLKPQLLQGVYAMGFNRPSKIQENAL-PLMLAEPPQNLIAQSQSGTGKTAAFVLA 151
Query: 97  ILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGD-YLGVKVHACVGGTSVREDQRILS 155
           +L Q++      Q L L+PT ELA Q  KV+  +G  Y  +K+   V G  +   Q+I  
Sbjct: 152 MLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKI-- 209
Query: 156 SGVHVVVGTPGRVFDMLRR-QSLRPDNIRIFVLDEADEML-SRGFKDQIYDIFQLLPPKI 213
               +V+GTPG V D   + + + P  I++FVLDEAD M+ ++G +DQ   I ++LP   
Sbjct: 210 -SEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNC 268
Query: 214 QVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLY 273
           Q+ +FSAT      +  +K +  P  I +KR+E TL+ IKQ++V     + K + LC+LY
Sbjct: 269 QMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVLCSSRDEKFQALCNLY 328
Query: 274 ETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLI 333
             + I Q++IF +TR+   WL  ++    H V+   G+M    R  ++  FR G  +VL+
Sbjct: 329 GAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLV 388
Query: 334 TTDLLARGIDVQQVSLVINYDLPT----QPEN--YLHRIGRSGRFGRKGVAINFV-TRDD 386
           TT++ ARGIDV+QVS+VIN+DLP      P+N  YLHRIGR+GRFG++G+A+N V ++  
Sbjct: 389 TTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHS 448
Query: 387 ERMLFDIQKFYNVVIEEL 404
             +L  IQ+ +N  IE L
Sbjct: 449 MNILNRIQEHFNKKIERL 466

>pdb|3G0H|A Chain A, Human Dead-box Rna Helicase Ddx19, In Complex With An Atp-analogue And Rna Length = 424

Iteration: 1
 Score =  259 bits (663), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 149/378 (39%), Positives = 226/378 (59%), Gaps = 17/378 (4%)
Query: 40  TFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKG---LDVIQQAQSGTGKTATFCSG 96
           +F+ + L+  LL+G+YA GF +PS IQ+  + P        ++I Q+QSGTGKTA F   
Sbjct: 42  SFEELRLKPQLLQGVYAMGFNRPSKIQENAL-PLMLAEPPQNLIAQSQSGTGKTAAFVLA 100
Query: 97  ILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGD-YLGVKVHACVGGTSVREDQRILS 155
           +L Q++      Q L L+PT ELA Q  KV+  +G  Y  +K+   V G  +   Q+I  
Sbjct: 101 MLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKI-- 158
Query: 156 SGVHVVVGTPGRVFDMLRR-QSLRPDNIRIFVLDEADEML-SRGFKDQIYDIFQLLPPKI 213
               +V+GTPG V D   + + + P  I++FVLDEAD M+ ++G +DQ   I ++LP   
Sbjct: 159 -SEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNC 217
Query: 214 QVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLY 273
           Q+ +FSAT      +  +K +  P  I +KR+E TL+ IKQ++V     + K + LC+LY
Sbjct: 218 QMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVLCSSRDEKFQALCNLY 277
Query: 274 ETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLI 333
             + I Q++IF +TR+   WL  ++    H V+   G+M    R  ++  FR G  +VL+
Sbjct: 278 GAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLV 337
Query: 334 TTDLLARGIDVQQVSLVINYDLPT----QPEN--YLHRIGRSGRFGRKGVAINFV-TRDD 386
           TT++ ARGIDV+QVS+VIN+DLP      P+N  YLHRIGR+GRFG++G+A+N V ++  
Sbjct: 338 TTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHS 397
Query: 387 ERMLFDIQKFYNVVIEEL 404
             +L  IQ+ +N  IE L
Sbjct: 398 MNILNRIQEHFNKKIERL 415

>pdb|3EWS|A Chain A, Human Dead-Box Rna-Helicase Ddx19 In Complex With Adp Length = 445

Iteration: 1
 Score =  259 bits (663), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 149/378 (39%), Positives = 226/378 (59%), Gaps = 17/378 (4%)
Query: 40  TFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKG---LDVIQQAQSGTGKTATFCSG 96
           +F+ + L+  LL+G+YA GF +PS IQ+  + P        ++I Q+QSGTGKTA F   
Sbjct: 63  SFEELRLKPQLLQGVYAMGFNRPSKIQENAL-PLMLAEPPQNLIAQSQSGTGKTAAFVLA 121
Query: 97  ILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGD-YLGVKVHACVGGTSVREDQRILS 155
           +L Q++      Q L L+PT ELA Q  KV+  +G  Y  +K+   V G  +   Q+I  
Sbjct: 122 MLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKI-- 179
Query: 156 SGVHVVVGTPGRVFDMLRR-QSLRPDNIRIFVLDEADEML-SRGFKDQIYDIFQLLPPKI 213
               +V+GTPG V D   + + + P  I++FVLDEAD M+ ++G +DQ   I ++LP   
Sbjct: 180 -SEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNC 238
Query: 214 QVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLY 273
           Q+ +FSAT      +  +K +  P  I +KR+E TL+ IKQ++V     + K + LC+LY
Sbjct: 239 QMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVLCSSRDEKFQALCNLY 298
Query: 274 ETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLI 333
             + I Q++IF +TR+   WL  ++    H V+   G+M    R  ++  FR G  +VL+
Sbjct: 299 GAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLV 358
Query: 334 TTDLLARGIDVQQVSLVINYDLPT----QPEN--YLHRIGRSGRFGRKGVAINFV-TRDD 386
           TT++ ARGIDV+QVS+VIN+DLP      P+N  YLHRIGR+GRFG++G+A+N V ++  
Sbjct: 359 TTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHS 418
Query: 387 ERMLFDIQKFYNVVIEEL 404
             +L  IQ+ +N  IE L
Sbjct: 419 MNILNRIQEHFNKKIERL 436

>pdb|3FHT|A Chain A, Crystal Structure Of Human Dbp5 In Complex With Amppnp And Rna Length = 412

Iteration: 1
 Score =  259 bits (663), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 149/378 (39%), Positives = 226/378 (59%), Gaps = 17/378 (4%)
Query: 40  TFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKG---LDVIQQAQSGTGKTATFCSG 96
           +F+ + L+  LL+G+YA GF +PS IQ+  + P        ++I Q+QSGTGKTA F   
Sbjct: 26  SFEELRLKPQLLQGVYAMGFNRPSKIQENAL-PLMLAEPPQNLIAQSQSGTGKTAAFVLA 84
Query: 97  ILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGD-YLGVKVHACVGGTSVREDQRILS 155
           +L Q++      Q L L+PT ELA Q  KV+  +G  Y  +K+   V G  +   Q+I  
Sbjct: 85  MLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKI-- 142
Query: 156 SGVHVVVGTPGRVFDMLRR-QSLRPDNIRIFVLDEADEML-SRGFKDQIYDIFQLLPPKI 213
               +V+GTPG V D   + + + P  I++FVLDEAD M+ ++G +DQ   I ++LP   
Sbjct: 143 -SEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNC 201
Query: 214 QVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLY 273
           Q+ +FSAT      +  +K +  P  I +KR+E TL+ IKQ++V     + K + LC+LY
Sbjct: 202 QMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVLCSSRDEKFQALCNLY 261
Query: 274 ETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLI 333
             + I Q++IF +TR+   WL  ++    H V+   G+M    R  ++  FR G  +VL+
Sbjct: 262 GAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLV 321
Query: 334 TTDLLARGIDVQQVSLVINYDLPT----QPEN--YLHRIGRSGRFGRKGVAINFV-TRDD 386
           TT++ ARGIDV+QVS+VIN+DLP      P+N  YLHRIGR+GRFG++G+A+N V ++  
Sbjct: 322 TTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHS 381
Query: 387 ERMLFDIQKFYNVVIEEL 404
             +L  IQ+ +N  IE L
Sbjct: 382 MNILNRIQEHFNKKIERL 399

>pdb|1QVA|A Chain A, Yeast Initiation Factor 4a N-Terminal Domain Length = 223

Iteration: 1
 Score =  253 bits (646), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 126/211 (59%), Positives = 155/211 (73%), Gaps = 1/211 (0%)
Query: 32  TSYDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTA 91
           T+Y +V   FD M L E LLRG++ YGFE+PSAIQQR I+P  +G DV+ QAQSGTGKT 
Sbjct: 14  TNYQKVVYKFDDMELDEQLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTG 73
Query: 92  TFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQ 151
           TF    LQ++D  +   QAL+LAPTRELA QI+KV+ AL  ++ +KVHAC+GGTS  ED 
Sbjct: 74  TFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDA 133
Query: 152 RILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPP 211
             L     +VVGTPGRVFD ++R+  R D I++F+LDEADEMLS GFK+QIY IF LLPP
Sbjct: 134 EGLRDA-QIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLPP 192
Query: 212 KIQVGVFSATMPPEALEITRKFMNKPVRILV 242
             QV + SATMP + LE+T KFM  PVRILV
Sbjct: 193 TTQVVLLSATMPNDVLEVTTKFMRNPVRILV 223

>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56 Length = 390

Iteration: 1
 Score =  251 bits (641), Expect = 5e-67,   Method: Compositional matrix adjust.
 Identities = 144/368 (39%), Positives = 216/368 (58%), Gaps = 6/368 (1%)
Query: 46  LQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGL 105
           L+  LLR I   GFE PS +Q   I     G+DV+ QA+SG GKTA F    LQQL+   
Sbjct: 14  LKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVT 73
Query: 106 VECQALVLAPTRELAQQIEKVMRALGDYL-GVKVHACVGGTSVREDQRILSSGV-HVVVG 163
            +   LV+  TRELA QI K       Y+  VKV    GG S+++D+ +L     H+VVG
Sbjct: 74  GQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVG 133
Query: 164 TPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSR-GFKDQIYDIFQLLPPKIQVGVFSATM 222
           TPGR+  + R +SL   +I+ F+LDEAD+ML +   +  + +IF++ P + QV +FSAT+
Sbjct: 134 TPGRILALARNKSLNLKHIKHFILDEADKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATL 193
Query: 223 PPEALEITRKFMNKPVRILVKRD-ELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQS 281
             E   + RKFM  P+ I V  + +LTL G++Q++V + K+  K   L DL + L   Q 
Sbjct: 194 SKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKL-KDNEKNRKLFDLLDVLEFNQV 252
Query: 282 VIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARG 341
           VIFV + ++   L   +  ++    A H  M Q  R    ++F+    R+L+ T+L  RG
Sbjct: 253 VIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRG 312
Query: 342 IDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVT-RDDERMLFDIQKFYNVV 400
           +D+++V++  NYD+P   + YLHR+ R+GRFG KG+AI FV+  +D ++L D+Q  + V 
Sbjct: 313 MDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVN 372
Query: 401 IEELPANV 408
           I ELP  +
Sbjct: 373 ISELPDEI 380

>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp Length = 386

Iteration: 1
 Score =  250 bits (638), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 143/368 (38%), Positives = 215/368 (58%), Gaps = 6/368 (1%)
Query: 46  LQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGL 105
           L+  LLR I   GFE PS +Q   I     G+DV+ QA+SG GKTA F    LQQL+   
Sbjct: 15  LKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVT 74
Query: 106 VECQALVLAPTRELAQQIEKVMRALGDYL-GVKVHACVGGTSVREDQRILSSGV-HVVVG 163
            +   LV+  TRELA QI K       Y+  VKV    GG S+++D+ +L     H+VVG
Sbjct: 75  GQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVG 134
Query: 164 TPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSR-GFKDQIYDIFQLLPPKIQVGVFSATM 222
           TPGR+  + R +SL   +I+ F+LDE D+ML +   +  + +IF++ P + QV +FSAT+
Sbjct: 135 TPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATL 194
Query: 223 PPEALEITRKFMNKPVRILVKRD-ELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQS 281
             E   + RKFM  P+ I V  + +LTL G++Q++V + K+  K   L DL + L   Q 
Sbjct: 195 SKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKL-KDNEKNRKLFDLLDVLEFNQV 253
Query: 282 VIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARG 341
           VIFV + ++   L   +  ++    A H  M Q  R    ++F+    R+L+ T+L  RG
Sbjct: 254 VIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRG 313
Query: 342 IDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVT-RDDERMLFDIQKFYNVV 400
           +D+++V++  NYD+P   + YLHR+ R+GRFG KG+AI FV+  +D ++L D+Q  + V 
Sbjct: 314 MDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVN 373
Query: 401 IEELPANV 408
           I ELP  +
Sbjct: 374 ISELPDEI 381

>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56 Length = 391

Iteration: 1
 Score =  249 bits (637), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 143/368 (38%), Positives = 215/368 (58%), Gaps = 6/368 (1%)
Query: 46  LQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGL 105
           L+  LLR I   GFE PS +Q   I     G+DV+ QA+SG GKTA F    LQQL+   
Sbjct: 15  LKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVT 74
Query: 106 VECQALVLAPTRELAQQIEKVMRALGDYL-GVKVHACVGGTSVREDQRILSSGV-HVVVG 163
            +   LV+  TRELA QI K       Y+  VKV    GG S+++D+ +L     H+VVG
Sbjct: 75  GQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVG 134
Query: 164 TPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSR-GFKDQIYDIFQLLPPKIQVGVFSATM 222
           TPGR+  + R +SL   +I+ F+LDE D+ML +   +  + +IF++ P + QV +FSAT+
Sbjct: 135 TPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATL 194
Query: 223 PPEALEITRKFMNKPVRILVKRD-ELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQS 281
             E   + RKFM  P+ I V  + +LTL G++Q++V + K+  K   L DL + L   Q 
Sbjct: 195 SKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKL-KDNEKNRKLFDLLDVLEFNQV 253
Query: 282 VIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARG 341
           VIFV + ++   L   +  ++    A H  M Q  R    ++F+    R+L+ T+L  RG
Sbjct: 254 VIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRG 313
Query: 342 IDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVT-RDDERMLFDIQKFYNVV 400
           +D+++V++  NYD+P   + YLHR+ R+GRFG KG+AI FV+  +D ++L D+Q  + V 
Sbjct: 314 MDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVN 373
Query: 401 IEELPANV 408
           I ELP  +
Sbjct: 374 ISELPDEI 381

>pdb|1HV8|A Chain A, Crystal Structure Of A Dead Box Protein From The Hyperthermophile Methanococcus Jannaschii Length = 367

Iteration: 1
 Score =  220 bits (560), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 125/359 (34%), Positives = 201/359 (55%), Gaps = 9/359 (2%)
Query: 38  YDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKG-LDVIQQAQSGTGKTATFCSG 96
           Y  F+ + L +N+L  I   GFEKP+ IQ + I  F     +++ QA++G+GKTA+F   
Sbjct: 5   YXNFNELNLSDNILNAIRNKGFEKPTDIQXKVIPLFLNDEYNIVAQARTGSGKTASFAIP 64
Query: 97  ILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSS 156
           +++ ++      +A++L PTRELA Q+   + +L     +K+    GG ++    + L +
Sbjct: 65  LIELVNEN-NGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALKN 123
Query: 157 GVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVG 216
             ++VVGTPGR+ D + R +L   N++ F+LDEADE L+ GF   +  I        ++ 
Sbjct: 124 A-NIVVGTPGRILDHINRGTLNLKNVKYFILDEADEXLNXGFIKDVEKILNACNKDKRIL 182
Query: 217 VFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETL 276
           +FSAT P E L + +K+      I  K +      I+Q +V V + E + E LC L +  
Sbjct: 183 LFSATXPREILNLAKKYXGDYSFIKAKINA----NIEQSYVEVNENE-RFEALCRLLKNK 237
Query: 277 AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTD 336
                ++F  T+R    L   +R       A HGD+ Q+ R+ ++R F+    R+LI TD
Sbjct: 238 EFY-GLVFCKTKRDTKELASXLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATD 296
Query: 337 LLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQK 395
           + +RGIDV  ++ VINY LP  PE+Y HRIGR+GR G+KG AI+ + R + + L  I++
Sbjct: 297 VXSRGIDVNDLNCVINYHLPQNPESYXHRIGRTGRAGKKGKAISIINRREYKKLRYIER 355

>pdb|1FUK|A Chain A, Crystal Structure Of The Carboxy Terminal Domain Of Yeast Eif4a Length = 165

Iteration: 1
 Score =  203 bits (517), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 110/164 (67%), Positives = 137/164 (83%)
Query: 249 LEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSAT 308
           LEGIKQF+VNVE+EE+K E L DLY+++++TQ+VIF NTRRKV+ LT K+R+   TVSA 
Sbjct: 1   LEGIKQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAI 60
Query: 309 HGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGR 368
           + D+ Q  RD IM+EFRSGSSR+LI+TDLLARGIDVQQVSLVINYDLP   ENY+HRIGR
Sbjct: 61  YSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGR 120
Query: 369 SGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVADLL 412
            GRFGRKGVAINFVT +D   + +++KFY+  IEELP+++A LL
Sbjct: 121 GGRFGRKGVAINFVTNEDVGAMRELEKFYSTQIEELPSDIATLL 164

>pdb|2DB3|A Chain A, Structural Basis For Rna Unwinding By The Dead-Box Protein Drosophila Vasa Length = 434

Iteration: 1
 Score =  196 bits (498), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 117/357 (32%), Positives = 194/357 (54%), Gaps = 9/357 (2%)
Query: 41  FDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQ 100
           F +  L++ ++  +   G++ P+ IQ+  I     G D++  AQ+G+GKTA F   IL +
Sbjct: 58  FTSADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPILSK 117
Query: 101 L-----DYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILS 155
           L     +  L   Q ++++PTRELA QI    R       +K+    GGTS R     ++
Sbjct: 118 LLEDPHELELGRPQVVIVSPTRELAIQIFNEARKFAFESYLKIGIVYGGTSFRHQNECIT 177
Query: 156 SGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQ--LLPPKI 213
            G HVV+ TPGR+ D + R  +  ++ R  VLDEAD ML  GF + +  I     + P+ 
Sbjct: 178 RGCHVVIATPGRLLDFVDRTFITFEDTRFVVLDEADRMLDMGFSEDMRRIMTHVTMRPEH 237
Query: 214 QVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLY 273
           Q  +FSAT P E   +  +F+   V + +         +KQ    V K   + + +  L 
Sbjct: 238 QTLMFSATFPEEIQRMAGEFLKNYVFVAIGIVGGACSDVKQTIYEVNKYAKRSKLIEILS 297
Query: 274 ETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLI 333
           E    T  ++FV T+R  D+L   +  ++   ++ HGD  Q+ R+  +R+F++GS +VLI
Sbjct: 298 EQADGT--IVFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSMKVLI 355
Query: 334 TTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERML 390
            T + +RG+D++ +  VINYD+P++ ++Y+HRIGR+GR G  G A +F   + +R +
Sbjct: 356 ATSVASRGLDIKNIKHVINYDMPSKIDDYVHRIGRTGRVGNNGRATSFFDPEKDRAI 412

>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x Length = 417

Iteration: 1
 Score =  195 bits (496), Expect = 4e-50,   Method: Compositional matrix adjust.
 Identities = 130/395 (32%), Positives = 205/395 (51%), Gaps = 22/395 (5%)
Query: 39  DTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGIL 98
           ++F  + + E ++  I    + +P+ +Q+  I    +  D++  AQ+G+GKTA F   IL
Sbjct: 15  ESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPIL 74
Query: 99  QQL----------------DYGLVECQ--ALVLAPTRELAQQIEKVMRALGDYLGVKVHA 140
            Q+                 YG  +    +LVLAPTRELA QI +  R       V+   
Sbjct: 75  SQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRPCV 134
Query: 141 CVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKD 200
             GG  + +  R L  G H++V TPGR+ DM+ R  +  D  +  VLDEAD ML  GF+ 
Sbjct: 135 VYGGADIGQQIRDLERGCHLLVATPGRLVDMMERGKIGLDFCKYLVLDEADRMLDMGFEP 194
Query: 201 QIYDIFQ--LLPPK--IQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFH 256
           QI  I +   +PPK      +FSAT P E   + R F+++ + + V R   T E I Q  
Sbjct: 195 QIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGRVGSTSENITQKV 254
Query: 257 VNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNT 316
           V VE+ + +   L  L  T   + +++FV T++  D L D +    +  ++ HGD  Q  
Sbjct: 255 VWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRD 314
Query: 317 RDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKG 376
           R+  + +FRSG S +L+ T + ARG+D+  V  VIN+DLP+  E Y+HRIGR+GR G  G
Sbjct: 315 REEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLG 374
Query: 377 VAINFVTRDDERMLFDIQKFYNVVIEELPANVADL 411
           +A +F    +  +  D+        +E+P+ + ++
Sbjct: 375 LATSFFNERNINITKDLLDLLVEAKQEVPSWLENM 409

>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna Helicase From Sulfolobus Tokodaii Length = 337

Iteration: 1
 Score =  165 bits (418), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 111/340 (32%), Positives = 183/340 (53%), Gaps = 23/340 (6%)
Query: 46  LQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGL 105
           + E + + I   GF+  + +Q + I    +G +V+ +A++G+GKTA +   IL+      
Sbjct: 1   MNEKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILE------ 54
Query: 106 VECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVRED-QRILSSGVHVVVGT 164
           +  ++LV+ PTREL +Q+   +R +G Y+  KV    GG   +    R+ ++   +VV T
Sbjct: 55  LGMKSLVVTPTRELTRQVASHIRDIGRYMDTKVAEVYGGMPYKAQINRVRNA--DIVVAT 112
Query: 165 PGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPP 224
           PGR+ D+  +  +   +  I ++DEAD M   GF D I  I      +   G+FSAT+P 
Sbjct: 113 PGRLLDLWSKGVIDLSSFEIVIIDEADLMFEMGFIDDIKIILAQTSNRKITGLFSATIPE 172
Query: 225 EALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEW--KLETLCDLYETLAITQSV 282
           E  ++ + F+     I      + L  ++   V+V K++W  K++ L +  +   I    
Sbjct: 173 EIRKVVKDFITNYEEI---EACIGLANVEHKFVHV-KDDWRSKVQALRENKDKGVI---- 224
Query: 283 IFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGI 342
           +FV TR +V  L   +R  D+ +    GD+ Q+ R+  +  FR G   +LITTD+ +RG+
Sbjct: 225 VFVRTRNRVAKL---VRLFDNAIE-LRGDLPQSVRNRNIDAFREGEYDMLITTDVASRGL 280
Query: 343 DVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFV 382
           D+  V  VIN+D P     Y+HRIGR+GR GRKG AI F+
Sbjct: 281 DIPLVEKVINFDAPQDLRTYIHRIGRTGRMGRKGEAITFI 320

>pdb|3I5X|A Chain A, Structure Of Mss116p Bound To Ssrna And Amp-Pnp Length = 563

Iteration: 1
 Score =  148 bits (373), Expect = 7e-36,   Method: Compositional matrix adjust.
 Identities = 115/387 (29%), Positives = 199/387 (51%), Gaps = 31/387 (8%)
Query: 46  LQENLLRGIYAYGFEKPSAIQQRGIVPF--CKGLDVIQQAQSGTGKTATFCSGILQQLDY 103
           L + + + I    F   + +QQ+ I P    +  DVI +A++GTGKT  F   I Q L  
Sbjct: 79  LDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLIN 138
Query: 104 GLVECQ----ALVLAPTRELAQQIEKVMRALGDY-LGVKVHACV---GGTSVREDQRILS 155
              + Q    A+++APTR+LA QIE  ++ + D   G+K +ACV   GGT  R     ++
Sbjct: 139 TKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMN 198
Query: 156 S-GVHVVVGTPGRVFDMLRRQSLRPDNIRIF-VLDEADEMLSRGFKDQIYDIFQLLPPK- 212
               ++V+ TPGR+ D+L + S +      + VLDEAD +L  GF+D +  I  +L  K 
Sbjct: 199 KLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGILNEKN 258
Query: 213 ------IQVGVFSATMPPEALEITRKFMNKPVRILV----KRDELTLEGIKQFHVNVEKE 262
                 I+  +FSAT+  +  ++    MNK   + +    K +    E I Q  V  EK 
Sbjct: 259 SKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEKF 318
Query: 263 EWKLETLCD-----LYETLAITQSVIFVNTRRKVDWLTDKMRS---RDHTVSATHGDMDQ 314
              +    +     + E  +  +++IF  T +   +L   +++   +D  +   HG + Q
Sbjct: 319 ANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQ 378
Query: 315 NTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGR 374
           N R  +++ F+   S +L+ TD+ ARG+D   V  V+   +P++  NY+HRIGR+ R G+
Sbjct: 379 NKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGK 438
Query: 375 KGVAINFVTRDDERMLFDIQKFYNVVI 401
           +G ++ F+ +D+   + +++   N+VI
Sbjct: 439 EGSSVLFICKDELPFVRELEDAKNIVI 465

>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 =  147 bits (372), Expect = 8e-36,   Method: Compositional matrix adjust.
 Identities = 115/387 (29%), Positives = 198/387 (51%), Gaps = 31/387 (8%)
Query: 46  LQENLLRGIYAYGFEKPSAIQQRGIVPFCKG--LDVIQQAQSGTGKTATFCSGILQQLDY 103
           L + + + I    F   + +QQ+ I P       DVI +A++GTGKT  F   I Q L  
Sbjct: 28  LDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLIN 87
Query: 104 GLVECQ----ALVLAPTRELAQQIEKVMRALGDY-LGVKVHACV---GGTSVREDQRILS 155
              + Q    A+++APTR+LA QIE  ++ + D   G+K +ACV   GGT  R     ++
Sbjct: 88  TKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMN 147
Query: 156 S-GVHVVVGTPGRVFDMLRRQSLRPDNIRIF-VLDEADEMLSRGFKDQIYDIFQLLPPK- 212
               ++V+ TPGR+ D+L + S +      + VLDEAD +L  GF+D +  I  +L  K 
Sbjct: 148 KLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGILNEKN 207
Query: 213 ------IQVGVFSATMPPEALEITRKFMNKPVRILV----KRDELTLEGIKQFHVNVEKE 262
                 I+  +FSAT+  +  ++    MNK   + +    K +    E I Q  V  EK 
Sbjct: 208 SKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEKF 267
Query: 263 EWKLETLCD-----LYETLAITQSVIFVNTRRKVDWLTDKMRS---RDHTVSATHGDMDQ 314
              +    +     + E  +  +++IF  T +   +L   +++   +D  +   HG + Q
Sbjct: 268 ANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQ 327
Query: 315 NTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGR 374
           N R  +++ F+   S +L+ TD+ ARG+D   V  V+   +P++  NY+HRIGR+ R G+
Sbjct: 328 NKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGK 387
Query: 375 KGVAINFVTRDDERMLFDIQKFYNVVI 401
           +G ++ F+ +D+   + +++   N+VI
Sbjct: 388 EGSSVLFICKDELPFVRELEDAKNIVI 414

>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And Amp-Pnp Length = 579

Iteration: 1
 Score =  147 bits (372), Expect = 9e-36,   Method: Compositional matrix adjust.
 Identities = 115/387 (29%), Positives = 199/387 (51%), Gaps = 31/387 (8%)
Query: 46  LQENLLRGIYAYGFEKPSAIQQRGIVPF--CKGLDVIQQAQSGTGKTATFCSGILQQLDY 103
           L + + + I    F   + +QQ+ I P    +  DVI +A++GTGKT  F   I Q L  
Sbjct: 28  LDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLIN 87
Query: 104 GLVECQ----ALVLAPTRELAQQIEKVMRALGDY-LGVKVHACV---GGTSVREDQRILS 155
              + Q    A+++APTR+LA QIE  ++ + D   G+K +ACV   GGT  R     ++
Sbjct: 88  TKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMN 147
Query: 156 S-GVHVVVGTPGRVFDMLRRQSLRPDNIRIF-VLDEADEMLSRGFKDQIYDIFQLLPPK- 212
               ++V+ TPGR+ D+L + S +      + VLDEAD +L  GF+D +  I  +L  K 
Sbjct: 148 KLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGILNEKN 207
Query: 213 ------IQVGVFSATMPPEALEITRKFMNKPVRILV----KRDELTLEGIKQFHVNVEKE 262
                 I+  +FSAT+  +  ++    MNK   + +    K +    E I Q  V  EK 
Sbjct: 208 SKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEKF 267
Query: 263 EWKLETLCD-----LYETLAITQSVIFVNTRRKVDWLTDKMRS---RDHTVSATHGDMDQ 314
              +    +     + E  +  +++IF  T +   +L   +++   +D  +   HG + Q
Sbjct: 268 ANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQ 327
Query: 315 NTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGR 374
           N R  +++ F+   S +L+ TD+ ARG+D   V  V+   +P++  NY+HRIGR+ R G+
Sbjct: 328 NKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGK 387
Query: 375 KGVAINFVTRDDERMLFDIQKFYNVVI 401
           +G ++ F+ +D+   + +++   N+VI
Sbjct: 388 EGSSVLFICKDELPFVRELEDAKNIVI 414

>pdb|1T6N|A Chain A, Crystal Structure Of The N-Terminal Domain Of Human Uap56 Length = 220

Iteration: 1
 Score =  146 bits (369), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 88/220 (40%), Positives = 124/220 (56%), Gaps = 4/220 (1%)
Query: 27  GQDFFTSYDEVYDT-FDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQS 85
           G D   SY  ++ + F    L+  LLR I   GFE PS +Q   I     G+DV+ QA+S
Sbjct: 1   GSDVKGSYVSIHSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKS 60
Query: 86  GTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYL-GVKVHACVGG 144
           G GKTA F    LQQL+    +   LV+  TRELA QI K       Y+  VKV    GG
Sbjct: 61  GMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGG 120
Query: 145 TSVREDQRILSSGV-HVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSR-GFKDQI 202
            S+++D+ +L     H+VVGTPGR+  + R +SL   +I+ F+LDE D+ML +   +  +
Sbjct: 121 LSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDV 180
Query: 203 YDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILV 242
            +IF++ P + QV +FSAT+  E   + RKFM  P+ I V
Sbjct: 181 QEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFV 220

>pdb|2RB4|A Chain A, Crystal Structure Of The Helicase Domain Of Human Ddx25 Rna Helicase Length = 175

Iteration: 1
 Score =  146 bits (369), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 74/170 (43%), Positives = 107/170 (62%), Gaps = 6/170 (3%)
Query: 247 LTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVS 306
           LTL  I+Q++V  E  + K + LC++Y ++ I Q++IF  TRR   WLT +M    H VS
Sbjct: 3   LTLNNIRQYYVLCEHRKDKYQALCNIYGSITIGQAIIFCQTRRNAKWLTVEMIQDGHQVS 62
Query: 307 ATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQP------E 360
              G++    R  I++ FR G  +VLITT++ ARGIDV+QV++V+N+DLP +       E
Sbjct: 63  LLSGELTVEQRASIIQRFRDGKEKVLITTNVCARGIDVKQVTIVVNFDLPVKQGEEPDYE 122
Query: 361 NYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVAD 410
            YLHRIGR+GRFG+KG+A N +  D+   L  IQ  +N  I++L A   D
Sbjct: 123 TYLHRIGRTGRFGKKGLAFNMIEVDELPSLMKIQDHFNSSIKQLNAEDMD 172

>pdb|2KBF|A Chain A, Solution Structure Of Carboxyl-Terminal Domain Of Dbp5p Length = 187

Iteration: 1
 Score =  145 bits (367), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 73/160 (45%), Positives = 108/160 (67%), Gaps = 7/160 (4%)
Query: 245 DELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHT 304
           +E+ ++ IKQ +++ + E  K + L +LY  + I  S+IFV T++  + L  K++S  H 
Sbjct: 2   NEVNVDAIKQLYMDCKNEADKFDVLTELYGLMTIGSSIIFVATKKTANVLYGKLKSEGHE 61
Query: 305 VSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPT------Q 358
           VS  HGD+    RD ++ +FR G S+VLITT++LARGID+  VS+V+NYDLPT       
Sbjct: 62  VSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQAD 121
Query: 359 PENYLHRIGRSGRFGRKGVAINFV-TRDDERMLFDIQKFY 397
           P  Y+HRIGR+GRFGRKGVAI+FV  ++   +L  IQK++
Sbjct: 122 PATYIHRIGRTGRFGRKGVAISFVHDKNSFNILSAIQKYF 161

>pdb|1VEC|A Chain A, Crystal Structure Of The N-Terminal Domain Of RckP54, A Human Dead-Box Protein Length = 206

Iteration: 1
 Score =  144 bits (364), Expect = 7e-35,   Method: Compositional matrix adjust.
 Identities = 75/203 (36%), Positives = 122/203 (60%), Gaps = 1/203 (0%)
Query: 39  DTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGIL 98
           + F+   L+  LL GI+  G+EKPS IQ+  I     G D++ +A++GTGK+  +   +L
Sbjct: 3   NEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLL 62
Query: 99  QQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLG-VKVHACVGGTSVREDQRILSSG 157
           ++LD      QA+V+ PTRELA Q+ ++   +  ++G  KV A  GGT++R+D   L   
Sbjct: 63  ERLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDT 122
Query: 158 VHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGV 217
           VHVV+ TPGR+ D++++   + D++++ VLDEAD++LS+ F   + DI   LP   Q+ +
Sbjct: 123 VHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNRQILL 182
Query: 218 FSATMPPEALEITRKFMNKPVRI 240
           +SAT P    +     + KP  I
Sbjct: 183 YSATFPLSVQKFMNSHLEKPYEI 205

>pdb|3PEU|A Chain A, S. Cerevisiae Dbp5 L327v C-Terminal Domain Bound To Gle1 H337r And Ip6 Length = 188

Iteration: 1
 Score =  143 bits (361), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 73/160 (45%), Positives = 105/160 (65%), Gaps = 7/160 (4%)
Query: 245 DELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHT 304
           +E+ ++ IKQ + + + E  K + L +LY    I  S+IFV T++  + L  K++S  H 
Sbjct: 3   NEVNVDAIKQLYXDCKNEADKFDVLTELYGVXTIGSSIIFVATKKTANVLYGKLKSEGHE 62
Query: 305 VSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPT------Q 358
           VS  HGD+    RD ++ +FR G S+VLITT++LARGID+  VS V+NYDLPT       
Sbjct: 63  VSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSXVVNYDLPTLANGQAD 122
Query: 359 PENYLHRIGRSGRFGRKGVAINFV-TRDDERMLFDIQKFY 397
           P  Y+HRIGR+GRFGRKGVAI+FV  ++   +L  IQK++
Sbjct: 123 PATYIHRIGRTGRFGRKGVAISFVHDKNSFNILSAIQKYF 162

>pdb|3GFP|A Chain A, Structure Of The C-Terminal Domain Of The Dead-Box Protein Dbp5 Length = 189

Iteration: 1
 Score =  143 bits (360), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 73/160 (45%), Positives = 105/160 (65%), Gaps = 7/160 (4%)
Query: 245 DELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHT 304
           +E+ ++ IKQ + + + E  K + L +LY    I  S+IFV T++  + L  K++S  H 
Sbjct: 4   NEVNVDAIKQLYXDCKNEADKFDVLTELYGLXTIGSSIIFVATKKTANVLYGKLKSEGHE 63
Query: 305 VSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPT------Q 358
           VS  HGD+    RD ++ +FR G S+VLITT++LARGID+  VS V+NYDLPT       
Sbjct: 64  VSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSXVVNYDLPTLANGQAD 123
Query: 359 PENYLHRIGRSGRFGRKGVAINFV-TRDDERMLFDIQKFY 397
           P  Y+HRIGR+GRFGRKGVAI+FV  ++   +L  IQK++
Sbjct: 124 PATYIHRIGRTGRFGRKGVAISFVHDKNSFNILSAIQKYF 163

>pdb|2OXC|A Chain A, Human Dead-Box Rna Helicase Ddx20, Dead Domain In Complex With Adp Length = 230

Iteration: 1
 Score =  139 bits (349), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 80/199 (40%), Positives = 118/199 (59%), Gaps = 3/199 (1%)
Query: 41  FDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQ 100
           F+++ L   +L G+ A GFE+PS +Q + I     GLD+I QA+SGTGKT  F +  L  
Sbjct: 26  FESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDS 85
Query: 101 LDYGLVECQALVLAPTRELAQQIEKVMRALGDYL-GVKVHACVGGTSVREDQRILSSGVH 159
           L    +  Q L+LAPTRE+A QI  V+ A+G  + G++ H  +GGT + +D+  L    H
Sbjct: 86  LVLENLSTQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRLKK-CH 144
Query: 160 VVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRG-FKDQIYDIFQLLPPKIQVGVF 218
           + VG+PGR+  ++    L P +IR+F+LDEAD++L  G F++QI  I+  LP   Q+   
Sbjct: 145 IAVGSPGRIKQLIELDYLNPGSIRLFILDEADKLLEEGSFQEQINWIYSSLPASKQMLAV 204
Query: 219 SATMPPEALEITRKFMNKP 237
           SAT P        K+M  P
Sbjct: 205 SATYPEFLANALTKYMRDP 223

>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 =  138 bits (347), Expect = 7e-33,   Method: Compositional matrix adjust.
 Identities = 69/164 (42%), Positives = 101/164 (61%), Gaps = 1/164 (0%)
Query: 245 DELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHT 304
           +ELTL+G+ Q++  V  E  K+  L  L+  L I QS+IF N+ ++V+ L  K+    ++
Sbjct: 12  EELTLKGVTQYYAYV-TERQKVHCLNTLFSRLQINQSIIFCNSSQRVELLAKKISQLGYS 70
Query: 305 VSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLH 364
               H  M Q  R+ +  +FR+G  R L+ TDL  RGID+Q V++VIN+D P   E YLH
Sbjct: 71  CFYIHAKMRQEHRNRVFHDFRNGLCRNLVCTDLFTRGIDIQAVNVVINFDFPKLAETYLH 130
Query: 365 RIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANV 408
           RIGRSGRFG  G+AIN +T DD   L  I++     I+ +P+N+
Sbjct: 131 RIGRSGRFGHLGLAINLITYDDRFNLKSIEEQLGTEIKPIPSNI 174

>pdb|2KBE|A Chain A, Solution Structure Of Amino-Terminal Domain Of Dbp5p Length = 226

Iteration: 1
 Score =  129 bits (325), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 75/185 (40%), Positives = 113/185 (61%), Gaps = 7/185 (3%)
Query: 40  TFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGL--DVIQQAQSGTGKTATFCSGI 97
           +FD +GL   LL+GIYA  F+KPS IQ+R +         ++I Q+QSGTGKTA F   +
Sbjct: 23  SFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTM 82
Query: 98  LQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSG 157
           L +++      QA+ LAP+RELA+Q  +V++ +G +  +     V   S  ++++I    
Sbjct: 83  LTRVNPEDASPQAICLAPSRELARQTLEVVQEMGKFTKITSQLIVPD-SFEKNKQI---N 138
Query: 158 VHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEML-SRGFKDQIYDIFQLLPPKIQVG 216
             V+VGTPG V D++RR+ ++   I+IFVLDEAD ML  +G  DQ   + + LP   Q+ 
Sbjct: 139 AQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVKRFLPKDTQLV 198
Query: 217 VFSAT 221
           +FSAT
Sbjct: 199 LFSAT 203

>pdb|2GXQ|A Chain A, Hera N-Terminal Domain In Complex With Amp, Crystal Form 1 Length = 207

Iteration: 1
 Score =  127 bits (318), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 76/203 (37%), Positives = 109/203 (53%), Gaps = 5/203 (2%)
Query: 41  FDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQ 100
           F    L+  +L  ++  G   P+ IQ   +    +G D+I QA++GTGKT  F   I ++
Sbjct: 3   FKDFPLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAER 62
Query: 101 LDYGLV---ECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSG 157
           L        + +ALVL PTRELA Q+   + A+  +L  KV A  GGT   + +  L  G
Sbjct: 63  LAPSQERGRKPRALVLTPTRELALQVASELTAVAPHL--KVVAVYGGTGYGKQKEALLRG 120
Query: 158 VHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGV 217
              VV TPGR  D LR+  L    + + VLDEADEMLS GF++++  +    PP  Q  +
Sbjct: 121 ADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSMGFEEEVEALLSATPPSRQTLL 180
Query: 218 FSATMPPEALEITRKFMNKPVRI 240
           FSAT+P  A  +  ++M  PV I
Sbjct: 181 FSATLPSWAKRLAERYMKNPVLI 203

>pdb|3MWJ|A Chain A, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Apo Form Length = 207

Iteration: 1
 Score =  125 bits (315), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 75/203 (36%), Positives = 109/203 (53%), Gaps = 5/203 (2%)
Query: 41  FDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQ 100
           F    L+  +L  ++  G   P+ I+   +    +G D+I QA++GTGKT  F   I ++
Sbjct: 3   FKDFPLKPEILEALHGRGLTTPTPIEAAALPLALEGKDLIGQARTGTGKTLAFALPIAER 62
Query: 101 LDYGLV---ECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSG 157
           L        + +ALVL PTRELA Q+   + A+  +L  KV A  GGT   + +  L  G
Sbjct: 63  LAPSQERGRKPRALVLTPTRELALQVASELTAVAPHL--KVVAVYGGTGYGKQKEALLRG 120
Query: 158 VHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGV 217
              VV TPGR  D LR+  L    + + VLDEADEMLS GF++++  +    PP  Q  +
Sbjct: 121 ADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSMGFEEEVEALLSATPPSRQTLL 180
Query: 218 FSATMPPEALEITRKFMNKPVRI 240
           FSAT+P  A  +  ++M  PV I
Sbjct: 181 FSATLPSWAKRLAERYMKNPVLI 203

>pdb|3FHC|B Chain B, Crystal Structure Of Human Dbp5 In Complex With Nup214 Length = 235

Iteration: 1
 Score =  122 bits (307), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 79/213 (37%), Positives = 121/213 (56%), Gaps = 10/213 (4%)
Query: 40  TFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFC---KGLDVIQQAQSGTGKTATFCSG 96
           +F+ + L+  LL+G+YA GF +PS IQ+  + P        ++I Q+QSGTGKTA F   
Sbjct: 26  SFEELRLKPQLLQGVYAMGFNRPSKIQENAL-PLMLAEPPQNLIAQSQSGTGKTAAFVLA 84
Query: 97  ILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGD-YLGVKVHACVGGTSVREDQRILS 155
           +L Q++      Q L L+PT ELA Q  KV+  +G  Y  +K+   V G  +   Q+I  
Sbjct: 85  MLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKI-- 142
Query: 156 SGVHVVVGTPGRVFDMLRR-QSLRPDNIRIFVLDEADEML-SRGFKDQIYDIFQLLPPKI 213
               +V+GTPG V D   + + + P  I++FVLDEAD M+ ++G +DQ   I ++LP   
Sbjct: 143 -SEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNC 201
Query: 214 QVGVFSATMPPEALEITRKFMNKPVRILVKRDE 246
           Q+ +FSAT      +  +K +  P  I +KR+E
Sbjct: 202 QMLLFSATFEDSVWKFAQKVVPDPNVIKLKREE 234

>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 = 66/160 (41%), Positives = 96/160 (60%), Gaps = 1/160 (0%)
Query: 247 LTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVS 306
           LT   I+   + V +EE K   L D+  T      +IF  T+  V+ LTD++    +   
Sbjct: 5   LTTRNIEHAVIQV-REENKFSLLKDVLMTENPDSCIIFCRTKEHVNQLTDELDDLGYPCD 63
Query: 307 ATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRI 366
             HG M Q  R  +M EF+ G  R L+ TD+ ARGID++ +SLVINYDLP + E+Y+HR 
Sbjct: 64  KIHGGMIQEDRFDVMNEFKRGEYRYLVATDVAARGIDIENISLVINYDLPLEKESYVHRT 123
Query: 367 GRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPA 406
           GR+GR G KG AI+FVT  ++R L DI+++    I+++ A
Sbjct: 124 GRTGRAGNKGKAISFVTAFEKRFLADIEEYIGFEIQKIEA 163

>pdb|3FMO|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex With The Dead- Box Helicase Ddx19 Length = 300

Iteration: 1
 Score =  122 bits (305), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 78/212 (36%), Positives = 120/212 (56%), Gaps = 10/212 (4%)
Query: 40  TFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFC---KGLDVIQQAQSGTGKTATFCSG 96
           +F+ + L+  LL+G+YA GF +PS IQ+  + P        ++I Q+QSGTGKTA F   
Sbjct: 93  SFEELRLKPQLLQGVYAMGFNRPSKIQENAL-PLMLAEPPQNLIAQSQSGTGKTAAFVLA 151
Query: 97  ILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGD-YLGVKVHACVGGTSVREDQRILS 155
           +L Q++      Q L L+PT ELA Q  KV+  +G  Y  +K+   V G  +   Q+I  
Sbjct: 152 MLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKI-- 209
Query: 156 SGVHVVVGTPGRVFDMLRR-QSLRPDNIRIFVLDEADEML-SRGFKDQIYDIFQLLPPKI 213
               +V+GTPG V D   + + + P  I++FVLDEAD M+ ++G +DQ   I ++LP   
Sbjct: 210 -SEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNC 268
Query: 214 QVGVFSATMPPEALEITRKFMNKPVRILVKRD 245
           Q+ +FSAT      +  +K +  P  I +KR+
Sbjct: 269 QMLLFSATFEDSVWKFAQKVVPDPNVIKLKRE 300

>pdb|3BER|A Chain A, Human Dead-Box Rna-Helicase Ddx47, Conserved Domain I In Complex With Amp Length = 249

Iteration: 1
 Score =  112 bits (281), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 69/209 (33%), Positives = 107/209 (51%), Gaps = 1/209 (0%)
Query: 35  DEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFC 94
           +E   TF  +G+ + L       G+ KP+ IQ   I    +G D+I  A++G+GKT  F 
Sbjct: 39  EEETKTFKDLGVTDVLCEACDQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFA 98
Query: 95  SGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL 154
             IL  L        ALVL PTRELA QI +   ALG  +GV+    VGG         L
Sbjct: 99  LPILNALLETPQRLFALVLTPTRELAFQISEQFEALGSSIGVQSAVIVGGIDSMSQSLAL 158
Query: 155 SSGVHVVVGTPGRVFDMLRR-QSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKI 213
           +   H+++ TPGR+ D L   +      ++  V+DEAD +L+  F+ ++  I +++P   
Sbjct: 159 AKKPHIIIATPGRLIDHLENTKGFNLRALKYLVMDEADRILNMDFETEVDKILKVIPRDR 218
Query: 214 QVGVFSATMPPEALEITRKFMNKPVRILV 242
           +  +FSATM  +  ++ R  +  PV+  V
Sbjct: 219 KTFLFSATMTKKVQKLQRAALKNPVKCAV 247

>pdb|1T5I|A Chain A, Crystal Structure Of The C-Terminal Domain Of Uap56 Length = 172

Iteration: 1
 Score =  110 bits (276), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 58/162 (35%), Positives = 96/162 (59%), Gaps = 2/162 (1%)
Query: 248 TLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSA 307
           +L G++Q++V + K+  K   L DL + L   Q VIFV + ++   L   +  ++    A
Sbjct: 2   SLHGLQQYYVKL-KDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIA 60
Query: 308 THGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIG 367
            H  M Q  R    ++F+    R+L+ T+L  RG+D+++V++  NYD+P   + YLHR+ 
Sbjct: 61  IHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVA 120
Query: 368 RSGRFGRKGVAINFVT-RDDERMLFDIQKFYNVVIEELPANV 408
           R+GRFG KG+AI FV+  +D ++L D+Q  + V I ELP  +
Sbjct: 121 RAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEI 162

>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 = 78/243 (32%), Positives = 117/243 (48%), Gaps = 19/243 (7%)
Query: 27  GQDFFTSYDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSG 86
           G D+  S   V + FD + L   +   I    +++P+ IQ+  I    +  D++  AQ+G
Sbjct: 13  GPDY--SATNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTG 70
Query: 87  TGKTATF---------CSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVK 137
           +GKTA F         C  + QQ        + L+LAPTRELA QI    +     L   
Sbjct: 71  SGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFS--LNTP 128
Query: 138 VHACV--GGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLS 195
           + +CV  GG       R +  G H++V TPGR+ D + +  +  +  +  VLDEAD ML 
Sbjct: 129 LRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEKNKISLEFCKYIVLDEADRMLD 188
Query: 196 RGFKDQIYDIFQL--LPPKI--QVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEG 251
            GF+ QI  I +   +P  I  Q  +FSAT P E  ++   F+   + + V R   T + 
Sbjct: 189 MGFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTVGRVGSTSDS 248
Query: 252 IKQ 254
           IKQ
Sbjct: 249 IKQ 251

>pdb|1Q0U|A Chain A, Crystal Structure Of The Bstdead N-Terminal Domain Length = 219

Iteration: 1
 Score =  108 bits (270), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 68/206 (33%), Positives = 102/206 (49%), Gaps = 4/206 (1%)
Query: 41  FDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQ 100
           F     Q  ++  I    F KP+ IQ+R I    +G   + Q+Q+GTGKT  +   I ++
Sbjct: 6   FTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESXVGQSQTGTGKTHAYLLPIXEK 65
Query: 101 LDYGLVECQALVLAPTRELAQQIE----KVMRALGDYLGVKVHACVGGTSVREDQRILSS 156
           +     E QA++ APTRELA QI     K+ +       +     +GGT  ++    L+ 
Sbjct: 66  IKPERAEVQAVITAPTRELATQIYHETLKITKFCPKDRXIVARCLIGGTDKQKALEKLNV 125
Query: 157 GVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVG 216
             H+V+GTPGR+ D +R Q+L      I V+DEAD  L  GF   +  I    P  +Q  
Sbjct: 126 QPHIVIGTPGRINDFIREQALDVHTAHILVVDEADLXLDXGFITDVDQIAARXPKDLQXL 185
Query: 217 VFSATMPPEALEITRKFMNKPVRILV 242
           VFSAT+P +     +K+   P  + V
Sbjct: 186 VFSATIPEKLKPFLKKYXENPTFVHV 211

>pdb|3FE2|A Chain A, Human Dead-Box Rna Helicase Ddx5 (P68), Conserved Domain I In Complex With Adp Length = 242

Iteration: 1
 Score = 99.4 bits (246), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 69/216 (31%), Positives = 101/216 (46%), Gaps = 11/216 (5%)
Query: 40  TFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQ 99
            F       N++  I    F +P+AIQ +G      GLD++  AQ+G+GKT ++    + 
Sbjct: 30  NFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIV 89
Query: 100 QLDY--------GLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQ 151
            +++        G +    LVLAPTRELAQQ+++V         +K     GG       
Sbjct: 90  HINHQPFLERGDGPI---CLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQI 146
Query: 152 RILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPP 211
           R L  GV + + TPGR+ D L             VLDEAD ML  GF+ QI  I   + P
Sbjct: 147 RDLERGVEICIATPGRLIDFLECGKTNLRRTTYLVLDEADRMLDMGFEPQIRKIVDQIRP 206
Query: 212 KIQVGVFSATMPPEALEITRKFMNKPVRILVKRDEL 247
             Q  ++SAT P E  ++   F+   + I +   EL
Sbjct: 207 DRQTLMWSATWPKEVRQLAEDFLKDYIHINIGALEL 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 = 99.0 bits (245), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 67/209 (32%), Positives = 98/209 (46%), Gaps = 11/209 (5%)
Query: 40  TFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQ 99
            F       N++  I    F +P+AIQ +G      GLD++  AQ+G+GKT ++    + 
Sbjct: 44  NFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIV 103
Query: 100 QLDY--------GLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQ 151
            +++        G +    LVLAPTRELAQQ+++V         +K     GG       
Sbjct: 104 HINHQPFLERGDGPI---CLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQI 160
Query: 152 RILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPP 211
           R L  GV + + TPGR+ D L             VLDEAD ML  GF+ QI  I   + P
Sbjct: 161 RDLERGVEICIATPGRLIDFLECGKTNLRRTTYLVLDEADRMLDMGFEPQIRKIVDQIRP 220
Query: 212 KIQVGVFSATMPPEALEITRKFMNKPVRI 240
             Q  ++SAT P E  ++   F+   + I
Sbjct: 221 DRQTLMWSATWPKEVRQLAEDFLKDYIHI 249

>pdb|3LY5|A Chain A, Ddx18 Dead-Domain Length = 262

Iteration: 1
 Score = 99.0 bits (245), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 61/196 (31%), Positives = 106/196 (54%), Gaps = 5/196 (2%)
Query: 46  LQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATF---CSGILQQLD 102
           + EN L+ I   GF   + IQ + I P  +G D++  A++G+GKT  F      ++ +L 
Sbjct: 61  VNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLR 120
Query: 103 YGLVECQA-LVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVV 161
           +        L+L+PTRELA Q   V++ L  +        +GG++   + + L +G++++
Sbjct: 121 FMPRNGTGVLILSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQKLGNGINII 180
Query: 162 VGTPGRVFD-MLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSA 220
           V TPGR+ D M         N++  V+DEAD +L  GF++++  I +LLP + Q  +FSA
Sbjct: 181 VATPGRLLDHMQNTPGFMYKNLQCLVIDEADRILDVGFEEELKQIIKLLPTRRQTMLFSA 240
Query: 221 TMPPEALEITRKFMNK 236
           T   +  ++ R  + K
Sbjct: 241 TQTRKVEDLARISLKK 256

>pdb|2JGN|A Chain A, Ddx3 Helicase Domain Length = 185

Iteration: 1
 Score = 96.7 bits (239), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 55/164 (33%), Positives = 91/164 (55%)
Query: 248 TLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSA 307
           T E I Q  V VE+ + +   L  L  T   + +++FV T++  D L D +    +  ++
Sbjct: 16  TSENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTS 75
Query: 308 THGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIG 367
            HGD  Q  R+  + +FRSG S +L+ T + ARG+D+  V  VIN+DLP+  E Y+HRIG
Sbjct: 76  IHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIG 135
Query: 368 RSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVADL 411
           R+GR G  G+A +F    +  +  D+        +E+P+ + ++
Sbjct: 136 RTGRVGNLGLATSFFNERNINITKDLLDLLVEAKQEVPSWLENM 179

>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 = 95.5 bits (236), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 56/161 (34%), Positives = 84/161 (52%), Gaps = 3/161 (1%)
Query: 252 IKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGD 311
           I Q++   +  E K   L  L +    T+S++FV  R +V  L + +R          G+
Sbjct: 4   IHQWYYRADDLEHKTALLVHLLKQPEATRSIVFVRKRERVHELANWLREAGINNCYLEGE 63
Query: 312 MDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGR 371
           M Q  R+  ++    G   VL+ TD+ ARGID+  VS V N+D+P   + YLHRIGR+ R
Sbjct: 64  MVQGKRNEAIKRLTEGRVNVLVATDVAARGIDIPDVSHVFNFDMPRSGDTYLHRIGRTAR 123
Query: 372 FGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVADLL 412
            GRKG AI+ V   D  +L  + ++   + E + A V D L
Sbjct: 124 AGRKGTAISLVEAHDHLLLGKVGRY---IEEPIKARVIDEL 161

>pdb|3IUY|A Chain A, Crystal Structure Of Ddx53 Dead-Box Domain Length = 228

Iteration: 1
 Score = 92.8 bits (229), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 66/207 (31%), Positives = 100/207 (48%), Gaps = 7/207 (3%)
Query: 42  DAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQL 101
           DA     +LL+ I   G  KP+ IQ +      +G+D+I  AQ+GTGKT ++       L
Sbjct: 23  DAFQQYPDLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIHL 82
Query: 102 DYGLVECQ------ALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILS 155
           D   +  +       LVL PTRELA  +E        Y G+K     GG +       +S
Sbjct: 83  DSQPISREQRNGPGMLVLTPTRELALHVEAECSKYS-YKGLKSICIYGGRNRNGQIEDIS 141
Query: 156 SGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQV 215
            GV +++ TPGR+ D+    S+   +I   V+DEAD+ML   F+ QI  I   + P  Q 
Sbjct: 142 KGVDIIIATPGRLNDLQMNNSVNLRSITYLVIDEADKMLDMEFEPQIRKILLDVRPDRQT 201
Query: 216 GVFSATMPPEALEITRKFMNKPVRILV 242
            + SAT P    ++   ++  P+ + V
Sbjct: 202 VMTSATWPDTVRQLALSYLKDPMIVYV 228

>pdb|2PL3|A Chain A, Human Dead-Box Rna Helicase Ddx10, Dead Domain In Complex With Adp Length = 236

Iteration: 1
 Score = 91.3 bits (225), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 63/209 (30%), Positives = 107/209 (51%), Gaps = 10/209 (4%)
Query: 41  FDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQ 100
           F    L +  L+G+    +   + IQ++ I    +G DV+  A++G+GKT  F   +L+ 
Sbjct: 27  FSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEA 86
Query: 101 LDYGLVECQA-----LVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVR-EDQRIL 154
           L Y L          L+++PTRELA Q  +V+R +G          +GG  ++ E +RI 
Sbjct: 87  L-YRLQWTSTDGLGVLIISPTRELAYQTFEVLRKVGKNHDFSAGLIIGGKDLKHEAERI- 144
Query: 155 SSGVHVVVGTPGRVFDMLRRQ-SLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKI 213
            + ++++V TPGR+   +    S    ++++ VLDEAD +L  GF D +  + + LP K 
Sbjct: 145 -NNINILVCTPGRLLQHMDETVSFHATDLQMLVLDEADRILDMGFADTMNAVIENLPKKR 203
Query: 214 QVGVFSATMPPEALEITRKFMNKPVRILV 242
           Q  +FSAT      ++ R  +  P  + V
Sbjct: 204 QTLLFSATQTKSVKDLARLSLKNPEYVWV 232

>pdb|2P6N|A Chain A, Human Dead-box Rna Helicase Ddx41, Helicase Domain Length = 191

Iteration: 1
 Score = 90.1 bits (222), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 47/137 (34%), Positives = 73/137 (53%), Gaps = 2/137 (1%)
Query: 261 KEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDII 320
           KEE K+  L +  +       +IF   +  VD + + +  +     A HG  DQ  R   
Sbjct: 38  KEEAKMVYLLECLQKTP-PPVLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKA 96
Query: 321 MREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAIN 380
           +  FR G   VL+ TD+ ++G+D   +  VINYD+P + ENY+HRIGR+G  G  G+A  
Sbjct: 97  IEAFREGKKDVLVATDVASKGLDFPAIQHVINYDMPEEIENYVHRIGRTGCSGNTGIATT 156
Query: 381 FVTRD-DERMLFDIQKF 396
           F+ +  DE +L D++  
Sbjct: 157 FINKACDESVLMDLKAL 173

>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 = 82.0 bits (201), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 37/100 (37%), Positives = 58/100 (58%)
Query: 265 KLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREF 324
           +LE L DL    +  ++++F  T+ + + +   +    H   A HGDM Q  R+ +M  F
Sbjct: 15  RLEVLSDLLYVASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQGERERVMGAF 74
Query: 325 RSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLH 364
           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 = 79.3 bits (194), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 36/100 (36%), Positives = 58/100 (58%)
Query: 265 KLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREF 324
           +LE L DL    +  ++++F  T+ + + +   +    H   A HGD+ Q  R+ ++  F
Sbjct: 18  RLEVLSDLLYVASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAF 77
Query: 325 RSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLH 364
           R G  RVL+ TD+ ARG+D+ QV LV++Y LP + E Y H
Sbjct: 78  RQGEVRVLVATDVAARGLDIPQVDLVVHYRLPDRAEAYQH 117

>pdb|3DKP|A Chain A, Human Dead-Box Rna-Helicase Ddx52, Conserved Domain I In Complex With Adp Length = 245

Iteration: 1
 Score = 78.6 bits (192), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 57/206 (27%), Positives = 104/206 (50%), Gaps = 11/206 (5%)
Query: 24  GSDGQDFFTSYDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQA 83
           G+D  D   ++ ++   +    +   LL+ I   GF+ P+ IQ + I     G +++  A
Sbjct: 17  GTDLPDPIATFQQLDQEYK---INSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASA 73
Query: 84  QSGTGKTATFCSGILQQLDYGLVE-CQALVLAPTRELAQQIEKVMRALGDYLGVKVHAC- 141
            +G+GKT  F   IL QL     +  +AL+++PTRELA QI + +  + +  G ++H   
Sbjct: 74  PTGSGKTLAFSIPILMQLKQPANKGFRALIISPTRELASQIHRELIKISEGTGFRIHMIH 133
Query: 142 VGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPD--NIRIFVLDEADEML---SR 196
               + ++     S    ++V TP R+  +L++     D  ++   V+DE+D++      
Sbjct: 134 KAAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPPGIDLASVEWLVVDESDKLFEDGKT 193
Query: 197 GFKDQIYDIF-QLLPPKIQVGVFSAT 221
           GF+DQ+  IF      K++  +FSAT
Sbjct: 194 GFRDQLASIFLACTSHKVRRAMFSAT 219

>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 = 8e-15,   Method: Compositional matrix adjust.
 Identities = 37/125 (29%), Positives = 74/125 (59%), Gaps = 3/125 (2%)
Query: 280 QSVIFVNTRRKVDWLTDKMRS---RDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTD 336
           +++IF  T +   +L   +++   +D  +   HG + QN R  +++ F+   S +L+ TD
Sbjct: 35  KAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTD 94
Query: 337 LLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKF 396
           + ARG+D   V  V+   +P++  NY+HRIGR+ R G++G ++ F+ +D+   + +++  
Sbjct: 95  VGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRELEDA 154
Query: 397 YNVVI 401
            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 = 8e-15,   Method: Compositional matrix adjust.
 Identities = 37/125 (29%), Positives = 74/125 (59%), Gaps = 3/125 (2%)
Query: 280 QSVIFVNTRRKVDWLTDKMRS---RDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTD 336
           +++IF  T +   +L   +++   +D  +   HG + QN R  +++ F+   S +L+ TD
Sbjct: 35  KAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTD 94
Query: 337 LLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKF 396
           + ARG+D   V  V+   +P++  NY+HRIGR+ R G++G ++ F+ +D+   + +++  
Sbjct: 95  VGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRELEDA 154
Query: 397 YNVVI 401
            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: 280 QSVIFVNTRRKVDWLTDKMRS---RDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTD 336
           +++IF  T +   +L   +++   +D  +   HG + QN R  +++ F+   S +L+ TD
Sbjct: 35  KAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTD 94
Query: 337 LLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKF 396
           + ARG+D   V  V+   +P++  NY+HRIGR+ R G++G ++ F+ +D+   + +++  
Sbjct: 95  VGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRELEDA 154
Query: 397 YNVVI 401
            N+VI
Sbjct: 155 KNIVI 159

>pdb|1OYY|A Chain A, Structure Of The Recq Catalytic Core Bound To Atp-Gamma-S Length = 523

Iteration: 1
 Score = 58.9 bits (141), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 27/100 (27%), Positives = 54/100 (54%)
Query: 282 VIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARG 341
           +I+ N+R KV+    +++S+  + +A H  ++ N R  +  +F+    ++++ T     G
Sbjct: 240 IIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMG 299
Query: 342 IDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINF 381
           I+   V  V+++D+P   E+Y    GR+GR G    A+ F
Sbjct: 300 INKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLF 339

>pdb|1OYW|A Chain A, Structure Of The Recq Catalytic Core Length = 523

Iteration: 1
 Score = 58.5 bits (140), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 83/348 (23%), Positives = 148/348 (42%), Gaps = 34/348 (9%)
Query: 57  YGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPT 116
           +G+++    Q+  I     G D +    +G GK+   C  I   L  GL     +V++P 
Sbjct: 21  FGYQQFRPGQEEIIDTVLSGRDCLVVXPTGGGKS--LCYQIPALLLNGLT----VVVSPL 74
Query: 117 RELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSG-----VHVVVGTPGRVFDM 171
             L +     ++A G        AC+  T  RE Q  + +G     + ++   P R+   
Sbjct: 75  ISLXKDQVDQLQANG-----VAAACLNSTQTREQQLEVXTGCRTGQIRLLYIAPERLXLD 129
Query: 172 LRRQSLRPDNIRIFVLDEADEMLSRG--FKDQIYDIFQLLP--PKIQVGVFSATMPPEAL 227
              + L   N  +  +DEA  +   G  F+ +   + QL    P +     +AT    A 
Sbjct: 130 NFLEHLAHWNPVLLAVDEAHCISQWGHDFRPEYAALGQLRQRFPTLPFXALTAT----AD 185
Query: 228 EITRKFMNKPVRILVKRDELTLEGIKQF-HVNVE---KEEWK-LETLCDLYETLAITQSV 282
           + TR+ +   VR+L   D L    I  F   N+     E++K L+ L    +       +
Sbjct: 186 DTTRQDI---VRLLGLNDPLI--QISSFDRPNIRYXLXEKFKPLDQLXRYVQEQRGKSGI 240
Query: 283 IFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGI 342
           I+ N+R KV+    +++S+  + +A H  ++ N R  +  +F+    ++++ T     GI
Sbjct: 241 IYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGXGI 300
Query: 343 DVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERML 390
           +   V  V+++D+P   E+Y    GR+GR G    A  F    D   L
Sbjct: 301 NKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAXLFYDPADXAWL 348

>pdb|4GL2|A Chain A, Structural Basis For Dsrna Duplex Backbone Recognition By Mda5 Length = 699

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 27/102 (26%), Positives = 48/102 (47%), Gaps = 14/102 (13%)
Query: 282 VIFVNTRRKV----DWLTDKMR------SRDHTVSATHGD----MDQNTRDIIMREFRSG 327
           +IF  TR+       W+T+  +         H + A H      M QN +  ++ +FR+G
Sbjct: 404 IIFTKTRQSAYALSQWITENEKFAEVGVKAHHLIGAGHSSEFKPMTQNEQKEVISKFRTG 463
Query: 328 SSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRS 369
              +LI T +   G+D+++ ++VI Y L T     +   GR+
Sbjct: 464 KINLLIATTVAEEGLDIKECNIVIRYGLVTNEIAMVQARGRA 505

>pdb|1GM5|A Chain A, Structure Of Recg Bound To Three-Way Dna Junction Length = 780

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 69/321 (21%), Positives = 138/321 (42%), Gaps = 39/321 (12%)
Query: 75  KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYL 134
           K ++ + Q   G+GKT      IL   + G    Q   + PT  LA  I+   R +  + 
Sbjct: 388 KPMNRLLQGDVGSGKTVVAQLAILDNYEAGF---QTAFMVPTSILA--IQHYRRTVESFS 442
Query: 135 GVKVHAC--VGGTSVREDQRILSS----GVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLD 188
              +H    +G T+  E ++I S      + VV+GT       L ++ +   N+ + ++D
Sbjct: 443 KFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHA-----LIQEDVHFKNLGLVIID 497
Query: 189 EADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEA--------LEITRKFMNKPVRI 240
           E       G K +  +        +   V SAT  P +        L++T      P R 
Sbjct: 498 EQHRF---GVKQR--EALMNKGKMVDTLVMSATPIPRSMALAFYGDLDVTVIDEMPPGRK 552
Query: 241 LVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRS 300
            V+   + ++ + + +  V +E  +      +Y  +  +  +   +     ++L+ ++  
Sbjct: 553 EVQTMLVPMDRVNEVYEFVRQEVMRGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFP 612
Query: 301 RDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPE 360
            +  +   HG + Q  +D +M EF  G   +L++T ++  GIDV + ++++  +    PE
Sbjct: 613 -EFKLGLMHGRLSQEEKDRVMLEFAEGRYDILVSTTVIEVGIDVPRANVMVIEN----PE 667
Query: 361 NY----LHRI-GRSGRFGRKG 376
            +    LH++ GR GR G++ 
Sbjct: 668 RFGLAQLHQLRGRVGRGGQEA 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: 241 LVKRDELTLEGIKQFHVNVEKEEWKLETLC----DLYETLAITQSVIFVNTRRKVDWLTD 296
           L +R E  L+ ++    +   E  KLE LC    + Y     T +++FV TR  VD L +
Sbjct: 348 LTQRFEEKLQELESVSRDPSNENPKLEDLCFILQEEYHLNPETITILFVKTRALVDALKN 407
Query: 297 ------KMRSRDHTVSATHGDMDQNT------RDIIMREFR-SGSSRVLITTDLLARGID 343
                 K+      +    G  +QNT      +  I+  F+ SG   +LI T +   GID
Sbjct: 408 WIEGNPKLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAFKASGDHNILIATSVADEGID 467
Query: 344 VQQVSLVINYD 354
           + 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: 241 LVKRDELTLEGIKQFHVNVEKEEWKLETLC----DLYETLAITQSVIFVNTRRKVDWLTD 296
           L +R E  L+ ++    +   E  KLE LC    + Y     T +++FV TR  VD L +
Sbjct: 356 LTQRFEEKLQELESVSRDPSNENPKLEDLCFILQEEYHLNPETITILFVKTRALVDALKN 415
Query: 297 ------KMRSRDHTVSATHGDMDQNT------RDIIMREFR-SGSSRVLITTDLLARGID 343
                 K+      +    G  +QNT      +  I+  F+ SG   +LI T +   GID
Sbjct: 416 WIEGNPKLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAFKASGDHNILIATSVADEGID 475
Query: 344 VQQVSLVINYD 354
           + 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 = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 39/131 (29%), Positives = 60/131 (45%), Gaps = 17/131 (12%)
Query: 241 LVKRDELTLEGIKQFHVNVEKEEWKLETLC----DLYETLAITQSVIFVNTRRKVDWLTD 296
           L +R E  L+ ++    +   E  KLE LC    + Y     T +++FV TR  VD L +
Sbjct: 357 LTQRFEEKLQELESVSRDPSNENPKLEDLCFILQEEYHLNPETITILFVKTRALVDALKN 416
Query: 297 ------KMRSRDHTVSATHGDMDQNT------RDIIMREFR-SGSSRVLITTDLLARGID 343
                 K+      +    G  +QNT      +  I+  F+ SG   +LI T +   GID
Sbjct: 417 WIEGNPKLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAFKASGDHNILIATSVADEGID 476
Query: 344 VQQVSLVINYD 354
           + 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 = 3e-04,   Method: Compositional matrix adjust.
 Identities = 20/90 (22%), Positives = 45/90 (50%)
Query: 282 VIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARG 341
           +I+  +++  + +T  +++      A H +++   +  + R++ +   +V++ T     G
Sbjct: 271 IIYCFSQKDSEQVTVSLQNLGIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATVAFGMG 330
Query: 342 IDVQQVSLVINYDLPTQPENYLHRIGRSGR 371
           ID   V  VI++ +    ENY    GR+GR
Sbjct: 331 IDKPDVRFVIHHSMSKSMENYYQESGRAGR 360

>pdb|4I1S|A Chain A, Melanoma Differentiation Associated Protein-5 Helicase Domain Complex With Inhibitor Non-structural Protein V Length = 243

Iteration: 1
 Score = 42.0 bits (97), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 25/90 (27%), Positives = 43/90 (47%), Gaps = 14/90 (15%)
Query: 282 VIFVNTRRKV----DWLTDKMR------SRDHTVSATHGD----MDQNTRDIIMREFRSG 327
           +IF  TR+       W+TD  +         H + A H        QN +  ++ +FR+G
Sbjct: 154 IIFTKTRQSAYALSQWITDNKKFAEVGVKAHHLIGAGHSSEFKPXTQNEQREVISKFRTG 213
Query: 328 SSRVLITTDLLARGIDVQQVSLVINYDLPT 357
              +LI T +   G+D+++ ++VI Y L T
Sbjct: 214 KINLLIATTVAEEGLDIKECNIVIRYGLVT 243

>pdb|1WP9|A Chain A, Crystal Structure Of Pyrococcus Furiosus Hef Helicase Domain Length = 494

Iteration: 1
 Score = 41.6 bits (96), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 41/165 (24%), Positives = 81/165 (49%), Gaps = 18/165 (10%)
Query: 232 KFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTR--- 288
           K M K + +LV+  E+ L+     H  ++K +   E + +  +    ++ ++F N R   
Sbjct: 323 KRMKKAISLLVQAKEIGLD-----HPKMDKLK---EIIREQLQRKQNSKIIVFTNYRETA 374
Query: 289 RKV--DWLTDKMRSRDHTVSATHGD---MDQNTRDIIMREFRSGSSRVLITTDLLARGID 343
           +K+  + + D ++++     A+  +   + Q  + +I+ EF  G   VL+ T +   G+D
Sbjct: 375 KKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVATSVGEEGLD 434
Query: 344 VQQVSLVINYDLPTQPENYLHRIGRSGRF--GRKGVAINFVTRDD 386
           V +V LV+ Y+        + R GR+GR   GR  + +   TRD+
Sbjct: 435 VPEVDLVVFYEPVPSAIRSIQRRGRTGRHMPGRVIILMAKGTRDE 479

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	412
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
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	0.0
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	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
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	1e-143
3bor_A	237	Human initiation factor 4A-II; translation initiat	1e-139
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	1e-136
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	1e-127
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	1e-122
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	1e-121
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	1e-118
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	1e-115
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	1e-113
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	1e-109
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	1e-109
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	1e-108
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	1e-107
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	1e-103
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	3e-99
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	2e-96
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	4e-90
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	8e-81
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	8e-73
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	1e-70
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	5e-62
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	7e-59
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	2e-58
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	9e-57
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	2e-56
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	9e-56
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	3e-55
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	4e-53
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	8e-52
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	5e-44
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	2e-43
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	2e-24
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	2e-16
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	5e-18
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	2e-15
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	6e-14
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	9e-14
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-12
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-09
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	2e-11
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	4e-06
1yks_A	440	Genome polyprotein [contains: flavivirin protease	4e-11
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	1e-10
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	6e-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	8e-07
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	2e-10
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	1e-05
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	8e-10
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	7e-07
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	9e-08
3b6e_A	216	Interferon-induced helicase C domain-containing P;	2e-07
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	3e-07
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	3e-07
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	3e-07
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	8e-07
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	1e-06
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	1e-06
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	2e-06
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	6e-06
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	2e-05
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	6e-05
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	5e-04
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	8e-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 =  706 bits (1825), Expect = 0.0
 Identities = 261/409 (63%), Positives = 317/409 (77%), Gaps = 7/409 (1%)

Query: 5   AEGSQFDARQFDARMNDLLGSDGQDFFTSYD-EVYDTFDAMGLQENLLRGIYAYGFEKPS 63
             GS       +  M  +      +F TS + +V  TFD MGL+E+LLRGIYAYGFEKPS
Sbjct: 8   TSGSARKRLLKEEDMTKV------EFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPS 61

Query: 64  AIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQI 123
           AIQQR I    KG DVI Q+QSGTGKTATF   +LQ LD  + E QAL+LAPTRELA QI
Sbjct: 62  AIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQI 121

Query: 124 EKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIR 183
           +K + ALGDY+ V+ HAC+GGT+V ED R L  G HVV GTPGRVFDM+RR+SLR   I+
Sbjct: 122 QKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIK 181

Query: 184 IFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVK 243
           + VLDEADEML++GFK+QIYD+++ LPP  QV + SAT+P E LE+T KFM  P+RILVK
Sbjct: 182 MLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVK 241

Query: 244 RDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDH 303
           RDELTLEGIKQF V VE+EEWK +TLCDLY+TL ITQ+VIF NT+RKVDWLT+KMR  + 
Sbjct: 242 RDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANF 301

Query: 304 TVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYL 363
           TVS+ HGDM Q  R+ IM+EFRSG+SRVLI+TD+ ARG+DV QVSL+INYDLP   E Y+
Sbjct: 302 TVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYI 361

Query: 364 HRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVADLL 412
           HRIGRSGR+GRKGVAINFV  DD R+L DI+++Y+  I+E+P NVADL+
Sbjct: 362 HRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVADLI 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 =  705 bits (1821), Expect = 0.0
 Identities = 279/412 (67%), Positives = 328/412 (79%), Gaps = 4/412 (0%)

Query: 5   AEGSQFDARQFDARMNDLLGSDGQD---FFTSYDEVYDTFDAMGLQENLLRGIYAYGFEK 61
               +F +   D+R  D      +      ++++E+ D+FD M L E+LLRGIYAYGFEK
Sbjct: 3   LGSPEFMSASQDSRSRDNGPDGMEPEGVIESNWNEIVDSFDDMNLSESLLRGIYAYGFEK 62

Query: 62  PSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQ 121
           PSAIQQR I+P  KG DVI QAQSGTGKTATF   ILQQ++  L   QALVLAPTRELAQ
Sbjct: 63  PSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQ 122

Query: 122 QIEKVMRALGDYLGVKVHACVGGTSVREDQRIL-SSGVHVVVGTPGRVFDMLRRQSLRPD 180
           QI+KV+ ALGDY+G   HAC+GGT+VR + + L     H++VGTPGRVFDML R+ L P 
Sbjct: 123 QIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPK 182

Query: 181 NIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRI 240
            I++FVLDEADEMLSRGFKDQIYDIFQ L    QV + SATMP + LE+T+KFM  P+RI
Sbjct: 183 YIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRI 242

Query: 241 LVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRS 300
           LVK++ELTLEGI+QF++NVE+EEWKL+TLCDLYETL ITQ+VIF+NTRRKVDWLT+KM +
Sbjct: 243 LVKKEELTLEGIRQFYINVEREEWKLDTLCDLYETLTITQAVIFINTRRKVDWLTEKMHA 302

Query: 301 RDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPE 360
           RD TVSA HGDMDQ  RD+IMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPT  E
Sbjct: 303 RDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRE 362

Query: 361 NYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVADLL 412
           NY+HRIGR GRFGRKGVAIN VT +D+R L DI+ FYN  IEE+P NVADL+
Sbjct: 363 NYIHRIGRGGRFGRKGVAINMVTEEDKRTLRDIETFYNTSIEEMPLNVADLI 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 =  700 bits (1810), Expect = 0.0
 Identities = 243/387 (62%), Positives = 301/387 (77%), Gaps = 1/387 (0%)

Query: 26  DGQDFFTSYDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQS 85
           +     T+YD+V   FD M L ENLLRG++ YGFE+PSAIQQR I+P  +G DV+ QAQS
Sbjct: 8   EESQIQTNYDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQS 67

Query: 86  GTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGT 145
           GTGKT TF    LQ++D  +   QAL+LAPTRELA QI+KV+ AL  ++ +KVHAC+GGT
Sbjct: 68  GTGKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGT 127

Query: 146 SVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDI 205
           S  ED   L     +VVGTPGRVFD ++R+  R D I++F+LDEADEMLS GFK+QIY I
Sbjct: 128 SFVEDAEGLR-DAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQI 186

Query: 206 FQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWK 265
           F LLPP  QV + SATMP + LE+T KFM  PVRILVK+DELTLEGIKQF+VNVE+EE+K
Sbjct: 187 FTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKDELTLEGIKQFYVNVEEEEYK 246

Query: 266 LETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFR 325
            E L DLY+++++TQ+VIF NTRRKV+ LT K+R+   TVSA + D+ Q  RD IM+EFR
Sbjct: 247 YECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFR 306

Query: 326 SGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRD 385
           SGSSR+LI+TDLLARGIDVQQVSLVINYDLP   ENY+HRIGR GRFGRKGVAINFVT +
Sbjct: 307 SGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNE 366

Query: 386 DERMLFDIQKFYNVVIEELPANVADLL 412
           D   + +++KFY+  IEELP+++A LL
Sbjct: 367 DVGAMRELEKFYSTQIEELPSDIATLL 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 =  657 bits (1697), Expect = 0.0
 Identities = 158/381 (41%), Positives = 226/381 (59%), Gaps = 2/381 (0%)

Query: 32  TSYDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTA 91
              +   +TF+   L+  LL GI+  GFEKPS IQ+  I     G D++ +A++GTGKTA
Sbjct: 14  DVLNTKGNTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTA 73

Query: 92  TFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQ 151
            F    L+++   L + QAL++ PTRELA Q  +V+R LG + G+      GGT++R+D 
Sbjct: 74  AFVIPTLEKVKPKLNKIQALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDI 133

Query: 152 RILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPP 211
             L+  VH++VGTPGRV D+  R+     +  +F++DEAD+MLSR FK  I  I   LPP
Sbjct: 134 LRLNETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSRDFKTIIEQILSFLPP 193

Query: 212 KIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCD 271
             Q  +FSAT P    E   K ++KP  I +  +ELTL+GI Q++  VE E  KL  L  
Sbjct: 194 THQSLLFSATFPLTVKEFMVKHLHKPYEINLM-EELTLKGITQYYAFVE-ERQKLHCLNT 251

Query: 272 LYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRV 331
           L+  L I Q++IF N+  +V+ L  K+    ++   +H  M Q  R+ +  EFR G  R 
Sbjct: 252 LFSKLQINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRT 311

Query: 332 LITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLF 391
           L+ +DLL RGID+Q V++VIN+D P   E YLHRIGRSGRFG  G+AIN +  +D   L+
Sbjct: 312 LVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWNDRFNLY 371

Query: 392 DIQKFYNVVIEELPANVADLL 412
            I++     I  +PA +   L
Sbjct: 372 KIEQELGTEIAAIPATIDKSL 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 =  641 bits (1655), Expect = 0.0
 Identities = 147/389 (37%), Positives = 225/389 (57%), Gaps = 15/389 (3%)

Query: 36  EVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGL--DVIQQAQSGTGKTATF 93
               +F+ + L+  LL+G+YA GF +PS IQ+  +         ++I Q+QSGTGKTA F
Sbjct: 22  YSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAF 81

Query: 94  CSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYL-GVKVHACVGGTSVREDQR 152
              +L Q++      Q L L+PT ELA Q  KV+  +G +   +K+   V G  +   Q+
Sbjct: 82  VLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQK 141

Query: 153 ILSSGVHVVVGTPGRVFDMLRR-QSLRPDNIRIFVLDEADEMLS-RGFKDQIYDIFQLLP 210
           I      +V+GTPG V D   + + + P  I++FVLDEAD M++ +G +DQ   I ++LP
Sbjct: 142 I---SEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLP 198

Query: 211 PKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLC 270
              Q+ +FSAT      +  +K +  P  I +KR+E TL+ IKQ++V     + K + LC
Sbjct: 199 RNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVLCSSRDEKFQALC 258

Query: 271 DLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSR 330
           +LY  + I Q++IF +TR+   WL  ++    H V+   G+M    R  ++  FR G  +
Sbjct: 259 NLYGAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEK 318

Query: 331 VLITTDLLARGIDVQQVSLVINYDLPTQP------ENYLHRIGRSGRFGRKGVAINFVT- 383
           VL+TT++ ARGIDV+QVS+VIN+DLP         E YLHRIGR+GRFG++G+A+N V  
Sbjct: 319 VLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDS 378

Query: 384 RDDERMLFDIQKFYNVVIEELPANVADLL 412
           +    +L  IQ+ +N  IE L  +  D +
Sbjct: 379 KHSMNILNRIQEHFNKKIERLDTDDLDEI 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 =  637 bits (1646), Expect = 0.0
 Identities = 147/389 (37%), Positives = 225/389 (57%), Gaps = 15/389 (3%)

Query: 36  EVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGL--DVIQQAQSGTGKTATF 93
               +F+ + L+  LL+G+YA GF +PS IQ+  +         ++I Q+QSGTGKTA F
Sbjct: 89  YSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAF 148

Query: 94  CSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYL-GVKVHACVGGTSVREDQR 152
              +L Q++      Q L L+PT ELA Q  KV+  +G +   +K+   V G  +   Q+
Sbjct: 149 VLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQK 208

Query: 153 ILSSGVHVVVGTPGRVFDMLRR-QSLRPDNIRIFVLDEADEMLS-RGFKDQIYDIFQLLP 210
           I      +V+GTPG V D   + + + P  I++FVLDEAD M++ +G +DQ   I ++LP
Sbjct: 209 I---SEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLP 265

Query: 211 PKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLC 270
              Q+ +FSAT      +  +K +  P  I +KR+E TL+ IKQ++V     + K + LC
Sbjct: 266 RNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVLCSSRDEKFQALC 325

Query: 271 DLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSR 330
           +LY  + I Q++IF +TR+   WL  ++    H V+   G+M    R  ++  FR G  +
Sbjct: 326 NLYGAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEK 385

Query: 331 VLITTDLLARGIDVQQVSLVINYDLPTQP------ENYLHRIGRSGRFGRKGVAINFVT- 383
           VL+TT++ ARGIDV+QVS+VIN+DLP         E YLHRIGR+GRFG++G+A+N V  
Sbjct: 386 VLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDS 445

Query: 384 RDDERMLFDIQKFYNVVIEELPANVADLL 412
           +    +L  IQ+ +N  IE L  +  D +
Sbjct: 446 KHSMNILNRIQEHFNKKIERLDTDDLDEI 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 =  634 bits (1637), Expect = 0.0
 Identities = 150/387 (38%), Positives = 234/387 (60%), Gaps = 15/387 (3%)

Query: 37  VYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGL--DVIQQAQSGTGKTATFC 94
           +  +FD +GL   LL+GIYA  F+KPS IQ+R +         ++I Q+QSGTGKTA F 
Sbjct: 3   MAKSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFS 62

Query: 95  SGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL 154
             +L +++      QA+ LAP+RELA+Q  +V++ +G +  +     V  +  +  Q   
Sbjct: 63  LTMLTRVNPEDASPQAICLAPSRELARQTLEVVQEMGKFTKITSQLIVPDSFEKNKQI-- 120

Query: 155 SSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEML-SRGFKDQIYDIFQLLPPKI 213
                V+VGTPG V D++RR+ ++   I+IFVLDEAD ML  +G  DQ   + + LP   
Sbjct: 121 --NAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVKRFLPKDT 178

Query: 214 QVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLY 273
           Q+ +FSAT      +  +K +     + ++ +E+ ++ IKQ +++ + E  K + L +LY
Sbjct: 179 QLVLFSATFADAVRQYAKKIVPNANTLELQTNEVNVDAIKQLYMDCKNEADKFDVLTELY 238

Query: 274 ETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLI 333
             + I  S+IFV T++  + L  K++S  H VS  HGD+    RD ++ +FR G S+VLI
Sbjct: 239 GLMTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLI 298

Query: 334 TTDLLARGIDVQQVSLVINYDLPTQ------PENYLHRIGRSGRFGRKGVAINFVT-RDD 386
           TT++LARGID+  VS+V+NYDLPT       P  Y+HRIGR+GRFGRKGVAI+FV  ++ 
Sbjct: 299 TTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDKNS 358

Query: 387 ERMLFDIQKFY-NVVIEELPANVADLL 412
             +L  IQK++ ++ +  +P +  D +
Sbjct: 359 FNILSAIQKYFGDIEMTRVPTDDWDEV 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 =  608 bits (1571), Expect = 0.0
 Identities = 145/381 (38%), Positives = 218/381 (57%), Gaps = 6/381 (1%)

Query: 33  SYDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTAT 92
           S   +   F    L+  LLR I   GFE PS +Q   I     G+DV+ QA+SG GKTA 
Sbjct: 2   SPGHMSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAV 61

Query: 93  FCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYL-GVKVHACVGGTSVREDQ 151
           F    LQQL+    +   LV+  TRELA QI K       Y+  VKV    GG S+++D+
Sbjct: 62  FVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDE 121

Query: 152 RILSSGV-HVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSR-GFKDQIYDIFQLL 209
            +L     H+VVGTPGR+  + R +SL   +I+ F+LDE D+ML +   +  + +IF++ 
Sbjct: 122 EVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMT 181

Query: 210 PPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRD-ELTLEGIKQFHVNVEKEEWKLET 268
           P + QV +FSAT+  E   + RKFM  P+ I V  + +LTL G++Q++V + K+  K   
Sbjct: 182 PHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKL-KDNEKNRK 240

Query: 269 LCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGS 328
           L DL + L   Q VIFV + ++   L   +  ++    A H  M Q  R    ++F+   
Sbjct: 241 LFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQ 300

Query: 329 SRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVT-RDDE 387
            R+L+ T+L  RG+D+++V++  NYD+P   + YLHR+ R+GRFG KG+AI FV+  +D 
Sbjct: 301 RRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDA 360

Query: 388 RMLFDIQKFYNVVIEELPANV 408
           ++L D+Q  + V I ELP  +
Sbjct: 361 KILNDVQDRFEVNISELPDEI 381

>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 =  405 bits (1042), Expect = e-143
 Identities = 135/225 (60%), Positives = 166/225 (73%), Gaps = 1/225 (0%)

Query: 26  DGQDFFTSYDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQS 85
           +     T+YD+V   FD M L ENLLRG++ YGFE+PSAIQQR I+P  +G DV+ QAQS
Sbjct: 1   EESQIQTNYDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQS 60

Query: 86  GTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGT 145
           GTGKT TF    LQ++D  +   QAL+LAPTRELA QI+KV+ AL  ++ +KVHAC+GGT
Sbjct: 61  GTGKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGT 120

Query: 146 SVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDI 205
           S  ED   L     +VVGTPGRVFD ++R+  R D I++F+LDEADEMLS GFK+QIY I
Sbjct: 121 SFVEDAEGL-RDAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQI 179

Query: 206 FQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLE 250
           F LLPP  QV + SATMP + LE+T KFM  PVRILVK+DELTLE
Sbjct: 180 FTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKDELTLE 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 =  396 bits (1021), Expect = e-139
 Identities = 145/234 (61%), Positives = 176/234 (75%), Gaps = 1/234 (0%)

Query: 13  RQFDARMNDLLGSDGQDFFTSYDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVP 72
               +   + L   G    ++++E+ D FD M L+E+LLRGIYAYGFEKPSAIQQR I+P
Sbjct: 4   HHHHSSGRENLYFQGGVIESNWNEIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIP 63

Query: 73  FCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGD 132
             KG DVI QAQSGTGKTATF   ILQQL+    E QALVLAPTRELAQQI+KV+ ALGD
Sbjct: 64  CIKGYDVIAQAQSGTGKTATFAISILQQLEIEFKETQALVLAPTRELAQQIQKVILALGD 123

Query: 133 YLGVKVHACVGGTSVREDQRIL-SSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEAD 191
           Y+G   HAC+GGT+VR + + L +   H+VVGTPGRVFDML R+ L P  I++FVLDEAD
Sbjct: 124 YMGATCHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEAD 183

Query: 192 EMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRD 245
           EMLSRGFKDQIY+IFQ L   IQV + SATMP + LE+T+KFM  P+RILVK++
Sbjct: 184 EMLSRGFKDQIYEIFQKLNTSIQVVLLSATMPTDVLEVTKKFMRDPIRILVKKE 237

>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 =  394 bits (1015), Expect = e-136
 Identities = 129/369 (34%), Positives = 206/369 (55%), Gaps = 15/369 (4%)

Query: 40  TFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKG-LDVIQQAQSGTGKTATFCSGIL 98
            F+ + L +N+L  I   GFEKP+ IQ + I  F     +++ QA++G+GKTA+F   ++
Sbjct: 7   NFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLI 66

Query: 99  QQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGV 158
           + ++      +A++L PTRELA Q+   + +L     +K+    GG ++    + L    
Sbjct: 67  ELVNEN-NGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALK-NA 124

Query: 159 HVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVF 218
           ++VVGTPGR+ D + R +L   N++ F+LDEADEML+ GF   +  I        ++ +F
Sbjct: 125 NIVVGTPGRILDHINRGTLNLKNVKYFILDEADEMLNMGFIKDVEKILNACNKDKRILLF 184

Query: 219 SATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLC---DLYET 275
           SATMP E L + +K+M     I  K        I+Q +V V  E  + E LC      E 
Sbjct: 185 SATMPREILNLAKKYMGDYSFIKAK----INANIEQSYVEV-NENERFEALCRLLKNKEF 239

Query: 276 LAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITT 335
             +    +F  T+R    L   +R       A HGD+ Q+ R+ ++R F+    R+LI T
Sbjct: 240 YGL----VFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIAT 295

Query: 336 DLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQK 395
           D+++RGIDV  ++ VINY LP  PE+Y+HRIGR+GR G+KG AI+ + R + + L  I++
Sbjct: 296 DVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKKGKAISIINRREYKKLRYIER 355

Query: 396 FYNVVIEEL 404
              + I++L
Sbjct: 356 AMKLKIKKL 364

>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 =  370 bits (953), Expect = e-127
 Identities = 104/351 (29%), Positives = 173/351 (49%), Gaps = 18/351 (5%)

Query: 46  LQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGL 105
           + E + + I   GF+  + +Q + I    +G +V+ +A++G+GKTA +   IL+      
Sbjct: 1   MNEKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILEL----- 55

Query: 106 VECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTP 165
              ++LV+ PTREL +Q+   +R +G Y+  KV    GG   +     +     +VV TP
Sbjct: 56  -GMKSLVVTPTRELTRQVASHIRDIGRYMDTKVAEVYGGMPYKAQINRVR-NADIVVATP 113

Query: 166 GRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPE 225
           GR+ D+  +  +   +  I ++DEAD M   GF D I  I      +   G+FSAT+P E
Sbjct: 114 GRLLDLWSKGVIDLSSFEIVIIDEADLMFEMGFIDDIKIILAQTSNRKITGLFSATIPEE 173

Query: 226 ALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFV 285
             ++ + F+     I      + L  ++   V+V+       +             ++FV
Sbjct: 174 IRKVVKDFITNYEEIEAC---IGLANVEHKFVHVKD---DWRSKVQALRENKDKGVIVFV 227

Query: 286 NTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQ 345
            TR +V  L     +         GD+ Q+ R+  +  FR G   +LITTD+ +RG+D+ 
Sbjct: 228 RTRNRVAKLVRLFDN----AIELRGDLPQSVRNRNIDAFREGEYDMLITTDVASRGLDIP 283

Query: 346 QVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKF 396
            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 =  365 bits (939), Expect = e-122
 Identities = 109/398 (27%), Positives = 194/398 (48%), Gaps = 31/398 (7%)

Query: 39  DTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVP--FCKGLDVIQQAQSGTGKTATFCSG 96
              +   L + + + I    F   + +QQ+ I P    +  DVI +A++GTGKT  F   
Sbjct: 21  SLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIP 80

Query: 97  ILQQLDYGLVE----CQALVLAPTRELAQQIEKVMRALGDY----LGVKVHACVGGTSV- 147
           I Q L     +     +A+++APTR+LA QIE  ++ + D           + VGGT   
Sbjct: 81  IFQHLINTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFR 140

Query: 148 REDQRILSSGVHVVVGTPGRVFDMLRRQSLR-PDNIRIFVLDEADEMLSRGFKDQIYDIF 206
               ++     ++V+ TPGR+ D+L + S +    +   VLDEAD +L  GF+D +  I 
Sbjct: 141 AAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLETIS 200

Query: 207 QLLPPK-------IQVGVFSATMPPEALEITRKFMNKPVRILV----KRDELTLEGIKQF 255
            +L  K       I+  +FSAT+  +  ++    MNK   + +    K +    E I Q 
Sbjct: 201 GILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQS 260

Query: 256 HVNVEKEEWKL-----ETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRS---RDHTVSA 307
            V  EK    +          + E  +  +++IF  T +   +L   +++   +D  +  
Sbjct: 261 VVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILE 320

Query: 308 THGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIG 367
            HG + QN R  +++ F+   S +L+ TD+ ARG+D   V  V+   +P++  NY+HRIG
Sbjct: 321 FHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIG 380

Query: 368 RSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELP 405
           R+ R G++G ++ F+ +D+   + +++   N+VI +  
Sbjct: 381 RTARSGKEGSSVLFICKDELPFVRELEDAKNIVIAKQE 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 =  361 bits (928), Expect = e-121
 Identities = 110/398 (27%), Positives = 195/398 (48%), Gaps = 31/398 (7%)

Query: 39  DTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPF--CKGLDVIQQAQSGTGKTATFCSG 96
              +   L + + + I    F   + +QQ+ I P    +  DVI +A++GTGKT  F   
Sbjct: 72  SLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIP 131

Query: 97  ILQQLDYGLVE----CQALVLAPTRELAQQIEKVMRALGDY----LGVKVHACVGGTSVR 148
           I Q L     +     +A+++APTR+LA QIE  ++ + D           + VGGT  R
Sbjct: 132 IFQHLINTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFR 191

Query: 149 EDQRILS-SGVHVVVGTPGRVFDMLRRQSLR-PDNIRIFVLDEADEMLSRGFKDQIYDIF 206
                ++    ++V+ TPGR+ D+L + S +    +   VLDEAD +L  GF+D +  I 
Sbjct: 192 AAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLETIS 251

Query: 207 QLLPPK-------IQVGVFSATMPPEALEITRKFMNKPVRILV----KRDELTLEGIKQF 255
            +L  K       I+  +FSAT+  +  ++    MNK   + +    K +    E I Q 
Sbjct: 252 GILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQS 311

Query: 256 HVNVEKEEWKL-----ETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRS---RDHTVSA 307
            V  EK    +          + E  +  +++IF  T +   +L   +++   +D  +  
Sbjct: 312 VVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILE 371

Query: 308 THGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIG 367
            HG + QN R  +++ F+   S +L+ TD+ ARG+D   V  V+   +P++  NY+HRIG
Sbjct: 372 FHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIG 431

Query: 368 RSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELP 405
           R+ R G++G ++ F+ +D+   + +++   N+VI +  
Sbjct: 432 RTARSGKEGSSVLFICKDELPFVRELEDAKNIVIAKQE 469

>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 =  342 bits (880), Expect = e-118
 Identities = 80/206 (38%), Positives = 120/206 (58%), Gaps = 3/206 (1%)

Query: 40  TFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQ 99
            F+++ L   +L G+ A GFE+PS +Q + I     GLD+I QA+SGTGKT  F +  L 
Sbjct: 25  DFESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALD 84

Query: 100 QLDYGLVECQALVLAPTRELAQQIEKVMRALGDYL-GVKVHACVGGTSVREDQRILSSGV 158
            L    +  Q L+LAPTRE+A QI  V+ A+G  + G++ H  +GGT + +D+  L    
Sbjct: 85  SLVLENLSTQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRL-KKC 143

Query: 159 HVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRG-FKDQIYDIFQLLPPKIQVGV 217
           H+ VG+PGR+  ++    L P +IR+F+LDEAD++L  G F++QI  I+  LP   Q+  
Sbjct: 144 HIAVGSPGRIKQLIELDYLNPGSIRLFILDEADKLLEEGSFQEQINWIYSSLPASKQMLA 203

Query: 218 FSATMPPEALEITRKFMNKPVRILVK 243
            SAT P        K+M  P  + + 
Sbjct: 204 VSATYPEFLANALTKYMRDPTFVRLN 229

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19 Length = 165

 Score =  331 bits (851), Expect = e-115
 Identities = 110/164 (67%), Positives = 137/164 (83%)

Query: 249 LEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSAT 308
           LEGIKQF+VNVE+EE+K E L DLY+++++TQ+VIF NTRRKV+ LT K+R+   TVSA 
Sbjct: 1   LEGIKQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAI 60

Query: 309 HGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGR 368
           + D+ Q  RD IM+EFRSGSSR+LI+TDLLARGIDVQQVSLVINYDLP   ENY+HRIGR
Sbjct: 61  YSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGR 120

Query: 369 SGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVADLL 412
            GRFGRKGVAINFVT +D   + +++KFY+  IEELP+++A LL
Sbjct: 121 GGRFGRKGVAINFVTNEDVGAMRELEKFYSTQIEELPSDIATLL 164

>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 =  333 bits (855), Expect = e-113
 Identities = 77/219 (35%), Positives = 119/219 (54%), Gaps = 8/219 (3%)

Query: 32  TSYDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGL--DVIQQAQSGTGK 89
            S      +F+ + L+  LL+G+YA GF +PS IQ+  +         ++I Q+QSGTGK
Sbjct: 85  NSPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGK 144

Query: 90  TATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYL-GVKVHACVGGTSVR 148
           TA F   +L Q++      Q L L+PT ELA Q  KV+  +G +   +K+   V G  + 
Sbjct: 145 TAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLE 204

Query: 149 EDQRILSSGVHVVVGTPGRVFDMLRRQ-SLRPDNIRIFVLDEADEMLS-RGFKDQIYDIF 206
             Q+I      +V+GTPG V D   +   + P  I++FVLDEAD M++ +G +DQ   I 
Sbjct: 205 RGQKI---SEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQ 261

Query: 207 QLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRD 245
           ++LP   Q+ +FSAT      +  +K +  P  I +KR+
Sbjct: 262 RMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKRE 300

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens} Length = 417

 Score =  327 bits (840), Expect = e-109
 Identities = 126/379 (33%), Positives = 188/379 (49%), Gaps = 24/379 (6%)

Query: 40  TFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFC----S 95
           +F  + + E ++  I    + +P+ +Q+  I    +  D++  AQ+G+GKTA F     S
Sbjct: 16  SFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILS 75

Query: 96  GILQQLDYGLVEC--------------QALVLAPTRELAQQIEKVMRALGDYLGVKVHAC 141
            I        +                 +LVLAPTRELA QI +  R       V+    
Sbjct: 76  QIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRPCVV 135

Query: 142 VGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQ 201
            GG  + +  R L  G H++V TPGR+ DM+ R  +  D  +  VLDEAD ML  GF+ Q
Sbjct: 136 YGGADIGQQIRDLERGCHLLVATPGRLVDMMERGKIGLDFCKYLVLDEADRMLDMGFEPQ 195

Query: 202 IYDIFQLL--PPKI--QVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHV 257
           I  I +    PPK      +FSAT P E   + R F+++ + + V R   T E I Q  V
Sbjct: 196 IRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGRVGSTSENITQKVV 255

Query: 258 NVEKEEWKLETLCDLYETLAITQSV-IFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNT 316
            VE+ + K   L DL           +FV T++  D L D +    +  ++ HGD  Q  
Sbjct: 256 WVEESD-KRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRD 314

Query: 317 RDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKG 376
           R+  + +FRSG S +L+ T + ARG+D+  V  VIN+DLP+  E Y+HRIGR+GR G  G
Sbjct: 315 REEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLG 374

Query: 377 VAINFVTRDDERMLFDIQK 395
           +A +F    +  +  D+  
Sbjct: 375 LATSFFNERNINITKDLLD 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 =  327 bits (841), Expect = e-109
 Identities = 114/358 (31%), Positives = 194/358 (54%), Gaps = 9/358 (2%)

Query: 40  TFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFC----S 95
            F +  L++ ++  +   G++ P+ IQ+  I     G D++  AQ+G+GKTA F     S
Sbjct: 57  HFTSADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPILS 116

Query: 96  GILQQ-LDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL 154
            +L+   +  L   Q ++++PTRELA QI    R       +K+    GGTS R     +
Sbjct: 117 KLLEDPHELELGRPQVVIVSPTRELAIQIFNEARKFAFESYLKIGIVYGGTSFRHQNECI 176

Query: 155 SSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQ--LLPPK 212
           + G HVV+ TPGR+ D + R  +  ++ R  VLDEAD ML  GF + +  I     + P+
Sbjct: 177 TRGCHVVIATPGRLLDFVDRTFITFEDTRFVVLDEADRMLDMGFSEDMRRIMTHVTMRPE 236

Query: 213 IQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDL 272
            Q  +FSAT P E   +  +F+   V + +         +KQ  +    +  K   L ++
Sbjct: 237 HQTLMFSATFPEEIQRMAGEFLKNYVFVAIGIVGGACSDVKQ-TIYEVNKYAKRSKLIEI 295

Query: 273 YETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVL 332
               A   +++FV T+R  D+L   +  ++   ++ HGD  Q+ R+  +R+F++GS +VL
Sbjct: 296 LSEQA-DGTIVFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSMKVL 354

Query: 333 ITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERML 390
           I T + +RG+D++ +  VINYD+P++ ++Y+HRIGR+GR G  G A +F   + +R +
Sbjct: 355 IATSVASRGLDIKNIKHVINYDMPSKIDDYVHRIGRTGRVGNNGRATSFFDPEKDRAI 412

>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 =  316 bits (811), Expect = e-108
 Identities = 74/173 (42%), Positives = 108/173 (62%), Gaps = 6/173 (3%)

Query: 246 ELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTV 305
            LTL  I+Q++V  E  + K + LC++Y ++ I Q++IF  TRR   WLT +M    H V
Sbjct: 2   MLTLNNIRQYYVLCEHRKDKYQALCNIYGSITIGQAIIFCQTRRNAKWLTVEMIQDGHQV 61

Query: 306 SATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQ------P 359
           S   G++    R  I++ FR G  +VLITT++ ARGIDV+QV++V+N+DLP +       
Sbjct: 62  SLLSGELTVEQRASIIQRFRDGKEKVLITTNVCARGIDVKQVTIVVNFDLPVKQGEEPDY 121

Query: 360 ENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVADLL 412
           E YLHRIGR+GRFG+KG+A N +  D+   L  IQ  +N  I++L A   D +
Sbjct: 122 ETYLHRIGRTGRFGKKGLAFNMIEVDELPSLMKIQDHFNSSIKQLNAEDMDEI 174

>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 =  313 bits (805), Expect = e-107
 Identities = 88/220 (40%), Positives = 124/220 (56%), Gaps = 4/220 (1%)

Query: 27  GQDFFTSYDEVYDT-FDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQS 85
           G D   SY  ++ + F    L+  LLR I   GFE PS +Q   I     G+DV+ QA+S
Sbjct: 1   GSDVKGSYVSIHSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKS 60

Query: 86  GTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYL-GVKVHACVGG 144
           G GKTA F    LQQL+    +   LV+  TRELA QI K       Y+  VKV    GG
Sbjct: 61  GMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGG 120

Query: 145 TSVREDQRILSSGV-HVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSR-GFKDQI 202
            S+++D+ +L     H+VVGTPGR+  + R +SL   +I+ F+LDE D+ML +   +  +
Sbjct: 121 LSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDV 180

Query: 203 YDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILV 242
            +IF++ P + QV +FSAT+  E   + RKFM  P+ I V
Sbjct: 181 QEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFV 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 =  304 bits (780), Expect = e-103
 Identities = 75/203 (36%), Positives = 122/203 (60%), Gaps = 1/203 (0%)

Query: 39  DTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGIL 98
           + F+   L+  LL GI+  G+EKPS IQ+  I     G D++ +A++GTGK+  +   +L
Sbjct: 3   NEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLL 62

Query: 99  QQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYL-GVKVHACVGGTSVREDQRILSSG 157
           ++LD      QA+V+ PTRELA Q+ ++   +  ++ G KV A  GGT++R+D   L   
Sbjct: 63  ERLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDT 122

Query: 158 VHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGV 217
           VHVV+ TPGR+ D++++   + D++++ VLDEAD++LS+ F   + DI   LP   Q+ +
Sbjct: 123 VHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNRQILL 182

Query: 218 FSATMPPEALEITRKFMNKPVRI 240
           +SAT P    +     + KP  I
Sbjct: 183 YSATFPLSVQKFMNSHLEKPYEI 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 =  292 bits (749), Expect = 3e-99
 Identities = 58/162 (35%), Positives = 96/162 (59%), Gaps = 2/162 (1%)

Query: 248 TLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSA 307
           +L G++Q++V + K+  K   L DL + L   Q VIFV + ++   L   +  ++    A
Sbjct: 2   SLHGLQQYYVKL-KDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIA 60

Query: 308 THGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIG 367
            H  M Q  R    ++F+    R+L+ T+L  RG+D+++V++  NYD+P   + YLHR+ 
Sbjct: 61  IHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVA 120

Query: 368 RSGRFGRKGVAINFVT-RDDERMLFDIQKFYNVVIEELPANV 408
           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 =  284 bits (729), Expect = 2e-96
 Identities = 66/161 (40%), Positives = 96/161 (59%), Gaps = 1/161 (0%)

Query: 246 ELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTV 305
            LT   I+   + V +EE K   L D+  T      +IF  T+  V+ LTD++    +  
Sbjct: 4   GLTTRNIEHAVIQV-REENKFSLLKDVLMTENPDSCIIFCRTKEHVNQLTDELDDLGYPC 62

Query: 306 SATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHR 365
              HG M Q  R  +M EF+ G  R L+ TD+ ARGID++ +SLVINYDLP + E+Y+HR
Sbjct: 63  DKIHGGMIQEDRFDVMNEFKRGEYRYLVATDVAARGIDIENISLVINYDLPLEKESYVHR 122

Query: 366 IGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPA 406
            GR+GR G KG AI+FVT  ++R L DI+++    I+++ A
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 =  277 bits (711), Expect = 4e-90
 Identities = 65/392 (16%), Positives = 130/392 (33%), Gaps = 50/392 (12%)

Query: 46  LQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGL 105
             E+          +  +  Q+       +G      A +G GKT       L     G 
Sbjct: 6   EYEDFRSFFKKKFGKDLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLARKGK 65

Query: 106 VECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSV----REDQRILSSGVHVV 161
              ++ ++ PT  L +Q  + ++ L D   VK+             + ++       H++
Sbjct: 66  ---KSALVFPTVTLVKQTLERLQKLADE-KVKIFGFYSSMKKEEKEKFEKSFEEDDYHIL 121

Query: 162 VGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSAT 221
           V +   V     R+ L         +D+ D +L          +   +P +I    FS  
Sbjct: 122 VFSTQFVSK--NREKLSQKRFDFVFVDDVDAVLKASRNIDTLLMMVGIPEEIIRKAFSTI 179

Query: 222 MPPEALEITRK---------------------FMNKPVRILVKRDELTLEGIKQFHVNVE 260
              +  E  +                           +   V R       I    ++  
Sbjct: 180 KQGKIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLLNFTVGRLVSVARNITHVRISSR 239

Query: 261 KEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDII 320
            +E KL  L +++    +    IF  T  +   L + ++     V  T  + ++N     
Sbjct: 240 SKE-KLVELLEIFRDGIL----IFAQTEEEGKELYEYLKRFKFNVGETWSEFEKN----- 289

Query: 321 MREFRSGSSRVLITTD----LLARGIDV-QQVSLVINYDLP--TQPENYLHRIGRSGRFG 373
             +F+ G   +LI        L RG+D+ +++  VI +  P       Y+   GRS R  
Sbjct: 290 FEDFKVGKINILIGVQAYYGKLTRGVDLPERIKYVIFWGTPSGPDVYTYIQASGRSSRIL 349

Query: 374 RKGV--AINFVTRDDERMLFDIQKFYNVVIEE 403
              +   ++ +  +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 =  246 bits (631), Expect = 8e-81
 Identities = 69/209 (33%), Positives = 107/209 (51%), Gaps = 4/209 (1%)

Query: 40  TFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQ 99
            F     Q  ++  I    F KP+ IQ+R I    +G  ++ Q+Q+GTGKT  +   I++
Sbjct: 5   QFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIME 64

Query: 100 QLDYGLVECQALVLAPTRELAQQIEKVMRALGDYL----GVKVHACVGGTSVREDQRILS 155
           ++     E QA++ APTRELA QI      +  +      +     +GGT  ++    L+
Sbjct: 65  KIKPERAEVQAVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLN 124

Query: 156 SGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQV 215
              H+V+GTPGR+ D +R Q+L      I V+DEAD ML  GF   +  I   +P  +Q+
Sbjct: 125 VQPHIVIGTPGRINDFIREQALDVHTAHILVVDEADLMLDMGFITDVDQIAARMPKDLQM 184

Query: 216 GVFSATMPPEALEITRKFMNKPVRILVKR 244
            VFSAT+P +     +K+M  P  + V  
Sbjct: 185 LVFSATIPEKLKPFLKKYMENPTFVHVLE 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 =  225 bits (577), Expect = 8e-73
 Identities = 77/208 (37%), Positives = 110/208 (52%), Gaps = 5/208 (2%)

Query: 40  TFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQ 99
            F    L+  +L  ++  G   P+ IQ   +    +G D+I QA++GTGKT  F   I +
Sbjct: 2   EFKDFPLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAE 61

Query: 100 QLDYGLVEC---QALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSS 156
           +L          +ALVL PTRELA Q+   + A+  +L  KV A  GGT   + +  L  
Sbjct: 62  RLAPSQERGRKPRALVLTPTRELALQVASELTAVAPHL--KVVAVYGGTGYGKQKEALLR 119

Query: 157 GVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVG 216
           G   VV TPGR  D LR+  L    + + VLDEADEMLS GF++++  +    PP  Q  
Sbjct: 120 GADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSMGFEEEVEALLSATPPSRQTL 179

Query: 217 VFSATMPPEALEITRKFMNKPVRILVKR 244
           +FSAT+P  A  +  ++M  PV I V +
Sbjct: 180 LFSATLPSWAKRLAERYMKNPVLINVIK 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 =  221 bits (566), Expect = 1e-70
 Identities = 68/205 (33%), Positives = 104/205 (50%), Gaps = 1/205 (0%)

Query: 40  TFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQ 99
           TF  +G+ + L       G+ KP+ IQ   I    +G D+I  A++G+GKT  F   IL 
Sbjct: 44  TFKDLGVTDVLCEACDQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPILN 103

Query: 100 QLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVH 159
            L        ALVL PTRELA QI +   ALG  +GV+    VGG         L+   H
Sbjct: 104 ALLETPQRLFALVLTPTRELAFQISEQFEALGSSIGVQSAVIVGGIDSMSQSLALAKKPH 163

Query: 160 VVVGTPGRVFDMLRRQ-SLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVF 218
           +++ TPGR+ D L          ++  V+DEAD +L+  F+ ++  I +++P   +  +F
Sbjct: 164 IIIATPGRLIDHLENTKGFNLRALKYLVMDEADRILNMDFETEVDKILKVIPRDRKTFLF 223

Query: 219 SATMPPEALEITRKFMNKPVRILVK 243
           SATM  +  ++ R  +  PV+  V 
Sbjct: 224 SATMTKKVQKLQRAALKNPVKCAVS 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 =  199 bits (507), Expect = 5e-62
 Identities = 59/208 (28%), Positives = 102/208 (49%), Gaps = 6/208 (2%)

Query: 40  TFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQ 99
            F    L +  L+G+    +   + IQ++ I    +G DV+  A++G+GKT  F   +L+
Sbjct: 26  RFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLE 85

Query: 100 QLDYGLVE----CQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILS 155
            L             L+++PTRELA Q  +V+R +G          +GG  ++  +    
Sbjct: 86  ALYRLQWTSTDGLGVLIISPTRELAYQTFEVLRKVGKNHDFSAGLIIGGKDLKH-EAERI 144

Query: 156 SGVHVVVGTPGRVFD-MLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQ 214
           + ++++V TPGR+   M    S    ++++ VLDEAD +L  GF D +  + + LP K Q
Sbjct: 145 NNINILVCTPGRLLQHMDETVSFHATDLQMLVLDEADRILDMGFADTMNAVIENLPKKRQ 204

Query: 215 VGVFSATMPPEALEITRKFMNKPVRILV 242
             +FSAT      ++ R  +  P  + V
Sbjct: 205 TLLFSATQTKSVKDLARLSLKNPEYVWV 232

>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 =  191 bits (487), Expect = 7e-59
 Identities = 54/212 (25%), Positives = 101/212 (47%), Gaps = 8/212 (3%)

Query: 39  DTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGIL 98
                  +   LL+ I   GF+ P+ IQ + I     G +++  A +G+GKT  F   IL
Sbjct: 29  QLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPIL 88

Query: 99  QQLDYGLVE-CQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQ-RILSS 156
            QL     +  +AL+++PTRELA QI + +  + +  G ++H         +      S 
Sbjct: 89  MQLKQPANKGFRALIISPTRELASQIHRELIKISEGTGFRIHMIHKAAVAAKKFGPKSSK 148

Query: 157 GVHVVVGTPGRVFDMLRRQSLRPD--NIRIFVLDEADEML---SRGFKDQIYDIF-QLLP 210
              ++V TP R+  +L++     D  ++   V+DE+D++      GF+DQ+  IF     
Sbjct: 149 KFDILVTTPNRLIYLLKQDPPGIDLASVEWLVVDESDKLFEDGKTGFRDQLASIFLACTS 208

Query: 211 PKIQVGVFSATMPPEALEITRKFMNKPVRILV 242
            K++  +FSAT   +  +  +  ++  + + +
Sbjct: 209 HKVRRAMFSATFAYDVEQWCKLNLDNVISVSI 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 =  190 bits (485), Expect = 2e-58
 Identities = 69/228 (30%), Positives = 105/228 (46%), Gaps = 13/228 (5%)

Query: 40  TFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQ 99
            FD + L   +   I    +++P+ IQ+  I    +  D++  AQ+G+GKTA F   I+ 
Sbjct: 24  NFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIIN 83

Query: 100 QL---------DYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVRED 150
            L                + L+LAPTRELA QI    +       ++     GG      
Sbjct: 84  HLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQ 143

Query: 151 QRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIF-QLL 209
            R +  G H++V TPGR+ D + +  +  +  +  VLDEAD ML  GF+ QI  I  +  
Sbjct: 144 IREVQMGCHLLVATPGRLVDFIEKNKISLEFCKYIVLDEADRMLDMGFEPQIRKIIEESN 203

Query: 210 PPKI---QVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQ 254
            P     Q  +FSAT P E  ++   F+   + + V R   T + IKQ
Sbjct: 204 MPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTVGRVGSTSDSIKQ 251

>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 =  183 bits (466), Expect = 9e-57
 Identities = 52/154 (33%), Positives = 80/154 (51%)

Query: 250 EGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATH 309
           + I Q++   +  E K   L  L +    T+S++FV  R +V  L + +R          
Sbjct: 2   KKIHQWYYRADDLEHKTALLVHLLKQPEATRSIVFVRKRERVHELANWLREAGINNCYLE 61

Query: 310 GDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRS 369
           G+M Q  R+  ++    G   VL+ TD+ ARGID+  VS V N+D+P   + YLHRIGR+
Sbjct: 62  GEMVQGKRNEAIKRLTEGRVNVLVATDVAARGIDIPDVSHVFNFDMPRSGDTYLHRIGRT 121

Query: 370 GRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEE 403
            R GRKG AI+ V   D  +L  + ++    I+ 
Sbjct: 122 ARAGRKGTAISLVEAHDHLLLGKVGRYIEEPIKA 155

>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 =  184 bits (469), Expect = 2e-56
 Identities = 67/210 (31%), Positives = 101/210 (48%), Gaps = 8/210 (3%)

Query: 40  TF-DAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGIL 98
            F DA     +LL+ I   G  KP+ IQ +      +G+D+I  AQ+GTGKT ++     
Sbjct: 20  RFKDAFQQYPDLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGF 79

Query: 99  QQLDYGLVECQ------ALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQR 152
             LD   +  +       LVL PTRELA  +E        Y G+K     GG +      
Sbjct: 80  IHLDSQPISREQRNGPGMLVLTPTRELALHVEAECSKYS-YKGLKSICIYGGRNRNGQIE 138

Query: 153 ILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPK 212
            +S GV +++ TPGR+ D+    S+   +I   V+DEAD+ML   F+ QI  I   + P 
Sbjct: 139 DISKGVDIIIATPGRLNDLQMNNSVNLRSITYLVIDEADKMLDMEFEPQIRKILLDVRPD 198

Query: 213 IQVGVFSATMPPEALEITRKFMNKPVRILV 242
            Q  + SAT P    ++   ++  P+ + V
Sbjct: 199 RQTVMTSATWPDTVRQLALSYLKDPMIVYV 228

>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 =  183 bits (466), Expect = 9e-56
 Identities = 68/208 (32%), Positives = 96/208 (46%), Gaps = 5/208 (2%)

Query: 40  TFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFC----S 95
            F       N++  I    F +P+AIQ +G      GLD++  AQ+G+GKT ++      
Sbjct: 30  NFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIV 89

Query: 96  GILQQLDYGLVEC-QALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL 154
            I  Q      +    LVLAPTRELAQQ+++V         +K     GG       R L
Sbjct: 90  HINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIRDL 149

Query: 155 SSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQ 214
             GV + + TPGR+ D L             VLDEAD ML  GF+ QI  I   + P  Q
Sbjct: 150 ERGVEICIATPGRLIDFLECGKTNLRRTTYLVLDEADRMLDMGFEPQIRKIVDQIRPDRQ 209

Query: 215 VGVFSATMPPEALEITRKFMNKPVRILV 242
             ++SAT P E  ++   F+   + I +
Sbjct: 210 TLMWSATWPKEVRQLAEDFLKDYIHINI 237

>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 =  182 bits (464), Expect = 3e-55
 Identities = 60/209 (28%), Positives = 112/209 (53%), Gaps = 8/209 (3%)

Query: 40  TFDAMG--LQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGI 97
           +F ++   + EN L+ I   GF   + IQ + I P  +G D++  A++G+GKT  F    
Sbjct: 53  SFASLCNLVNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPA 112

Query: 98  LQQLDYGLVECQ----ALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRI 153
           ++ +       +     L+L+PTRELA Q   V++ L  +        +GG++   + + 
Sbjct: 113 VELIVKLRFMPRNGTGVLILSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQK 172

Query: 154 LSSGVHVVVGTPGRVFDMLRRQ-SLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPK 212
           L +G++++V TPGR+ D ++        N++  V+DEAD +L  GF++++  I +LLP +
Sbjct: 173 LGNGINIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEADRILDVGFEEELKQIIKLLPTR 232

Query: 213 IQVGVFSATMPPEALEITRK-FMNKPVRI 240
            Q  +FSAT   +  ++ R     +P+ +
Sbjct: 233 RQTMLFSATQTRKVEDLARISLKKEPLYV 261

>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 =  175 bits (445), Expect = 4e-53
 Identities = 46/154 (29%), Positives = 79/154 (51%), Gaps = 1/154 (0%)

Query: 252 IKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGD 311
            ++  V       +LE L DL    +  ++++F  T+ + + +   +    H   A HGD
Sbjct: 6   YEEEAVPA-PVRGRLEVLSDLLYVASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGD 64

Query: 312 MDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGR 371
           + Q  R+ ++  FR G  RVL+ TD+ ARG+D+ QV LV++Y LP + E Y HR GR+GR
Sbjct: 65  LSQGERERVLGAFRQGEVRVLVATDVAARGLDIPQVDLVVHYRLPDRAEAYQHRSGRTGR 124

Query: 372 FGRKGVAINFVTRDDERMLFDIQKFYNVVIEELP 405
            GR G  +      + R +  +++      + + 
Sbjct: 125 AGRGGRVVLLYGPRERRDVEALERAVGRRFKRVN 158

>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 =  174 bits (444), Expect = 8e-52
 Identities = 47/154 (30%), Positives = 79/154 (51%), Gaps = 1/154 (0%)

Query: 252 IKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGD 311
            ++  V       +LE L DL    +  ++++F  T+ + + +   +    H   A HGD
Sbjct: 3   YEEEAVPA-PVRGRLEVLSDLLYVASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGD 61

Query: 312 MDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGR 371
           M Q  R+ +M  FR G  RVL+ TD+ ARG+D+ QV LV++Y +P + E Y HR GR+GR
Sbjct: 62  MSQGERERVMGAFRQGEVRVLVATDVAARGLDIPQVDLVVHYRMPDRAEAYQHRSGRTGR 121

Query: 372 FGRKGVAINFVTRDDERMLFDIQKFYNVVIEELP 405
            GR G  +      + R +  +++      + + 
Sbjct: 122 AGRGGRVVLLYGPRERRDVEALERAVGRRFKRVN 155

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens} Length = 191

 Score =  150 bits (382), Expect = 5e-44
 Identities = 46/166 (27%), Positives = 76/166 (45%), Gaps = 9/166 (5%)

Query: 233 FMNKPVRILVKRDELTL-------EGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFV 285
             +    + +  + L           + Q  V   KEE K+  L +  +       +IF 
Sbjct: 4   HHHHSSGVDLGTENLYFQSMGAASLDVIQ-EVEYVKEEAKMVYLLECLQKTP-PPVLIFA 61

Query: 286 NTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQ 345
             +  VD + + +  +     A HG  DQ  R   +  FR G   VL+ TD+ ++G+D  
Sbjct: 62  EKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVASKGLDFP 121

Query: 346 QVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLF 391
            +  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 =  148 bits (377), Expect = 2e-43
 Identities = 52/145 (35%), Positives = 78/145 (53%), Gaps = 2/145 (1%)

Query: 252 IKQFHVNVEKEEWKLETLCDLYETLAITQSV-IFVNTRRKVDWLTDKMRSRDHTVSATHG 310
           I Q  V VE+ + K   L DL           +FV T++  D L D +    +  ++ HG
Sbjct: 20  ITQKVVWVEESD-KRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHG 78

Query: 311 DMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSG 370
           D  Q  R+  + +FRSG S +L+ T + ARG+D+  V  VIN+DLP+  E Y+HRIGR+G
Sbjct: 79  DRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTG 138

Query: 371 RFGRKGVAINFVTRDDERMLFDIQK 395
           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 =  103 bits (258), Expect = 2e-24
 Identities = 37/210 (17%), Positives = 77/210 (36%), Gaps = 21/210 (10%)

Query: 186 VLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRD 245
            L  A E+L       +    + L  + + G   A+    + +  +K ++          
Sbjct: 281 KLHHAIELLETQGLSALRAYIKKLYEEAKAGSTKASKEIFSDKRMKKAISL--------- 331

Query: 246 ELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRD--- 302
              L   K+  ++  K +   E + +  +    ++ ++F N R     + +++       
Sbjct: 332 ---LVQAKEIGLDHPKMDKLKEIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKDGIKA 388

Query: 303 -----HTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPT 357
                         + Q  + +I+ EF  G   VL+ T +   G+DV +V LV+ Y+   
Sbjct: 389 KRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVATSVGEEGLDVPEVDLVVFYEPVP 448

Query: 358 QPENYLHRIGRSGRFGRKGVAINFVTRDDE 387
                + 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 = 79.8 bits (196), Expect = 2e-16
 Identities = 53/344 (15%), Positives = 113/344 (32%), Gaps = 19/344 (5%)

Query: 67  QRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKV 126
           Q  I   CK  + +    +G GKT         +L       + L+LAPT+ L  Q  + 
Sbjct: 14  QEVIYAKCKETNCLIVLPTGLGKTLIAMMIAEYRLTKYGG--KVLMLAPTKPLVLQHAES 71

Query: 127 MRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFV 186
            R L +    K+ A  G  S  E  +  +    V+V TP  + + L    +  +++ + V
Sbjct: 72  FRRLFNLPPEKIVALTGEKSPEERSKAWAR-AKVIVATPQTIENDLLAGRISLEDVSLIV 130

Query: 187 LDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDE 246
            DEA   +       I   ++       V   +A+      +I     N  +  +  R E
Sbjct: 131 FDEAHRAVGNYAYVFIAREYKRQAKNPLVIGLTASPGSTPEKIMEVINNLGIEHIEYRSE 190

Query: 247 LTLEGIKQFHVNVEKEEWKLETLCDLYETL-----AITQSVIFVNTRRKVDWLTDKMRSR 301
            + +     +V   + EW    L ++Y+ +      + +  +       +   +     +
Sbjct: 191 NSPDVRP--YVKGIRFEWVRVDLPEIYKEVRKLLREMLRDALKPLAETGLLESSSPDIPK 248

Query: 302 DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPEN 361
              + A           II  E   G+  +       A  + +     ++     +    
Sbjct: 249 KEVLRA---------GQIINEEMAKGNHDLRGLLLYHAMALKLHHAIELLETQGLSALRA 299

Query: 362 YLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELP 405
           Y+ ++    + G    +    +    +    +      +  + P
Sbjct: 300 YIKKLYEEAKAGSTKASKEIFSDKRMKKAISLLVQAKEIGLDHP 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 = 85.1 bits (210), Expect = 5e-18
 Identities = 62/386 (16%), Positives = 104/386 (26%), Gaps = 83/386 (21%)

Query: 19  MNDLLGSDGQDFFTSYDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQ----RGIVPFC 74
           ++ L GS G             F A  +     RG+       P    +      +    
Sbjct: 167 VSYLKGSSGGPLLCPSGHAVGIFRA-AV---CTRGVAKAVDFVPVESMETTMRSPVFTDN 222

Query: 75  --------KGLDVIQQAQSGTGKTATFCSGILQQL-DYGLVECQALVLAPTRELAQQIEK 125
                           A +G+GK+      +       G    + LVL P+         
Sbjct: 223 SSPPAVPQSFQVAHLHAPTGSGKST----KVPAAYAAQGY---KVLVLNPSVAATLGFGA 275

Query: 126 VMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIF 185
            M       G+  +   G        R +++G  V   T G+    L           I 
Sbjct: 276 YMSKA---HGIDPNIRTGV-------RTITTGAPVTYSTYGK---FLADGGCSGGAYDII 322

Query: 186 VLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRD 245
           + DE            I  +           V  AT  P    +T    N     L    
Sbjct: 323 ICDECHST-DSTTILGIGTVLDQAETAGARLVVLATATPPG-SVTVPHPNIEEVALSNTG 380

Query: 246 ELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTV 305
           E+   G       +                    + +IF ++++K D L  K+       
Sbjct: 381 EIPFYGKAIPIEAIRGG-----------------RHLIFCHSKKKCDELAAKLSGLGINA 423

Query: 306 SATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARG--IDV-------QQVSLVINYD-- 354
            A +  +D       +    +    V++ TD L  G   D          V+  +++   
Sbjct: 424 VAYYRGLD-------VSVIPTIGDVVVVATDALMTGYTGDFDSVIDCNTCVTQTVDFSLD 476

Query: 355 ------LPTQP---ENYLHRIGRSGR 371
                   T P    +   R GR+GR
Sbjct: 477 PTFTIETTTVPQDAVSRSQRRGRTGR 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 = 77.2 bits (190), Expect = 2e-15
 Identities = 63/412 (15%), Positives = 137/412 (33%), Gaps = 89/412 (21%)

Query: 45  GLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYG 104
            +    +  +   G E+    Q   +     G +++    +  GKT      ++++   G
Sbjct: 9   SISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKG 68

Query: 105 LVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGT 164
               ++L + P R LA +  +  +     +G+++    G    R++         ++V T
Sbjct: 69  ---GKSLYVVPLRALAGEKYESFKKWEK-IGLRIGISTGDYESRDEHL---GDCDIIVTT 121

Query: 165 PGRVFDMLRRQSLRPDNIRIFVLDE----ADE--------MLSRGFKDQIYDIFQLLPPK 212
             +   ++R ++     +   V+DE      E        ++++          + +   
Sbjct: 122 SEKADSLIRNRASWIKAVSCLVVDEIHLLDSEKRGATLEILVTK---------MRRMNKA 172

Query: 213 IQ-VGVFSATMP-PEALEITRKFMNKPVRILVKRD----ELTLEGIKQFHVNVEKEEWKL 266
           ++ +G+ SAT P    +    ++++         D     L  EG+         +    
Sbjct: 173 LRVIGL-SATAPNVTEIA---EWLDAD---YYVSDWRPVPLV-EGVLCEGTLELFDGAFS 224

Query: 267 ETLCDLYETLAIT------QSVIFVNTRRKV----------------------DWLTDKM 298
            +    +E L           ++F +TRR                          L +  
Sbjct: 225 TSRRVKFEELVEECVAENGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENE 284

Query: 299 RSRDHTVSAT--------HGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLV 350
                 ++          H  +    R ++   FR G+ +V++ T  LA G+++     V
Sbjct: 285 GEMSRKLAECVRKGAAFHHAGLLNGQRRVVEDAFRRGNIKVVVATPTLAAGVNL-PARRV 343

Query: 351 INYDL--------PTQPENYLHRIGRSGRFG--RKGVAINFVTRDDERMLFD 392
           I   L          +   Y    GR+GR G   +G AI  V + D  +   
Sbjct: 344 IVRSLYRFDGYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIVGKRDREIAVK 395

>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 = 72.6 bits (178), Expect = 6e-14
 Identities = 77/410 (18%), Positives = 150/410 (36%), Gaps = 78/410 (19%)

Query: 42  DAMGLQENLLRGIYAYGFEKPSAIQQRGI-VPFCKGLDVIQQAQSGTGKTATFCSGILQQ 100
           D + + E +   +   G E     Q   +     +G + +    + +GKT      ++ +
Sbjct: 4   DELRVDERIKSTLKERGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHR 63

Query: 101 LDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHV 160
           +       +A+ + P + LA++  +  +     +G++V    G    +++         +
Sbjct: 64  ILTQ--GGKAVYIVPLKALAEEKFQEFQDWEK-IGLRVAMATGDYDSKDEWL---GKYDI 117

Query: 161 VVGTPGRVFDMLRRQSLRPDNIRIFVLDE----ADEMLSRGFKDQIYDIFQLLPPKIQ-V 215
           ++ T  +   +LR  S    +++I V DE          RG    +  I   +  K Q +
Sbjct: 118 IIATAEKFDSLLRHGSSWIKDVKILVADEIHLIGSR--DRG--ATLEVILAHMLGKAQII 173

Query: 216 GVFSATMP-PEALEITRKFMNKPVRILVKRD----ELTLEGIK--QFHVNVEKEEWKLET 268
           G+ SAT+  PE L    +++N     L+  D    +L   G+    F    +    +  +
Sbjct: 174 GL-SATIGNPEELA---EWLNAE---LIVSDWRPVKLR-RGVFYQGFVTWEDGSIDRFSS 225

Query: 269 LCDL-YETLA-ITQSVIFVNTRRKV----DWLTDKMRSRDHT------------------ 304
             +L Y+ +     ++IFVN RRK       L+ K++S                      
Sbjct: 226 WEELVYDAIRKKKGALIFVNMRRKAERVALELSKKVKSLLTKPEIRALNELADSLEENPT 285

Query: 305 -----------VSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVI-- 351
                      V+  H  + ++ R ++   FR G  + ++ T  L+ GI+      VI  
Sbjct: 286 NEKLAKAIRGGVAFHHAGLGRDERVLVEENFRKGIIKAVVATPTLSAGINT-PAFRVIIR 344

Query: 352 ---NYDLPTQPE----NYLHRIGRSGRFG--RKGVAINFVTRDDERMLFD 392
               Y                +GR+GR      G  I   T DD R + +
Sbjct: 345 DIWRYSDFGMERIPIIEVHQMLGRAGRPKYDEVGEGIIVSTSDDPREVMN 394

>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 = 9e-14
 Identities = 26/153 (16%), Positives = 52/153 (33%), Gaps = 7/153 (4%)

Query: 261 KEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSR-DHTVSATHGDMDQNTRDI 319
             + ++E L     +    + ++          L   +R R     +  H  M    RD 
Sbjct: 486 NFDPRVEWLMGYLTSHRSQKVLVICAKAATALQLEQVLREREGIRAAVFHEGMSIIERDR 545

Query: 320 IMREFRSGSS--RVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKG- 376
               F    +  +VL+ +++ + G + Q  S ++ +DLP  P+    RIGR  R G+   
Sbjct: 546 AAAWFAEEDTGAQVLLCSEIGSEGRNFQFASHMVMFDLPFNPDLLEQRIGRLDRIGQAHD 605

Query: 377 -VAINFVTRD--DERMLFDIQKFYNVVIEELPA 406
                          ++    +  +      P 
Sbjct: 606 IQIHVPYLEKTAQSVLVRWYHEGLDAFEHTCPT 638

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 67.6 bits (164), Expect = 3e-12
 Identities = 68/487 (13%), Positives = 131/487 (26%), Gaps = 179/487 (36%)

Query: 10  FDARQFDARMNDLLGSDGQDFFTSYDEVYDTFDAMGLQENLLRGIYAYG-----FEKPSA 64
           F+  +   +  D+L      F  ++D   D        +++ + I +            A
Sbjct: 9   FETGEHQYQYKDILSVFEDAFVDNFD-CKDV-------QDMPKSILSKEEIDHIIMSKDA 60

Query: 65  IQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLV------ECQA-------- 110
           +     +        +   Q        F   +L+  +Y  +      E +         
Sbjct: 61  VSGTLRL-----FWTLLSKQEEM--VQKFVEEVLRI-NYKFLMSPIKTEQRQPSMMTRMY 112

Query: 111 -----------LVLAP---TR-ELAQQIEKVMRALGDYLGVKVHACVG-GTSV------R 148
                       V A    +R +   ++ + +  L     V +   +G G +        
Sbjct: 113 IEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCL 172

Query: 149 ED--QRILSSGVH-VVVG---TPGRVFDMLRRQSL-------------RPDNIRIFVLDE 189
               Q  +   +  + +    +P  V +ML  Q L                NI++  +  
Sbjct: 173 SYKVQCKMDFKIFWLNLKNCNSPETVLEML--QKLLYQIDPNWTSRSDHSSNIKL-RIHS 229

Query: 190 ADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEAL---------EITRKFMNKPVRI 240
               L R  K + Y                       L         +    F     +I
Sbjct: 230 IQAELRRLLKSKPY--------------------ENCLLVLLNVQNAKAWNAFNLS-CKI 268

Query: 241 LV-KRD-ELT--LEGIKQFHVNVEKEEWKL---ETLCDLYET------------------ 275
           L+  R  ++T  L      H++++     L   E    L                     
Sbjct: 269 LLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVK-SLLLKYLDCRPQDLPREVLTTNP 327

Query: 276 LAITQSVIFVNTRRKVD----WL---TDKM-RSRDHTVSA-THGDMDQNTRDIIMREFRS 326
             +  S+I  + R  +     W     DK+    + +++     +  +    + +  F  
Sbjct: 328 RRL--SIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSV--FPP 383

Query: 327 GSSRVLITTDLLAR------GIDVQQV-------SLV-------------INYDLPTQPE 360
                 I T LL+         DV  V       SLV             I  +L  + E
Sbjct: 384 S---AHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLE 440

Query: 361 N--YLHR 365
           N   LHR
Sbjct: 441 NEYALHR 447

>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 = 2e-09
 Identities = 78/523 (14%), Positives = 148/523 (28%), Gaps = 181/523 (34%)

Query: 18  RMNDLLGSDG----QDFF-----TSYDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQR 68
           R+   L S      Q F       +Y  +         Q +++  +Y    ++       
Sbjct: 66  RLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDR----LYN 121

Query: 69  GIVPFCKGLDV------------IQQAQS----------GTGKT---ATFCS--GILQQL 101
               F K  +V            + + +           G+GKT      C    +  ++
Sbjct: 122 DNQVFAK-YNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKM 180

Query: 102 DY-------GLVECQALVLAPTRELAQQIEKVMRALGDYL-GVKVHACVGGTSVR-EDQR 152
           D+               VL   ++L  QI+    +  D+   +K+       S++ E +R
Sbjct: 181 DFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRI----HSIQAELRR 236

Query: 153 ILSSGVH----VV---VGTPG--RVFD----ML---RRQS----LRPDNIRIFVLDEADE 192
           +L S  +    +V   V        F+    +L   R +     L         LD    
Sbjct: 237 LLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSM 296

Query: 193 MLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRI-----LVKRDEL 247
            L+    D++  +         +      +P E L         P R+      ++    
Sbjct: 297 TLT---PDEVKSLLLKY-----LDCRPQDLPREVLTTN------PRRLSIIAESIRDGLA 342

Query: 248 TLEGIKQFHVNVEKE----EWKLETLC-----DLYETLA-------ITQSVIFV----NT 287
           T +  K  HVN +K     E  L  L       +++ L+       I   ++ +      
Sbjct: 343 TWDNWK--HVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVI 400

Query: 288 RRKVDWLTDKMRSRDHTVSATHGDMDQNTRDI--IMREFRSGSS------RVLITTDLLA 339
           +  V  + +K+       S       ++T  I  I  E +          R ++    + 
Sbjct: 401 KSDVMVVVNKLHKY----SLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIP 456

Query: 340 RGIDVQQVSLVINYDLPTQPE-NY--------LHRIGRSGRF-------------GRK-- 375
           +  D        + DL       Y        L  I    R               +K  
Sbjct: 457 KTFD--------SDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIR 508

Query: 376 --GVAIN-----------------FVTRDD---ERMLFDIQKF 396
               A N                 ++  +D   ER++  I  F
Sbjct: 509 HDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDF 551

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A* Length = 696

 Score = 64.6 bits (156), Expect = 2e-11
 Identities = 41/185 (22%), Positives = 71/185 (38%), Gaps = 17/185 (9%)

Query: 228 EITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDL----YETLAITQSVI 283
            +     ++  + L +R E  L+ ++    +   E  KLE LC +    Y     T +++
Sbjct: 344 NVRAAGFDEIEQDLTQRFEEKLQELESVSRDPSNENPKLEDLCFILQEEYHLNPETITIL 403

Query: 284 FVNTRRKVDWLTDKMRSRD------------HTVSATHGDMDQNTRDIIMREFR-SGSSR 330
           FV TR  VD L + +                   +  +  M    +  I+  F+ SG   
Sbjct: 404 FVKTRALVDALKNWIEGNPKLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAFKASGDHN 463

Query: 331 VLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERML 390
           +LI T +   GID+ Q +LVI Y+        +   GR    G K   +       E+  
Sbjct: 464 ILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTRGRGRARGSKCFLLTSNAGVIEKEQ 523

Query: 391 FDIQK 395
            ++ 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 = 48.1 bits (113), Expect = 4e-06
 Identities = 31/202 (15%), Positives = 67/202 (33%), Gaps = 8/202 (3%)

Query: 61  KPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLD--YGLVECQALVLAPTRE 118
           KP   Q    +P  KG + I  A +G GKT          L       + + +  A    
Sbjct: 13  KPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQIP 72

Query: 119 LAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLR 178
           + +Q + V     +  G +V    G T+       +     +++ TP  + + L++ ++ 
Sbjct: 73  VYEQNKSVFSKYFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTIP 132

Query: 179 P-DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKP 237
                 + + DE      +   + I   +       Q    S+   P+ + +T       
Sbjct: 133 SLSIFTLMIFDECHNTSKQHPYNMIMFNY-----LDQKLGGSSGPLPQVIGLTASVGVGD 187

Query: 238 VRILVKRDELTLEGIKQFHVNV 259
            +   +  +   +       +V
Sbjct: 188 AKTTDEALDYICKLCASLDASV 209

>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 = 63.3 bits (154), Expect = 4e-11
 Identities = 49/322 (15%), Positives = 98/322 (30%), Gaps = 62/322 (19%)

Query: 75  KGLDVIQQAQSGTGKTATFCSGILQQL--DYGLVECQALVLAPTRELAQQIEKVMRALGD 132
           KG+  +     G GKT       L Q+  +      + LVLAPTR +  ++++       
Sbjct: 7   KGMTTVLDFHPGAGKT----RRFLPQILAECARRRLRTLVLAPTRVVLSEMKEAFH---- 58

Query: 133 YLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRP---DNIRIFVLDE 189
             G+ V       S     R +     +           L  + L P    N  + ++DE
Sbjct: 59  --GLDVKFHTQAFSAHGSGREV-----IDAMCHA----TLTYRMLEPTRVVNWEVIIMDE 107

Query: 190 ADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTL 249
           A  +       + +   +    +    + +AT P  + E    F +    I   + ++  
Sbjct: 108 AHFLDPASIAARGWAAHRARANESATILMTATPPGTSDE----FPHSNGEIEDVQTDIPS 163

Query: 250 EGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATH 309
           E     H  +  ++                    F+ + R  + +   +R    +V   +
Sbjct: 164 EPWNTGHDWILADKRPT---------------AWFLPSIRAANVMAASLRKAGKSVVVLN 208

Query: 310 GDMDQNTRDIIMREFRSGSSRVLITTDLLARG--IDVQQV-----SLVINYD-------- 354
                 T +      +      ++ TD+   G  + V++V     +              
Sbjct: 209 RK----TFEREYPTIKQKKPDFILATDIAEMGANLCVERVLDCRTAFKPVLVDEGRKVAI 264

Query: 355 LPTQPENYLHRIGRSGRFGRKG 376
                 +      R GR GR  
Sbjct: 265 KGPLRISASSAAQRRGRIGRNP 286

>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 = 62.7 bits (151), Expect = 1e-10
 Identities = 32/186 (17%), Positives = 62/186 (33%), Gaps = 19/186 (10%)

Query: 228 EITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDL----YETLAITQSVI 283
            +      +  + L  + +     +     +   E  KLE L  +    Y     T++++
Sbjct: 577 NVKNGPYTELEQHLTAKFQEKEPELIALSKDETNENPKLEELVCILDDAYRYNPQTRTLL 636

Query: 284 FVNTRRKVDWLTDKMRS------------RDHTVSATHGDMDQNTRDIIMREFRSGSS-R 330
           F  TR  V  L   M                         M   ++  ++  F++    R
Sbjct: 637 FAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNR 696

Query: 331 VLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERML 390
           +LI T +   GID+ Q +LV+ Y+        +   GR GR       I   ++ +    
Sbjct: 697 LLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GR-AAGSKCILVTSKTEVVEN 754

Query: 391 FDIQKF 396
               ++
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 = 41.1 bits (95), Expect = 6e-04
 Identities = 26/142 (18%), Positives = 49/142 (34%), Gaps = 5/142 (3%)

Query: 57  YGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKT---ATFCSGILQQLDYGLVECQALVL 113
           Y  +K  + Q     P   G + +  A +G+GKT      C    Q +  G  + + + L
Sbjct: 244 YETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGR-KAKVVFL 302

Query: 114 APTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLR 173
           A    + +Q + V +   +  G  V    G          +     ++V TP  + +   
Sbjct: 303 ATKVPVYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFE 362

Query: 174 RQSLRP-DNIRIFVLDEADEML 194
             +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 = 61.9 bits (149), Expect = 2e-10
 Identities = 32/177 (18%), Positives = 60/177 (33%), Gaps = 19/177 (10%)

Query: 228 EITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDL----YETLAITQSVI 283
            +      +  + L  + +     +     +   E  KLE L  +    Y     T++++
Sbjct: 577 NVKNGPYTELEQHLTAKFQEKEPELIALSKDETNENPKLEELVCILDDAYRYNPQTRTLL 636

Query: 284 FVNTRRKVDWLTDKMRS------------RDHTVSATHGDMDQNTRDIIMREFRSGSS-R 330
           F  TR  V  L   M                         M   ++  ++  F++    R
Sbjct: 637 FAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNR 696

Query: 331 VLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDE 387
           +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 = 50.4 bits (119), Expect = 8e-07
 Identities = 48/371 (12%), Positives = 116/371 (31%), Gaps = 23/371 (6%)

Query: 57  YGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKT---ATFCSGILQQLDYGLVECQALVL 113
           Y  +K  + Q     P   G + +  A +G+GKT      C    Q +  G  + + + L
Sbjct: 244 YETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGR-KAKVVFL 302

Query: 114 APTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLR 173
           A    + +Q + V +   +  G  V    G          +     ++V TP  + +   
Sbjct: 303 ATKVPVYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFE 362

Query: 174 RQSLRP-DNIRIFVLDEADEMLSRGFKDQIYDIFQLLP-----PKIQVGVFSATMPPEAL 227
             +L       + + DE          + +   +            Q+   +A++     
Sbjct: 363 DGTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQKFNSASQLPQILGLTASVGVGNA 422

Query: 228 EITRKFM--------NKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETL--- 276
           +   + +           ++ +    E   E  +  +            + + +  +   
Sbjct: 423 KNIEETIEHICSLCSYLDIQAISTVRENIQELQRFMNKPEIDVRLVKRRIHNPFAAIISN 482

Query: 277 AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRD-IIMREFRSGSSRVLITT 335
            ++++   + T   VD L+   +    T +  H  +    +  ++  E +   SR+    
Sbjct: 483 LMSETEALMRTIYSVDTLSQNSKKDFGTQNYEHWIVVTQRKCRLLQLEDKEEESRICRAL 542

Query: 336 DLLARGIDVQQVSLVINYDLP-TQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQ 394
            +    +     +L+I+ D       +YL     + + G        +T   +    ++ 
Sbjct: 543 FICTEHLRKYNDALIISEDARIIDALSYLTEFFTNVKNGPYTELEQHLTAKFQEKEPELI 602

Query: 395 KFYNVVIEELP 405
                   E P
Sbjct: 603 ALSKDETNENP 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 = 61.5 bits (148), Expect = 2e-10
 Identities = 31/169 (18%), Positives = 57/169 (33%), Gaps = 15/169 (8%)

Query: 232 KFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKV 291
           +          +++   +   K       K E  +  L D Y     T++++F  TR  V
Sbjct: 344 ELEQHLTAKFQEKEPELIALSKDETNENPKLEELVCILDDAYRYNPQTRTLLFAKTRALV 403

Query: 292 DWLTDKMRS------------RDHTVSATHGDMDQNTRDIIMREFRSGSS-RVLITTDLL 338
             L   M                         M   ++  ++  F++    R+LI T + 
Sbjct: 404 SALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVA 463

Query: 339 ARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDE 387
             GID+ Q +LV+ Y+        +   GR GR       I   ++ + 
Sbjct: 464 DEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-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 = 46.5 bits (109), Expect = 1e-05
 Identities = 46/366 (12%), Positives = 113/366 (30%), Gaps = 21/366 (5%)

Query: 61  KPSAIQQRGIVPFCKGLDVIQQAQSGTGKT--ATFCSGILQQLDYGLVECQALVLAPTRE 118
           K  + Q     P   G + +  A +G+GKT  +        Q      + + + LA    
Sbjct: 7   KARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVP 66

Query: 119 LAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLR 178
           + +Q + V +   +  G  V    G          +     ++V TP  + +     +L 
Sbjct: 67  VYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLT 126

Query: 179 P-DNIRIFVLDEA-----DEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRK 232
                 + + DE      +   +      +   F       Q+   +A++     +   +
Sbjct: 127 SLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQKFNSASQLPQILGLTASVGVGNAKNIEE 186

Query: 233 FM--------NKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETL---AITQS 281
            +           ++ +    E   E  +  +            + + +  +    ++++
Sbjct: 187 TIEHICSLCSYLDIQAISTVRENIQELQRFMNKPEIDVRLVKRRIHNPFAAIISNLMSET 246

Query: 282 VIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRD-IIMREFRSGSSRVLITTDLLAR 340
              + T   VD L+   +    T +  H  +    +  ++  E +   SR+     +   
Sbjct: 247 EALMRTIYSVDTLSQNSKKDFGTQNYEHWIVVTQRKCRLLQLEDKEEESRICRALFICTE 306

Query: 341 GIDVQQVSLVINYDLPTQPE-NYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNV 399
            +     +L+I+ D       +YL     + + G        +T   +    ++      
Sbjct: 307 HLRKYNDALIISEDARIIDALSYLTEFFTNVKNGPYTELEQHLTAKFQEKEPELIALSKD 366

Query: 400 VIEELP 405
              E P
Sbjct: 367 ETNENP 372

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus} Length = 555

 Score = 59.5 bits (143), Expect = 8e-10
 Identities = 40/178 (22%), Positives = 68/178 (38%), Gaps = 19/178 (10%)

Query: 228 EITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDL----YETLAITQSVI 283
           ++     ++  R L +R E  LE +++   +   E  KL  L  +    Y     T++++
Sbjct: 335 DVREAAFDETERELTRRFEEKLEELEKVSRDPSNENPKLRDLYLVLQEEYHLKPETKTIL 394

Query: 284 FVNTRRKVDWLTDKMRSR------------DHTVSATHGDMDQNTRDIIMREFR-SGSSR 330
           FV TR  VD L   +                   +     M    +  ++  FR SG + 
Sbjct: 395 FVKTRALVDALKKWIEENPALSFLKPGILTGRGRTNRATGMTLPAQKCVLEAFRASGDNN 454

Query: 331 VLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDER 388
           +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 = 50.3 bits (119), Expect = 7e-07
 Identities = 37/274 (13%), Positives = 84/274 (30%), Gaps = 22/274 (8%)

Query: 66  QQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQ--ALVLAPTRELAQQI 123
           Q    +P  KG + I  A +G GKT          L       +   +  A    + +Q 
Sbjct: 9   QLELALPAKKGKNTIICAPTGCGKTFVSLLICEHHLKKFPCGQKGKVVFFANQIPVYEQQ 68

Query: 124 EKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRP-DNI 182
             V     + LG  + +  G TS     + +     +++ TP  + + L   ++      
Sbjct: 69  ATVFSRYFERLGYNIASISGATSDSVSVQHIIEDNDIIILTPQILVNNLNNGAIPSLSVF 128

Query: 183 RIFVLDEADEMLSRGFKDQIYDIFQLLP------PKIQVGVFSATMPPEALEITRKFMNK 236
            + + DE          +QI   +          P  QV   +A++     +   + M  
Sbjct: 129 TLMIFDECHNTSKNHPYNQIMFRYLDHKLGESRDPLPQVVGLTASVGVGDAKTAEEAMQH 188

Query: 237 PVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTD 296
             ++    D   +  ++     +E+  +K + +     +             R  +    
Sbjct: 189 ICKLCAALDASVIATVRDNVAELEQVVYKPQKISRKVAS-------------RTSNTFKC 235

Query: 297 KMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSR 330
            +            D+ +    +   + R   ++
Sbjct: 236 IISQLMKETEKLAKDVSEELGKLFQIQNREFGTQ 269

>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 = 9e-08
 Identities = 29/129 (22%), Positives = 58/129 (44%), Gaps = 12/129 (9%)

Query: 282 VIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLA-- 339
           +I+  +++  + +T  +++      A H +++   +  + R++ +   +V++ T  +A  
Sbjct: 271 IIYCFSQKDSEQVTVSLQNLGIHAGAYHANLEPEDKTTVHRKWSANEIQVVVAT--VAFG 328

Query: 340 RGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDD----ERMLF---- 391
            GID   V  VI++ +    ENY    GR+GR   K   I +    D      M+     
Sbjct: 329 MGIDKPDVRFVIHHSMSKSMENYYQESGRAGRDDMKADCILYYGFGDIFRISSMVVMENV 388

Query: 392 DIQKFYNVV 400
             QK Y +V
Sbjct: 389 GQQKLYEMV 397

>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 = 50.2 bits (120), Expect = 2e-07
 Identities = 16/114 (14%), Positives = 38/114 (33%), Gaps = 9/114 (7%)

Query: 86  GTGKT---ATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACV 142
           G+GKT          L +        + +VL     L +Q+ +           +V    
Sbjct: 58  GSGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEFQPFLKKWYRVIGLS 117

Query: 143 GGTSVREDQRILSSGVHVVVGTPGRVFDML------RRQSLRPDNIRIFVLDEA 190
           G T ++     +     +++ T   + + L          ++  +  + ++DE 
Sbjct: 118 GDTQLKISFPEVVKSCDIIISTAQILENSLLNLENGEDAGVQLSDFSLIIIDEC 171

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A Length = 431

 Score = 51.4 bits (123), Expect = 3e-07
 Identities = 50/328 (15%), Positives = 92/328 (28%), Gaps = 70/328 (21%)

Query: 75  KGLDVIQQAQSGTGKTATFCSGILQQL--DYGLVECQALVLAPTRELAQQIEKVMRALGD 132
           K    +     G GKT      +L QL  +      + ++LAPTR +A    ++  AL  
Sbjct: 1   KRELTVLDLHPGAGKT-R---RVLPQLVREAVKKRLRTVILAPTRVVA---SEMYEALRG 53

Query: 133 YLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRP---DNIRIFVLDE 189
                    +   +        +    V              + L+     N  ++++DE
Sbjct: 54  EP-------IRYMTPAVQSER-TGNEIVDFMCHS----TFTMKLLQGVRVPNYNLYIMDE 101

Query: 190 A-----DEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKR 244
           A       + +RG+ +      ++          +AT P             P       
Sbjct: 102 AHFLDPASVAARGYIET-----RVSMGDAGAIFMTATPPGTTEAF-------PPSNSPII 149

Query: 245 DELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHT 304
           DE   E            EW  E              V FV++ ++   +   ++     
Sbjct: 150 DE---ETRIPDKAWNSGYEWITEFDGRT---------VWFVHSIKQGAEIGTCLQKAGKK 197

Query: 305 VSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARG--IDVQQV----SLVINYD---- 354
           V   +    ++       + +S     +ITTD+   G      +V      +        
Sbjct: 198 VLYLNRKTFES----EYPKCKSEKWDFVITTDISEMGANFKADRVIDPRKTIKPILLDGR 253

Query: 355 ---LPTQPENYLHRIGRSGRFGRKGVAI 379
                           R GR GR    +
Sbjct: 254 VSMQGPIAITPASAAQRRGRIGRNPEKL 281

>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: 282 VIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARG 341
           +I+ N+R KV+    +++S+  + +A H  ++ N R  +  +F+    ++++ T     G
Sbjct: 240 IIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMG 299

Query: 342 IDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERML 390
           I+   V  V+++D+P   E+Y    GR+GR G    A+ F    D   L
Sbjct: 300 INKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWL 348

>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 = 51.0 bits (122), Expect = 3e-07
 Identities = 48/325 (14%), Positives = 92/325 (28%), Gaps = 71/325 (21%)

Query: 75  KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQA-LVLAPTRELAQQIEKVMRALGDY 133
           K    I     G GKT      +   +   L+     L+LAPTR +A ++E+ +R L   
Sbjct: 18  KKRLTIMDLHPGAGKTKRI---LPSIVREALLRRLRTLILAPTRVVAAEMEEALRGLP-- 72

Query: 134 LGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRP---DNIRIFVLDEA 190
                   +   +           +  ++            + L      N  + V+DEA
Sbjct: 73  --------IRYQTPAVKSDHTGREIVDLM-CHA----TFTTRLLSSTRVPNYNLIVMDEA 119

Query: 191 -----DEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRD 245
                  + +RG+        ++   +      +AT  P          N P+  + +  
Sbjct: 120 HFTDPCSVAARGYIST-----RVEMGEAAAIFMTAT--PPGSTDPFPQSNSPIEDIEREI 172

Query: 246 ELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTV 305
                      +   +                  ++V FV + +  + + + +R     V
Sbjct: 173 PERSWNTGFDWITDYQG-----------------KTVWFVPSIKAGNDIANCLRKSGKRV 215

Query: 306 SATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARG--IDV-------QQVSLVINYD-- 354
                            + +      ++TTD+   G            + +  VI  D  
Sbjct: 216 IQLSRKTFDT----EYPKTKLTDWDFVVTTDISEMGANFRAGRVIDPRRCLKPVILTDGP 271

Query: 355 -----LPTQPENYLHRIGRSGRFGR 374
                    P        R GR GR
Sbjct: 272 ERVILAGPIPVTPASAAQRRGRIGR 296

>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 = 50.3 bits (120), Expect = 8e-07
 Identities = 54/321 (16%), Positives = 86/321 (26%), Gaps = 63/321 (19%)

Query: 75  KGLDVIQQAQSGTGKTATFCSGILQQL--DYGLVECQALVLAPTRELAQQIEKVMRALGD 132
           K    +     G GKT      IL Q+  D      +  VLAPTR            +  
Sbjct: 240 KRQLTVLDLHPGAGKT-R---RILPQIIKDAIQKRLRTAVLAPTR-----------VVAA 284

Query: 133 YLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRP---DNIRIFVLDE 189
            +   +            QR  S    V V         L  + + P    N  +FV+DE
Sbjct: 285 EMAEALRGLPVRYLTPAVQREHSGNEIVDVMCHA----TLTHRLMSPLRVPNYNLFVMDE 340

Query: 190 ADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTL 249
           A          + Y   ++   +      +AT P  +        N PV  +        
Sbjct: 341 AHFTDPASIAARGYIATRVEAGEAAAIFMTATPPGTSDPFPD--TNSPVHDVSSEIP--- 395

Query: 250 EGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATH 309
                        EW  +              V FV + +  + +   ++     V   +
Sbjct: 396 -----DRAWSSGFEWITDYAGKT---------VWFVASVKMSNEIAQCLQRAGKRVIQLN 441

Query: 310 GDMDQNTRDIIMREFRSGSSRVLITTDLLARG--IDV-------QQVSLVINYD------ 354
                        + ++G    +ITTD+   G            + V   I  +      
Sbjct: 442 RKSYDT----EYPKCKNGDWDFVITTDISEMGANFGASRVIDCRKSVKPTILDEGEGRVI 497

Query: 355 -LPTQPENYLHRIGRSGRFGR 374
                         R GR GR
Sbjct: 498 LSVPSAITSASAAQRRGRVGR 518

>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 = 49.6 bits (118), Expect = 1e-06
 Identities = 51/326 (15%), Positives = 86/326 (26%), Gaps = 73/326 (22%)

Query: 75  KGLDVIQQAQSGTGKTATFCSGILQQL-DYGLVECQA-LVLAPTRELAQQIEKVMRALGD 132
           K    I     G GKT      IL  +    L      L+LAPTR +A    ++  AL  
Sbjct: 185 KKRLTIMDLHPGAGKT----KRILPSIVREALKRRLRTLILAPTRVVA---AEMEEALRG 237

Query: 133 YLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRP---DNIRIFVLDE 189
                             +   +    V +            + L      N  + V+DE
Sbjct: 238 L--------PIRYQTPAVKSDHTGREIVDLMCHA----TFTTRLLSSTRVPNYNLIVMDE 285

Query: 190 -----ADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKR 244
                   + +RG+        ++   +      +AT  P          N P+      
Sbjct: 286 AHFTDPCSVAARGYIST-----RVEMGEAAAIFMTAT--PPGSTDPFPQSNSPI------ 332

Query: 245 DELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHT 304
               +E            +W  +              V FV + +  + + + +R     
Sbjct: 333 --EDIEREIPERSWNTGFDWITDYQGKT---------VWFVPSIKAGNDIANCLRKSGKR 381

Query: 305 VSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARG--IDV-------QQVSLVINYD- 354
           V                 + +      ++TTD+   G            + +  VI  D 
Sbjct: 382 VIQLSRKTFDT----EYPKTKLTDWDFVVTTDISEMGANFRAGRVIDPRRCLKPVILTDG 437

Query: 355 ------LPTQPENYLHRIGRSGRFGR 374
                     P        R GR GR
Sbjct: 438 PERVILAGPIPVTPASAAQRRGRIGR 463

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus} Length = 715

 Score = 49.7 bits (119), Expect = 1e-06
 Identities = 70/416 (16%), Positives = 142/416 (34%), Gaps = 86/416 (20%)

Query: 42  DAMGLQENLLRGIYAYGFEKPSAIQQRGIVP-FCKGLDVIQQAQSGTGKTATFCSGILQQ 100
           + + L  N++  I   G +K +  Q   +     +G  ++  + +G+GKT     GI+  
Sbjct: 11  EDLKLPSNVIEIIKKRGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGIISF 70

Query: 101 LDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHV 160
           L       +A+ + P R L  +     +     +G KV    G     +          +
Sbjct: 71  LLKN--GGKAIYVTPLRALTNEKYLTFKDWEL-IGFKVAMTSGDYDTDDAWL---KNYDI 124

Query: 161 VVGTPGRVFDMLRRQSLRPDNIRIFVLDE----ADEMLSRGFKDQIYDIFQLLPPKIQ-V 215
           ++ T  ++  + R +    + +  FVLDE     D    RG    + +   +   +   +
Sbjct: 125 IITTYEKLDSLWRHRPEWLNEVNYFVLDELHYLNDP--ERG---PVVESVTIRAKRRNLL 179

Query: 216 GVFSATMP-PEALEITRKFMNK--------PVRI---LVKRDELTLEGIKQFHVNVEKEE 263
            + SAT+   + +    K++          PV +   ++  +    E    F  N  K+ 
Sbjct: 180 AL-SATISNYKQIA---KWLGAEPVATNWRPVPLIEGVIYPERKKKEYNVIFKDNTTKKV 235

Query: 264 WKLETLCDL-YETLAITQSV-IFVNTRR----------------------------KVDW 293
              + +     ++L+    V +F N+R+                            ++D 
Sbjct: 236 HGDDAIIAYTLDSLSKNGQVLVFRNSRKMAESTALKIANYMNFVSLDENALSEILKQLDD 295

Query: 294 LTDKMRSRDHTVSAT--------HGDMDQNTRDIIMREFRSGSSRVLITTDLLA------ 339
           + +        + +         H  + +  RD+I   FR    +V++ T  LA      
Sbjct: 296 IEEGGSDEKELLKSLISKGVAYHHAGLSKALRDLIEEGFRQRKIKVIVATPTLAAGVNLP 355

Query: 340 ------RGIDVQQVSLVINYDLPTQPENYLHRIGRSGR--FGRKGVAINFVTRDDE 387
                   I      +   YD       Y    GR+GR  F + G +I  V   ++
Sbjct: 356 ARTVIIGDIYRFNKKIAGYYD-EIPIMEYKQMSGRAGRPGFDQIGESIVVVRDKED 410

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4} Length = 510

 Score = 48.4 bits (114), Expect = 2e-06
 Identities = 49/341 (14%), Positives = 101/341 (29%), Gaps = 42/341 (12%)

Query: 61  KPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELA 120
           +P   Q+  +         I    +  G++          L+    E + L++ PT  L 
Sbjct: 113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENY--EGKILIIVPTTALT 170

Query: 121 QQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPD 180
            Q+         +    +    GG           +   VVVGT   V    ++      
Sbjct: 171 TQMADDFVDYRLFSHAMIKKIGGG---ASKDDKYKNDAPVVVGTWQTVV---KQPKEWFS 224

Query: 181 NIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMN-KPVR 239
              + + DE            I  I   L   +     S ++      I +       + 
Sbjct: 225 QFGMMMNDECHLATG----KSISSIISGLNNCMFKFGLSGSLRDGKANIMQYVGMFGEIF 280

Query: 240 ILVKRDELTLEG---------IKQFHVNVEKEEWKLETLCDLYETLAITQ---------- 280
             V   +L  +G         I   + +    + K +T  +  + +              
Sbjct: 281 KPVTTSKLMEDGQVTELKINSIFLRYPDEFTTKLKGKTYQEEIKIITGLSKRNKWIAKLA 340

Query: 281 ---------SVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRV 331
                    + +          + D +++    V    G++D  TR+I+     +G   +
Sbjct: 341 IKLAQKDENAFVMFKHVSHGKAIFDLIKNEYDKVYYVSGEVDTETRNIMKTLAENGKGII 400

Query: 332 LITT-DLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGR 371
           ++ +  + + GI V+ +  V+           L  IGR  R
Sbjct: 401 IVASYGVFSTGISVKNLHHVVLAHGVKSKIIVLQTIGRVLR 441

>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 = 47.1 bits (112), Expect = 6e-06
 Identities = 42/326 (12%), Positives = 95/326 (29%), Gaps = 86/326 (26%)

Query: 86  GTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGT 145
           G+GKT    + I +      +    L++ PT  LA+Q ++ +   G+    +      G 
Sbjct: 118 GSGKTHVAMAAINE------LSTPTLIVVPTLALAEQWKERLGIFGE----EYVGEFSGR 167

Query: 146 SVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFK------ 199
                         + V T    +    +   R   +   + DE   + +  +       
Sbjct: 168 IKELKP--------LTVSTYDSAYVNAEKLGNRFMLL---IFDEVHHLPAESYVQIAQMS 216

Query: 200 ----------------DQIYDIFQLLPPKI----------------QVGVFSATMPPEAL 227
                            +   + +++  K+                 +      +  +  
Sbjct: 217 IAPFRLGLTATFEREDGRHEILKEVVGGKVFELFPDSLAGKHLAKYTIKRIFVPLAEDER 276

Query: 228 EITRKFMNKPVRILVKRDE--LTLEGIKQFHVNVEKEEW--------------------K 265
               K      + L  R       E   +  +    +E                     K
Sbjct: 277 VEYEKREKVYKQFLRARGITLRRAEDFNKIVMASGYDERAYEALRAWEEARRIAFNSKNK 336

Query: 266 LETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFR 325
           +  L ++ E     + +IF      V  ++         + A      +  R+ I+  FR
Sbjct: 337 IRKLREILERHRKDKIIIFTRHNELVYRISKVFL-----IPAITHRTSREEREEILEGFR 391

Query: 326 SGSSRVLITTDLLARGIDVQQVSLVI 351
           +G  R ++++ +L  GIDV   ++ +
Sbjct: 392 TGRFRAIVSSQVLDEGIDVPDANVGV 417

>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 = 46.0 bits (109), Expect = 2e-05
 Identities = 56/318 (17%), Positives = 93/318 (29%), Gaps = 65/318 (20%)

Query: 79  VIQQAQSGTGKTATFCSGILQQL-DYGLVECQA-LVLAPTRELAQQIEKVMRALGDYLGV 136
            +     G+GKT      IL Q+    + +     VLAPTR +A    ++  AL    G+
Sbjct: 24  TVLDLHPGSGKT----RKILPQIIKDAIQQRLRTAVLAPTRVVA---AEMAEALR---GL 73

Query: 137 KVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRP---DNIRIFVLDEADEM 193
            V            QR       V V         L  + + P    N  +FV+DEA   
Sbjct: 74  PV-----RYQTSAVQREHQGNEIVDVMCHA----TLTHRLMSPNRVPNYNLFVMDEAHFT 124

Query: 194 LSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEI-TRKFMNKPVRILVKRDELTLEGI 252
                  + Y   ++   +      +AT P                 I   +DE+     
Sbjct: 125 DPASIAARGYIATKVELGEAAAIFMTATPPGTTDPFPDSNA-----PIHDLQDEIPDRAW 179

Query: 253 KQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDM 312
              +  + +   K                V FV + +  + +   ++     V   +   
Sbjct: 180 SSGYEWITEYAGKT---------------VWFVASVKMGNEIAMCLQRAGKKVIQLNRKS 224

Query: 313 DQNTRDIIMREFRSGSSRVLITTDLLARG--IDV-------QQVSLVINYD-------LP 356
                     + ++G    +ITTD+   G            + V   I  +         
Sbjct: 225 YDT----EYPKCKNGDWDFVITTDISEMGANFGASRVIDCRKSVKPTILEEGEGRVILGN 280

Query: 357 TQPENYLHRIGRSGRFGR 374
             P        R GR GR
Sbjct: 281 PSPITSASAAQRRGRVGR 298

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A Length = 677

 Score = 44.2 bits (103), Expect = 6e-05
 Identities = 26/187 (13%), Positives = 61/187 (32%), Gaps = 20/187 (10%)

Query: 234 MNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDW 293
               V  L+      +E      +           L  L         V F  ++  +  
Sbjct: 280 AIDLVMELMYTTGEEVEVRDYKRLT--PISVLDHALESLDNLRPGDCIVCF--SKNDIYS 335

Query: 294 LTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRV--LITTDLLARGIDVQQVSLVI 351
           ++ ++  R    +  +G +   T+    ++F   +     L+ TD +  G+++    ++ 
Sbjct: 336 VSRQIEIRGLESAVIYGSLPPGTKLAQAKKFNDPNDPCKILVATDAIGMGLNLSIRRIIF 395

Query: 352 N----YDLPTQPENYLHRI---------GRSGRFGRKGVAINFVTRDDERMLFDIQKFYN 398
                  +  + E  L  I         GR+GRF  +      VT  +   L  +++   
Sbjct: 396 YSLIKPSINEKGERELEPITTSQALQIAGRAGRFSSRF-KEGEVTTMNHEDLSLLKEILK 454

Query: 399 VVIEELP 405
             ++ + 
Sbjct: 455 RPVDPIR 461

>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 = 41.6 bits (98), Expect = 5e-04
 Identities = 59/290 (20%), Positives = 102/290 (35%), Gaps = 58/290 (20%)

Query: 83  AQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACV 142
           A +G GKT +F  G+   L   L   +  V+ PT  L  Q  + +R   +  GV     +
Sbjct: 78  APTGVGKT-SF--GLAMSLFLALKGKRCYVIFPTSLLVIQAAETIRKYAEKAGVGTENLI 134

Query: 143 G------GTSVREDQRILSSGVHVVVGTPG---RVFDMLRRQSLRPDNIRIFVLDEADEM 193
           G          +E+         +V+ T     + +  L           IFV D+ D +
Sbjct: 135 GYYHGRIPKREKENFMQNLRNFKIVITTTQFLSKHYRELGHFDF------IFV-DDVDAI 187

Query: 194 L--SR---------GFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILV 242
           L  S+         GF   +     +   +  + V +AT              K  +  +
Sbjct: 188 LKASKNVDKLLHLLGFHYDLKTKSWVGEARGCLMVSTAT------------AKKGKKAEL 235

Query: 243 KRDELTLE-GIKQFHV-NVE---KEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDK 297
            R  L  + G  +  V NVE     +  + TL  + E L  T  +I+  T  + + + + 
Sbjct: 236 FRQLLNFDIGSSRITVRNVEDVAVNDESISTLSSILEKLG-TGGIIYARTGEEAEEIYES 294

Query: 298 MRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITT----DLLARGID 343
           ++++      T        +     +F  G    LI T      L RG+D
Sbjct: 295 LKNKFRIGIVTAT------KKGDYEKFVEGEIDHLIGTAHYYGTLVRGLD 338

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae} Length = 1010

 Score = 40.5 bits (94), Expect = 8e-04
 Identities = 38/171 (22%), Positives = 62/171 (36%), Gaps = 19/171 (11%)

Query: 55  YAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKT--ATFCSGILQQLDYGLVECQALV 112
             Y F      Q   I    +G  V+  A +  GKT  A +   I Q L       + + 
Sbjct: 81  RTYPFT-LDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEY--AIAQSLKNK---QRVIY 134

Query: 113 LAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDML 172
            +P + L+ Q  + + A    +G+      G  ++  D          +V T   +  ML
Sbjct: 135 TSPIKALSNQKYRELLAEFGDVGL----MTGDITINPDA-------GCLVMTTEILRSML 183

Query: 173 RRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMP 223
            R S     +   + DE   M  +       +   LLP K++    SAT+P
Sbjct: 184 YRGSEVMREVAWVIFDEVHYMRDKERGVVWEETIILLPDKVRYVFLSATIP 234

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	412
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	100.0
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	100.0
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	100.0
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	100.0
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	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
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	100.0
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	100.0
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	100.0
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	100.0
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	100.0
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	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
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	100.0
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	100.0
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	100.0
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	100.0
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	100.0
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	100.0
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	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
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	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
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	100.0
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	100.0
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	100.0
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	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
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
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	100.0
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	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
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	100.0
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	100.0
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	100.0
1yks_A	440	Genome polyprotein [contains: flavivirin protease	100.0
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	100.0
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	100.0
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	100.0
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	100.0
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	100.0
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	100.0
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	100.0
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	100.0
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	100.0
3bor_A	237	Human initiation factor 4A-II; translation initiat	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
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	100.0
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	100.0
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	100.0
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	100.0
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	100.0
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	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
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	99.98
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	99.98
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	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
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	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
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	99.95
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	99.95
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	99.94
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
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	99.86
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	99.91
3b6e_A	216	Interferon-induced helicase C domain-containing P;	99.91
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	99.9
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	99.88
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	99.85
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	99.84
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	99.83
1z5z_A	271	Helicase of the SNF2/RAD54 family; hydrolase, reco	99.77
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	98.79
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	98.63
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	98.56
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	98.54
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	98.51
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	98.5
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	98.48
3lfu_A	647	DNA helicase II; SF1 helicase, ATP-binding, DNA da	98.34
3hgt_A	328	HDA1 complex subunit 3; RECA-like domain, SWI2/SNF	98.05
2o0j_A	385	Terminase, DNA packaging protein GP17; nucleotide-	97.7
3cpe_A	592	Terminase, DNA packaging protein GP17; large termi	97.51
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	97.41
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	97.38
1uaa_A	673	REP helicase, protein (ATP-dependent DNA helicase	97.35
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	97.35
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	97.28
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	97.23
2orv_A	234	Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2	97.22
1pjr_A	724	PCRA; DNA repair, DNA replication, SOS response, h	97.14
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	97.14
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	97.1
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	97.09
2chg_A	226	Replication factor C small subunit; DNA-binding pr	97.06
3e2i_A	219	Thymidine kinase; Zn-binding, ATP-binding, DNA syn	97.05
3u4q_A	1232	ATP-dependent helicase/nuclease subunit A; helicas	97.04
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	97.0
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	96.89
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	96.79
3co5_A	143	Putative two-component system transcriptional RES	96.71
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	96.69
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	96.5
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	96.48
2zpa_A	671	Uncharacterized protein YPFI; RNA modification enz	96.46
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	96.34
3bos_A	242	Putative DNA replication factor; P-loop containing	96.27
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	96.24
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	96.19
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	96.17
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	96.13
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	96.12
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	96.06
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	95.99
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	95.98
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	95.96
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	95.85
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	95.75
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	95.63
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	95.56
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	95.5
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	95.34
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	95.27
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	95.26
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	95.19
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	95.02
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	94.6
2chq_A	319	Replication factor C small subunit; DNA-binding pr	94.55
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	94.53
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	94.49
3pvs_A	447	Replication-associated recombination protein A; ma	94.47
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	94.25
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	94.18
2r6a_A	454	DNAB helicase, replicative helicase; replication,	93.89
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	93.79
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	93.67
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	93.43
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	93.28
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	93.19
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	93.08
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	92.88
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	92.79
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	92.64
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	92.55
3hjh_A	483	Transcription-repair-coupling factor; MFD, mutatio	91.89
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	91.33
2fna_A	357	Conserved hypothetical protein; structural genomic	90.86
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	90.76
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	90.67
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	90.25
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	90.23
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	89.92
2qgz_A	308	Helicase loader, putative primosome component; str	89.86
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	89.64
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	89.54
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	89.45
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	89.32
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	89.08
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	89.07
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	89.01
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	88.86
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	88.58
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	88.42
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	88.37
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	88.32
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	88.04
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	87.91
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	87.58
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	87.38
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	87.34
3u4q_B	1166	ATP-dependent helicase/deoxyribonuclease subunit;	87.1
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	87.04
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	86.93
1p9r_A	418	General secretion pathway protein E; bacterial typ	86.84
2ius_A	512	DNA translocase FTSK; nucleotide-binding, chromoso	86.6
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	86.57
2l82_A	162	Designed protein OR32; structural genomics, northe	86.56
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	86.54
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	86.38
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	86.35
1sky_E	473	F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alp	86.34
2eyu_A	261	Twitching motility protein PILT; pilus retraction	86.3
1e9r_A	437	Conjugal transfer protein TRWB; coupling protein,	86.17
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	86.06
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	86.04
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	85.96
2cvh_A	220	DNA repair and recombination protein RADB; filamen	85.94
1w36_B	1180	RECB, exodeoxyribonuclease V beta chain; recombina	85.93
3bor_A	237	Human initiation factor 4A-II; translation initiat	85.91
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	85.89
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	85.83
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	85.71
2l8b_A	189	Protein TRAI, DNA helicase I; RECD, hydrolase; NMR	85.64
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	85.61
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	85.48
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	85.45
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	85.39
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	85.25
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	85.06
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	85.01
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	85.0
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	84.76
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	84.69
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	84.59
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	84.53
2z43_A	324	DNA repair and recombination protein RADA; archaea	84.46
4ag6_A	392	VIRB4 ATPase, type IV secretory pathway VIRB4 comp	84.42
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	84.39
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	84.34
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	84.33
2r44_A	331	Uncharacterized protein; putative ATPase, structur	83.89
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	83.75
2iut_A	574	DNA translocase FTSK; nucleotide-binding, chromoso	83.65
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	83.63
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	83.59
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	83.55
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	83.52
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	83.48
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	83.46
1u94_A	356	RECA protein, recombinase A; homologous recombinat	83.36
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	83.3
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	83.19
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	83.16
1tue_A	212	Replication protein E1; helicase, replication, E1E	83.05
2r2a_A	199	Uncharacterized protein; zonular occludens toxin,	82.92
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	82.88
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	82.84
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	82.84
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	82.79
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	82.7
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	82.61
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	82.57
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	82.52
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	82.36
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	82.26
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	82.15
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	82.14
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	82.08
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	82.06
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	82.05
2ewv_A	372	Twitching motility protein PILT; pilus retraction	82.04
3io5_A	333	Recombination and repair protein; storage dimer, i	82.01
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	81.96
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	81.72
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	81.67
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	81.61
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	81.46
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	81.26
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	81.22
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	81.18
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	81.15
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	81.1
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	80.78
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	80.71
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	80.65
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	80.61
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	80.6
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	80.58
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	80.55
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	80.53
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	80.53
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	80.51
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	80.47
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	80.14
1xp8_A	366	RECA protein, recombinase A; recombination, radior	80.13
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	80.06

>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=3.1e-60  Score=446.57  Aligned_cols=373  Identities=32%  Similarity=0.516  Sum_probs=337.2

Q ss_pred             hccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCC-----CceeEE
Q 015158           37 VYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGL-----VECQAL  111 (412)
Q Consensus        37 ~~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~-----~~~~~l  111 (412)
                      +..+|+++++++.+.+.+...||..|+|+|+++++.+++|+++++++|||||||++|+++++..+....     .++++|
T Consensus        54 ~~~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~ai~~i~~g~d~i~~a~TGsGKT~a~~lpil~~l~~~~~~~~~~~~~~l  133 (434)
T 2db3_A           54 PIQHFTSADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPILSKLLEDPHELELGRPQVV  133 (434)
T ss_dssp             CCCCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHSCCCCCTTCCSEE
T ss_pred             CcCChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEECCCCCCchHHHHHHHHHHHHhcccccccCCccEE
Confidence            466899999999999999999999999999999999999999999999999999999999998775432     356899


Q ss_pred             EEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCc
Q 015158          112 VLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEAD  191 (412)
Q Consensus       112 il~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h  191 (412)
                      |++|+++|+.|+.+++.++....++.+..++|+............+++|+|+||++|.+.+.+....+.+++++|+||||
T Consensus       134 il~PtreLa~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Ivv~Tp~~l~~~l~~~~~~l~~~~~lVlDEah  213 (434)
T 2db3_A          134 IVSPTRELAIQIFNEARKFAFESYLKIGIVYGGTSFRHQNECITRGCHVVIATPGRLLDFVDRTFITFEDTRFVVLDEAD  213 (434)
T ss_dssp             EECSSHHHHHHHHHHHHHHTTTSSCCCCEECTTSCHHHHHHHHTTCCSEEEECHHHHHHHHHTTSCCCTTCCEEEEETHH
T ss_pred             EEecCHHHHHHHHHHHHHHhccCCcEEEEEECCCCHHHHHHHhhcCCCEEEEChHHHHHHHHhCCcccccCCeEEEccHh
Confidence            99999999999999999998877888889999988777766677789999999999999998888888999999999999


Q ss_pred             hhhccCcHHHHHHHHHhC--CCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhHHHH
Q 015158          192 EMLSRGFKDQIYDIFQLL--PPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETL  269 (412)
Q Consensus       192 ~~~~~~~~~~~~~i~~~~--~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  269 (412)
                      ++.+++|...+..++..+  ++..+++++|||++.........++..+..+...........+.+.+..... ..+...+
T Consensus       214 ~~~~~gf~~~~~~i~~~~~~~~~~q~l~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~i~~~~~~~~~-~~k~~~l  292 (434)
T 2db3_A          214 RMLDMGFSEDMRRIMTHVTMRPEHQTLMFSATFPEEIQRMAGEFLKNYVFVAIGIVGGACSDVKQTIYEVNK-YAKRSKL  292 (434)
T ss_dssp             HHTSTTTHHHHHHHHHCTTSCSSCEEEEEESCCCHHHHHHHHTTCSSCEEEEESSTTCCCTTEEEEEEECCG-GGHHHHH
T ss_pred             hhhccCcHHHHHHHHHhcCCCCCceEEEEeccCCHHHHHHHHHhccCCEEEEeccccccccccceEEEEeCc-HHHHHHH
Confidence            999999999999998875  5688999999999999988888889888888877766666677777776655 4577788


Q ss_pred             HHHHHhcCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCE
Q 015158          270 CDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSL  349 (412)
Q Consensus       270 ~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~  349 (412)
                      .+++..... ++||||++++.++.+++.|.+.++.+..+||+++..+|..+++.|++|+.+|||||+++++|+|+|++++
T Consensus       293 ~~~l~~~~~-~~lVF~~t~~~a~~l~~~L~~~~~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT~v~~rGlDi~~v~~  371 (434)
T 2db3_A          293 IEILSEQAD-GTIVFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATSVASRGLDIKNIKH  371 (434)
T ss_dssp             HHHHHHCCT-TEEEECSSHHHHHHHHHHHHHTTCCEEEESTTSCHHHHHHHHHHHHTSSCSEEEECGGGTSSCCCTTCCE
T ss_pred             HHHHHhCCC-CEEEEEeCcHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHHHcCCCcEEEEchhhhCCCCcccCCE
Confidence            888887654 5999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEccCCCChhhHHHhhhhcccCCCCceEEEEecc-CcHHHHHHHHHHhccccccCChhhhhc
Q 015158          350 VINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTR-DDERMLFDIQKFYNVVIEELPANVADL  411 (412)
Q Consensus       350 vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~l  411 (412)
                      ||+++.|.+..+|+||+||+||.|+.|.+++|+++ .+...+..+.+.++...+++|++|.++
T Consensus       372 VI~~d~p~~~~~y~qriGR~gR~g~~G~a~~~~~~~~~~~~~~~l~~~l~~~~~~vp~~l~~~  434 (434)
T 2db3_A          372 VINYDMPSKIDDYVHRIGRTGRVGNNGRATSFFDPEKDRAIAADLVKILEGSGQTVPDFLRTC  434 (434)
T ss_dssp             EEESSCCSSHHHHHHHHTTSSCTTCCEEEEEEECTTTCGGGHHHHHHHHHHTTCCCCGGGC--
T ss_pred             EEEECCCCCHHHHHHHhcccccCCCCCEEEEEEeccccHHHHHHHHHHHHHcCCCCCHHHHhC
Confidence            99999999999999999999999999999999994 577888999999999999999998753

>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation, rRNA processing, mRNA splicing, mRNA transport; HET: ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B 2zu6_A

Probab=100.00  E-value=1.5e-60  Score=447.84  Aligned_cols=377  Identities=68%  Similarity=1.073  Sum_probs=348.0

Q ss_pred             hhccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcC
Q 015158           36 EVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAP  115 (412)
Q Consensus        36 ~~~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P  115 (412)
                      ....+|+++++++.+.+.+..+||..|+++|+++++.+++++++++.+|||+|||++++++++..+.....+.++||++|
T Consensus        34 ~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~ai~~i~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~P  113 (410)
T 2j0s_A           34 DVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAP  113 (410)
T ss_dssp             CCCCSGGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTTSCSCCEEEECS
T ss_pred             cCCCCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCCCchHHHHHHHHHHHhhccCCceEEEEcC
Confidence            34568999999999999999999999999999999999999999999999999999999999988765556679999999


Q ss_pred             CHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhc
Q 015158          116 TRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLS  195 (412)
Q Consensus       116 ~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~  195 (412)
                      +++|+.|+.+.+..+....++.+..+.|+.....+......+++|+|+||+.+...+.+......++++||+||||++.+
T Consensus       114 t~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~ivv~Tp~~l~~~l~~~~~~~~~~~~vViDEah~~~~  193 (410)
T 2j0s_A          114 TRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLN  193 (410)
T ss_dssp             SHHHHHHHHHHHHHHTTTTTCCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHTS
T ss_pred             cHHHHHHHHHHHHHHhccCCeEEEEEECCCCHHHHHHHhhcCCCEEEcCHHHHHHHHHhCCccHhheeEEEEccHHHHHh
Confidence            99999999999999988888899999998887776666667789999999999999988877888999999999999999


Q ss_pred             cCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhHHHHHHHHHh
Q 015158          196 RGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYET  275 (412)
Q Consensus       196 ~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  275 (412)
                      +++...+..+...+++..+++++|||++.........++..+..+...........+...+........+...+.+++..
T Consensus       194 ~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~~~~  273 (410)
T 2j0s_A          194 KGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDT  273 (410)
T ss_dssp             TTTHHHHHHHHTTSCTTCEEEEEESCCCHHHHTTGGGTCSSCEEECCCGGGCSCTTEEEEEEEESSTTHHHHHHHHHHHH
T ss_pred             hhhHHHHHHHHHhCccCceEEEEEcCCCHHHHHHHHHHcCCCEEEEecCccccCCCceEEEEEeCcHHhHHHHHHHHHHh
Confidence            99999999999999999999999999998887777888888888777777777778888888887777788899999988


Q ss_pred             cCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccC
Q 015158          276 LAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDL  355 (412)
Q Consensus       276 ~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~  355 (412)
                      ...+++||||++++.++.+++.|.+.+..+..+||+++..+|..+++.|++|+.+|||+|+++++|+|+|++++||+++.
T Consensus       274 ~~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~v~~Vi~~~~  353 (410)
T 2j0s_A          274 LTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDL  353 (410)
T ss_dssp             HTSSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHHTSSCEEEECGGGSSSCCCTTEEEEEESSC
T ss_pred             cCCCcEEEEEcCHHHHHHHHHHHHhCCCceEEeeCCCCHHHHHHHHHHHHCCCCCEEEECChhhCcCCcccCCEEEEECC
Confidence            88889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHHhccccccCChhhhhcC
Q 015158          356 PTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVADLL  412 (412)
Q Consensus       356 ~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  412 (412)
                      |++...|.||+||+||.|++|.+++++++.+...++.++++++.+++++|.+..+++
T Consensus       354 p~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~  410 (410)
T 2j0s_A          354 PNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVADLI  410 (410)
T ss_dssp             CSSHHHHHHHHTTSSGGGCCEEEEEEEEGGGHHHHHHHHHHTTCCCEECCSCCTTTC
T ss_pred             CCCHHHHHHhcccccCCCCceEEEEEecHHHHHHHHHHHHHhCCCceecccchhhcC
Confidence            999999999999999999999999999999999999999999999999998887764

>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=4.9e-60  Score=445.14  Aligned_cols=384  Identities=72%  Similarity=1.115  Sum_probs=334.6

Q ss_pred             CCCCChhhhccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCce
Q 015158           29 DFFTSYDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVEC  108 (412)
Q Consensus        29 ~~~~~~~~~~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~  108 (412)
                      .....+.....+|+.+++++.+.+.+..+++..|+++|+++++.+++++++++.+|||+|||++++++++..+.....+.
T Consensus        30 ~~~~~~~~~~~~f~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~~~~~  109 (414)
T 3eiq_A           30 VIESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDLKAT  109 (414)
T ss_dssp             CCCCCCCCCCCCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEECCCSCSSSHHHHHHHHHHHCCTTSCSC
T ss_pred             ccCCCccchhcCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHhHHHhCCCCEEEECCCCCcccHHHHHHHHHHHhhcCCce
Confidence            34455667778999999999999999999999999999999999999999999999999999999999998887655667


Q ss_pred             eEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhc-CCCcEEEeChHHHHHHHHcCCCCCCCceEEEE
Q 015158          109 QALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILS-SGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVL  187 (412)
Q Consensus       109 ~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~iii~T~~~l~~~~~~~~~~~~~~~~iii  187 (412)
                      +++|++|+++|+.|+.+.+..+....+..+....|+........... ..++|+|+||++|.+.+.+..+...++++||+
T Consensus       110 ~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~l~~~~~~~~~~~~vVi  189 (414)
T 3eiq_A          110 QALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVL  189 (414)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHGGGSCCCEEECCCCTTHHHHHHHHTTTCCSEEEECHHHHHHHHHHTSSCSTTCCEEEE
T ss_pred             eEEEEeChHHHHHHHHHHHHHHhcccCceEEEEECCcchHHHHHHHhcCCCCEEEECHHHHHHHHHcCCcccccCcEEEE
Confidence            89999999999999999999998888888888888877655544433 67899999999999999888777888999999


Q ss_pred             eCCchhhccCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhHH
Q 015158          188 DEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLE  267 (412)
Q Consensus       188 DE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  267 (412)
                      ||||++.++++...+..++..++++.+++++|||++.........++..+..+...........+...+........+..
T Consensus       190 DEah~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  269 (414)
T 3eiq_A          190 DEADEMLSRGFKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLD  269 (414)
T ss_dssp             CSHHHHHHTTTHHHHHHHHTTSCTTCEEEEECSCCCHHHHHHHTTTCSSCEEECCCCCCCCTTSCCEEEEECSSSTTHHH
T ss_pred             ECHHHhhccCcHHHHHHHHHhCCCCCeEEEEEEecCHHHHHHHHHHcCCCEEEEecCCccCCCCceEEEEEeChHHhHHH
Confidence            99999999999999999999999999999999999999888888899999888887777778888888888888788899


Q ss_pred             HHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCC
Q 015158          268 TLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQV  347 (412)
Q Consensus       268 ~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~  347 (412)
                      .+.+++.....+++||||++++.++.+++.|.+.+..+..+||+++..+|..+++.|++|+.+|||+|+++++|+|+|++
T Consensus       270 ~l~~~~~~~~~~~~lvf~~~~~~~~~l~~~l~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidip~v  349 (414)
T 3eiq_A          270 TLCDLYETLTITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQV  349 (414)
T ss_dssp             HHHHHHHSSCCSSCEEECSCHHHHHHHHHHHHTTTCCCEEC---CHHHHHHHHHHHHSCC---CEEECSSCC--CCGGGC
T ss_pred             HHHHHHHhCCCCcEEEEeCCHHHHHHHHHHHHhcCCeEEEecCCCCHHHHHHHHHHHHcCCCcEEEECCccccCCCccCC
Confidence            99999999888999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHHhccccccCChhhhhcC
Q 015158          348 SLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVADLL  412 (412)
Q Consensus       348 ~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  412 (412)
                      ++||+++.|+|...|.||+||+||.|++|.|++++++.+...++.++++++..++++|.++.+||
T Consensus       350 ~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  414 (414)
T 3eiq_A          350 SLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTEEDKRTLRDIETFYNTSIEEMPLNVADLI  414 (414)
T ss_dssp             SCEEESSCCSSTHHHHHHSCCC-------CEEEEECSTHHHHHHHHHHHTTCCCEECCC------
T ss_pred             CEEEEeCCCCCHHHhhhhcCcccCCCCCceEEEEEcHHHHHHHHHHHHHHcCCccccChhhhhcC
Confidence            99999999999999999999999999999999999999999999999999999999999998876

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=100.00  E-value=2.6e-58  Score=433.72  Aligned_cols=375  Identities=34%  Similarity=0.509  Sum_probs=330.8

Q ss_pred             hhccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCC----------
Q 015158           36 EVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGL----------  105 (412)
Q Consensus        36 ~~~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~----------  105 (412)
                      .+..+|+++++++.+.+.|...||..|+|+|.++++.++.++++++.+|||+|||++|+++++..+....          
T Consensus        12 ~~~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~~~~~~~~~~~~~   91 (417)
T 2i4i_A           12 PHIESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYSDGPGEALRAMKE   91 (417)
T ss_dssp             CCCSSGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHHCCCHHHHHHHH
T ss_pred             cccCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHccCCCEEEEcCCCCHHHHHHHHHHHHHHHhccccchhhcccc
Confidence            3445799999999999999999999999999999999999999999999999999999999987764321          


Q ss_pred             --------CceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCC
Q 015158          106 --------VECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSL  177 (412)
Q Consensus       106 --------~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~  177 (412)
                              ..+++||++|+++|+.|+.+.+.++....++.+..++|+............+++|+|+||++|...+....+
T Consensus        92 ~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~  171 (417)
T 2i4i_A           92 NGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRPCVVYGGADIGQQIRDLERGCHLLVATPGRLVDMMERGKI  171 (417)
T ss_dssp             CBTTBSCSBCCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCHHHHHHHHTTCCSEEEECHHHHHHHHHTTSB
T ss_pred             ccccccccCCccEEEECCcHHHHHHHHHHHHHHhCcCCceEEEEECCCCHHHHHHHhhCCCCEEEEChHHHHHHHHcCCc
Confidence                    225799999999999999999999987778889999998887776666677889999999999999988877


Q ss_pred             CCCCceEEEEeCCchhhccCcHHHHHHHHHh--CCC--CceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCce
Q 015158          178 RPDNIRIFVLDEADEMLSRGFKDQIYDIFQL--LPP--KIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIK  253 (412)
Q Consensus       178 ~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~--~~~--~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  253 (412)
                      ...++++||+||||++.+++|...+..+...  ++.  ..+++++|||+++........++..+..+...........+.
T Consensus       172 ~~~~~~~iViDEah~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~  251 (417)
T 2i4i_A          172 GLDFCKYLVLDEADRMLDMGFEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGRVGSTSENIT  251 (417)
T ss_dssp             CCTTCCEEEESSHHHHHHTTCHHHHHHHHTSSSCCCBTTBEEEEEESCCCHHHHHHHHHHCSSCEEEEEC----CCSSEE
T ss_pred             ChhhCcEEEEEChhHhhccCcHHHHHHHHHhccCCCcCCcEEEEEEEeCCHHHHHHHHHHcCCCEEEEeCCCCCCccCce
Confidence            7889999999999999999999999998874  332  578999999999988888888888888777766666666777


Q ss_pred             EEEEEeccchhhHHHHHHHHHhc-CCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEE
Q 015158          254 QFHVNVEKEEWKLETLCDLYETL-AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVL  332 (412)
Q Consensus       254 ~~~~~~~~~~~~~~~l~~~~~~~-~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vl  332 (412)
                      ..+..... ..+...+.++++.. ..+++||||++++.++.+++.|++.+..+..+||+++..+|..+++.|++|+.+||
T Consensus       252 ~~~~~~~~-~~~~~~l~~~l~~~~~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vl  330 (417)
T 2i4i_A          252 QKVVWVEE-SDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPIL  330 (417)
T ss_dssp             EEEEECCG-GGHHHHHHHHHHTCCTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHHTSSCEE
T ss_pred             EEEEEecc-HhHHHHHHHHHHhcCCCCeEEEEECCHHHHHHHHHHHHHCCCCeeEecCCCCHHHHHHHHHHHHcCCCCEE
Confidence            76666654 55777888888876 45789999999999999999999999999999999999999999999999999999


Q ss_pred             EEcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHHhccccccCChhhhhc
Q 015158          333 ITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVADL  411 (412)
Q Consensus       333 v~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  411 (412)
                      |+|+++++|+|+|++++||+++.|.|...|.||+||+||.|+.|.+++++++.+...++.+.++++...++++.++.++
T Consensus       331 vaT~~~~~Gidip~v~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~~  409 (417)
T 2i4i_A          331 VATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINITKDLLDLLVEAKQEVPSWLENM  409 (417)
T ss_dssp             EECHHHHTTSCCCCEEEEEESSCCSSHHHHHHHHTTBCC--CCEEEEEEECGGGGGGHHHHHHHHHHTTCCCCHHHHHH
T ss_pred             EECChhhcCCCcccCCEEEEEcCCCCHHHHHHhcCccccCCCCceEEEEEccccHHHHHHHHHHHHHhcCcCCHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999999888654

>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=6.1e-58  Score=428.78  Aligned_cols=372  Identities=42%  Similarity=0.682  Sum_probs=333.1

Q ss_pred             hccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCC
Q 015158           37 VYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPT  116 (412)
Q Consensus        37 ~~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~  116 (412)
                      ...+|+++++++.+.+.|...||..|+++|.++++.+++++++++.+|||+|||++++++++..+.....+.+++|++|+
T Consensus        19 ~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~li~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~   98 (400)
T 1s2m_A           19 KGNTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVPT   98 (400)
T ss_dssp             --CCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEECSS
T ss_pred             ccCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEECCCCcHHHHHHHHHHHHHHhhccCCccEEEEcCC
Confidence            34679999999999999999999999999999999999999999999999999999999999887665556689999999


Q ss_pred             HHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhcc
Q 015158          117 RELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSR  196 (412)
Q Consensus       117 ~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~  196 (412)
                      ++|+.|+.+.+..+....++.+....|+............+++|+|+||++|.+.+.+......++++||+||||++.+.
T Consensus        99 ~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~T~~~l~~~~~~~~~~~~~~~~vIiDEaH~~~~~  178 (400)
T 1s2m_A           99 RELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLNETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSR  178 (400)
T ss_dssp             HHHHHHHHHHHHHHTTTTTCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEEESHHHHSSH
T ss_pred             HHHHHHHHHHHHHHhcccCceEEEEeCCcchHHHHHHhcCCCCEEEEchHHHHHHHHhCCcccccCCEEEEeCchHhhhh
Confidence            99999999999999887788899999988776666666678899999999999988887777889999999999999888


Q ss_pred             CcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhHHHHHHHHHhc
Q 015158          197 GFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETL  276 (412)
Q Consensus       197 ~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  276 (412)
                      ++...+..+...+++..+++++|||++......+...+..+..+.... ......+...+..... ..+...+..++...
T Consensus       179 ~~~~~~~~i~~~~~~~~~~i~lSAT~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~-~~k~~~l~~~~~~~  256 (400)
T 1s2m_A          179 DFKTIIEQILSFLPPTHQSLLFSATFPLTVKEFMVKHLHKPYEINLME-ELTLKGITQYYAFVEE-RQKLHCLNTLFSKL  256 (400)
T ss_dssp             HHHHHHHHHHTTSCSSCEEEEEESCCCHHHHHHHHHHCSSCEEESCCS-SCBCTTEEEEEEECCG-GGHHHHHHHHHHHS
T ss_pred             chHHHHHHHHHhCCcCceEEEEEecCCHHHHHHHHHHcCCCeEEEecc-ccccCCceeEEEEech-hhHHHHHHHHHhhc
Confidence            888889999998988999999999999988888888888776554433 2344455555554443 56778888888888


Q ss_pred             CCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccCC
Q 015158          277 AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLP  356 (412)
Q Consensus       277 ~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~~  356 (412)
                      ..+++||||++++.++.+++.|++.+..+..+||+++..+|..+++.|++|+.+|||+|+++++|+|+|++++||+++.|
T Consensus       257 ~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vLv~T~~~~~Gidip~~~~Vi~~~~p  336 (400)
T 1s2m_A          257 QINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQAVNVVINFDFP  336 (400)
T ss_dssp             CCSEEEEECSSHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESSCSSSSCCCTTEEEEEESSCC
T ss_pred             CCCcEEEEEecHHHHHHHHHHHHhcCCCeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCccccCCCccCCCEEEEeCCC
Confidence            88899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHHhccccccCChhhhh
Q 015158          357 TQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVAD  410 (412)
Q Consensus       357 ~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  410 (412)
                      +|...|.||+||+||.|++|.|++++++.+...++.+++.++..++++|.++.+
T Consensus       337 ~s~~~~~Qr~GR~gR~g~~g~~~~l~~~~~~~~~~~i~~~~~~~~~~~~~~~~~  390 (400)
T 1s2m_A          337 KTAETYLHRIGRSGRFGHLGLAINLINWNDRFNLYKIEQELGTEIAAIPATIDK  390 (400)
T ss_dssp             SSHHHHHHHHCBSSCTTCCEEEEEEECGGGHHHHHHHHHHHTCCCEECCSSCCG
T ss_pred             CCHHHHHHhcchhcCCCCCceEEEEeccchHHHHHHHHHHhCCCcccccccccc
Confidence            999999999999999999999999999999999999999999999999987755

>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=1.1e-56  Score=419.04  Aligned_cols=369  Identities=39%  Similarity=0.654  Sum_probs=325.7

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHH
Q 015158           39 DTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRE  118 (412)
Q Consensus        39 ~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  118 (412)
                      .+|+++++++.+.+.|...||..|+|+|.++++.++.++++++.+|||+|||++++++++..+.....+.++||++|+++
T Consensus         8 ~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~P~~~   87 (391)
T 1xti_A            8 SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRE   87 (391)
T ss_dssp             -CGGGGCCCHHHHHHHHHHSCCSCCHHHHHHHHHHTTTCCEEEECSSCSSHHHHHHHHHHHHCCCCTTCCCEEEECSCHH
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHHHHHHHhhcccCCCeeEEEECCCHH
Confidence            47999999999999999999999999999999999999999999999999999999999988766555678999999999


Q ss_pred             HHHHHHHHHHHhhccc-CcEEEEEEcCcchHHHHHHh-cCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhcc
Q 015158          119 LAQQIEKVMRALGDYL-GVKVHACVGGTSVREDQRIL-SSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSR  196 (412)
Q Consensus       119 L~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~-~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~  196 (412)
                      |+.|+.+.+.++.... ++.+..++|+.......... ...++|+|+||+++...+........++++||+||||++.++
T Consensus        88 L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~iiv~T~~~l~~~~~~~~~~~~~~~~vViDEaH~~~~~  167 (391)
T 1xti_A           88 LAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQ  167 (391)
T ss_dssp             HHHHHHHHHHHHTTTCTTCCEEEECTTSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTTSSCCTTCSEEEECSHHHHTSS
T ss_pred             HHHHHHHHHHHHHhhCCCeEEEEEeCCCCHHHHHHHHhcCCCCEEEECHHHHHHHHHcCCccccccCEEEEeCHHHHhhc
Confidence            9999999999987665 78888899887765554433 345799999999999998888777889999999999998873


Q ss_pred             -CcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCc-cccCCceEEEEEeccchhhHHHHHHHHH
Q 015158          197 -GFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDE-LTLEGIKQFHVNVEKEEWKLETLCDLYE  274 (412)
Q Consensus       197 -~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~l~~~~~  274 (412)
                       ++...+..++...+...+++++|||+++........++..+..+...... .....+...+..... ..+...+.+++.
T Consensus       168 ~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~l~~~l~  246 (391)
T 1xti_A          168 LDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKD-NEKNRKLFDLLD  246 (391)
T ss_dssp             HHHHHHHHHHHHTSCSSSEEEEEESSCCSTHHHHHHHHCSSCEEEECCCCCCCCCTTCEEEEEECCG-GGHHHHHHHHHH
T ss_pred             cchHHHHHHHHhhCCCCceEEEEEeeCCHHHHHHHHHHcCCCeEEEecCccccCcccceEEEEEcCc-hhHHHHHHHHHH
Confidence             67788888888888899999999999998888888888888877665443 333455555555443 567788888888


Q ss_pred             hcCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEcc
Q 015158          275 TLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYD  354 (412)
Q Consensus       275 ~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~  354 (412)
                      ....+++||||++++.++.+++.|.+.+..+..+||+++..+|..+++.|++|+.+|||+|+++++|+|+|++++||+++
T Consensus       247 ~~~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gidi~~~~~Vi~~~  326 (391)
T 1xti_A          247 VLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYD  326 (391)
T ss_dssp             HSCCSEEEEECSCHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTCCSEEEESCCCSSCBCCTTEEEEEESS
T ss_pred             hcCCCcEEEEeCcHHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCcEEEECChhhcCCCcccCCEEEEeC
Confidence            88889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCChhhHHHhhhhcccCCCCceEEEEeccC-cHHHHHHHHHHhccccccCChhh
Q 015158          355 LPTQPENYLHRIGRSGRFGRKGVAINFVTRD-DERMLFDIQKFYNVVIEELPANV  408 (412)
Q Consensus       355 ~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~  408 (412)
                      .|+|...|.||+||+||.|++|.+++++++. +.+.++.+++.++..++++|.++
T Consensus       327 ~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  381 (391)
T 1xti_A          327 MPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEI  381 (391)
T ss_dssp             CCSSHHHHHHHHCBCSSSCCCCEEEEEECSHHHHHHHHHHHHHTTCCCEECCSCC
T ss_pred             CCCCHHHHHHhcccccCCCCceEEEEEEcccchHHHHHHHHHHhcCChhhCCccc
Confidence            9999999999999999999999999999876 56778999999999999888654

>1fuu_A Yeast initiation factor 4A; IF4A, helicase, DEAD-box protein, translation; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 2vso_A* 2vsx_A*

Probab=100.00  E-value=1.6e-59  Score=438.88  Aligned_cols=386  Identities=63%  Similarity=0.973  Sum_probs=191.3

Q ss_pred             CCCCCCCChhhhccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCC
Q 015158           26 DGQDFFTSYDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGL  105 (412)
Q Consensus        26 ~~~~~~~~~~~~~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~  105 (412)
                      ++..+....+....+|+++++++.+.+.+..+|+..|+++|+++++.+.+++++++.+|||+|||++++++++..+....
T Consensus         8 ~~~~~~~~~~~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~l~~~~   87 (394)
T 1fuu_A            8 EESQIQTNYDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSV   87 (394)
T ss_dssp             ---CEEESSCCCCCSSGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCCEEECCCSSHHHHHHHHHHHHHHCCTTC
T ss_pred             cccchhhhcccccCChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhhccC
Confidence            34444555666677899999999999999999999999999999999999999999999999999999999998877665


Q ss_pred             CceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEE
Q 015158          106 VECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIF  185 (412)
Q Consensus       106 ~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~i  185 (412)
                      .+++++|++|+++|+.|+.+.+.++....+..+..++|+........... +++|+|+||+++...+.+......++++|
T Consensus        88 ~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~-~~~i~v~T~~~l~~~~~~~~~~~~~~~~v  166 (394)
T 1fuu_A           88 KAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLR-DAQIVVGTPGRVFDNIQRRRFRTDKIKMF  166 (394)
T ss_dssp             CSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEECSSCCHHHHHHHHH-HCSEEEECHHHHHHHHHTTSSCCTTCCEE
T ss_pred             CCCCEEEEcCCHHHHHHHHHHHHHHhccCCeeEEEEeCCCchHHHHhhcC-CCCEEEECHHHHHHHHHhCCcchhhCcEE
Confidence            66799999999999999999999998877888999998887655444333 57899999999999998877778899999


Q ss_pred             EEeCCchhhccCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhh
Q 015158          186 VLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWK  265 (412)
Q Consensus       186 iiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  265 (412)
                      |+||||++.++++...+..+...+++..+++++|||+++........++..+..+...........+...+........+
T Consensus       167 IiDEah~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  246 (394)
T 1fuu_A          167 ILDEADEMLSSGFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKDELTLEGIKQFYVNVEEEEYK  246 (394)
T ss_dssp             EEETHHHHHHTTCHHHHHHHHHHSCTTCEEEEECSSCCHHHHHHHHHHCCSCEEEEECC---------------------
T ss_pred             EEEChHHhhCCCcHHHHHHHHHhCCCCceEEEEEEecCHHHHHHHHHhcCCCeEEEecCccccCCCceEEEEEcCchhhH
Confidence            99999999988899999999999999999999999999988888888898888887777666666666666666655556


Q ss_pred             HHHHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCC
Q 015158          266 LETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQ  345 (412)
Q Consensus       266 ~~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~  345 (412)
                      ...+..++.....+++||||++++.++.+++.|++.+..+..+||+++..+|..+++.|++|+.+|||+|+++++|+|+|
T Consensus       247 ~~~l~~~~~~~~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gldi~  326 (394)
T 1fuu_A          247 YECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQ  326 (394)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHHHHHhcCCCCcEEEEECCHHHHHHHHHHHHHcCCeEEEeeCCCCHHHHHHHHHHHHCCCCcEEEECChhhcCCCcc
Confidence            77777777777778999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHHhccccccCChhhhhcC
Q 015158          346 QVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVADLL  412 (412)
Q Consensus       346 ~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  412 (412)
                      ++++||+++.|+|...|.||+||+||.|++|.|++++++.+...++.++++++..+++++.++.++|
T Consensus       327 ~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~  393 (394)
T 1fuu_A          327 QVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELEKFYSTQIEELPSDIATLL  393 (394)
T ss_dssp             -------------------------------------------------------------------
T ss_pred             cCCEEEEeCCCCCHHHHHHHcCcccCCCCCceEEEEEchhHHHHHHHHHHHhCCcccccCcchhhhc
Confidence            9999999999999999999999999999999999999999999999999999999999998877654

>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=9.4e-56  Score=413.45  Aligned_cols=366  Identities=40%  Similarity=0.701  Sum_probs=327.2

Q ss_pred             hccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcC--ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEc
Q 015158           37 VYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKG--LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLA  114 (412)
Q Consensus        37 ~~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~--~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~  114 (412)
                      ...+|+++++++.+.+.+...++..|+|+|.++++.++.+  +++++.+|||+|||++++++++..+.....+.++||++
T Consensus         3 ~~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~   82 (395)
T 3pey_A            3 MAKSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRVNPEDASPQAICLA   82 (395)
T ss_dssp             -CCSSTTSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHCSSCCCEEEECCTTSCHHHHHHHHHHHHCCTTCCSCCEEEEC
T ss_pred             cccCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCcHHHHHHHHHHHHhccCCCCccEEEEC
Confidence            4578999999999999999999999999999999999998  89999999999999999999998877655667899999


Q ss_pred             CCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhh
Q 015158          115 PTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEML  194 (412)
Q Consensus       115 P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~  194 (412)
                      |+++|+.|+.+.+.++....+..+....++.....    ...+++|+|+||+.+...+.+......++++||+||||++.
T Consensus        83 P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~iiv~T~~~l~~~~~~~~~~~~~~~~iIiDEah~~~  158 (395)
T 3pey_A           83 PSRELARQTLEVVQEMGKFTKITSQLIVPDSFEKN----KQINAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNML  158 (395)
T ss_dssp             SSHHHHHHHHHHHHHHTTTSCCCEEEESTTSSCTT----SCBCCSEEEECHHHHHHHHHTTCBCCTTCCEEEEETHHHHH
T ss_pred             CCHHHHHHHHHHHHHHhcccCeeEEEEecCchhhh----ccCCCCEEEEcHHHHHHHHHcCCcccccCCEEEEEChhhhc
Confidence            99999999999999988777777777776654222    23467999999999999998877778899999999999988


Q ss_pred             c-cCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhHHHHHHHH
Q 015158          195 S-RGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLY  273 (412)
Q Consensus       195 ~-~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~  273 (412)
                      + .++...+..+...++++.+++++|||+++........++..+..+...........+...+........+...+..++
T Consensus       159 ~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~  238 (395)
T 3pey_A          159 DQQGLGDQCIRVKRFLPKDTQLVLFSATFADAVRQYAKKIVPNANTLELQTNEVNVDAIKQLYMDCKNEADKFDVLTELY  238 (395)
T ss_dssp             HSTTHHHHHHHHHHTSCTTCEEEEEESCCCHHHHHHHHHHSCSCEEECCCGGGCSCTTEEEEEEECSSHHHHHHHHHHHH
T ss_pred             CccccHHHHHHHHHhCCCCcEEEEEEecCCHHHHHHHHHhCCCCeEEEccccccccccccEEEEEcCchHHHHHHHHHHH
Confidence            7 677888888999999999999999999998888888888888888777777777778888888777777888888888


Q ss_pred             HhcCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEc
Q 015158          274 ETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINY  353 (412)
Q Consensus       274 ~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~  353 (412)
                      .....+++||||++++.++.+++.|++.+..+..+||+++..+|..+++.|++|+.+|||+|+++++|+|+|++++||++
T Consensus       239 ~~~~~~~~lvf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidip~~~~Vi~~  318 (395)
T 3pey_A          239 GLMTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNY  318 (395)
T ss_dssp             TTTTSSEEEEECSCHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHTTSCCEEEECGGGSSSCCCTTEEEEEES
T ss_pred             HhccCCCEEEEeCCHHHHHHHHHHHHhcCCcEEEeCCCCCHHHHHHHHHHHHCCCCCEEEECChhhcCCCcccCCEEEEc
Confidence            88888999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCC------ChhhHHHhhhhcccCCCCceEEEEecc-CcHHHHHHHHHHhc-cccccCCh
Q 015158          354 DLPT------QPENYLHRIGRSGRFGRKGVAINFVTR-DDERMLFDIQKFYN-VVIEELPA  406 (412)
Q Consensus       354 ~~~~------s~~~~~Q~~GR~~R~g~~g~~~~~~~~-~~~~~~~~~~~~~~-~~~~~~~~  406 (412)
                      +.|+      |...|.||+||+||.|++|.+++++++ .+...+..+++++. .++..++.
T Consensus       319 ~~p~~~~~~~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~  379 (395)
T 3pey_A          319 DLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDKNSFNILSAIQKYFGDIEMTRVPT  379 (395)
T ss_dssp             SCCBCTTSSBCHHHHHHHHTTSSCTTCCEEEEEEECSHHHHHHHHHHHHHTTSCCCEECCS
T ss_pred             CCCCCCcCCCCHHHhhHhccccccCCCCceEEEEEechHHHHHHHHHHHHhCCceeecCCh
Confidence            9998      999999999999999999999999986 45667788888888 66666663

>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein, ATPase, RNA binding protein; 3.00A {Methanocaldococcus jannaschii} SCOP: c.37.1.19 c.37.1.19

Probab=100.00  E-value=4.3e-55  Score=404.93  Aligned_cols=361  Identities=36%  Similarity=0.618  Sum_probs=318.3

Q ss_pred             hccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcC-ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcC
Q 015158           37 VYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKG-LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAP  115 (412)
Q Consensus        37 ~~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~-~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P  115 (412)
                      ...+|+++++++.+.+.|...|+..|+|+|+++++.++++ +++++.+|||+|||++++.+++..+... .+.+++|++|
T Consensus         4 ~~~~f~~~~l~~~~~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~~l~~~~TGsGKT~~~~~~~~~~~~~~-~~~~~lil~P   82 (367)
T 1hv8_A            4 EYMNFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNEN-NGIEAIILTP   82 (367)
T ss_dssp             CCCCGGGSSCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCSS-SSCCEEEECS
T ss_pred             ccCchhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCEEEECCCCChHHHHHHHHHHHHhccc-CCCcEEEEcC
Confidence            3467999999999999999999999999999999999988 7999999999999999999888776543 4568999999


Q ss_pred             CHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhc
Q 015158          116 TRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLS  195 (412)
Q Consensus       116 ~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~  195 (412)
                      +++|+.|+.+.+..+....+..+....|+........... +++|+|+||+++.+.+........++++||+||||.+.+
T Consensus        83 ~~~L~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~-~~~iiv~T~~~l~~~~~~~~~~~~~~~~iIiDEah~~~~  161 (367)
T 1hv8_A           83 TRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALK-NANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEMLN  161 (367)
T ss_dssp             CHHHHHHHHHHHHHHHCSSCCCEEEECTTSCHHHHHHHHH-TCSEEEECHHHHHHHHHTTCSCTTSCCEEEEETHHHHHT
T ss_pred             CHHHHHHHHHHHHHHhCCCCceEEEEECCcchHHHHhhcC-CCCEEEecHHHHHHHHHcCCcccccCCEEEEeCchHhhh
Confidence            9999999999999998777888888888877655544443 579999999999999988777788999999999999999


Q ss_pred             cCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhHHHHHHHHHh
Q 015158          196 RGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYET  275 (412)
Q Consensus       196 ~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  275 (412)
                      +++...+..++..+++..+++++|||++.........+++....+.....    ..+...+..... ..+...+..++. 
T Consensus       162 ~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~-~~~~~~l~~~l~-  235 (367)
T 1hv8_A          162 MGFIKDVEKILNACNKDKRILLFSATMPREILNLAKKYMGDYSFIKAKIN----ANIEQSYVEVNE-NERFEALCRLLK-  235 (367)
T ss_dssp             TTTHHHHHHHHHTSCSSCEEEEECSSCCHHHHHHHHHHCCSEEEEECCSS----SSSEEEEEECCG-GGHHHHHHHHHC-
T ss_pred             hchHHHHHHHHHhCCCCceEEEEeeccCHHHHHHHHHHcCCCeEEEecCC----CCceEEEEEeCh-HHHHHHHHHHHh-
Confidence            99999999999999899999999999999888888888776655443322    244555555443 456677777776 


Q ss_pred             cCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccC
Q 015158          276 LAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDL  355 (412)
Q Consensus       276 ~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~  355 (412)
                      ...+++||||++++.++.+++.|++.+..+..+||+++..+|..+++.|++|+.+|||+|+++++|+|+|++++||+++.
T Consensus       236 ~~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gid~~~~~~Vi~~~~  315 (367)
T 1hv8_A          236 NKEFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVMSRGIDVNDLNCVINYHL  315 (367)
T ss_dssp             STTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECTTHHHHCCCSCCSEEEESSC
T ss_pred             cCCCcEEEEECCHHHHHHHHHHHHhcCCCeEEeeCCCCHHHHHHHHHHHHcCCCeEEEECChhhcCCCcccCCEEEEecC
Confidence            34578999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHHhccccccCC
Q 015158          356 PTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELP  405 (412)
Q Consensus       356 ~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  405 (412)
                      |+|...|.||+||+||.|++|.+++++++.+...++.+++.++..+++++
T Consensus       316 ~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~  365 (367)
T 1hv8_A          316 PQNPESYMHRIGRTGRAGKKGKAISIINRREYKKLRYIERAMKLKIKKLK  365 (367)
T ss_dssp             CSCHHHHHHHSTTTCCSSSCCEEEEEECTTSHHHHHHHHHHHTCCCCCBC
T ss_pred             CCCHHHhhhcccccccCCCccEEEEEEcHHHHHHHHHHHHHhCCCCceec
Confidence            99999999999999999999999999999999999999999999888765

>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=2.1e-55  Score=413.38  Aligned_cols=368  Identities=39%  Similarity=0.674  Sum_probs=326.5

Q ss_pred             hccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcC--ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEc
Q 015158           37 VYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKG--LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLA  114 (412)
Q Consensus        37 ~~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~--~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~  114 (412)
                      ...+|+++++++.+.+.+...||..|+++|.++++.++++  +++++.+|||+|||++++++++..+.....+++++|++
T Consensus        23 ~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~~~~~~~~lil~  102 (412)
T 3fht_A           23 SVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLS  102 (412)
T ss_dssp             CSSCTGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHSSSCCCEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEEC
T ss_pred             ccCCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCchHHHHHHHHHHHHhhhcCCCCCEEEEC
Confidence            3568999999999999999999999999999999999987  89999999999999999999998887766677899999


Q ss_pred             CCHHHHHHHHHHHHHhhccc-CcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHc-CCCCCCCceEEEEeCCch
Q 015158          115 PTRELAQQIEKVMRALGDYL-GVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRR-QSLRPDNIRIFVLDEADE  192 (412)
Q Consensus       115 P~~~L~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~-~~~~~~~~~~iiiDE~h~  192 (412)
                      |+++|+.|+.+.+.++.... +..+....++......   ....++|+|+||+++...+.+ ..+...++++||+||||+
T Consensus       103 P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~ivv~T~~~l~~~~~~~~~~~~~~~~~iViDEah~  179 (412)
T 3fht_A          103 PTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERG---QKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADV  179 (412)
T ss_dssp             SSHHHHHHHHHHHHHHTTTSTTCCEEEECTTCCCCTT---CCCCCSEEEECHHHHHHHHTTSCSSCGGGCCEEEEETHHH
T ss_pred             CCHHHHHHHHHHHHHHHhhcccceEEEeecCcchhhh---hcCCCCEEEECchHHHHHHHhcCCcChhhCcEEEEeCHHH
Confidence            99999999999999987653 5667777766553322   234578999999999998865 445567899999999999


Q ss_pred             hhc-cCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhHHHHHH
Q 015158          193 MLS-RGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCD  271 (412)
Q Consensus       193 ~~~-~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  271 (412)
                      +.+ .++...+..+...++.+.+++++|||+++.........+..+..+...........+...+........+...+..
T Consensus       180 ~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  259 (412)
T 3fht_A          180 MIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVLCSSRDEKFQALCN  259 (412)
T ss_dssp             HHSTTTTHHHHHHHHHTSCTTCEEEEEESCCCHHHHHHHHHHSSSCEEECCCGGGSSCTTEEEEEEECSSHHHHHHHHHH
T ss_pred             HhhcCCcHHHHHHHHhhCCCCceEEEEEeecCHHHHHHHHHhcCCCeEEeeccccccccCceEEEEEcCChHHHHHHHHH
Confidence            886 6788888899999999999999999999998899999999988888777777777888888888877788889999


Q ss_pred             HHHhcCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEE
Q 015158          272 LYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVI  351 (412)
Q Consensus       272 ~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi  351 (412)
                      ++.....+++||||++++.++.+++.|.+.+..+..+||+++..+|..+++.|++|+.+|||+|+++++|+|+|++++||
T Consensus       260 ~~~~~~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidip~~~~Vi  339 (412)
T 3fht_A          260 LYGAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVI  339 (412)
T ss_dssp             HHHHHSSSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHTTSCSEEEECGGGTSSCCCTTEEEEE
T ss_pred             HHhhcCCCCEEEEeCCHHHHHHHHHHHHhCCCeEEEecCCCCHHHHHHHHHHHHCCCCcEEEEcCccccCCCccCCCEEE
Confidence            99888889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EccCCC------ChhhHHHhhhhcccCCCCceEEEEeccCc-HHHHHHHHHHhccccccCChh
Q 015158          352 NYDLPT------QPENYLHRIGRSGRFGRKGVAINFVTRDD-ERMLFDIQKFYNVVIEELPAN  407 (412)
Q Consensus       352 ~~~~~~------s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~  407 (412)
                      +++.|+      +...|.||+||+||.|+.|.+++++++.+ ...++.+++.+...+++++.+
T Consensus       340 ~~~~p~~~~~~~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~  402 (412)
T 3fht_A          340 NFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHSMNILNRIQEHFNKKIERLDTD  402 (412)
T ss_dssp             ESSCCBCSSSSBCHHHHHHHHTTSSCTTCCEEEEEEECSHHHHHHHHHHHHHHTCCCEEC---
T ss_pred             EECCCCCCCCCcchheeecccCcccCCCCCceEEEEEcChhhHHHHHHHHHHHCCccccCCCc
Confidence            999994      66899999999999999999999998764 888899999999988888753

>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=5.4e-55  Score=417.51  Aligned_cols=366  Identities=39%  Similarity=0.677  Sum_probs=174.7

Q ss_pred             ccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcC--ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcC
Q 015158           38 YDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKG--LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAP  115 (412)
Q Consensus        38 ~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~--~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P  115 (412)
                      ..+|+.+++++.+.+.|..+||..|+|+|.++++.++.+  +++++.+|||||||++|+++++..+.....++++||++|
T Consensus        91 ~~~f~~~~l~~~l~~~l~~~g~~~p~~~Q~~ai~~il~~~~~~~l~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~P  170 (479)
T 3fmp_B           91 VKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSP  170 (479)
T ss_dssp             CCCSGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHTSBSCCEEEEECCSSSSHHHHHHHHHHTTCCTTSCSCCEEEECS
T ss_pred             cCCHHHcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCcEEEEcCCCCchhHHHHHHHHHHHhhcCCCCcEEEEeC
Confidence            568999999999999999999999999999999999987  899999999999999999999998877666678999999


Q ss_pred             CHHHHHHHHHHHHHhhccc-CcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHc-CCCCCCCceEEEEeCCchh
Q 015158          116 TRELAQQIEKVMRALGDYL-GVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRR-QSLRPDNIRIFVLDEADEM  193 (412)
Q Consensus       116 ~~~L~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~-~~~~~~~~~~iiiDE~h~~  193 (412)
                      +++|+.|+.+.+..+.... +..+....++......   .....+|+|+||+.+..++.+ ..+.+.++++||+||+|++
T Consensus       171 t~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~~~iViDEah~~  247 (479)
T 3fmp_B          171 TYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERG---QKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVM  247 (479)
T ss_dssp             SHHHHHHHHHHHHHHHTTSTTCCEEEESTTCCCCTT---CCCCCSEEEECHHHHHHHHTTSCCCCGGGCCEEEECCHHHH
T ss_pred             hHHHHHHHHHHHHHHHhhCCCceEEEEeCCcccccc---ccCCCCEEEECchHHHHHHHhcCCcCcccCCEEEEECHHHH
Confidence            9999999999998886543 5566666665543222   133568999999999998865 3455688999999999998


Q ss_pred             hc-cCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhHHHHHHH
Q 015158          194 LS-RGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDL  272 (412)
Q Consensus       194 ~~-~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  272 (412)
                      .+ .++...+..+...++.+.+++++|||++.........++..+..+...........+.+.+........+...+..+
T Consensus       248 ~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  327 (479)
T 3fmp_B          248 IATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVLCSSRDEKFQALCNL  327 (479)
T ss_dssp             HTSTTHHHHHHHHHTTSCTTSEEEEEESCCCHHHHHHHHHHSSSEEEEEEC-----------------------------
T ss_pred             hhcCCcHHHHHHHHhhCCccceEEEEeCCCCHHHHHHHHHHcCCCeEEeccccccCcCCceEEEEEeCCHHHHHHHHHHH
Confidence            86 57788888899999999999999999999988999999998888888777766677777777766666677788888


Q ss_pred             HHhcCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEE
Q 015158          273 YETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVIN  352 (412)
Q Consensus       273 ~~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~  352 (412)
                      +.....+++||||++++.++.+++.|.+.+..+..+||+++..+|..+++.|++|+.+|||+|+++++|+|+|++++||+
T Consensus       328 ~~~~~~~~~lvF~~s~~~~~~l~~~L~~~~~~v~~lh~~~~~~~R~~~~~~f~~g~~~iLv~T~~~~~GlDip~v~~VI~  407 (479)
T 3fmp_B          328 YGAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVIN  407 (479)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HhhccCCceEEEeCcHHHHHHHHHHHHhCCccEEEecCCCCHHHHHHHHHHHHcCCCcEEEEccccccCCccccCCEEEE
Confidence            88777789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCC------ChhhHHHhhhhcccCCCCceEEEEeccCc-HHHHHHHHHHhccccccCCh
Q 015158          353 YDLPT------QPENYLHRIGRSGRFGRKGVAINFVTRDD-ERMLFDIQKFYNVVIEELPA  406 (412)
Q Consensus       353 ~~~~~------s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~  406 (412)
                      ++.|.      +...|.||+||+||.|+.|.+++++++.+ ...++.+++++...++.++.
T Consensus       408 ~d~p~~~~~~~s~~~~~Qr~GRagR~g~~G~~i~~~~~~~~~~~~~~i~~~~~~~~~~l~~  468 (479)
T 3fmp_B          408 FDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHSMNILNRIQEHFNKKIERLDT  468 (479)
T ss_dssp             -------------------------------------------------------------
T ss_pred             ecCCCCCccCCCHHHHHHHhcccccCCCCceEEEEEcCcchHHHHHHHHHHhCCCceECCC
Confidence            99994      66899999999999999999999998765 78888999999988887764

>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=3.3e-52  Score=381.02  Aligned_cols=335  Identities=31%  Similarity=0.538  Sum_probs=287.5

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHH
Q 015158           46 LQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEK  125 (412)
Q Consensus        46 l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~  125 (412)
                      +++.+.+.+..+|+..|+|+|+++++.+.+++++++.+|||+|||++++++++..      +.+++|++|+++|+.|+.+
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            4688999999999999999999999999999999999999999999998888764      3479999999999999999


Q ss_pred             HHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHH
Q 015158          126 VMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDI  205 (412)
Q Consensus       126 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i  205 (412)
                      .+.++....+..+..++|+........... .++|+|+||++|.+.+........++++||+||||++.++++...+..+
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            999998777888988988877655544433 4799999999999988877777788999999999999999999999999


Q ss_pred             HHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhHHHHHHHHHhcCCCcEEEEE
Q 015158          206 FQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFV  285 (412)
Q Consensus       206 ~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lif~  285 (412)
                      +...+...+++++|||+++........++..+..+...   .....+...+.......   ......+.....+++||||
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            99999899999999999998888888888776655322   23344555555444322   2223556666778999999


Q ss_pred             cchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccCCCChhhHHHh
Q 015158          286 NTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHR  365 (412)
Q Consensus       286 ~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~  365 (412)
                      ++++.++.+++.|.    .+..+||+++..+|.++++.|++|+.+|||+|+++++|+|+|++++||+++.|+|...|.||
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            99999999999887    57899999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhcccCCCCceEEEEeccCcHHHHHHHHHHhc
Q 015158          366 IGRSGRFGRKGVAINFVTRDDERMLFDIQKFYN  398 (412)
Q Consensus       366 ~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~  398 (412)
                      +||+||.|++|.+++++. .+...++.+++.++
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 88888888877665

>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=3.3e-52  Score=406.29  Aligned_cols=358  Identities=30%  Similarity=0.456  Sum_probs=295.9

Q ss_pred             CCCHHHHHHHHHCCCCCChHHHHhhhhhhh--cCccEEEECCCCCCchhHhHHHHHHhhccCC----CceeEEEEcCCHH
Q 015158           45 GLQENLLRGIYAYGFEKPSAIQQRGIVPFC--KGLDVIQQAQSGTGKTATFCSGILQQLDYGL----VECQALVLAPTRE  118 (412)
Q Consensus        45 ~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~--~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~----~~~~~lil~P~~~  118 (412)
                      .+++.+.+.+..+||..|+|+|.++++.++  .++++++.+|||+|||++|+++++..+....    .+.++||++|+++
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  7889999999999999999999998775542    2458999999999


Q ss_pred             HHHHHHHHHHHhhc----ccCcEEEEEEcCcchHHHHHHh-cCCCcEEEeChHHHHHHHHcC-CCCCCCceEEEEeCCch
Q 015158          119 LAQQIEKVMRALGD----YLGVKVHACVGGTSVREDQRIL-SSGVHVVVGTPGRVFDMLRRQ-SLRPDNIRIFVLDEADE  192 (412)
Q Consensus       119 L~~q~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~-~~~~~iii~T~~~l~~~~~~~-~~~~~~~~~iiiDE~h~  192 (412)
                      |+.|+.+.+.++..    .....+....|+.......... ..+++|+|+||++|...+.+. ...+..+++||+||||+
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    2345677777777655544333 447899999999998877653 23457799999999999


Q ss_pred             hhccCcHHHHHHHHHhCC-------CCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCc----cccCCceEEEEEecc
Q 015158          193 MLSRGFKDQIYDIFQLLP-------PKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDE----LTLEGIKQFHVNVEK  261 (412)
Q Consensus       193 ~~~~~~~~~~~~i~~~~~-------~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~  261 (412)
                      +.+++|...+..+...++       .+.+++++|||+++........++..+..+......    .....+.........
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            999999988888876653       367999999999998888888888877666554322    222344444444443


Q ss_pred             chhh----HHHHHHHHHh-cCCCcEEEEEcchhHHHHHHHHHhcC---CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEE
Q 015158          262 EEWK----LETLCDLYET-LAITQSVIFVNTRRKVDWLTDKMRSR---DHTVSATHGDMDQNTRDIIMREFRSGSSRVLI  333 (412)
Q Consensus       262 ~~~~----~~~l~~~~~~-~~~~k~lif~~~~~~~~~~~~~L~~~---~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv  333 (412)
                      ....    ...+...+.. ...+++||||++++.++.+++.|++.   +..+..+||+++..+|..+++.|++|+.+|||
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            2222    2233333333 45679999999999999999999876   88999999999999999999999999999999


Q ss_pred             EcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHHhccccc
Q 015158          334 TTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIE  402 (412)
Q Consensus       334 ~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~  402 (412)
                      ||+++++|+|+|++++||+++.|.+...|+||+||+||.|+.|.|++++++.+...++.+++.....+.
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            999999999999999999999999999999999999999999999999999999999999988776554

>3i5x_A ATP-dependent RNA helicase MSS116; protein-RNA complex, RNA helicase, DEAD-BOX, ATP-binding, HE hydrolase, mitochondrion; HET: ANP; 1.90A {Saccharomyces cerevisiae} PDB: 3i5y_A* 3i61_A* 3i62_A* 3sqx_A* 4db2_A 4db4_A

Probab=100.00  E-value=1.1e-51  Score=402.52  Aligned_cols=357  Identities=30%  Similarity=0.461  Sum_probs=293.8

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHhhhhhhh--cCccEEEECCCCCCchhHhHHHHHHhhccCC----CceeEEEEcCCHHH
Q 015158           46 LQENLLRGIYAYGFEKPSAIQQRGIVPFC--KGLDVIQQAQSGTGKTATFCSGILQQLDYGL----VECQALVLAPTREL  119 (412)
Q Consensus        46 l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~--~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~----~~~~~lil~P~~~L  119 (412)
                      +++.+.+.+..+||..|+|+|.++++.++  .++++++.+|||+|||++|+++++..+....    .+.++||++|+++|
T Consensus        79 l~~~l~~~l~~~g~~~~~~~Q~~~i~~~l~~~~~~~lv~apTGsGKTl~~~lpil~~l~~~~~~~~~~~~~lil~Ptr~L  158 (563)
T 3i5x_A           79 LDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDL  158 (563)
T ss_dssp             SCHHHHHHHHTTCCSSCCHHHHHHHHHHHSSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTSSTTSCCEEEECSSHHH
T ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCCCccHHHHHHHHHHHHhccccccCCeeEEEEcCcHHH
Confidence            89999999999999999999999999999  6789999999999999999999998876543    23589999999999


Q ss_pred             HHHHHHHHHHhhcc----cCcEEEEEEcCcchHHHHHHh-cCCCcEEEeChHHHHHHHHcC-CCCCCCceEEEEeCCchh
Q 015158          120 AQQIEKVMRALGDY----LGVKVHACVGGTSVREDQRIL-SSGVHVVVGTPGRVFDMLRRQ-SLRPDNIRIFVLDEADEM  193 (412)
Q Consensus       120 ~~q~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~-~~~~~iii~T~~~l~~~~~~~-~~~~~~~~~iiiDE~h~~  193 (412)
                      +.|+.+.+.++...    ....+..+.|+.......... ..+++|+|+||++|...+.+. ...++++++||+||||++
T Consensus       159 a~Q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~l~~~~~~~~~~~~~lViDEah~l  238 (563)
T 3i5x_A          159 ALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRL  238 (563)
T ss_dssp             HHHHHHHHHHHHHHCGGGTTSCEEEECTTSCHHHHHHHHHHHCCSEEEECHHHHHHHHHHHHHHHCTTCCEEEEETHHHH
T ss_pred             HHHHHHHHHHHHhhccccCceeEEEEECCcCHHHHHHHHhcCCCCEEEECcHHHHHHHHhccccccccceEEEEeCHHHH
Confidence            99999999986432    245677777777655443333 457899999999998877653 223567999999999999


Q ss_pred             hccCcHHHHHHHHHhCC-------CCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCc----cccCCceEEEEEeccc
Q 015158          194 LSRGFKDQIYDIFQLLP-------PKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDE----LTLEGIKQFHVNVEKE  262 (412)
Q Consensus       194 ~~~~~~~~~~~i~~~~~-------~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~  262 (412)
                      .+++|...+..+...++       ++.+++++|||+++........++..+..+......    .....+...+......
T Consensus       239 ~~~~f~~~~~~i~~~l~~~~~~~~~~~~~l~~SAT~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  318 (563)
T 3i5x_A          239 LEIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEKF  318 (563)
T ss_dssp             TSTTTHHHHHHHHHHHHHHCSSCTTCCEEEEEESSCCTHHHHHTTTTCCSSEEEEEESSCSSSCSSCTTEEEEEEEESST
T ss_pred             hccchHHHHHHHHHhhhhccccCccCceEEEEEccCCHHHHHHHHHhcCCCceEEEeccCCCCccccccCceEEEECchh
Confidence            99999888888776652       377899999999988888888888777666543322    1223344444444433


Q ss_pred             hhhH----HHHHHHHHh-cCCCcEEEEEcchhHHHHHHHHHhcC---CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEE
Q 015158          263 EWKL----ETLCDLYET-LAITQSVIFVNTRRKVDWLTDKMRSR---DHTVSATHGDMDQNTRDIIMREFRSGSSRVLIT  334 (412)
Q Consensus       263 ~~~~----~~l~~~~~~-~~~~k~lif~~~~~~~~~~~~~L~~~---~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~  334 (412)
                      ....    ..+...+.. ...+++||||++++.++.+++.|++.   +..+..+||+++..+|..+++.|++|+.+||||
T Consensus       319 ~~~~~~~~~~l~~~~~~~~~~~~~iVF~~s~~~~~~l~~~L~~~~~~~~~v~~~h~~~~~~~R~~~~~~f~~g~~~vLva  398 (563)
T 3i5x_A          319 ANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVC  398 (563)
T ss_dssp             THHHHHHHHHHHHHHHHTTTCCEEEEECSCHHHHHHHHHHHHHHHTTTSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEE
T ss_pred             HhhHHHHHHHHHHHHhhcCCCCcEEEEcCcHHHHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcCCCCEEEE
Confidence            2222    223333333 45679999999999999999999876   889999999999999999999999999999999


Q ss_pred             cCCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHHhccccc
Q 015158          335 TDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIE  402 (412)
Q Consensus       335 t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~  402 (412)
                      |+++++|+|+|++++||+++.|.+...|+||+||+||.|+.|.|++++.+.+...++.+++..+..++
T Consensus       399 T~~~~~GiDip~v~~VI~~~~p~s~~~y~Qr~GRagR~g~~g~~i~~~~~~e~~~~~~l~~~~~~~~~  466 (563)
T 3i5x_A          399 TDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRELEDAKNIVIA  466 (563)
T ss_dssp             CGGGTSSCCCTTCCEEEEESCCSSTTHHHHHHTTSSCTTCCEEEEEEEEGGGHHHHHHHHHHHCCCCC
T ss_pred             cchhhcCCCcccCCEEEEECCCCchhhhhhhcCccccCCCCceEEEEEchhHHHHHHHHHHHhCCCcc
Confidence            99999999999999999999999999999999999999999999999999999999999988775544

>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=7.8e-51  Score=393.01  Aligned_cols=344  Identities=17%  Similarity=0.221  Sum_probs=275.5

Q ss_pred             ccccc--cCCCCHHHHHHHHH-CCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEc
Q 015158           38 YDTFD--AMGLQENLLRGIYA-YGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLA  114 (412)
Q Consensus        38 ~~~f~--~~~l~~~~~~~l~~-~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~  114 (412)
                      ...|.  .+++++.+.+.|+. +||..|+|+|.++++.++.|+++++.+|||+|||++|+++++..      .+++||++
T Consensus        18 ~~~w~~~~~~l~~~l~~~L~~~fg~~~~rp~Q~~~i~~il~g~d~lv~~pTGsGKTl~~~lpal~~------~g~~lVis   91 (591)
T 2v1x_A           18 PAAWNKEDFPWSGKVKDILQNVFKLEKFRPLQLETINVTMAGKEVFLVMPTGGGKSLCYQLPALCS------DGFTLVIC   91 (591)
T ss_dssp             GGGGCCSCSTTHHHHHHHHHHTSCCCSCCTTHHHHHHHHHTTCCEEEECCTTSCTTHHHHHHHHTS------SSEEEEEC
T ss_pred             hhccccccCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEEECCCChHHHHHHHHHHHc------CCcEEEEe
Confidence            34444  47788999999998 79999999999999999999999999999999999999988753      24899999


Q ss_pred             CCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHH------hcCCCcEEEeChHHHH------HHHHcCCCCCCCc
Q 015158          115 PTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRI------LSSGVHVVVGTPGRVF------DMLRRQSLRPDNI  182 (412)
Q Consensus       115 P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~iii~T~~~l~------~~~~~~~~~~~~~  182 (412)
                      |+++|+.|+.+.+.++    ++.+..++++.........      .....+|+|+||++|.      +.+.. .....++
T Consensus        92 P~~~L~~q~~~~l~~~----gi~~~~l~~~~~~~~~~~~~~~l~~~~~~~~Ilv~Tpe~L~~~~~~~~~l~~-~~~~~~i  166 (591)
T 2v1x_A           92 PLISLMEDQLMVLKQL----GISATMLNASSSKEHVKWVHAEMVNKNSELKLIYVTPEKIAKSKMFMSRLEK-AYEARRF  166 (591)
T ss_dssp             SCHHHHHHHHHHHHHH----TCCEEECCSSCCHHHHHHHHHHHHCTTCCCCEEEECHHHHHSCHHHHHHHHH-HHHTTCE
T ss_pred             CHHHHHHHHHHHHHhc----CCcEEEEeCCCCHHHHHHHHHHhhcccCCCCEEEEChhHhhccHHHHHHHHh-hhhccCC
Confidence            9999999999999987    7788888888765544322      2467899999999874      22221 2234678


Q ss_pred             eEEEEeCCchhhccC--cHHHHHH--HHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEE
Q 015158          183 RIFVLDEADEMLSRG--FKDQIYD--IFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVN  258 (412)
Q Consensus       183 ~~iiiDE~h~~~~~~--~~~~~~~--i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  258 (412)
                      ++||+||||++.+|+  |...+..  .+....++.+++++|||+++.....+...++.+....... ....+++......
T Consensus       167 ~~iViDEAH~is~~g~dfr~~~~~l~~l~~~~~~~~ii~lSAT~~~~v~~~i~~~l~~~~~~~~~~-~~~r~nl~~~v~~  245 (591)
T 2v1x_A          167 TRIAVDEVHCCSQWGHDFRPDYKALGILKRQFPNASLIGLTATATNHVLTDAQKILCIEKCFTFTA-SFNRPNLYYEVRQ  245 (591)
T ss_dssp             EEEEEETGGGGSTTCTTCCGGGGGGGHHHHHCTTSEEEEEESSCCHHHHHHHHHHTTCCSCEEEEC-CCCCTTEEEEEEE
T ss_pred             cEEEEECcccccccccccHHHHHHHHHHHHhCCCCcEEEEecCCCHHHHHHHHHHhCCCCcEEEec-CCCCcccEEEEEe
Confidence            999999999998876  5544433  2333335789999999999988787777766543332222 2233444433333


Q ss_pred             ecc-chhhHHHHHHHHHh-cCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcC
Q 015158          259 VEK-EEWKLETLCDLYET-LAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTD  336 (412)
Q Consensus       259 ~~~-~~~~~~~l~~~~~~-~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~  336 (412)
                      ... .......+.+++.. ...+++||||++++.++.+++.|++.++.+..+||+++..+|..+++.|.+|+.+|||+|+
T Consensus       246 ~~~~~~~~~~~l~~~l~~~~~~~~~IVf~~sr~~~e~la~~L~~~g~~~~~~h~~l~~~~R~~~~~~F~~g~~~VlVAT~  325 (591)
T 2v1x_A          246 KPSNTEDFIEDIVKLINGRYKGQSGIIYCFSQKDSEQVTVSLQNLGIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATV  325 (591)
T ss_dssp             CCSSHHHHHHHHHHHHTTTTTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEECT
T ss_pred             CCCcHHHHHHHHHHHHHHhccCCCeEEEeCcHHHHHHHHHHHHHCCCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEec
Confidence            222 23345566666654 3568999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHH
Q 015158          337 LLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDI  393 (412)
Q Consensus       337 ~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~  393 (412)
                      ++++|+|+|++++||+++.|.|...|.|++||+||.|++|.|++++.+.|...+..+
T Consensus       326 a~~~GID~p~V~~VI~~~~p~s~~~y~Qr~GRaGR~G~~g~~i~l~~~~D~~~~~~~  382 (591)
T 2v1x_A          326 AFGMGIDKPDVRFVIHHSMSKSMENYYQESGRAGRDDMKADCILYYGFGDIFRISSM  382 (591)
T ss_dssp             TSCTTCCCSCEEEEEESSCCSSHHHHHHHHTTSCTTSSCEEEEEEECHHHHHHHHHH
T ss_pred             hhhcCCCcccccEEEEeCCCCCHHHHHHHhccCCcCCCCceEEEEEChHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999998877655443

>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=9.1e-51  Score=388.97  Aligned_cols=339  Identities=18%  Similarity=0.274  Sum_probs=276.2

Q ss_pred             cccccCCCCHHHHHHHHH-CCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCH
Q 015158           39 DTFDAMGLQENLLRGIYA-YGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTR  117 (412)
Q Consensus        39 ~~f~~~~l~~~~~~~l~~-~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~  117 (412)
                      .+|+.+++++.+.+.|.. +|+..|+|+|.++++.+++|+++++.+|||+|||++|+++++..      .+.+||++|++
T Consensus         2 ~~fe~l~L~~~~~~~l~~~~g~~~~r~~Q~~~i~~il~g~d~lv~apTGsGKTl~~~lp~l~~------~g~~lvi~P~~   75 (523)
T 1oyw_A            2 AQAEVLNLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLL------NGLTVVVSPLI   75 (523)
T ss_dssp             CCCCCSSHHHHHHHHHHHTTCCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHS------SSEEEEECSCH
T ss_pred             CChhhCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEECCCCcHHHHHHHHHHHHh------CCCEEEECChH
Confidence            578999999999999998 89999999999999999999999999999999999999888743      24799999999


Q ss_pred             HHHHHHHHHHHHhhcccCcEEEEEEcCcchHHH----HHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchh
Q 015158          118 ELAQQIEKVMRALGDYLGVKVHACVGGTSVRED----QRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEM  193 (412)
Q Consensus       118 ~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~  193 (412)
                      +|+.|+.+.+..+    ++.+..++++......    .....+..+|+++||+++........+...++++||+||||++
T Consensus        76 aL~~q~~~~l~~~----gi~~~~l~~~~~~~~~~~~~~~~~~~~~~ilv~Tpe~l~~~~~~~~l~~~~~~~vViDEaH~i  151 (523)
T 1oyw_A           76 SLMKDQVDQLQAN----GVAAACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDNFLEHLAHWNPVLLAVDEAHCI  151 (523)
T ss_dssp             HHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHHTCCSEEEECHHHHTSTTHHHHHTTSCEEEEEESSGGGG
T ss_pred             HHHHHHHHHHHHc----CCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhChHHHHHHhhCCCCEEEEeCcccc
Confidence            9999999999886    6778888877664433    2233567899999999985322111223367899999999999


Q ss_pred             hccC--cHHHHH---HHHHhCCCCceEEEEeecCChHHHHHHHHhcC--CCeEEEecCCccccCCceEEEEEeccchhhH
Q 015158          194 LSRG--FKDQIY---DIFQLLPPKIQVGVFSATMPPEALEITRKFMN--KPVRILVKRDELTLEGIKQFHVNVEKEEWKL  266 (412)
Q Consensus       194 ~~~~--~~~~~~---~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  266 (412)
                      .+++  |...+.   .+...++ +.+++++|||+++.....+...++  .+..+ ..  ....+++......   ...+.
T Consensus       152 ~~~g~~fr~~~~~l~~l~~~~~-~~~~i~lSAT~~~~~~~~i~~~l~~~~~~~~-~~--~~~r~~l~~~v~~---~~~~~  224 (523)
T 1oyw_A          152 SQWGHDFRPEYAALGQLRQRFP-TLPFMALTATADDTTRQDIVRLLGLNDPLIQ-IS--SFDRPNIRYMLME---KFKPL  224 (523)
T ss_dssp             CTTSSCCCHHHHGGGGHHHHCT-TSCEEEEESCCCHHHHHHHHHHHTCCSCEEE-EC--CCCCTTEEEEEEE---CSSHH
T ss_pred             CcCCCccHHHHHHHHHHHHhCC-CCCEEEEeCCCCHHHHHHHHHHhCCCCCeEE-eC--CCCCCceEEEEEe---CCCHH
Confidence            8876  444433   3444453 688999999999877665555443  33322 22  2223344333332   24466


Q ss_pred             HHHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCC
Q 015158          267 ETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQ  346 (412)
Q Consensus       267 ~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~  346 (412)
                      ..+.+++.....+++||||++++.++.+++.|++.++.+..+||+++..+|..+++.|.+|+.+|||+|+++++|+|+|+
T Consensus       225 ~~l~~~l~~~~~~~~IVf~~sr~~~e~l~~~L~~~g~~~~~~h~~l~~~~R~~~~~~f~~g~~~vlVaT~a~~~GiD~p~  304 (523)
T 1oyw_A          225 DQLMRYVQEQRGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMGINKPN  304 (523)
T ss_dssp             HHHHHHHHHTTTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECTTSCTTTCCTT
T ss_pred             HHHHHHHHhcCCCcEEEEeCCHHHHHHHHHHHHHCCCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEechhhCCCCccC
Confidence            77888888877789999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHH
Q 015158          347 VSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQ  394 (412)
Q Consensus       347 ~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~  394 (412)
                      +++||+++.|.|...|.|++||+||.|.+|.|++++++.|...++.+.
T Consensus       305 v~~VI~~~~p~s~~~y~Qr~GRaGR~g~~~~~~l~~~~~d~~~~~~~~  352 (523)
T 1oyw_A          305 VRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLRRCL  352 (523)
T ss_dssp             CCEEEESSCCSSHHHHHHHHTTSCTTSSCEEEEEEECHHHHHHHHHHH
T ss_pred             ccEEEEECCCCCHHHHHHHhccccCCCCCceEEEEeCHHHHHHHHHHH
Confidence            999999999999999999999999999999999999988776655444

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=100.00  E-value=6.5e-48  Score=361.98  Aligned_cols=325  Identities=21%  Similarity=0.263  Sum_probs=257.1

Q ss_pred             HHHHHHH-CCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHH
Q 015158           50 LLRGIYA-YGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMR  128 (412)
Q Consensus        50 ~~~~l~~-~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~  128 (412)
                      +.+.++. +++ +|+|+|.++++.+++++++++.+|||+|||++++++++....   .+++++|++|+++|+.|+.+.+.
T Consensus        10 ~~~~l~~~~~~-~~~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~l~~~~~~~~---~~~~~lil~Pt~~L~~q~~~~~~   85 (414)
T 3oiy_A           10 FRSFFKKKFGK-DLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLAR---KGKKSALVFPTVTLVKQTLERLQ   85 (414)
T ss_dssp             HHHHHHHHHSS-CCCHHHHHHHHHHTTTCCEECCSCSSSSHHHHHHHHHHHHHT---TTCCEEEEESSHHHHHHHHHHHH
T ss_pred             HHHHHHHhcCC-CCCHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHhc---CCCEEEEEECCHHHHHHHHHHHH
Confidence            3444444 466 499999999999999999999999999999999888877653   34689999999999999999999


Q ss_pred             HhhcccCcEEEEEEcCcchH---HHHHHh-cCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhc---------
Q 015158          129 ALGDYLGVKVHACVGGTSVR---EDQRIL-SSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLS---------  195 (412)
Q Consensus       129 ~~~~~~~~~~~~~~~~~~~~---~~~~~~-~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~---------  195 (412)
                      .+.. .++.+..++|+....   ...... .+.++|+|+||+.+...+..  +...++++||+||||++..         
T Consensus        86 ~~~~-~~~~v~~~~g~~~~~~~~~~~~~l~~~~~~Iiv~Tp~~l~~~l~~--~~~~~~~~iViDEaH~~~~~~~~~d~~l  162 (414)
T 3oiy_A           86 KLAD-EKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREK--LSQKRFDFVFVDDVDAVLKASRNIDTLL  162 (414)
T ss_dssp             HHCC-SSCCEEECCTTSCHHHHHHHHHHHHHTCCSEEEEEHHHHHHCHHH--HTTCCCSEEEESCHHHHHHCHHHHHHHH
T ss_pred             HHcc-CCceEEEEECCCChhhHHHHHHHhhcCCCCEEEECHHHHHHHHHH--hccccccEEEEeChHhhhhccchhhhHH
Confidence            9877 788999999988763   223333 34489999999999877664  4456899999999998764         


Q ss_pred             --cCcHHH-HHHHHHhCC-----------CCceEEEEeec-CChHHH-HHHHHhcCCCeEEEecCCccccCCceEEEEEe
Q 015158          196 --RGFKDQ-IYDIFQLLP-----------PKIQVGVFSAT-MPPEAL-EITRKFMNKPVRILVKRDELTLEGIKQFHVNV  259 (412)
Q Consensus       196 --~~~~~~-~~~i~~~~~-----------~~~~~i~~SAT-~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  259 (412)
                        .+|... +..++..++           ...+++++||| ++.... ........    +...........+.+.+...
T Consensus       163 ~~~~~~~~~~~~i~~~~~~~~~~~~l~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~----~~~~~~~~~~~~i~~~~~~~  238 (414)
T 3oiy_A          163 MMVGIPEEIIRKAFSTIKQGKIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLLN----FTVGRLVSVARNITHVRISS  238 (414)
T ss_dssp             HHTTCCHHHHHHHHHHHHHTCCCCCCTTCCCCEEEESSCCSSCCSSTTHHHHHHHS----CCSSCCCCCCCSEEEEEESS
T ss_pred             hhcCCcHHHHHHHHHhcccchhhhhcccCCCceEEEEecCCCcchhHHHHHHHhhc----cCcCccccccccchheeecc
Confidence              455556 677777665           78899999999 443322 22233322    11122233344455555443


Q ss_pred             ccchhhHHHHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcCCCeeE-EecCCCCHHHHHHHHHHHhcCCCcEEEE----
Q 015158          260 EKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVS-ATHGDMDQNTRDIIMREFRSGSSRVLIT----  334 (412)
Q Consensus       260 ~~~~~~~~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~-~~~~~~~~~~r~~~~~~f~~g~~~vlv~----  334 (412)
                          .+...+.++++.. .+++||||++++.++.+++.|++.++.+. .+||.    +|.  ++.|++|+.+||||    
T Consensus       239 ----~~~~~l~~~l~~~-~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~h~~----~r~--~~~f~~g~~~vLvat~s~  307 (414)
T 3oiy_A          239 ----RSKEKLVELLEIF-RDGILIFAQTEEEGKELYEYLKRFKFNVGETWSEF----EKN--FEDFKVGKINILIGVQAY  307 (414)
T ss_dssp             ----CCHHHHHHHHHHH-CSSEEEEESSHHHHHHHHHHHHHTTCCEEESSSCH----HHH--HHHHHTTSCSEEEEECCT
T ss_pred             ----CHHHHHHHHHHHc-CCCEEEEECCHHHHHHHHHHHHHcCCceehhhcCc----chH--HHHHhCCCCeEEEEecCc
Confidence                2455666677663 38999999999999999999999999998 88984    344  99999999999999    


Q ss_pred             cCCCcCCCCCCC-CCEEEEccCC--CChhhHHHhhhhcccCC----CCceEEEEeccCcHHHHHHHHHHhc
Q 015158          335 TDLLARGIDVQQ-VSLVINYDLP--TQPENYLHRIGRSGRFG----RKGVAINFVTRDDERMLFDIQKFYN  398 (412)
Q Consensus       335 t~~~~~G~d~~~-~~~vi~~~~~--~s~~~~~Q~~GR~~R~g----~~g~~~~~~~~~~~~~~~~~~~~~~  398 (412)
                      |+++++|+|+|+ +++||+++.|  .|...|.||+||+||.|    ..|.+++++  .+...+..++++++
T Consensus       308 T~~~~~GiDip~~v~~VI~~~~p~~~~~~~y~qr~GR~gR~g~~~~~~g~~i~~~--~~~~~~~~l~~~~~  376 (414)
T 3oiy_A          308 YGKLTRGVDLPERIKYVIFWGTPSGPDVYTYIQASGRSSRILNGVLVKGVSVIFE--EDEEIFESLKTRLL  376 (414)
T ss_dssp             TCCCCCCCCCTTTCCEEEEESCCTTTCHHHHHHHHGGGCCEETTEECCEEEEEEC--CCHHHHHHHHHHHH
T ss_pred             CchhhccCccccccCEEEEECCCCCCCHHHHHHHhCccccCCCCCCcceEEEEEE--ccHHHHHHHHHHhc
Confidence            999999999999 9999999999  99999999999999987    478888888  67778888888888

>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=1.2e-46  Score=375.88  Aligned_cols=350  Identities=19%  Similarity=0.256  Sum_probs=273.4

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHHhhhhh-hhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHH
Q 015158           40 TFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVP-FCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRE  118 (412)
Q Consensus        40 ~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~-~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  118 (412)
                      +|+++++++.+.+.+..+||..|+++|.++++. +..++++++++|||||||+++.++++..+...  +.+++|++|+++
T Consensus         2 ~f~~l~l~~~~~~~l~~~g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~--~~~~l~i~P~ra   79 (720)
T 2zj8_A            2 RVDELRVDERIKSTLKERGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRILTQ--GGKAVYIVPLKA   79 (720)
T ss_dssp             BGGGCCSCHHHHHHHHHTTCCBCCHHHHHHHTTTGGGTCEEEEECCGGGCHHHHHHHHHHHHHHHH--CSEEEEECSSGG
T ss_pred             cHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCcEEEEcCCccHHHHHHHHHHHHHHHhC--CCEEEEEcCcHH
Confidence            588999999999999999999999999999998 88899999999999999999999998776521  358999999999


Q ss_pred             HHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCc
Q 015158          119 LAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGF  198 (412)
Q Consensus       119 L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~  198 (412)
                      |+.|+++.++.+.. .++.+..++|+......   ...+++|+|+||++|...+.+....++++++||+||+|.+.++.+
T Consensus        80 La~q~~~~~~~l~~-~g~~v~~~~G~~~~~~~---~~~~~~Iiv~Tpe~l~~~~~~~~~~l~~~~~vIiDE~H~l~~~~r  155 (720)
T 2zj8_A           80 LAEEKFQEFQDWEK-IGLRVAMATGDYDSKDE---WLGKYDIIIATAEKFDSLLRHGSSWIKDVKILVADEIHLIGSRDR  155 (720)
T ss_dssp             GHHHHHHHTGGGGG-GTCCEEEECSCSSCCCG---GGGGCSEEEECHHHHHHHHHHTCTTGGGEEEEEEETGGGGGCTTT
T ss_pred             HHHHHHHHHHHHHh-cCCEEEEecCCCCcccc---ccCCCCEEEECHHHHHHHHHcChhhhhcCCEEEEECCcccCCCcc
Confidence            99999999965543 48889999987654332   224679999999999998887665578899999999999988788


Q ss_pred             HHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEE-----Eecc-----chhhHHH
Q 015158          199 KDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHV-----NVEK-----EEWKLET  268 (412)
Q Consensus       199 ~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~-----~~~~~~~  268 (412)
                      ...+..++..++.+.+++++|||+++.  ..+..+++.... ...   ..+..+...+.     ....     .......
T Consensus       156 ~~~~~~ll~~l~~~~~ii~lSATl~n~--~~~~~~l~~~~~-~~~---~rp~~l~~~~~~~~~~~~~~~~~~~~~~~~~~  229 (720)
T 2zj8_A          156 GATLEVILAHMLGKAQIIGLSATIGNP--EELAEWLNAELI-VSD---WRPVKLRRGVFYQGFVTWEDGSIDRFSSWEEL  229 (720)
T ss_dssp             HHHHHHHHHHHBTTBEEEEEECCCSCH--HHHHHHTTEEEE-ECC---CCSSEEEEEEEETTEEEETTSCEEECSSTTHH
T ss_pred             cHHHHHHHHHhhcCCeEEEEcCCcCCH--HHHHHHhCCccc-CCC---CCCCcceEEEEeCCeeeccccchhhhhHHHHH
Confidence            888888888877789999999999752  334444442211 110   01111111111     0111     1233444


Q ss_pred             HHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcC---------------------------------CCeeEEecCCCCHH
Q 015158          269 LCDLYETLAITQSVIFVNTRRKVDWLTDKMRSR---------------------------------DHTVSATHGDMDQN  315 (412)
Q Consensus       269 l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~---------------------------------~~~~~~~~~~~~~~  315 (412)
                      +.+.+.  ..+++||||++++.++.+++.|.+.                                 ...+..+||+++..
T Consensus       230 ~~~~~~--~~~~~LVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~l~~~~~~~v~~~h~~l~~~  307 (720)
T 2zj8_A          230 VYDAIR--KKKGALIFVNMRRKAERVALELSKKVKSLLTKPEIRALNELADSLEENPTNEKLAKAIRGGVAFHHAGLGRD  307 (720)
T ss_dssp             HHHHHH--TTCCEEEECSCHHHHHHHHHHHHHHHGGGSCHHHHHHHHHHHHTSCSCHHHHHHHHHHTTTEEEECTTSCHH
T ss_pred             HHHHHh--CCCCEEEEecCHHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHhcccchHHHHHHHhcCeeeecCCCCHH
Confidence            444444  3479999999999999999998753                                 12489999999999


Q ss_pred             HHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEE----cc----CCCChhhHHHhhhhcccCC--CCceEEEEeccC
Q 015158          316 TRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVIN----YD----LPTQPENYLHRIGRSGRFG--RKGVAINFVTRD  385 (412)
Q Consensus       316 ~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~----~~----~~~s~~~~~Q~~GR~~R~g--~~g~~~~~~~~~  385 (412)
                      +|..+++.|.+|+++|||||+++++|+|+|++++||.    ++    .|.|..+|.||+||+||.|  ..|.|++++++.
T Consensus       308 ~R~~v~~~f~~g~~~vlvaT~~l~~Gvdip~~~~VI~~~~~yd~~g~~~~s~~~~~Qr~GRaGR~g~~~~G~~~~l~~~~  387 (720)
T 2zj8_A          308 ERVLVEENFRKGIIKAVVATPTLSAGINTPAFRVIIRDIWRYSDFGMERIPIIEVHQMLGRAGRPKYDEVGEGIIVSTSD  387 (720)
T ss_dssp             HHHHHHHHHHTTSSCEEEECSTTGGGCCCCBSEEEECCSEECCSSSCEECCHHHHHHHHTTBCCTTTCSEEEEEEECSSS
T ss_pred             HHHHHHHHHHCCCCeEEEECcHhhccCCCCceEEEEcCCeeecCCCCccCCHHHHHHHHhhcCCCCCCCCceEEEEecCc
Confidence            9999999999999999999999999999999999997    44    5899999999999999998  468899999887


Q ss_pred             cHHHHHHHHHHhccccccCC
Q 015158          386 DERMLFDIQKFYNVVIEELP  405 (412)
Q Consensus       386 ~~~~~~~~~~~~~~~~~~~~  405 (412)
                      +..  ..+++++....+++.
T Consensus       388 ~~~--~~~~~~~~~~~~~i~  405 (720)
T 2zj8_A          388 DPR--EVMNHYIFGKPEKLF  405 (720)
T ss_dssp             CHH--HHHHHHTTSCCCCCC
T ss_pred             cHH--HHHHHHhcCCCCCcE
Confidence            733  234456655555554

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=100.00  E-value=7.5e-46  Score=370.40  Aligned_cols=351  Identities=18%  Similarity=0.243  Sum_probs=267.8

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHHhhhhh-hhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCH
Q 015158           39 DTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVP-FCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTR  117 (412)
Q Consensus        39 ~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~-~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~  117 (412)
                      .+|+++++++.+.+.+...||..|+++|.++++. +.+++++++++|||||||+++.++++..+...  +.+++|++|++
T Consensus         8 ~~~~~l~l~~~~~~~l~~~g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~--~~~il~i~P~r   85 (715)
T 2va8_A            8 MPIEDLKLPSNVIEIIKKRGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGIISFLLKN--GGKAIYVTPLR   85 (715)
T ss_dssp             CBGGGSSSCHHHHHHHHTTSCCBCCHHHHHHHHTTTTTTCCEEEECCTTSCHHHHHHHHHHHHHHHS--CSEEEEECSCH
T ss_pred             CcHHHcCCCHHHHHHHHhCCCCCCCHHHHHHHHHHhcCCCcEEEEcCCCCcHHHHHHHHHHHHHHHC--CCeEEEEeCcH
Confidence            4699999999999999999999999999999999 78899999999999999999999998776532  35899999999


Q ss_pred             HHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccC
Q 015158          118 ELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRG  197 (412)
Q Consensus       118 ~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~  197 (412)
                      +|+.|+++.++.+ ...+..+...+|+......   ....++|+|+||++|...+.+....++++++||+||+|++.+..
T Consensus        86 ~La~q~~~~~~~~-~~~g~~v~~~~G~~~~~~~---~~~~~~Iiv~Tpe~l~~~~~~~~~~l~~~~~vIiDE~H~l~~~~  161 (715)
T 2va8_A           86 ALTNEKYLTFKDW-ELIGFKVAMTSGDYDTDDA---WLKNYDIIITTYEKLDSLWRHRPEWLNEVNYFVLDELHYLNDPE  161 (715)
T ss_dssp             HHHHHHHHHHGGG-GGGTCCEEECCSCSSSCCG---GGGGCSEEEECHHHHHHHHHHCCGGGGGEEEEEECSGGGGGCTT
T ss_pred             HHHHHHHHHHHHh-hcCCCEEEEEeCCCCCchh---hcCCCCEEEEcHHHHHHHHhCChhHhhccCEEEEechhhcCCcc
Confidence            9999999999644 3348888888887654332   12367999999999999888765557789999999999988777


Q ss_pred             cHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEE-----------EEecc-----
Q 015158          198 FKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFH-----------VNVEK-----  261 (412)
Q Consensus       198 ~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----------~~~~~-----  261 (412)
                      +...+..++..++ +.+++++|||+++.  ..+..+++.+.. ....   .+..+...+           .....     
T Consensus       162 ~~~~l~~i~~~~~-~~~ii~lSATl~n~--~~~~~~l~~~~~-~~~~---r~~~l~~~~~~~~~~~~~~~~~~~~~~~~~  234 (715)
T 2va8_A          162 RGPVVESVTIRAK-RRNLLALSATISNY--KQIAKWLGAEPV-ATNW---RPVPLIEGVIYPERKKKEYNVIFKDNTTKK  234 (715)
T ss_dssp             THHHHHHHHHHHH-TSEEEEEESCCTTH--HHHHHHHTCEEE-ECCC---CSSCEEEEEEEECSSTTEEEEEETTSCEEE
T ss_pred             cchHHHHHHHhcc-cCcEEEEcCCCCCH--HHHHHHhCCCcc-CCCC---CCCCceEEEEecCCcccceeeecCcchhhh
Confidence            7888888877766 88999999999752  333344443221 1100   011111111           00110     


Q ss_pred             ---chhhHHHHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcCC------------------------------------
Q 015158          262 ---EEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRD------------------------------------  302 (412)
Q Consensus       262 ---~~~~~~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~------------------------------------  302 (412)
                         .......+.+.+.  ..+++||||++++.++.+++.|.+..                                    
T Consensus       235 ~~~~~~~~~~~~~~~~--~~~~~LVF~~s~~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~l~~~~~  312 (715)
T 2va8_A          235 VHGDDAIIAYTLDSLS--KNGQVLVFRNSRKMAESTALKIANYMNFVSLDENALSEILKQLDDIEEGGSDEKELLKSLIS  312 (715)
T ss_dssp             EESSSHHHHHHHHHHT--TTCCEEEECSSHHHHHHHHHHHHHTTTSSCCCHHHHHHHHHHHHTCCSSCHHHHHHHHHHHT
T ss_pred             cccchHHHHHHHHHHh--cCCCEEEEECCHHHHHHHHHHHHHHHhhccCChHHHHHHHHHHHHhhhccccccHHHHHHHh
Confidence               1223344444443  45899999999999999999998642                                    


Q ss_pred             CeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEE----cc-------CCCChhhHHHhhhhccc
Q 015158          303 HTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVIN----YD-------LPTQPENYLHRIGRSGR  371 (412)
Q Consensus       303 ~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~----~~-------~~~s~~~~~Q~~GR~~R  371 (412)
                      ..+..+||+++..+|..+++.|.+|+.+|||||+++++|+|+|++++||.    ++       .|.|..+|.||+||+||
T Consensus       313 ~~v~~~h~~l~~~~r~~v~~~f~~g~~~vlvaT~~l~~Gidip~~~~VI~~~~~~d~~~~~~~~~~s~~~~~Qr~GRaGR  392 (715)
T 2va8_A          313 KGVAYHHAGLSKALRDLIEEGFRQRKIKVIVATPTLAAGVNLPARTVIIGDIYRFNKKIAGYYDEIPIMEYKQMSGRAGR  392 (715)
T ss_dssp             TTEEEECTTSCHHHHHHHHHHHHTTCSCEEEECGGGGGSSCCCBSEEEECCC--------------CHHHHHHHHTTBCC
T ss_pred             cCEEEECCCCCHHHHHHHHHHHHcCCCeEEEEChHHhcccCCCceEEEEeCCeeccccCCCCCCcCCHHHHHHHhhhcCC
Confidence            24899999999999999999999999999999999999999999999998    77       78999999999999999


Q ss_pred             CC--CCceEEEEeccCcHHHHHHHHHHhccccccCC
Q 015158          372 FG--RKGVAINFVTRDDERMLFDIQKFYNVVIEELP  405 (412)
Q Consensus       372 ~g--~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  405 (412)
                      .|  .+|.|+++++..+. ....+++++....+++.
T Consensus       393 ~g~~~~G~~~~l~~~~~~-~~~~~~~~l~~~~e~~~  427 (715)
T 2va8_A          393 PGFDQIGESIVVVRDKED-VDRVFKKYVLSDVEPIE  427 (715)
T ss_dssp             TTTCSCEEEEEECSCGGG-HHHHHHHTTSSCCCCCC
T ss_pred             CCCCCCceEEEEeCCchH-HHHHHHHHHcCCCCCce
Confidence            88  47899999887653 11234455544444444

>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=1.5e-46  Score=374.19  Aligned_cols=349  Identities=16%  Similarity=0.230  Sum_probs=265.5

Q ss_pred             ccccCC--CCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCH
Q 015158           40 TFDAMG--LQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTR  117 (412)
Q Consensus        40 ~f~~~~--l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~  117 (412)
                      +|++++  +++.+.+.++.+||..|+++|.++++.+.+++++++++|||||||+++.++++..+..   +.+++|++|++
T Consensus         2 ~f~~l~~~l~~~~~~~l~~~g~~~l~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~~l~il~~~~~---~~~~l~i~P~r   78 (702)
T 2p6r_A            2 KVEELAESISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIK---GGKSLYVVPLR   78 (702)
T ss_dssp             CSHHHHHHHHHHHHHHHHCC---CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHHT---TCCEEEEESSH
T ss_pred             chhhhhhccCHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCcEEEEcCCccHHHHHHHHHHHHHHHh---CCcEEEEeCcH
Confidence            477777  8999999999999999999999999999999999999999999999999999987654   35899999999


Q ss_pred             HHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccC
Q 015158          118 ELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRG  197 (412)
Q Consensus       118 ~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~  197 (412)
                      +|+.|+++.++.+. ..+..+..++|+......   ...+++|+|+||++|...+.+....++++++||+||+|++.+++
T Consensus        79 ~La~q~~~~~~~~~-~~g~~v~~~~G~~~~~~~---~~~~~~Iiv~Tpe~l~~~l~~~~~~l~~~~~vIiDE~H~l~~~~  154 (702)
T 2p6r_A           79 ALAGEKYESFKKWE-KIGLRIGISTGDYESRDE---HLGDCDIIVTTSEKADSLIRNRASWIKAVSCLVVDEIHLLDSEK  154 (702)
T ss_dssp             HHHHHHHHHHTTTT-TTTCCEEEECSSCBCCSS---CSTTCSEEEEEHHHHHHHHHTTCSGGGGCCEEEETTGGGGGCTT
T ss_pred             HHHHHHHHHHHHHH-hcCCEEEEEeCCCCcchh---hccCCCEEEECHHHHHHHHHcChhHHhhcCEEEEeeeeecCCCC
Confidence            99999999996543 347889999987764332   12468999999999999888766557789999999999998877


Q ss_pred             cHHHHHHHHHhC---CCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEE-------EEec-----cc
Q 015158          198 FKDQIYDIFQLL---PPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFH-------VNVE-----KE  262 (412)
Q Consensus       198 ~~~~~~~i~~~~---~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~-----~~  262 (412)
                      +...+..++..+   .++.+++++|||+++ . ..+..+++.+.. ....   .+..+...+       ....     ..
T Consensus       155 r~~~~~~ll~~l~~~~~~~~ii~lSATl~n-~-~~~~~~l~~~~~-~~~~---r~~~l~~~~~~~~~~~~~~~~~~~~~~  228 (702)
T 2p6r_A          155 RGATLEILVTKMRRMNKALRVIGLSATAPN-V-TEIAEWLDADYY-VSDW---RPVPLVEGVLCEGTLELFDGAFSTSRR  228 (702)
T ss_dssp             THHHHHHHHHHHHHHCTTCEEEEEECCCTT-H-HHHHHHTTCEEE-ECCC---CSSCEEEEEECSSEEEEEETTEEEEEE
T ss_pred             cccHHHHHHHHHHhcCcCceEEEECCCcCC-H-HHHHHHhCCCcc-cCCC---CCccceEEEeeCCeeeccCcchhhhhh
Confidence            777776665554   568999999999975 2 344445553321 1111   111111111       1100     00


Q ss_pred             hhhHHHHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcC------------------------------CCeeEEecCCC
Q 015158          263 EWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSR------------------------------DHTVSATHGDM  312 (412)
Q Consensus       263 ~~~~~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~------------------------------~~~~~~~~~~~  312 (412)
                      ......+.+.+.  ..+++||||++++.++.+++.|.+.                              +..+..+||++
T Consensus       229 ~~~~~~~~~~~~--~~~~~LVF~~s~~~~~~~a~~L~~~~~~~~~~~~~~~~i~~~~~~~~~~~l~~~~~~~v~~~h~~l  306 (702)
T 2p6r_A          229 VKFEELVEECVA--ENGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGL  306 (702)
T ss_dssp             CCHHHHHHHHHH--TTCCEEEECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECTTS
T ss_pred             hhHHHHHHHHHh--cCCCEEEEcCCHHHHHHHHHHHHHHHHhhcChHHHHHHHHhhccccccHHHHHHHhcCeEEecCCC
Confidence            013444555443  4579999999999999999988752                              13578899999


Q ss_pred             CHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEE----cc---CCCChhhHHHhhhhcccCC--CCceEEEEec
Q 015158          313 DQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVIN----YD---LPTQPENYLHRIGRSGRFG--RKGVAINFVT  383 (412)
Q Consensus       313 ~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~----~~---~~~s~~~~~Q~~GR~~R~g--~~g~~~~~~~  383 (412)
                      +..+|..+++.|.+|+.+|||||+++++|+|+|++++||.    ++   .|.|..+|.||+||+||.|  .+|.|+++++
T Consensus       307 ~~~~R~~v~~~f~~g~~~vlvaT~~l~~Gidip~~~~VI~~~~~yd~~~~~~s~~~~~Qr~GRaGR~g~~~~G~~~~l~~  386 (702)
T 2p6r_A          307 LNGQRRVVEDAFRRGNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIVG  386 (702)
T ss_dssp             CHHHHHHHHHHHHTTSCCEEEECSTTTSSSCCCBSEEEECCSEEESSSEEECCHHHHHHHHTTBSCTTTCSCEEEEEECC
T ss_pred             CHHHHHHHHHHHHCCCCeEEEECcHHhccCCCCceEEEEcCceeeCCCCCcCCHHHHHHHhhhcCCCCCCCCceEEEEec
Confidence            9999999999999999999999999999999999999997    43   6899999999999999998  4789999998


Q ss_pred             cCcHHHHHHHHHHhccccccCC
Q 015158          384 RDDERMLFDIQKFYNVVIEELP  405 (412)
Q Consensus       384 ~~~~~~~~~~~~~~~~~~~~~~  405 (412)
                      +.+..  ..+++++....+++.
T Consensus       387 ~~~~~--~~~~~~l~~~~e~~~  406 (702)
T 2p6r_A          387 KRDRE--IAVKRYIFGEPERIT  406 (702)
T ss_dssp             GGGHH--HHHHTTTSSCCCCCC
T ss_pred             CccHH--HHHHHHhcCCCCCce
Confidence            87733  223344444444443

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=100.00  E-value=2.2e-46  Score=374.36  Aligned_cols=353  Identities=22%  Similarity=0.258  Sum_probs=229.1

Q ss_pred             HHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCC--ceeEEEEcCCHHHHHHHHHHHH
Q 015158           51 LRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLV--ECQALVLAPTRELAQQIEKVMR  128 (412)
Q Consensus        51 ~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~--~~~~lil~P~~~L~~q~~~~~~  128 (412)
                      ...+..+|+..|+++|.++++.++.|+++++++|||+|||++++++++..+.....  ++++||++|+++|+.|+.+.+.
T Consensus         3 ~~~l~~~g~~~lr~~Q~~~i~~~l~g~~~iv~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~lvl~Pt~~L~~Q~~~~~~   82 (696)
T 2ykg_A            3 VSDTNLYSPFKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQIPVYEQNKSVFS   82 (696)
T ss_dssp             ----CTTC--CCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHSCTTCCCCEEEECSSHHHHHHHHHHHH
T ss_pred             CCcccccCCCCccHHHHHHHHHHHcCCCEEEEcCCCchHHHHHHHHHHHHHHhCccCCCCeEEEEECCHHHHHHHHHHHH
Confidence            34566789999999999999999999999999999999999999999887654322  2589999999999999999999


Q ss_pred             HhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCC-CCCCceEEEEeCCchhhccCc-HHHHHHHH
Q 015158          129 ALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSL-RPDNIRIFVLDEADEMLSRGF-KDQIYDIF  206 (412)
Q Consensus       129 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~-~~~~~~~iiiDE~h~~~~~~~-~~~~~~i~  206 (412)
                      ++....++.+..++|+............+++|+|+||+.|.+.+....+ ...++++||+||||++.+... ...+...+
T Consensus        83 ~~~~~~~~~v~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~L~~~l~~~~~~~l~~~~~vViDEaH~~~~~~~~~~i~~~~l  162 (696)
T 2ykg_A           83 KYFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTIPSLSIFTLMIFDECHNTSKQHPYNMIMFNYL  162 (696)
T ss_dssp             HHTTTTTCCEEEECSSSCSSSCHHHHHHTCSEEEECHHHHHHHHHTTSSCCGGGCSEEEEETGGGCSTTCHHHHHHHHHH
T ss_pred             HHhccCCceEEEEeCCccccccHHHhccCCCEEEECHHHHHHHHhcCcccccccccEEEEeCCCcccCcccHHHHHHHHH
Confidence            9987778899999998765444444445689999999999999887666 578899999999999875542 22222222


Q ss_pred             Hh-----CCCCceEEEEeecCC-------hHHHHHHHHhc----------------------CCCeEEEecCCccccC--
Q 015158          207 QL-----LPPKIQVGVFSATMP-------PEALEITRKFM----------------------NKPVRILVKRDELTLE--  250 (412)
Q Consensus       207 ~~-----~~~~~~~i~~SAT~~-------~~~~~~~~~~~----------------------~~~~~~~~~~~~~~~~--  250 (412)
                      ..     .++..++++|||||.       .+....+....                      ..|.............  
T Consensus       163 ~~~~~~~~~~~~~il~LTATp~~~~~~~~~~~~~~i~~~~~~l~~~~~~~~~~~~~~l~~~~~~p~~~~~~~~~~~~~~f  242 (696)
T 2ykg_A          163 DQKLGGSSGPLPQVIGLTASVGVGDAKTTDEALDYICKLCASLDASVIATVKHNLEELEQVVYKPQKFFRKVESRISDKF  242 (696)
T ss_dssp             HHHHTTCCSCCCEEEEEESCCCCSSCCSHHHHHHHHHHHHHHTTCCEEECCCTTHHHHHHHSCCCEEEEEECCCCSCCHH
T ss_pred             HHhhcccCCCCCeEEEEeCccccCccccHHHHHHHHHHHHHhcCCceEeecccchHHHHhhcCCCceeEEecCcccCChH
Confidence            22     246789999999997       22222222211                      1121111000000000  


Q ss_pred             --------------------------------------------------------------------------------
Q 015158          251 --------------------------------------------------------------------------------  250 (412)
Q Consensus       251 --------------------------------------------------------------------------------  250 (412)
                                                                                                      
T Consensus       243 s~~~~~l~~~i~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~  322 (696)
T 2ykg_A          243 KYIIAQLMRDTESLAKRICKDLENLSQIQNREFGTQKYEQWIVTVQKACMVFQMPDKDEESRICKALFLYTSHLRKYNDA  322 (696)
T ss_dssp             HHHHHHHHHHHHHHHHHHSTTGGGSSSCCSCCSSSHHHHHHHHHHHHTSCC------CCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhccccccccchhHHHHHHHHHHHHHHhhcccchhhhHHHHHHHHHHHHHHHHhHH
Confidence                                                                                            


Q ss_pred             -----------------------------CceEEEE---------------EeccchhhHHHHHHHHHhc----CCCcEE
Q 015158          251 -----------------------------GIKQFHV---------------NVEKEEWKLETLCDLYETL----AITQSV  282 (412)
Q Consensus       251 -----------------------------~~~~~~~---------------~~~~~~~~~~~l~~~~~~~----~~~k~l  282 (412)
                                                   .+...+.               .......+...+.+++...    ..+++|
T Consensus       323 ~~i~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~k~~~L~~ll~~~~~~~~~~~~I  402 (696)
T 2ykg_A          323 LIISEHARMKDALDYLKDFFSNVRAAGFDEIEQDLTQRFEEKLQELESVSRDPSNENPKLEDLCFILQEEYHLNPETITI  402 (696)
T ss_dssp             HHHHHHSCHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHTTHHHHHHHHHCGGGCCHHHHHHHHHHHHHHTTCTTCCEE
T ss_pred             HhccchhhHHHHHHHHHHHHHHHhhcccchHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhccCCCCcEE
Confidence                                         0000000               0001233556666666665    567999


Q ss_pred             EEEcchhHHHHHHHHHhcCC----CeeEEe--------cCCCCHHHHHHHHHHHhc-CCCcEEEEcCCCcCCCCCCCCCE
Q 015158          283 IFVNTRRKVDWLTDKMRSRD----HTVSAT--------HGDMDQNTRDIIMREFRS-GSSRVLITTDLLARGIDVQQVSL  349 (412)
Q Consensus       283 if~~~~~~~~~~~~~L~~~~----~~~~~~--------~~~~~~~~r~~~~~~f~~-g~~~vlv~t~~~~~G~d~~~~~~  349 (412)
                      |||++++.++.+++.|++.+    +.+..+        |++++..+|.+++++|++ |+.+|||+|+++++|+|+|++++
T Consensus       403 IF~~~~~~~~~l~~~L~~~~~~~~~~~~~l~G~~~~~~h~~~~~~eR~~v~~~F~~~g~~~vLVaT~v~~~GiDip~v~~  482 (696)
T 2ykg_A          403 LFVKTRALVDALKNWIEGNPKLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAFKASGDHNILIATSVADEGIDIAQCNL  482 (696)
T ss_dssp             EECSCHHHHHHHHHHHHHCTTCCSCCEEC-----------------------------CCSCSEEEESSCCC---CCCSE
T ss_pred             EEeCcHHHHHHHHHHHHhCCCccccceeEEEccCCCccccCCCHHHHHHHHHHHHhcCCccEEEEechhhcCCcCccCCE
Confidence            99999999999999999987    778877        559999999999999998 99999999999999999999999


Q ss_pred             EEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHH----HHHhccccccCC
Q 015158          350 VINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDI----QKFYNVVIEELP  405 (412)
Q Consensus       350 vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~  405 (412)
                      ||+++.|+|+..|.||+|| ||. .+|.++++++..+......+    ++++...+++++
T Consensus       483 VI~~d~p~s~~~~~Qr~GR-GR~-~~g~~~~l~~~~~~~~~~~~~~~~e~~~~~~~~~~~  540 (696)
T 2ykg_A          483 VILYEYVGNVIKMIQTRGR-GRA-RGSKCFLLTSNAGVIEKEQINMYKEKMMNDSILRLQ  540 (696)
T ss_dssp             EEEESCC--CCCC-----------CCCEEEEEESCHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             EEEeCCCCCHHHHHHhhcc-CcC-CCceEEEEecCCCHHHHHHHHHHHHHHHHHHHHHhh
Confidence            9999999999999999999 998 78999999998877555555    555555554444

>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=8.2e-46  Score=361.45  Aligned_cols=328  Identities=18%  Similarity=0.202  Sum_probs=200.1

Q ss_pred             CCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCC--ceeEEEEcCCHHHHHHHHHHHHHhhcccCcE
Q 015158           60 EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLV--ECQALVLAPTRELAQQIEKVMRALGDYLGVK  137 (412)
Q Consensus        60 ~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~--~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~  137 (412)
                      .+|+|+|.++++.++.++++++.+|||+|||++++++++..+.....  ++++||++|+++|+.||.+.+..+....++.
T Consensus         6 ~~~~~~Q~~~i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~   85 (556)
T 4a2p_A            6 KKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFERQGYS   85 (556)
T ss_dssp             --CCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHGGGTCC
T ss_pred             CCCCHHHHHHHHHHHcCCCEEEEcCCCChHHHHHHHHHHHHHHhCcccCCCeEEEEeCCHHHHHHHHHHHHHHhcccCce
Confidence            35999999999999999999999999999999999999888765422  5689999999999999999999998877899


Q ss_pred             EEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCC-CCCCceEEEEeCCchhhccCcHHHH-HHHHHh----CCC
Q 015158          138 VHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSL-RPDNIRIFVLDEADEMLSRGFKDQI-YDIFQL----LPP  211 (412)
Q Consensus       138 ~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~-~~~~~~~iiiDE~h~~~~~~~~~~~-~~i~~~----~~~  211 (412)
                      +..++|+............+++|+|+||++|.+.+....+ ...++++||+||||++.+++....+ ..++..    ..+
T Consensus        86 ~~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~~vViDEah~~~~~~~~~~~~~~~~~~~~~~~~~  165 (556)
T 4a2p_A           86 VQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQKFNSASQ  165 (556)
T ss_dssp             EEECCCC-----CHHHHHHHCSEEEECHHHHHHHHHSSSCCCSTTCSEEEEETGGGCSTTSHHHHHHHHHHHHHHCC---
T ss_pred             EEEEeCCCCcchhHHHhhCCCCEEEECHHHHHHHHHhCcccccccCCEEEEECCcccCCcchHHHHHHHHHHhhhcccCC
Confidence            9999998865554444455689999999999999988766 6788999999999999877643332 222222    135


Q ss_pred             CceEEEEeecCChH----HH---H---HHHHhcCCCeEEEecCC------ccccCCceEEEEE-----------------
Q 015158          212 KIQVGVFSATMPPE----AL---E---ITRKFMNKPVRILVKRD------ELTLEGIKQFHVN-----------------  258 (412)
Q Consensus       212 ~~~~i~~SAT~~~~----~~---~---~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~-----------------  258 (412)
                      ..+++++||||+..    ..   .   .+...+...........      ....+........                 
T Consensus       166 ~~~~l~lSAT~~~~~~~~~~~~~~~i~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  245 (556)
T 4a2p_A          166 LPQILGLTASVGVGNAKNIEETIEHICSLCSYLDIQAISTVRENIQELQRFMNKPEIDVRLVKRRIHNPFAAIISNLMSE  245 (556)
T ss_dssp             CCEEEEEESCCCCTTCSSHHHHHHHHHHHHHHHTCSEEECCCTTHHHHHHHTCCCCEEEEECCCCSCCHHHHHHHHHHHH
T ss_pred             CCeEEEEeCCcccCchhhHHHHHHHHHHHHHhcCCeEecchhcchHHHHhcCCCCceEEEEcCCCcCChHHHHHHHHHHH
Confidence            68899999999531    00   1   11111221111100000      0000000000000                 


Q ss_pred             --------------------------------------------------------------------------------
Q 015158          259 --------------------------------------------------------------------------------  258 (412)
Q Consensus       259 --------------------------------------------------------------------------------  258 (412)
                                                                                                      
T Consensus       246 ~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~  325 (556)
T 4a2p_A          246 TEALMRTIYSVDTLSQNSKKDFGTQNYEHWIVVTQRKCRLLQLEDKEEESRICRALFICTEHLRKYNDALIISEDARIID  325 (556)
T ss_dssp             HHHHHHHHCC---------CCCSSHHHHHHHHHHHHHHHHC---CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCHHH
T ss_pred             HHHHHHHHhhhhhhhcccccccchhhHHHHHHHHHHHHHhhcccccchhHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHH
Confidence                                                                                            


Q ss_pred             -----------------------------------------eccchhhHHHHHHHHHh----cCCCcEEEEEcchhHHHH
Q 015158          259 -----------------------------------------VEKEEWKLETLCDLYET----LAITQSVIFVNTRRKVDW  293 (412)
Q Consensus       259 -----------------------------------------~~~~~~~~~~l~~~~~~----~~~~k~lif~~~~~~~~~  293 (412)
                                                               ......+...+.+++..    ...+++||||+++..++.
T Consensus       326 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~K~~~L~~~l~~~~~~~~~~k~lVF~~~~~~~~~  405 (556)
T 4a2p_A          326 ALSYLTEFFTNVKNGPYTELEQHLTAKFQEKEPELIALSKDETNENPKLEELVCILDDAYRYNPQTRTLLFAKTRALVSA  405 (556)
T ss_dssp             HHHHHHHHHHHHHHSCCCHHHHHHHHHHHTTHHHHHHHHHCSSSCCHHHHHHHHHHHHHHHHCTTCCEEEEESSHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCCCHHHHHHHHHHhhHHHHhhhhccCCCCCChHHHHHHHHHHHHhcCCCCceEEEEEccHHHHHH
Confidence                                                     00012234444445543    456899999999999999


Q ss_pred             HHHHHhcC------------CCeeEEecCCCCHHHHHHHHHHHhc-CCCcEEEEcCCCcCCCCCCCCCEEEEccCCCChh
Q 015158          294 LTDKMRSR------------DHTVSATHGDMDQNTRDIIMREFRS-GSSRVLITTDLLARGIDVQQVSLVINYDLPTQPE  360 (412)
Q Consensus       294 ~~~~L~~~------------~~~~~~~~~~~~~~~r~~~~~~f~~-g~~~vlv~t~~~~~G~d~~~~~~vi~~~~~~s~~  360 (412)
                      +++.|++.            |.....+||+++..+|..++++|++ |+.+|||||+++++|+|+|++++||++++|+|+.
T Consensus       406 l~~~L~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~R~~~~~~F~~~g~~~vLvaT~~~~~GiDip~v~~VI~~d~p~s~~  485 (556)
T 4a2p_A          406 LKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVT  485 (556)
T ss_dssp             HHHHHTTCSGGGSCCEEC------------------------------CCEEEEEC-----------CEEEEETCCSCHH
T ss_pred             HHHHHHhCCCcceeeeeEEEccCCcccccccCHHHHHHHHHHhcccCceEEEEEcCchhcCCCchhCCEEEEeCCCCCHH
Confidence            99999876            4555666788999999999999999 9999999999999999999999999999999999


Q ss_pred             hHHHhhhhcccCCCCceEEEEeccCcHHH
Q 015158          361 NYLHRIGRSGRFGRKGVAINFVTRDDERM  389 (412)
Q Consensus       361 ~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~  389 (412)
                      .|+||+|| ||. .+|.+++++++.+...
T Consensus       486 ~~~Qr~GR-gR~-~~g~~~~l~~~~~~~~  512 (556)
T 4a2p_A          486 KMIQVRGR-GRA-AGSKCILVTSKTEVVE  512 (556)
T ss_dssp             HHHHC----------CCEEEEESCHHHHH
T ss_pred             HHHHhcCC-CCC-CCceEEEEEeCcchHH
Confidence            99999999 999 7899999998876543

>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=6.6e-44  Score=362.40  Aligned_cols=318  Identities=20%  Similarity=0.278  Sum_probs=254.3

Q ss_pred             HCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccC
Q 015158           56 AYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLG  135 (412)
Q Consensus        56 ~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~  135 (412)
                      .++|. |+++|.++++.+..++++++++|||+|||+++.++++..+..+   .+++|++|+++|+.|+++.+.++..   
T Consensus        82 ~~~f~-L~~~Q~eai~~l~~g~~vLV~apTGSGKTlva~lai~~~l~~g---~rvL~l~PtkaLa~Q~~~~l~~~~~---  154 (1010)
T 2xgj_A           82 TYPFT-LDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKNK---QRVIYTSPIKALSNQKYRELLAEFG---  154 (1010)
T ss_dssp             CCSSC-CCHHHHHHHHHHHHTCEEEEECCTTSCHHHHHHHHHHHHHHTT---CEEEEEESSHHHHHHHHHHHHHHHS---
T ss_pred             hCCCC-CCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHhccC---CeEEEECChHHHHHHHHHHHHHHhC---
Confidence            45776 9999999999999999999999999999999999888877543   5899999999999999999998764   


Q ss_pred             cEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceE
Q 015158          136 VKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQV  215 (412)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~  215 (412)
                       .+..++|+....       ..++|+|+||++|.+.+.+....+.++++||+||+|++.++++...+..++..++.+.++
T Consensus       155 -~vglltGd~~~~-------~~~~IvV~Tpe~L~~~L~~~~~~l~~l~lVViDEaH~l~d~~rg~~~e~il~~l~~~~~i  226 (1010)
T 2xgj_A          155 -DVGLMTGDITIN-------PDAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMRDKERGVVWEETIILLPDKVRY  226 (1010)
T ss_dssp             -CEEEECSSCEEC-------TTCSEEEEEHHHHHHHHHHTCTTGGGEEEEEEETGGGGGCTTTHHHHHHHHHHSCTTCEE
T ss_pred             -CEEEEeCCCccC-------CCCCEEEEcHHHHHHHHHcCcchhhcCCEEEEechhhhcccchhHHHHHHHHhcCCCCeE
Confidence             577788877643       357899999999999888777777899999999999999988888899999999999999


Q ss_pred             EEEeecCChHHH--HHHHHhcCCCeEEEecCCccccCCceEEEEEec---------cc----------------------
Q 015158          216 GVFSATMPPEAL--EITRKFMNKPVRILVKRDELTLEGIKQFHVNVE---------KE----------------------  262 (412)
Q Consensus       216 i~~SAT~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------~~----------------------  262 (412)
                      +++|||+++...  ..+....+.+..+.......  ..+...+....         ..                      
T Consensus       227 l~LSATi~n~~e~a~~l~~~~~~~~~vi~~~~rp--~pl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  304 (1010)
T 2xgj_A          227 VFLSATIPNAMEFAEWICKIHSQPCHIVYTNFRP--TPLQHYLFPAHGDGIYLVVDEKSTFREENFQKAMASISNQIGDD  304 (1010)
T ss_dssp             EEEECCCTTHHHHHHHHHHHHTSCEEEEEECCCS--SCEEEEEEETTSSCCEEEECTTCCBCHHHHHHHHHTCC------
T ss_pred             EEEcCCCCCHHHHHHHHHhhcCCCeEEEecCCCc--ccceEEEEecCCcceeeeeccccccchHHHHHHHHHHhhhhccc
Confidence            999999976422  33333344444443332211  12222222110         00                      


Q ss_pred             -----------------------hhhHHHHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcCCCe---------------
Q 015158          263 -----------------------EWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHT---------------  304 (412)
Q Consensus       263 -----------------------~~~~~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~---------------  304 (412)
                                             ......+...+......++||||+++..|+.+++.|...++.               
T Consensus       305 ~~~~~~~g~~~~~~k~~~~~~~~~~~l~~l~~~l~~~~~~~~IVF~~sr~~~e~la~~L~~~~~~~~~e~~~i~~~~~~~  384 (1010)
T 2xgj_A          305 PNSTDSRGKKGQTYKGGSAKGDAKGDIYKIVKMIWKKKYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEALTKIFNNA  384 (1010)
T ss_dssp             ------------------------CHHHHHHHHHHHHTCCSEEEEESSHHHHHHHHHTTTTSCCCCHHHHHHHHHHHHHH
T ss_pred             ccccccccccccccccccccccchHHHHHHHHHHHhcCCCCEEEEECCHHHHHHHHHHHHhCCCCChHHHHHHHHHHHHH
Confidence                                   111223444444445569999999999999999999875432               


Q ss_pred             ------------------------eEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEE----ccC-
Q 015158          305 ------------------------VSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVIN----YDL-  355 (412)
Q Consensus       305 ------------------------~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~----~~~-  355 (412)
                                              +..+||++++.+|..+++.|++|.++|||||+++++|+|+|.+++||.    ++. 
T Consensus       385 ~~~l~~~d~~l~~~~~l~~~l~~gI~~~Hggl~~~eR~~ve~~F~~G~ikVLVAT~~la~GIDiP~~~vVI~~~~kfd~~  464 (1010)
T 2xgj_A          385 IALLPETDRELPQIKHILPLLRRGIGIHHSGLLPILKEVIEILFQEGFLKVLFATETFSIGLNMPAKTVVFTSVRKWDGQ  464 (1010)
T ss_dssp             HTTSCGGGTTCHHHHHHHHHHHHTEEEESTTSCHHHHHHHHHHHHTTCCSEEEEEGGGGGSTTCCBSEEEESCSEEECSS
T ss_pred             HHhcchhhhcchhHHHHHHHHhCCeeEECCCCCHHHHHHHHHHHhcCCCcEEEEehHhhccCCCCCceEEEeCCcccCCc
Confidence                                    788999999999999999999999999999999999999999999998    777 


Q ss_pred             ---CCChhhHHHhhhhcccCCC--CceEEEEeccC-cHHHH
Q 015158          356 ---PTQPENYLHRIGRSGRFGR--KGVAINFVTRD-DERML  390 (412)
Q Consensus       356 ---~~s~~~~~Q~~GR~~R~g~--~g~~~~~~~~~-~~~~~  390 (412)
                         |.|+.+|.||+||+||.|.  .|.|++++++. +...+
T Consensus       465 ~~rp~s~~~y~Qr~GRAGR~G~d~~G~vi~l~~~~~e~~~~  505 (1010)
T 2xgj_A          465 QFRWVSGGEYIQMSGRAGRRGLDDRGIVIMMIDEKMEPQVA  505 (1010)
T ss_dssp             CEEECCHHHHHHHHTTBCCTTTCSSEEEEEEECSCCCHHHH
T ss_pred             CCccCCHHHHhHhhhhcccCCCCCceEEEEEECCCCCHHHH
Confidence               8899999999999999997  49999999876 44433

>3l9o_A ATP-dependent RNA helicase DOB1; REC-A fold, winged-helix-turn-helix, antiparallel-coiled-COI domain, ATP-binding, helicase, hydrolase; 3.39A {Saccharomyces cerevisiae}

Probab=100.00  E-value=2.6e-45  Score=375.81  Aligned_cols=348  Identities=19%  Similarity=0.214  Sum_probs=264.5

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHH
Q 015158           40 TFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTREL  119 (412)
Q Consensus        40 ~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L  119 (412)
                      .|...++++.+...+...+...|+++|.++++.+..|+++++++|||||||++|+++++..+..+   .+++|++|+++|
T Consensus       163 ~~~~~~l~~~~~~~~~~~~~f~ltp~Q~~AI~~i~~g~dvLV~ApTGSGKTlva~l~i~~~l~~g---~rvlvl~PtraL  239 (1108)
T 3l9o_A          163 NYDYTPIAEHKRVNEARTYPFTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKNK---QRVIYTSPIKAL  239 (1108)
T ss_dssp             CCCSSTTTTTCCCSCSSCCSSCCCHHHHHHHHHHTTTCCEEEECCSSSHHHHHHHHHHHHHHHTT---CEEEEEESSHHH
T ss_pred             CcccCCCChhhhHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHHhcC---CeEEEEcCcHHH
Confidence            45555555555555544445559999999999999999999999999999999999999887554   589999999999


Q ss_pred             HHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcH
Q 015158          120 AQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFK  199 (412)
Q Consensus       120 ~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~  199 (412)
                      +.|+++.+.++..    .+..++|+...       ..+++|+|+||++|.+.+.+....+.++++||+||||++.++++.
T Consensus       240 a~Q~~~~l~~~~~----~VglltGd~~~-------~~~~~IlV~Tpe~L~~~L~~~~~~l~~l~lVVIDEaH~l~d~~rg  308 (1108)
T 3l9o_A          240 SNQKYRELLAEFG----DVGLMTGDITI-------NPDAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMRDKERG  308 (1108)
T ss_dssp             HHHHHHHHHHHTS----SEEEECSSCBC-------CCSCSEEEEEHHHHHHHHHHCSSHHHHEEEEEEETGGGTTSHHHH
T ss_pred             HHHHHHHHHHHhC----CccEEeCcccc-------CCCCCEEEeChHHHHHHHHcCccccccCCEEEEhhhhhccccchH
Confidence            9999999999764    56778887763       345899999999999998877666778999999999999998889


Q ss_pred             HHHHHHHHhCCCCceEEEEeecCChH--HHHHHHHhcCCCeEEEecCCccccCCceEEEEEecc---------c------
Q 015158          200 DQIYDIFQLLPPKIQVGVFSATMPPE--ALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEK---------E------  262 (412)
Q Consensus       200 ~~~~~i~~~~~~~~~~i~~SAT~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------~------  262 (412)
                      ..+..++..++++.+++++|||+++.  ....+......+..+........  .+..+++....         .      
T Consensus       309 ~~~e~ii~~l~~~~qvl~lSATipn~~e~a~~l~~~~~~~~~vi~~~~rp~--pl~~~~~~~~~~~~~~~vd~~~~~~~~  386 (1108)
T 3l9o_A          309 VVWEETIILLPDKVRYVFLSATIPNAMEFAEWICKIHSQPCHIVYTNFRPT--PLQHYLFPAHGDGIYLVVDEKSTFREE  386 (1108)
T ss_dssp             HHHHHHHHHSCTTSEEEEEECSCSSCHHHHHHHHHHTCSCEEEEEECCCSS--CEEEEEEETTSSCCEEEEETTTEECHH
T ss_pred             HHHHHHHHhcCCCceEEEEcCCCCCHHHHHHHHHhhcCCCeEEEecCCCcc--cceEEEeecCCcceeeeeccccchhhh
Confidence            99999999999999999999998764  33455555555554443322211  12222211000         0      


Q ss_pred             ---------------------------------------hhhHHHHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcCCC
Q 015158          263 ---------------------------------------EWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDH  303 (412)
Q Consensus       263 ---------------------------------------~~~~~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~~  303 (412)
                                                             ......+...+.....+++||||++++.|+.++..|...+.
T Consensus       387 ~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~li~~l~~~~~~~vIVF~~sr~~~e~la~~L~~~~~  466 (1108)
T 3l9o_A          387 NFQKAMASISNQIGDDPNSTDSRGKKGQTYKGGSAKGDAKGDIYKIVKMIWKKKYNPVIVFSFSKRDCEELALKMSKLDF  466 (1108)
T ss_dssp             HHHHHHTTC-----------------------------CHHHHHHHHHHHHHTTCCCEEEEESCHHHHHHHHHHTCSHHH
T ss_pred             hHHHHHHHHHhhhcccccccccccccccccccccccccchhHHHHHHHHHHhcCCCCEEEEeCcHHHHHHHHHHHHhccC
Confidence                                                   11222333444445567999999999999999999865322


Q ss_pred             e---------------------------------------eEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCC
Q 015158          304 T---------------------------------------VSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDV  344 (412)
Q Consensus       304 ~---------------------------------------~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~  344 (412)
                      .                                       +..+||++++.+|..+++.|.+|.++|||||+++++|+|+
T Consensus       467 ~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~gV~~~Hg~l~~~~R~~v~~~F~~G~ikVLVAT~vla~GIDi  546 (1108)
T 3l9o_A          467 NSDDEKEALTKIFNNAIALLPETDRELPQIKHILPLLRRGIGIHHSGLLPILKEVIEILFQEGFLKVLFATETFSIGLNM  546 (1108)
T ss_dssp             HCC----CHHHHGGGSCTHHHHHTTCCHHHHHHTHHHHHTEEEECSCSCHHHHHHHHHHHHHTCCCEEEEESCCCSCCCC
T ss_pred             CCHHHHHHHHHHHHHHHhhcchhhhhhhhHHHHHHhhhcCeeeecCCCCHHHHHHHHHHHhCCCCeEEEECcHHhcCCCC
Confidence            1                                       7899999999999999999999999999999999999999


Q ss_pred             CCCCEEEEccC--------CCChhhHHHhhhhcccCC--CCceEEEEeccCcHHHHHHHHHHhccccccCC
Q 015158          345 QQVSLVINYDL--------PTQPENYLHRIGRSGRFG--RKGVAINFVTRDDERMLFDIQKFYNVVIEELP  405 (412)
Q Consensus       345 ~~~~~vi~~~~--------~~s~~~~~Q~~GR~~R~g--~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  405 (412)
                      |++++||....        |.|..+|.||+||+||.|  ..|.|++++++....  ..+.+++.....++.
T Consensus       547 P~v~~VI~~~~~~d~~~~r~iS~~eyiQr~GRAGR~G~d~~G~~ill~~~~~~~--~~~~~l~~~~~~~L~  615 (1108)
T 3l9o_A          547 PAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLDDRGIVIMMIDEKMEP--QVAKGMVKGQADRLD  615 (1108)
T ss_dssp             --CEEEESCSEEESSSCEEECCHHHHHHHHHHSCCSSSCSSEEEEEEECCCCCH--HHHHHHHHCCCCCCC
T ss_pred             CCceEEEecCcccCccccccCCHHHHHHhhcccCCCCCCCceEEEEEecCCcCH--HHHHHHhcCCCcccc
Confidence            99999997655        346778999999999999  578888888776332  234445544444433

>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=2.2e-44  Score=345.96  Aligned_cols=323  Identities=20%  Similarity=0.237  Sum_probs=247.7

Q ss_pred             CChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEE
Q 015158           61 KPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHA  140 (412)
Q Consensus        61 ~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~  140 (412)
                      +|+|+|.++++.+..+ ++++.+|||+|||++++.++...+.  ..+.++||++|+++|+.||.+++.++....+..+..
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            3999999999999999 9999999999999999988887765  234589999999999999999999987444457888


Q ss_pred             EEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEee
Q 015158          141 CVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSA  220 (412)
Q Consensus       141 ~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SA  220 (412)
                      ++|+......... ...++|+|+||+.+.+.+....+...++++||+||||++.+......+...+....+..+++++||
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            8888765543332 235799999999999998887777889999999999998765444555555555566888999999


Q ss_pred             cCChH---HHHHHHHhcCCCeEEEecCCcc-----ccCCceEEEEEec--------------------------------
Q 015158          221 TMPPE---ALEITRKFMNKPVRILVKRDEL-----TLEGIKQFHVNVE--------------------------------  260 (412)
Q Consensus       221 T~~~~---~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~--------------------------------  260 (412)
                      ||..+   .......+..............     ............+                                
T Consensus       165 Tp~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  244 (494)
T 1wp9_A          165 SPGSTPEKIMEVINNLGIEHIEYRSENSPDVRPYVKGIRFEWVRVDLPEIYKEVRKLLREMLRDALKPLAETGLLESSSP  244 (494)
T ss_dssp             CSCSSHHHHHHHHHHTTCCEEEECCTTSTTTGGGCCCCCEEEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHTSSSCCCT
T ss_pred             CCCCCcHHHHHHHHhcChheeeccCCCcHHHHHhcCCCceeEEecCCcHHHHHHHHHHHHHHHHHHHHHHHhccccccCC
Confidence            99743   2223322221111111100000     0000000000000                                


Q ss_pred             --------------------------------------------------------------------------------
Q 015158          261 --------------------------------------------------------------------------------  260 (412)
Q Consensus       261 --------------------------------------------------------------------------------  260 (412)
                                                                                                      
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             ---------------cchhhHHHHHHHHHh----cCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecC--------CCC
Q 015158          261 ---------------KEEWKLETLCDLYET----LAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHG--------DMD  313 (412)
Q Consensus       261 ---------------~~~~~~~~l~~~~~~----~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~--------~~~  313 (412)
                                     ....+...+.+++..    ...+++||||++++.++.+++.|++.++.+..+||        +++
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                           112244555566655    46789999999999999999999999999999999        999


Q ss_pred             HHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHH
Q 015158          314 QNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDER  388 (412)
Q Consensus       314 ~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~  388 (412)
                      ..+|.+++++|++|+.+|||+|+++++|+|+|.+++||++++|+|+..|.||+||+||.|+ |.++.++++.+.+
T Consensus       405 ~~~r~~~~~~F~~~~~~vLv~T~~~~~Gldl~~~~~Vi~~d~~~~~~~~~Qr~GR~~R~g~-g~~~~l~~~~t~e  478 (494)
T 1wp9_A          405 QREQKLILDEFARGEFNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRHMP-GRVIILMAKGTRD  478 (494)
T ss_dssp             CCHHHHHHHHHHHTSCSEEEECGGGGGGGGSTTCCEEEESSCCHHHHHHHHHHTTSCSCCC-SEEEEEEETTSHH
T ss_pred             HHHHHHHHHHHhcCCceEEEECCccccCCCchhCCEEEEeCCCCCHHHHHHHHhhccCCCC-ceEEEEEecCCHH
Confidence            9999999999999999999999999999999999999999999999999999999999998 9999999987654

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=100.00  E-value=5.5e-45  Score=355.59  Aligned_cols=331  Identities=20%  Similarity=0.231  Sum_probs=229.0

Q ss_pred             CChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCC--ceeEEEEcCCHHHHHHHHHHHHHhhcccCcEE
Q 015158           61 KPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLV--ECQALVLAPTRELAQQIEKVMRALGDYLGVKV  138 (412)
Q Consensus        61 ~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~--~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~  138 (412)
                      +|+|+|.++++.++.++++++.+|||+|||++++++++..+.....  +.++||++|+++|+.|+.+.+.++....++.+
T Consensus         4 ~~~~~Q~~~i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~   83 (555)
T 3tbk_A            4 KPRNYQLELALPAKKGKNTIICAPTGCGKTFVSLLICEHHLKKFPCGQKGKVVFFANQIPVYEQQATVFSRYFERLGYNI   83 (555)
T ss_dssp             CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHHTTTCCE
T ss_pred             CCcHHHHHHHHHHhCCCCEEEEeCCCChHHHHHHHHHHHHHHhcccCCCCEEEEEeCCHHHHHHHHHHHHHHhccCCcEE
Confidence            3999999999999999999999999999999999999888765422  56899999999999999999999988778999


Q ss_pred             EEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCC-CCCCceEEEEeCCchhhccC-cHHHHHHHHHhC-----CC
Q 015158          139 HACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSL-RPDNIRIFVLDEADEMLSRG-FKDQIYDIFQLL-----PP  211 (412)
Q Consensus       139 ~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~-~~~~~~~iiiDE~h~~~~~~-~~~~~~~i~~~~-----~~  211 (412)
                      ..++|+............+++|+|+||++|...+..... ...++++||+||||++.+.+ +...+...+...     .+
T Consensus        84 ~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~~vViDEah~~~~~~~~~~~~~~~~~~~~~~~~~~  163 (555)
T 3tbk_A           84 ASISGATSDSVSVQHIIEDNDIIILTPQILVNNLNNGAIPSLSVFTLMIFDECHNTSKNHPYNQIMFRYLDHKLGESRDP  163 (555)
T ss_dssp             EEECTTTGGGSCHHHHHHHCSEEEECHHHHHHHHHTSSSCCGGGCSEEEETTGGGCSTTCHHHHHHHHHHHHHTSSCCSC
T ss_pred             EEEcCCCcchhhHHHHhcCCCEEEECHHHHHHHHhcCcccccccCCEEEEECccccCCcchHHHHHHHHHHhhhccccCC
Confidence            999999876554444555689999999999999887766 67789999999999988764 223333333322     24


Q ss_pred             CceEEEEeecCChHH-------HH---HHHHhcCCCeEEEecC------CccccCCceEEEEEe----------------
Q 015158          212 KIQVGVFSATMPPEA-------LE---ITRKFMNKPVRILVKR------DELTLEGIKQFHVNV----------------  259 (412)
Q Consensus       212 ~~~~i~~SAT~~~~~-------~~---~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~----------------  259 (412)
                      ..+++++||||....       ..   .+...+..........      .....+.........                
T Consensus       164 ~~~~l~lSAT~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  243 (555)
T 3tbk_A          164 LPQVVGLTASVGVGDAKTAEEAMQHICKLCAALDASVIATVRDNVAELEQVVYKPQKISRKVASRTSNTFKCIISQLMKE  243 (555)
T ss_dssp             CCEEEEEESCCCCTTCCSHHHHHHHHHHHHHHTTCSEEECCCSCHHHHHTTCCCCCEEEEECCCCSCCHHHHHHHHHHHH
T ss_pred             CCeEEEEecCcccCccccHHHHHHHHHHHHHhcCCeeeeccccCHHHHHhhcCCCceEEEEecCcccChHHHHHHHHHHH
Confidence            678999999995421       11   1122222111111110      000000000000000                


Q ss_pred             --------------------------------------------------------------------------------
Q 015158          260 --------------------------------------------------------------------------------  259 (412)
Q Consensus       260 --------------------------------------------------------------------------------  259 (412)
                                                                                                      
T Consensus       244 ~~~~~~~~~~~l~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~  323 (555)
T 3tbk_A          244 TEKLAKDVSEELGKLFQIQNREFGTQKYEQWIVGVHKACSVFQMADKEEESRVCKALFLYTSHLRKYNDALIISEDAQMT  323 (555)
T ss_dssp             HHHHHHTSCHHHHGGGGCCSCCSSSHHHHHHHHHHHHHHHTCCCSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCHH
T ss_pred             HHHHHHHHHHhhhhhhhcccccccchhhhHHHHHHHHHhhhhhccchhhHHHHHHHHHHHHHHHHHHHHHHhhhhhhhHH
Confidence                                                                                            


Q ss_pred             -------------------------------------------ccchhhHHHHHHHHHh----cCCCcEEEEEcchhHHH
Q 015158          260 -------------------------------------------EKEEWKLETLCDLYET----LAITQSVIFVNTRRKVD  292 (412)
Q Consensus       260 -------------------------------------------~~~~~~~~~l~~~~~~----~~~~k~lif~~~~~~~~  292 (412)
                                                                 .....+...+.+++..    ...+++||||+++..++
T Consensus       324 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~k~lVF~~~~~~~~  403 (555)
T 3tbk_A          324 DALNYLKAFFHDVREAAFDETERELTRRFEEKLEELEKVSRDPSNENPKLRDLYLVLQEEYHLKPETKTILFVKTRALVD  403 (555)
T ss_dssp             HHHHHHHHHHHHHCC-----HHHHHHHHHHTTHHHHHHHHHCGGGCCHHHHHHHHHHHHHHHHCTTCCEEEECSSHHHHH
T ss_pred             HHHHHHHHHHHHHhhcccchHHHHHHHHHhhhhhhhhhhccCCCcCCHHHHHHHHHHHHHhccCCCceEEEEeCcHHHHH
Confidence                                                       0012234444444443    35589999999999999


Q ss_pred             HHHHHHhcCC------------CeeEEecCCCCHHHHHHHHHHHhc-CCCcEEEEcCCCcCCCCCCCCCEEEEccCCCCh
Q 015158          293 WLTDKMRSRD------------HTVSATHGDMDQNTRDIIMREFRS-GSSRVLITTDLLARGIDVQQVSLVINYDLPTQP  359 (412)
Q Consensus       293 ~~~~~L~~~~------------~~~~~~~~~~~~~~r~~~~~~f~~-g~~~vlv~t~~~~~G~d~~~~~~vi~~~~~~s~  359 (412)
                      .+++.|++.+            .....+||+++..+|.+++++|++ |+.+|||||+++++|+|+|++++||+++.|+|+
T Consensus       404 ~l~~~L~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~R~~~~~~F~~~g~~~vLvaT~~~~~GlDlp~v~~VI~~d~p~s~  483 (555)
T 3tbk_A          404 ALKKWIEENPALSFLKPGILTGRGRTNRATGMTLPAQKCVLEAFRASGDNNILIATSVADEGIDIAECNLVILYEYVGNV  483 (555)
T ss_dssp             HHHHHHHHCGGGTTCCEEECCC--------------------------CCSEEEECCCTTCCEETTSCSEEEEESCCSSC
T ss_pred             HHHHHHhhCcCcCceeeeEEEecCCcccccccCHHHHHHHHHHHhcCCCeeEEEEcchhhcCCccccCCEEEEeCCCCCH
Confidence            9999998763            344555679999999999999999 999999999999999999999999999999999


Q ss_pred             hhHHHhhhhcccCCCCceEEEEeccCcHHHHHHH
Q 015158          360 ENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDI  393 (412)
Q Consensus       360 ~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~  393 (412)
                      ..|.||+|| ||. .+|.+++++++.+......+
T Consensus       484 ~~~~Qr~GR-gR~-~~g~~~~l~~~~~~~~~~~~  515 (555)
T 3tbk_A          484 IKMIQTRGR-GRA-RDSKCFLLTSSADVIEKEKA  515 (555)
T ss_dssp             CCEECSSCC-CTT-TSCEEEEEESCHHHHHHHHH
T ss_pred             HHHHHhcCc-CcC-CCceEEEEEcCCCHHHHHHH
Confidence            999999999 998 89999999999877666555

>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=3.3e-44  Score=361.64  Aligned_cols=331  Identities=18%  Similarity=0.207  Sum_probs=207.8

Q ss_pred             HCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCC--ceeEEEEcCCHHHHHHHHHHHHHhhcc
Q 015158           56 AYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLV--ECQALVLAPTRELAQQIEKVMRALGDY  133 (412)
Q Consensus        56 ~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~--~~~~lil~P~~~L~~q~~~~~~~~~~~  133 (412)
                      .+|+..|+|+|.++++.++.|+++++.+|||+|||++++++++..+.....  ++++||++|+++|+.|+.+.+.++...
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            346778999999999999999999999999999999999999988765421  568999999999999999999999887


Q ss_pred             cCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCC-CCCCceEEEEeCCchhhccCcHHH-HHHHHHh---
Q 015158          134 LGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSL-RPDNIRIFVLDEADEMLSRGFKDQ-IYDIFQL---  208 (412)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~-~~~~~~~iiiDE~h~~~~~~~~~~-~~~i~~~---  208 (412)
                      .++.+..++|+............+++|+|+||++|.+.+....+ ...++++||+||||++.+...... +..+...   
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            78999999998876555555556789999999999999887666 677899999999999886653322 2233322   


Q ss_pred             -CCCCceEEEEeecCCh-----------HHHHHHHHhcCCCeEEEecCC------ccccCCceEEEEE------------
Q 015158          209 -LPPKIQVGVFSATMPP-----------EALEITRKFMNKPVRILVKRD------ELTLEGIKQFHVN------------  258 (412)
Q Consensus       209 -~~~~~~~i~~SAT~~~-----------~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~------------  258 (412)
                       ..+..+++++||||..           .... +...++..........      ....+........            
T Consensus       403 ~~~~~~~~l~lSATp~~~~~~~~~~~~~~i~~-l~~~L~~~~i~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~  481 (797)
T 4a2q_A          403 SASQLPQILGLTASVGVGNAKNIEETIEHICS-LCSYLDIQAISTVRENIQELQRFMNKPEIDVRLVKRRIHNPFAAIIS  481 (797)
T ss_dssp             TCCCCCEEEEEESCCCCTTCCSHHHHHHHHHH-HHHHHTCSEEECCCTTHHHHHHHSCCCCCEEEECCCCSCCHHHHHHH
T ss_pred             cCCCCCeEEEEcCCccccccccHHHHHHHHHH-HHHhcCCcEEecccccHHHHHHhcCCCceEEEecCCCCCcHHHHHHH
Confidence             1456889999999952           1111 1111221111100000      0000000000000            


Q ss_pred             --------------------------ec----------------------------------------------------
Q 015158          259 --------------------------VE----------------------------------------------------  260 (412)
Q Consensus       259 --------------------------~~----------------------------------------------------  260 (412)
                                                ..                                                    
T Consensus       482 ~l~~~i~~~~~~~~~l~~l~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~~~  561 (797)
T 4a2q_A          482 NLMSETEALMRTIYSVDTLSQNSKKDFGTQNYEHWIVVTQRKCRLLQLEDKEEESRICRALFICTEHLRKYNDALIISED  561 (797)
T ss_dssp             HHHHHHHHHHHHC------------CCSSHHHHHHHHHHHHHHHHCCCSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhHHhhhhccccccchhHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHHHHHHHHHHHHhhhcc
Confidence                                      00                                                    


Q ss_pred             ------------------------------------------------cchhhHHHHHHHHHh----cCCCcEEEEEcch
Q 015158          261 ------------------------------------------------KEEWKLETLCDLYET----LAITQSVIFVNTR  288 (412)
Q Consensus       261 ------------------------------------------------~~~~~~~~l~~~~~~----~~~~k~lif~~~~  288 (412)
                                                                      ....+...+.+++..    ...+++||||+++
T Consensus       562 ~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~~~~~~~~K~~~L~~lL~~~~~~~~~~kvLIF~~~~  641 (797)
T 4a2q_A          562 ARIIDALSYLTEFFTNVKNGPYTELEQHLTAKFQEKEPELIALSKDETNENPKLEELVCILDDAYRYNPQTRTLLFAKTR  641 (797)
T ss_dssp             SCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHTTHHHHHHHHHCTTCCCHHHHHHHHHHHHHHHHCSSCCEEEEESSH
T ss_pred             ccHHHHHHHHHHHHHHHhccCccHHHHHHHHHHHHHHHHHHHhhcCCCCCChHHHHHHHHHHHHhccCCCCeEEEEECcH
Confidence                                                            011233444445543    4568999999999


Q ss_pred             hHHHHHHHHHhcC------------CCeeEEecCCCCHHHHHHHHHHHhc-CCCcEEEEcCCCcCCCCCCCCCEEEEccC
Q 015158          289 RKVDWLTDKMRSR------------DHTVSATHGDMDQNTRDIIMREFRS-GSSRVLITTDLLARGIDVQQVSLVINYDL  355 (412)
Q Consensus       289 ~~~~~~~~~L~~~------------~~~~~~~~~~~~~~~r~~~~~~f~~-g~~~vlv~t~~~~~G~d~~~~~~vi~~~~  355 (412)
                      ..++.+++.|++.            |.....+||+++..+|..++++|++ |+.+|||||+++++|+|+|.+++||+++.
T Consensus       642 ~~~~~L~~~L~~~~~~~~~~~~~l~G~~~~~~hg~~~~~eR~~~l~~F~~~g~~~vLVaT~~~~~GIDlp~v~~VI~yd~  721 (797)
T 4a2q_A          642 ALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEY  721 (797)
T ss_dssp             HHHHHHHHHHHTCSTTCSCCCEEC----------------------------CCSEEEEECC-------CCCSEEEEESC
T ss_pred             HHHHHHHHHHHhCcccccccceEEEecCCcccCCCCCHHHHHHHHHHhhccCCceEEEEcCchhcCCCchhCCEEEEeCC
Confidence            9999999999874            5566677889999999999999999 99999999999999999999999999999


Q ss_pred             CCChhhHHHhhhhcccCCCCceEEEEeccCcHHH
Q 015158          356 PTQPENYLHRIGRSGRFGRKGVAINFVTRDDERM  389 (412)
Q Consensus       356 ~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~  389 (412)
                      |+|+..|+||+|| ||. .+|.++++++..+...
T Consensus       722 p~s~~~~iQr~GR-GR~-~~g~~i~l~~~~~~ee  753 (797)
T 4a2q_A          722 SGNVTKMIQVRGR-GRA-AGSKCILVTSKTEVVE  753 (797)
T ss_dssp             CSCHHHHHTC---------CCCEEEEECCHHHHH
T ss_pred             CCCHHHHHHhcCC-CCC-CCceEEEEEeCCcHHH
Confidence            9999999999999 999 8899999998876543

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=100.00  E-value=1.4e-42  Score=352.72  Aligned_cols=310  Identities=17%  Similarity=0.261  Sum_probs=244.9

Q ss_pred             HCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccC
Q 015158           56 AYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLG  135 (412)
Q Consensus        56 ~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~  135 (412)
                      .++|. |+++|.++++.+.+|+++++.+|||+|||+++++++......+   .+++|++|+++|+.|+++.+.++..  +
T Consensus        35 ~~~f~-l~~~Q~~aI~~il~g~~vlv~apTGsGKTlv~~~~i~~~~~~g---~~vlvl~PtraLa~Q~~~~l~~~~~--~  108 (997)
T 4a4z_A           35 SWPFE-LDTFQKEAVYHLEQGDSVFVAAHTSAGKTVVAEYAIAMAHRNM---TKTIYTSPIKALSNQKFRDFKETFD--D  108 (997)
T ss_dssp             CCSSC-CCHHHHHHHHHHHTTCEEEEECCTTSCSHHHHHHHHHHHHHTT---CEEEEEESCGGGHHHHHHHHHTTC----
T ss_pred             hCCCC-CCHHHHHHHHHHHcCCCEEEEECCCCcHHHHHHHHHHHHHhcC---CeEEEEeCCHHHHHHHHHHHHHHcC--C
Confidence            45676 9999999999999999999999999999999988888766543   5899999999999999999988653  6


Q ss_pred             cEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceE
Q 015158          136 VKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQV  215 (412)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~  215 (412)
                      ..+..++|+....       ...+|+|+||+.|.+.+......+.++++||+||||++.++++...+..++..++++.++
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 VNIGLITGDVQIN-------PDANCLIMTTEILRSMLYRGADLIRDVEFVIFDEVHYVNDQDRGVVWEEVIIMLPQHVKF  181 (997)
T ss_dssp             CCEEEECSSCEEC-------TTSSEEEEEHHHHHHHHHHTCSGGGGEEEEEECCTTCCCTTCTTCCHHHHHHHSCTTCEE
T ss_pred             CeEEEEeCCCccC-------CCCCEEEECHHHHHHHHHhCchhhcCCCEEEEECcccccccchHHHHHHHHHhcccCCCE
Confidence            7788888877533       347999999999999888777667889999999999999998888899999999999999


Q ss_pred             EEEeecCChHHHHHHHHhc---CCCeEEEecCCccccCCceEEE------------------------------------
Q 015158          216 GVFSATMPPEALEITRKFM---NKPVRILVKRDELTLEGIKQFH------------------------------------  256 (412)
Q Consensus       216 i~~SAT~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~------------------------------------  256 (412)
                      +++|||+++.. ++..++.   .....+......  +..+...+                                    
T Consensus       182 IlLSAT~~n~~-ef~~~l~~~~~~~~~vi~~~~r--~~pl~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  258 (997)
T 4a4z_A          182 ILLSATVPNTY-EFANWIGRTKQKNIYVISTPKR--PVPLEINIWAKKELIPVINQNSEFLEANFRKHKEILNGESAKGA  258 (997)
T ss_dssp             EEEECCCTTHH-HHHHHHHHHHTCCEEEEECSSC--SSCEEEEEEETTEEEEEECTTCCBCHHHHHHHHHHHC-------
T ss_pred             EEEcCCCCChH-HHHHHHhcccCCceEEEecCCC--CccceEEEecCCcchhcccchhhhhHHHHHHHHHHhhccccccc
Confidence            99999987542 3333221   122222111111  00111110                                    


Q ss_pred             --------------------------------------------------------EEeccchhhHHHHHHHHHhcCCCc
Q 015158          257 --------------------------------------------------------VNVEKEEWKLETLCDLYETLAITQ  280 (412)
Q Consensus       257 --------------------------------------------------------~~~~~~~~~~~~l~~~~~~~~~~k  280 (412)
                                                                              ............+...+......+
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                                                                    000011233556667777777789


Q ss_pred             EEEEEcchhHHHHHHHHHhcCCC---------------------------------------eeEEecCCCCHHHHHHHH
Q 015158          281 SVIFVNTRRKVDWLTDKMRSRDH---------------------------------------TVSATHGDMDQNTRDIIM  321 (412)
Q Consensus       281 ~lif~~~~~~~~~~~~~L~~~~~---------------------------------------~~~~~~~~~~~~~r~~~~  321 (412)
                      +||||++++.|+.++..|.+.++                                       .+..+||++++.+|..++
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            99999999999999999987655                                       478999999999999999


Q ss_pred             HHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccCCC---------ChhhHHHhhhhcccCC--CCceEEEEe
Q 015158          322 REFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPT---------QPENYLHRIGRSGRFG--RKGVAINFV  382 (412)
Q Consensus       322 ~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~~~---------s~~~~~Q~~GR~~R~g--~~g~~~~~~  382 (412)
                      +.|.+|.++|||+|+++++|+|+|+ ..||+.+.+.         |..+|.||+||+||.|  ..|.|++++
T Consensus       419 ~~F~~G~~kVLvAT~~~a~GIDiP~-~~VVi~~~~k~dg~~~~~~s~~~y~Qr~GRAGR~G~~~~G~vi~l~  489 (997)
T 4a4z_A          419 ILFSKGFIKVLFATETFAMGLNLPT-RTVIFSSIRKHDGNGLRELTPGEFTQMAGRAGRRGLDSTGTVIVMA  489 (997)
T ss_dssp             HHHHTTCCSEEEECTHHHHSCCCCC-SEEEESCSEEEETTEEEECCHHHHHHHHGGGCCTTTCSSEEEEEEC
T ss_pred             HHHHCCCCcEEEEchHhhCCCCCCC-ceEEEeccccccCccCCCCCHHHHhHHhcccccCCCCcceEEEEec
Confidence            9999999999999999999999999 6666666655         9999999999999998  457777777

>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=6.9e-43  Score=355.39  Aligned_cols=331  Identities=18%  Similarity=0.218  Sum_probs=205.9

Q ss_pred             HCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCC--ceeEEEEcCCHHHHHHHHHHHHHhhcc
Q 015158           56 AYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLV--ECQALVLAPTRELAQQIEKVMRALGDY  133 (412)
Q Consensus        56 ~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~--~~~~lil~P~~~L~~q~~~~~~~~~~~  133 (412)
                      ..++..|+++|.++++.++.|+++++.+|||+|||++++++++..+.....  +.++||++|+++|+.|+.+++.++...
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            345777999999999999999999999999999999999999887765421  568999999999999999999999887


Q ss_pred             cCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCC-CCCCceEEEEeCCchhhccCc-HHHHHHHHHh---
Q 015158          134 LGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSL-RPDNIRIFVLDEADEMLSRGF-KDQIYDIFQL---  208 (412)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~-~~~~~~~iiiDE~h~~~~~~~-~~~~~~i~~~---  208 (412)
                      .++.+..++|+............+++|+|+||++|.+.+....+ ...++++||+||||++...+. ...+..+...   
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            78999999998865443333444679999999999999887666 577899999999999886642 2223333332   


Q ss_pred             -CCCCceEEEEeecCCh-----------HHHHHHH------------------HhcCCCeEEEecCCccccCC-------
Q 015158          209 -LPPKIQVGVFSATMPP-----------EALEITR------------------KFMNKPVRILVKRDELTLEG-------  251 (412)
Q Consensus       209 -~~~~~~~i~~SAT~~~-----------~~~~~~~------------------~~~~~~~~~~~~~~~~~~~~-------  251 (412)
                       ..+..+++++||||..           .......                  .+...+..............       
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             1456889999999952           1111111                  11111111111100000000       


Q ss_pred             -----------------ceEEE-EEec-----------------------------------------------------
Q 015158          252 -----------------IKQFH-VNVE-----------------------------------------------------  260 (412)
Q Consensus       252 -----------------~~~~~-~~~~-----------------------------------------------------  260 (412)
                                       +.... ....                                                     
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                             00000 0000                                                     


Q ss_pred             -----------------------------------------------cchhhHHHHHHHHHh----cCCCcEEEEEcchh
Q 015158          261 -----------------------------------------------KEEWKLETLCDLYET----LAITQSVIFVNTRR  289 (412)
Q Consensus       261 -----------------------------------------------~~~~~~~~l~~~~~~----~~~~k~lif~~~~~  289 (412)
                                                                     ....+...+.+++..    ...+++||||++++
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                                                           011233344455554    34589999999999


Q ss_pred             HHHHHHHHHhcC------------CCeeEEecCCCCHHHHHHHHHHHhc-CCCcEEEEcCCCcCCCCCCCCCEEEEccCC
Q 015158          290 KVDWLTDKMRSR------------DHTVSATHGDMDQNTRDIIMREFRS-GSSRVLITTDLLARGIDVQQVSLVINYDLP  356 (412)
Q Consensus       290 ~~~~~~~~L~~~------------~~~~~~~~~~~~~~~r~~~~~~f~~-g~~~vlv~t~~~~~G~d~~~~~~vi~~~~~  356 (412)
                      .++.+++.|.+.            |.....+||+++..+|.+++++|++ |+++|||+|+++++|+|+|.+++||+++.|
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            999999999976            5556667888999999999999999 999999999999999999999999999999


Q ss_pred             CChhhHHHhhhhcccCCCCceEEEEeccCcHH
Q 015158          357 TQPENYLHRIGRSGRFGRKGVAINFVTRDDER  388 (412)
Q Consensus       357 ~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~  388 (412)
                      +|+..|+||+|| ||. ..|.++++++..+..
T Consensus       723 ~s~~~~iQr~GR-GR~-~~g~vi~Li~~~t~e  752 (936)
T 4a2w_A          723 GNVTKMIQVRGR-GRA-AGSKCILVTSKTEVV  752 (936)
T ss_dssp             SCSHHHHCC---------CCCEEEEESCHHHH
T ss_pred             CCHHHHHHhcCC-CCC-CCCEEEEEEeCCCHH
Confidence            999999999999 999 789999998886554

>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=7.3e-43  Score=357.60  Aligned_cols=321  Identities=20%  Similarity=0.246  Sum_probs=255.4

Q ss_pred             HCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccC
Q 015158           56 AYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLG  135 (412)
Q Consensus        56 ~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~  135 (412)
                      ..||. |+++|.++++.+++|+++++++|||||||++++.+++..+.   .+.++||++|+++|+.|+.+.+.++. ..+
T Consensus        74 ~~gf~-pt~iQ~~ai~~il~g~dvlv~ApTGSGKTl~~l~~il~~~~---~~~~~Lil~PtreLa~Q~~~~l~~l~-~~~  148 (1104)
T 4ddu_A           74 KFGKD-LTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLAR---KGKKSALVFPTVTLVKQTLERLQKLA-DEK  148 (1104)
T ss_dssp             HSSSC-CCHHHHHHHHHHTTTCCEEECCSTTCCHHHHHHHHHHHHHT---TTCCEEEEESSHHHHHHHHHHHHTTS-CTT
T ss_pred             hcCCC-CCHHHHHHHHHHHcCCCEEEEeCCCCcHHHHHHHHHHHHHh---cCCeEEEEechHHHHHHHHHHHHHhh-CCC
Confidence            36885 99999999999999999999999999999988888877663   34589999999999999999999976 668


Q ss_pred             cEEEEEEcCcch---HHHHHHhc-CCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhc-----------cCcHH
Q 015158          136 VKVHACVGGTSV---REDQRILS-SGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLS-----------RGFKD  200 (412)
Q Consensus       136 ~~~~~~~~~~~~---~~~~~~~~-~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~-----------~~~~~  200 (412)
                      +.+..++|+...   ......+. +.++|+|+||++|.+++..  +...++++||+||||++..           ++|..
T Consensus       149 i~v~~l~Gg~~~~er~~~~~~l~~g~~~IlV~Tp~rL~~~l~~--l~~~~l~~lViDEaH~l~~~~r~~Dr~L~~~gf~~  226 (1104)
T 4ddu_A          149 VKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREK--LSQKRFDFVFVDDVDAVLKASRNIDTLLMMVGIPE  226 (1104)
T ss_dssp             SCEEEECTTCCTTHHHHHHHHHHTSCCSEEEEEHHHHHHSHHH--HHTSCCSEEEESCHHHHTTSSHHHHHHHHTSSCCH
T ss_pred             CeEEEEeCCCCHHHHHHHHHHHhCCCCCEEEECHHHHHHHHHh--hcccCcCEEEEeCCCccccccccchhhhHhcCCCH
Confidence            899999999876   33333344 4589999999999877654  4456899999999997664           56666


Q ss_pred             H-HHHHHHhCC-----------CCceEEEEeecC-ChHHH-HHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhH
Q 015158          201 Q-IYDIFQLLP-----------PKIQVGVFSATM-PPEAL-EITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKL  266 (412)
Q Consensus       201 ~-~~~i~~~~~-----------~~~~~i~~SAT~-~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  266 (412)
                      . +..++..++           .+.+++++|||+ +.... ........    +..........++.+.+...    .+.
T Consensus       227 ~~i~~il~~l~~~~~~~~~~~~~~~q~ll~SAT~~p~~~~~~~~~~~l~----i~v~~~~~~~~~i~~~~~~~----~k~  298 (1104)
T 4ddu_A          227 EIIRKAFSTIKQGKIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLLN----FTVGRLVSVARNITHVRISS----RSK  298 (1104)
T ss_dssp             HHHHHHHHHHHHTSCCCCCSSCCCCEEEEECBSSCCCSSTTHHHHHHTC----CCCCBCCCCCCCEEEEEESC----CCH
T ss_pred             HHHHHHHHhcccchhhhhhccCCCceEEEEcCCCCcHHHHHHHhhccee----EEeccCCCCcCCceeEEEec----CHH
Confidence            6 778887776           789999999994 43322 22333332    22233333445555555544    245


Q ss_pred             HHHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcCCCeeE-EecCCCCHHHHHHHHHHHhcCCCcEEEE----cCCCcCC
Q 015158          267 ETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVS-ATHGDMDQNTRDIIMREFRSGSSRVLIT----TDLLARG  341 (412)
Q Consensus       267 ~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~-~~~~~~~~~~r~~~~~~f~~g~~~vlv~----t~~~~~G  341 (412)
                      ..+.+++.... +++||||++++.++.+++.|++.++.+. .+||.     |.+ ++.|++|+.+||||    |+++++|
T Consensus       299 ~~L~~ll~~~~-~~~LVF~~s~~~a~~l~~~L~~~g~~~~~~lhg~-----rr~-l~~F~~G~~~VLVatas~TdvlarG  371 (1104)
T 4ddu_A          299 EKLVELLEIFR-DGILIFAQTEEEGKELYEYLKRFKFNVGETWSEF-----EKN-FEDFKVGKINILIGVQAYYGKLTRG  371 (1104)
T ss_dssp             HHHHHHHHHHC-SSEEEEESSSHHHHHHHHHHHHTTCCEEESSSSH-----HHH-HHHHHHTSCSEEEEETTTHHHHCCS
T ss_pred             HHHHHHHHhcC-CCEEEEECcHHHHHHHHHHHHhCCCCeeeEecCc-----HHH-HHHHHCCCCCEEEEecCCCCeeEec
Confidence            56667776643 8999999999999999999999999998 99982     555 99999999999999    9999999


Q ss_pred             CCCCC-CCEEEEccCCC---------------------------------------------------------------
Q 015158          342 IDVQQ-VSLVINYDLPT---------------------------------------------------------------  357 (412)
Q Consensus       342 ~d~~~-~~~vi~~~~~~---------------------------------------------------------------  357 (412)
                      +|+|+ +++||+++.|.                                                               
T Consensus       372 IDip~~V~~VI~~d~P~~~~Sle~~~~~~~~~~~l~~l~~~~~~~~~~~~~~~~e~~~~~l~~~~~~~~i~~~~~~l~~~  451 (1104)
T 4ddu_A          372 VDLPERIKYVIFWGTPSMRFSLELDKAPRFVLARVLKEMGLIKAQENPDVEELRKIAKEHLTQKEFVEKVKEMFRGVVVK  451 (1104)
T ss_dssp             CCCTTTCCEEEEESCCEEEEECSSSSCCHHHHHHHHHHHSSCSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHCCSSEEE
T ss_pred             CcCCCCCCEEEEECCCCCCCCcccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccHHHHHHHhhccceEEec
Confidence            99999 99999999998                                                               


Q ss_pred             ---------ChhhHHHhhhhcccCCCCc--eEEEEeccCcHHHHHHHHHHhc
Q 015158          358 ---------QPENYLHRIGRSGRFGRKG--VAINFVTRDDERMLFDIQKFYN  398 (412)
Q Consensus       358 ---------s~~~~~Q~~GR~~R~g~~g--~~~~~~~~~~~~~~~~~~~~~~  398 (412)
                               +...|+||+||+||.|..|  .++.++..+|.+.++.+++.++
T Consensus       452 ~~~~~~~~pd~~tYihr~GRtgR~~~gg~~~Glsi~~~~d~~~~~~l~~~~~  503 (1104)
T 4ddu_A          452 DEDLELIIPDVYTYIQASGRSSRILNGVLVKGVSVIFEEDEEIFESLKTRLL  503 (1104)
T ss_dssp             TTTTEEEEECHHHHHHHHHTTCCEETTEECCEEEEEECCCHHHHHHHHHHHH
T ss_pred             CCeeEEEecChhhhhcccCchhcccCCCcccceEEEEEecHHHHHHHHHHHh
Confidence                     6778999999999976543  4555555688888888888876

>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=7.1e-43  Score=349.16  Aligned_cols=322  Identities=18%  Similarity=0.225  Sum_probs=221.0

Q ss_pred             CChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCC---CceeEEEEcCCHHHHHHH-HHHHHHhhcccCc
Q 015158           61 KPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGL---VECQALVLAPTRELAQQI-EKVMRALGDYLGV  136 (412)
Q Consensus        61 ~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~---~~~~~lil~P~~~L~~q~-~~~~~~~~~~~~~  136 (412)
                      +|+++|.++++.++.|+++++.+|||+|||++|++++...+..+.   ...++||++|+++|+.|| .+++.++... ++
T Consensus         7 ~l~~~Q~~~i~~il~g~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~vlvl~P~~~L~~Q~~~~~l~~~~~~-~~   85 (699)
T 4gl2_A            7 QLRPYQMEVAQPALEGKNIIICLPTGCGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEFQPFLKK-WY   85 (699)
T ss_dssp             CCCHHHHHHHHHHHSSCCEEECCCTTSCHHHHHHHHHHHHHHHHHHHTCCCCBCCEESCSHHHHHHHHHTHHHHHTT-TS
T ss_pred             CccHHHHHHHHHHHhCCCEEEEcCCCCcHHHHHHHHHHHHHHhccccCCCCeEEEEECCHHHHHHHHHHHHHHHcCc-Cc
Confidence            399999999999999999999999999999999999988765431   125799999999999999 9999998754 47


Q ss_pred             EEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHH------HcCCCCCCCceEEEEeCCchhhccC-cHHHHHHHHHhC
Q 015158          137 KVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDML------RRQSLRPDNIRIFVLDEADEMLSRG-FKDQIYDIFQLL  209 (412)
Q Consensus       137 ~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~------~~~~~~~~~~~~iiiDE~h~~~~~~-~~~~~~~i~~~~  209 (412)
                      .+..++|+..............+|+|+||+.|.+.+      ....+...++++||+||||++.... +...+..+....
T Consensus        86 ~v~~~~g~~~~~~~~~~~~~~~~Ilv~Tp~~L~~~l~~~~~~~~~~~~~~~~~lvViDEaH~~~~~~~~~~i~~~~l~~~  165 (699)
T 4gl2_A           86 RVIGLSGDTQLKISFPEVVKSCDIIISTAQILENSLLNLENGEDAGVQLSDFSLIIIDECHHTNKEAVYNNIMRHYLMQK  165 (699)
T ss_dssp             CEEEEC----CCCCHHHHHHSCSEEEEEHHHHHHHTC--------CCCGGGCSEEEEESGGGCBTTBSSCSHHHHHHHHH
T ss_pred             eEEEEeCCcchhhHHHhhhcCCCEEEECHHHHHHHHhccccccccceecccCcEEEEECccccCccchHHHHHHHHHHhh
Confidence            888888887655444445567899999999999887      3444667789999999999876433 333333222211


Q ss_pred             -------------CCCceEEEEeecCChH-------HHHHHH---HhcCC-CeEEEecC-Cc----cccCCceEEEEEec
Q 015158          210 -------------PPKIQVGVFSATMPPE-------ALEITR---KFMNK-PVRILVKR-DE----LTLEGIKQFHVNVE  260 (412)
Q Consensus       210 -------------~~~~~~i~~SAT~~~~-------~~~~~~---~~~~~-~~~~~~~~-~~----~~~~~~~~~~~~~~  260 (412)
                                   .+..+++++||||...       ....+.   ..+.. .+...... ..    ...+..........
T Consensus       166 ~~~~~~~~~~~~~~~~~~il~lTATp~~~~~~~~~~~~~~i~~l~~~l~~~~i~~~~~~~~~l~~~~~~p~~~~~~~~~~  245 (699)
T 4gl2_A          166 LKNNRLKKENKPVIPLPQILGLTASPGVGGATKQAKAEEHILKLCANLDAFTIKTVKENLDQLKNQIQEPCKKFAIADAT  245 (699)
T ss_dssp             HHHHHHHC----CCCCCEEEEECSCCCCCSCCSHHHHHHHHHHHHHHHTCSCCCCCCTTHHHHHHHSCCCEEEEEEEC--
T ss_pred             hcccccccccccCCCCCEEEEecccccccccccHHHHHHHHHHHHhhcCCCEEEeecCchHHHhhhcCCCceEEEEcccc
Confidence                         1567899999999862       111111   11111 00000000 00    00000000000000


Q ss_pred             --------------------------------------------------------------------------------
Q 015158          261 --------------------------------------------------------------------------------  260 (412)
Q Consensus       261 --------------------------------------------------------------------------------  260 (412)
                                                                                                      
T Consensus       246 ~~~~~~~~l~~l~~~i~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~  325 (699)
T 4gl2_A          246 REDPFKEKLLEIMTRIQTYCQMSPMSDFGTQPYEQWAIQMEKKAAKEGNRKERVCAEHLRKYNEALQINDTIRMIDAYTH  325 (699)
T ss_dssp             ---CHHHHHHHHHHHHHHHHTCCCCSCSSSHHHHHHHHHHHHHHHHHTCTTTHHHHHHHHHHHHHHHHHHHSCHHHHHHH
T ss_pred             cCChHHHHHHHHHHHHHHHhccCcchhccchHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence                                                                                            


Q ss_pred             ---------------------------c-------------------------chhh----HHHHHHHHHhcC-CCcEEE
Q 015158          261 ---------------------------K-------------------------EEWK----LETLCDLYETLA-ITQSVI  283 (412)
Q Consensus       261 ---------------------------~-------------------------~~~~----~~~l~~~~~~~~-~~k~li  283 (412)
                                                 .                         ...+    ...+.+.+.... .+++||
T Consensus       326 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~~~~~~~~k~~~L~~~L~~~~~~~~~~~~~IV  405 (699)
T 4gl2_A          326 LETFYNEEKDKKFAVIEDDLKKPLKLDETDRFLMTLFFENNKMLKRLAENPEYENEKLTKLRNTIMEQYTRTEESARGII  405 (699)
T ss_dssp             HHHHHHHHHHHHC------------CCHHHHHHHHHHHHHHHHHHHHHTCCC----CSSCSHHHHHHHHHHSSSCCCEEE
T ss_pred             HHHHHHHHHhhhccccccccccccccchhHHHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHhcCCCCCcEEE
Confidence                                       0                         0001    111222222223 689999


Q ss_pred             EEcchhHHHHHHHHHhcC------CCeeEEecCC--------CCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCE
Q 015158          284 FVNTRRKVDWLTDKMRSR------DHTVSATHGD--------MDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSL  349 (412)
Q Consensus       284 f~~~~~~~~~~~~~L~~~------~~~~~~~~~~--------~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~  349 (412)
                      ||++++.++.+++.|++.      |+.+..+||+        ++..+|.+++++|++|+.+|||+|+++++|+|+|++++
T Consensus       406 F~~s~~~~~~l~~~L~~~~~l~~~g~~~~~lhg~~~~~~~~~~~~~eR~~~~~~F~~g~~~VLVaT~~~~~GIDip~v~~  485 (699)
T 4gl2_A          406 FTKTRQSAYALSQWITENEKFAEVGVKAHHLIGAGHSSEFKPMTQNEQKEVISKFRTGKINLLIATTVAEEGLDIKECNI  485 (699)
T ss_dssp             ECSCHHHHHHHHHHHHSSCSCC-----CEECCCSCCCTTCCCCCHHHHHHHHHHHCC---CCSEEECSCCTTSCCCSCCC
T ss_pred             EECcHHHHHHHHHHHHhCccccccCcceEEEECCCCccCCCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCccccCCE
Confidence            999999999999999987      8999999999        99999999999999999999999999999999999999


Q ss_pred             EEEccCCCChhhHHHhhhhcccCCCCceEEEEeccC
Q 015158          350 VINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRD  385 (412)
Q Consensus       350 vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~  385 (412)
                      ||++++|+|+..|.||+||+||.|  +.++++....
T Consensus       486 VI~~d~p~s~~~~~Qr~GRArr~g--~~~~l~~~~~  519 (699)
T 4gl2_A          486 VIRYGLVTNEIAMVQARGRARADE--STYVLVAHSG  519 (699)
T ss_dssp             CEEESCCCCHHHHHHHHTTSCSSS--CEEEEEEESS
T ss_pred             EEEeCCCCCHHHHHHHcCCCCCCC--ceEEEEEeCC
Confidence            999999999999999999986654  4444444433

>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=5.7e-43  Score=358.73  Aligned_cols=321  Identities=19%  Similarity=0.273  Sum_probs=252.1

Q ss_pred             HHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhccc
Q 015158           55 YAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYL  134 (412)
Q Consensus        55 ~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~  134 (412)
                      ..+||. | ++|.++++.++.|+++++.+|||||||+ +.++++..+..  .+.+++|++|+++|+.|+.+.+..++...
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            347999 9 9999999999999999999999999998 66666655543  34689999999999999999999998877


Q ss_pred             Cc----EEEEEEcCcchHHH---HHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHH
Q 015158          135 GV----KVHACVGGTSVRED---QRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQ  207 (412)
Q Consensus       135 ~~----~~~~~~~~~~~~~~---~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~  207 (412)
                      ++    .+..++|+......   ...+.. ++|+|+||++|...+.+    +.++++||+||||++.++  ...+..++.
T Consensus       127 ~i~~~~~v~~~~Gg~~~~~~~~~~~~l~~-~~IlV~TP~~L~~~l~~----L~~l~~lViDEah~~l~~--~~~~~~i~~  199 (1054)
T 1gku_B          127 GVGTENLIGYYHGRIPKREKENFMQNLRN-FKIVITTTQFLSKHYRE----LGHFDFIFVDDVDAILKA--SKNVDKLLH  199 (1054)
T ss_dssp             CCSGGGSEEECCSSCCSHHHHHHHHSGGG-CSEEEEEHHHHHHCSTT----SCCCSEEEESCHHHHHTS--THHHHHHHH
T ss_pred             CCCccceEEEEeCCCChhhHHHHHhhccC-CCEEEEcHHHHHHHHHH----hccCCEEEEeChhhhhhc--cccHHHHHH
Confidence            77    88999998876553   233344 89999999999987664    458999999999998884  477777776


Q ss_pred             hCC-----------CCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhHHHHHHHHHhc
Q 015158          208 LLP-----------PKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETL  276 (412)
Q Consensus       208 ~~~-----------~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  276 (412)
                      .+.           ...+.+++|||++.. ......++..+..+...........+.+.+..    ..+...+.++++..
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            663           456789999998875 32222222222222223333334445555442    33455566666665


Q ss_pred             CCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEE----cCCCcCCCCCCCC-CEEE
Q 015158          277 AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLIT----TDLLARGIDVQQV-SLVI  351 (412)
Q Consensus       277 ~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~----t~~~~~G~d~~~~-~~vi  351 (412)
                       .+++||||++++.++.+++.|++. +.+..+||++     ..+++.|++|+.+||||    |+++++|+|+|++ ++||
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             EccCC-----------------------------------------------------------------------CChh
Q 015158          352 NYDLP-----------------------------------------------------------------------TQPE  360 (412)
Q Consensus       352 ~~~~~-----------------------------------------------------------------------~s~~  360 (412)
                      +++.|                                                                       .|..
T Consensus       348 ~~~~P~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~  427 (1054)
T 1gku_B          348 FVGCPSFRVTIEDIDSLSPQMVKLLAYLYRNVDEIERLLPAVERHIDEVREILKKVMGKERPQAKDVVVREGEVIFPDLR  427 (1054)
T ss_dssp             EESCCEEEEECSCGGGSCHHHHHHHHTTTSCHHHHHTTCTTTSSCHHHHHHHHHHHHTTSCCSCSSSEEETTEEEEECHH
T ss_pred             EeCCCcccccccccccChHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHhccccccccceeEeecceecCcHH
Confidence            99999                                                                       7899


Q ss_pred             hHHHhhhhcccCCCCc--eEEEEeccCcHHHHHHHHHHhcc
Q 015158          361 NYLHRIGRSGRFGRKG--VAINFVTRDDERMLFDIQKFYNV  399 (412)
Q Consensus       361 ~~~Q~~GR~~R~g~~g--~~~~~~~~~~~~~~~~~~~~~~~  399 (412)
                      .|+||+||+||.|..|  .+++++...+.+.+..+++.++.
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            9999999999988776  48888888899999999988884

>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=2.7e-42  Score=340.15  Aligned_cols=326  Identities=18%  Similarity=0.243  Sum_probs=242.2

Q ss_pred             HHHHHHHHHCCCCCChHHHHhhhhhhhcC------ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHH
Q 015158           48 ENLLRGIYAYGFEKPSAIQQRGIVPFCKG------LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQ  121 (412)
Q Consensus        48 ~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~------~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~  121 (412)
                      +.+...+...+| +|+++|+++++.+.++      .+.++++|||||||.+++++++..+..+   .+++|++|+++|+.
T Consensus       356 ~~~~~~~~~lpf-~lt~~Q~~ai~~I~~~l~~~~~~~~Ll~a~TGSGKTlvall~il~~l~~g---~qvlvlaPtr~La~  431 (780)
T 1gm5_A          356 KLAEEFIKSLPF-KLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEAG---FQTAFMVPTSILAI  431 (780)
T ss_dssp             HHHHHHHHHSSS-CCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHHT---SCEEEECSCHHHHH
T ss_pred             HHHHHHHHhCCC-CCCHHHHHHHHHHHhhccccCCCcEEEEcCCCCCHHHHHHHHHHHHHHcC---CeEEEEeCcHHHHH
Confidence            445556677899 6999999999998875      5899999999999999999999887654   48999999999999


Q ss_pred             HHHHHHHHhhcccCcEEEEEEcCcchHHHH----HHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccC
Q 015158          122 QIEKVMRALGDYLGVKVHACVGGTSVREDQ----RILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRG  197 (412)
Q Consensus       122 q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~  197 (412)
                      |+.+.+.++....++.+..++|+.......    ....+.++|+|+||+.+..     ...+.++++||+||+|++....
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            999999999887789999999988765432    2234568999999988754     3456789999999999853221


Q ss_pred             cHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhHHHHHHHHHh-c
Q 015158          198 FKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYET-L  276 (412)
Q Consensus       198 ~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~  276 (412)
                           ...+.....+.++++|||||.+......  .++................+.....   . ......+.+.+.. .
T Consensus       507 -----r~~l~~~~~~~~vL~mSATp~p~tl~~~--~~g~~~~s~i~~~p~~r~~i~~~~~---~-~~~~~~l~~~i~~~l  575 (780)
T 1gm5_A          507 -----REALMNKGKMVDTLVMSATPIPRSMALA--FYGDLDVTVIDEMPPGRKEVQTMLV---P-MDRVNEVYEFVRQEV  575 (780)
T ss_dssp             ------CCCCSSSSCCCEEEEESSCCCHHHHHH--HTCCSSCEEECCCCSSCCCCEECCC---C-SSTHHHHHHHHHHHT
T ss_pred             -----HHHHHHhCCCCCEEEEeCCCCHHHHHHH--HhCCcceeeeeccCCCCcceEEEEe---c-cchHHHHHHHHHHHH
Confidence                 1122223346889999999977544433  2332211111111111122222111   1 1223333344433 2


Q ss_pred             -CCCcEEEEEcch--------hHHHHHHHHHhc---CCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCC
Q 015158          277 -AITQSVIFVNTR--------RKVDWLTDKMRS---RDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDV  344 (412)
Q Consensus       277 -~~~k~lif~~~~--------~~~~~~~~~L~~---~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~  344 (412)
                       .+++++|||+..        ..++.+++.|.+   .+..+..+||+++..+|..+++.|++|+.+|||||+++++|+|+
T Consensus       576 ~~g~qvlVf~~~ie~se~l~~~~a~~l~~~L~~~~~~~~~v~~lHG~m~~~eR~~v~~~F~~G~~~ILVaT~vie~GIDi  655 (780)
T 1gm5_A          576 MRGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDILVSTTVIEVGIDV  655 (780)
T ss_dssp             TTSCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHHHHHTTTSSSBCCCSSCCCSCSCC
T ss_pred             hcCCcEEEEecchhhhhhhhHHHHHHHHHHHHhhhcCCCcEEEEeCCCCHHHHHHHHHHHHCCCCeEEEECCCCCccccC
Confidence             457899999965        457888999988   46789999999999999999999999999999999999999999


Q ss_pred             CCCCEEEEccCCC-ChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHH
Q 015158          345 QQVSLVINYDLPT-QPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDI  393 (412)
Q Consensus       345 ~~~~~vi~~~~~~-s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~  393 (412)
                      |++++||+++.|. +...+.|++||+||.|.+|.|++++++.+......+
T Consensus       656 P~v~~VIi~d~~r~~l~~l~Qr~GRaGR~g~~g~~ill~~~~~~~~~~rl  705 (780)
T 1gm5_A          656 PRANVMVIENPERFGLAQLHQLRGRVGRGGQEAYCFLVVGDVGEEAMERL  705 (780)
T ss_dssp             TTCCEEEBCSCSSSCTTHHHHHHHTSCCSSTTCEEECCCCSCCHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCHHHHHHHhcccCcCCCCCEEEEEECCCChHHHHHH
Confidence            9999999999885 789999999999999999999999985444433333

>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=1.4e-40  Score=343.00  Aligned_cols=321  Identities=17%  Similarity=0.214  Sum_probs=247.2

Q ss_pred             CCCHHHHHHH-HHCCCCCChHHHHhhhhhhhc----Cc--cEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCH
Q 015158           45 GLQENLLRGI-YAYGFEKPSAIQQRGIVPFCK----GL--DVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTR  117 (412)
Q Consensus        45 ~l~~~~~~~l-~~~~~~~l~~~Q~~a~~~~~~----~~--~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~  117 (412)
                      +.+....+.+ ..++|. ++|+|.++++.++.    ++  ++++++|||+|||.+++.+++.....+   .+++|++||+
T Consensus       587 ~~~~~~~~~~~~~f~~~-~t~~Q~~ai~~il~~~~~g~p~d~ll~~~TGsGKT~val~aa~~~~~~g---~~vlvlvPt~  662 (1151)
T 2eyq_A          587 KHDREQYQLFCDSFPFE-TTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDNH---KQVAVLVPTT  662 (1151)
T ss_dssp             CCCHHHHHHHHHTCCSC-CCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHTTT---CEEEEECSSH
T ss_pred             CCCHHHHHHHHHhCCCC-CCHHHHHHHHHHHHHHhcCCcCcEEEECCCCCCHHHHHHHHHHHHHHhC---CeEEEEechH
Confidence            4455555555 446887 79999999999886    55  899999999999999988887765543   4899999999


Q ss_pred             HHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHH----HHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchh
Q 015158          118 ELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQ----RILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEM  193 (412)
Q Consensus       118 ~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~  193 (412)
                      +|+.|+.+.+.++....++.+..+++........    ....+..+|+|+|++.+.     ....+.++++||+||+|++
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            9999999999988777778888888765544332    223456899999998663     3455688999999999994


Q ss_pred             hccCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhHHHHHHHH
Q 015158          194 LSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLY  273 (412)
Q Consensus       194 ~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~  273 (412)
                           .......+..++.+.+++++||||.+...............+  .........+.........    ......++
T Consensus       738 -----g~~~~~~l~~l~~~~~vl~lSATp~p~~l~~~~~~~~~~~~i--~~~~~~r~~i~~~~~~~~~----~~i~~~il  806 (1151)
T 2eyq_A          738 -----GVRHKERIKAMRANVDILTLTATPIPRTLNMAMSGMRDLSII--ATPPARRLAVKTFVREYDS----MVVREAIL  806 (1151)
T ss_dssp             -----CHHHHHHHHHHHTTSEEEEEESSCCCHHHHHHHTTTSEEEEC--CCCCCBCBCEEEEEEECCH----HHHHHHHH
T ss_pred             -----ChHHHHHHHHhcCCCCEEEEcCCCChhhHHHHHhcCCCceEE--ecCCCCccccEEEEecCCH----HHHHHHHH
Confidence                 233445555566788999999999876655554443332221  1111222233443333322    12222233


Q ss_pred             Hhc-CCCcEEEEEcchhHHHHHHHHHhcC--CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEE
Q 015158          274 ETL-AITQSVIFVNTRRKVDWLTDKMRSR--DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLV  350 (412)
Q Consensus       274 ~~~-~~~k~lif~~~~~~~~~~~~~L~~~--~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~v  350 (412)
                      ... .+++++|||++++.++.+++.|++.  +..+..+||+++..+|.+++++|.+|+.+|||||+++++|+|+|++++|
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            332 4579999999999999999999887  7889999999999999999999999999999999999999999999999


Q ss_pred             EEccC-CCChhhHHHhhhhcccCCCCceEEEEeccC
Q 015158          351 INYDL-PTQPENYLHRIGRSGRFGRKGVAINFVTRD  385 (412)
Q Consensus       351 i~~~~-~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~  385 (412)
                      |+.+. +++..++.|++||+||.|+.|.|++++++.
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            98877 579999999999999999999999998764

>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=2e-40  Score=350.84  Aligned_cols=340  Identities=18%  Similarity=0.204  Sum_probs=254.7

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHhhhhhhhc-CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHH
Q 015158           46 LQENLLRGIYAYGFEKPSAIQQRGIVPFCK-GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIE  124 (412)
Q Consensus        46 l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~-~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~  124 (412)
                      +.....+.+...+|..++|.|.++++.++. ++++++.+|||||||+++.++++..+... .+.+++|++|+++|+.|.+
T Consensus       911 L~~~~~e~l~~~~f~~fnpiQ~q~~~~l~~~~~nvlv~APTGSGKTliaelail~~l~~~-~~~kavyi~P~raLa~q~~  989 (1724)
T 4f92_B          911 LRNSAFESLYQDKFPFFNPIQTQVFNTVYNSDDNVFVGAPTGSGKTICAEFAILRMLLQS-SEGRCVYITPMEALAEQVY  989 (1724)
T ss_dssp             SCCHHHHTTTTTTCSBCCHHHHHHHHHHHSCCSCEEEECCTTSCCHHHHHHHHHHHHHHC-TTCCEEEECSCHHHHHHHH
T ss_pred             ccCHHHHHHHHhcCCCCCHHHHHHHHHHhcCCCcEEEEeCCCCCchHHHHHHHHHHHHhC-CCCEEEEEcChHHHHHHHH
Confidence            445666777777899999999999999975 57899999999999999999999888654 3458999999999999999


Q ss_pred             HHHHH-hhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCC--CCCceEEEEeCCchhhccCcHHH
Q 015158          125 KVMRA-LGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLR--PDNIRIFVLDEADEMLSRGFKDQ  201 (412)
Q Consensus       125 ~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~--~~~~~~iiiDE~h~~~~~~~~~~  201 (412)
                      +.+.+ +....+..+..++|+......   ...+++|+|+||++|..++.++...  ++++++||+||+|.+.+. .+..
T Consensus       990 ~~~~~~f~~~~g~~V~~ltGd~~~~~~---~~~~~~IiV~TPEkld~llr~~~~~~~l~~v~lvViDE~H~l~d~-rg~~ 1065 (1724)
T 4f92_B          990 MDWYEKFQDRLNKKVVLLTGETSTDLK---LLGKGNIIISTPEKWDILSRRWKQRKNVQNINLFVVDEVHLIGGE-NGPV 1065 (1724)
T ss_dssp             HHHHHHHTTTSCCCEEECCSCHHHHHH---HHHHCSEEEECHHHHHHHHTTTTTCHHHHSCSEEEECCGGGGGST-THHH
T ss_pred             HHHHHHhchhcCCEEEEEECCCCcchh---hcCCCCEEEECHHHHHHHHhCcccccccceeeEEEeechhhcCCC-CCcc
Confidence            99876 555678899999998664322   2234689999999998777654332  467899999999988764 4444


Q ss_pred             HHHHH-------HhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhh------HHH
Q 015158          202 IYDIF-------QLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWK------LET  268 (412)
Q Consensus       202 ~~~i~-------~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~  268 (412)
                      +..++       ...+++.|+|++|||+++ ..+...++...............+..+.............      ...
T Consensus      1066 le~il~rl~~i~~~~~~~~riI~lSATl~N-~~dla~WL~~~~~~~~~~~~~~RPvpL~~~i~~~~~~~~~~~~~~~~~~ 1144 (1724)
T 4f92_B         1066 LEVICSRMRYISSQIERPIRIVALSSSLSN-AKDVAHWLGCSATSTFNFHPNVRPVPLELHIQGFNISHTQTRLLSMAKP 1144 (1724)
T ss_dssp             HHHHHHHHHHHHHTTSSCCEEEEEESCBTT-HHHHHHHHTCCSTTEEECCGGGCSSCEEEEEEEECCCSHHHHHHTTHHH
T ss_pred             HHHHHHHHHHHHhhcCCCceEEEEeCCCCC-HHHHHHHhCCCCCCeEEeCCCCCCCCeEEEEEeccCCCchhhhhhhcch
Confidence            44333       345678999999999974 3455555543333333333333343444444444332211      122


Q ss_pred             HHHHHHh-cCCCcEEEEEcchhHHHHHHHHHhcC----------------------------------CCeeEEecCCCC
Q 015158          269 LCDLYET-LAITQSVIFVNTRRKVDWLTDKMRSR----------------------------------DHTVSATHGDMD  313 (412)
Q Consensus       269 l~~~~~~-~~~~k~lif~~~~~~~~~~~~~L~~~----------------------------------~~~~~~~~~~~~  313 (412)
                      +...+.. ...+++||||++++.|+.++..|...                                  ...+..+|++++
T Consensus      1145 ~~~~i~~~~~~~~~lVF~~sR~~~~~~A~~L~~~~~~~~~~~~~~~~~~~~l~~~l~~~~d~~L~~~l~~GIa~hHagL~ 1224 (1724)
T 4f92_B         1145 VYHAITKHSPKKPVIVFVPSRKQTRLTAIDILTTCAADIQRQRFLHCTEKDLIPYLEKLSDSTLKETLLNGVGYLHEGLS 1224 (1724)
T ss_dssp             HHHHHHHHCSSSCEEEEESSHHHHHHHHHHHHHHHHHTTCTTTTBCSCHHHHHHHHTTCCCHHHHHHHHTTEEEECTTSC
T ss_pred             HHHHHHHhcCCCCeeeeCCCHHHHHHHHHHHHHHHhhccchhhhhcccHHHHHHHHhhcccHHHHHHHhCCEEEECCCCC
Confidence            2333333 45689999999999998887766321                                  235889999999


Q ss_pred             HHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEc----------cCCCChhhHHHhhhhcccCCC--CceEEEE
Q 015158          314 QNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINY----------DLPTQPENYLHRIGRSGRFGR--KGVAINF  381 (412)
Q Consensus       314 ~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~----------~~~~s~~~~~Q~~GR~~R~g~--~g~~~~~  381 (412)
                      +.+|..+++.|++|.++|||||++++.|+|+|...+||.-          ..|.+..+|.||+||+||.|.  .|.|+++
T Consensus      1225 ~~~R~~VE~lF~~G~i~VLvaT~tlA~GVnlPa~~VVI~~~~~~dg~~~~~~~~s~~~~~Qm~GRAGR~g~d~~G~avll 1304 (1724)
T 4f92_B         1225 PMERRLVEQLFSSGAIQVVVASRSLCWGMNVAAHLVIIMDTQYYNGKIHAYVDYPIYDVLQMVGHANRPLQDDEGRCVIM 1304 (1724)
T ss_dssp             HHHHHHHHHHHHHTSBCEEEEEGGGSSSCCCCBSEEEEECSEEEETTTTEEEECCHHHHHHHHTTBCCTTTCSCEEEEEE
T ss_pred             HHHHHHHHHHHHCCCCeEEEEChHHHcCCCCCccEEEEecCccccCcccccCCCCHHHHHHhhccccCCCCCCceEEEEE
Confidence            9999999999999999999999999999999988777731          235789999999999999986  6889999


Q ss_pred             eccCcHHHHH
Q 015158          382 VTRDDERMLF  391 (412)
Q Consensus       382 ~~~~~~~~~~  391 (412)
                      +.+.+...++
T Consensus      1305 ~~~~~~~~~~ 1314 (1724)
T 4f92_B         1305 CQGSKKDFFK 1314 (1724)
T ss_dssp             EEGGGHHHHH
T ss_pred             ecchHHHHHH
Confidence            8887776543

>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=1.3e-41  Score=327.69  Aligned_cols=309  Identities=17%  Similarity=0.148  Sum_probs=230.4

Q ss_pred             CChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEE
Q 015158           61 KPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHA  140 (412)
Q Consensus        61 ~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~  140 (412)
                      +|+++|.++++.+++++++++++|||+|||.+++.++...+..+  ..++||++|+++|+.||.+.+.++....+..+..
T Consensus       113 ~l~~~Q~~ai~~~~~~~~~ll~~~tGsGKT~~~~~~~~~~~~~~--~~~vlvl~P~~~L~~Q~~~~~~~~~~~~~~~v~~  190 (510)
T 2oca_A          113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENY--EGKILIIVPTTALTTQMADDFVDYRLFSHAMIKK  190 (510)
T ss_dssp             CCCHHHHHHHHHHHHHSEEEEECCSTTTHHHHHHHHHHHHHHHC--SSEEEEEESSHHHHHHHHHHHHHTTSSCGGGEEE
T ss_pred             CCCHHHHHHHHHHHhcCCcEEEeCCCCCHHHHHHHHHHHHHhCC--CCeEEEEECcHHHHHHHHHHHHHhhcCCccceEE
Confidence            59999999999999999999999999999999988888766533  2489999999999999999999886555567777


Q ss_pred             EEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEee
Q 015158          141 CVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSA  220 (412)
Q Consensus       141 ~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SA  220 (412)
                      ++++......   .....+|+|+|++.+...   ....+.++++||+||||++..    ..+..++..+++..+++++||
T Consensus       191 ~~~~~~~~~~---~~~~~~I~i~T~~~l~~~---~~~~~~~~~liIiDE~H~~~~----~~~~~il~~~~~~~~~l~lSA  260 (510)
T 2oca_A          191 IGGGASKDDK---YKNDAPVVVGTWQTVVKQ---PKEWFSQFGMMMNDECHLATG----KSISSIISGLNNCMFKFGLSG  260 (510)
T ss_dssp             CGGGCCTTGG---GCTTCSEEEEEHHHHTTS---CGGGGGGEEEEEEETGGGCCH----HHHHHHGGGCTTCCEEEEEES
T ss_pred             EecCCccccc---cccCCcEEEEeHHHHhhc---hhhhhhcCCEEEEECCcCCCc----ccHHHHHHhcccCcEEEEEEe
Confidence            7777654432   345689999999977542   223356789999999999765    456677777877889999999


Q ss_pred             cCChHHHHH--HHHhcCCCeEEEecCC------ccccCCceEEEEEeccc--------------------hhhHHHHHHH
Q 015158          221 TMPPEALEI--TRKFMNKPVRILVKRD------ELTLEGIKQFHVNVEKE--------------------EWKLETLCDL  272 (412)
Q Consensus       221 T~~~~~~~~--~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~--------------------~~~~~~l~~~  272 (412)
                      ||+......  ...+++. ........      ...+..+.......+..                    ..+...+.++
T Consensus       261 Tp~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  339 (510)
T 2oca_A          261 SLRDGKANIMQYVGMFGE-IFKPVTTSKLMEDGQVTELKINSIFLRYPDEFTTKLKGKTYQEEIKIITGLSKRNKWIAKL  339 (510)
T ss_dssp             CGGGCSSCHHHHHHHHCS-EECCCCCC---------CCEEEEEEEECCHHHHHHHTTCCHHHHHHHHHTCHHHHHHHHHH
T ss_pred             CCCCCcccHHHhHHhhCC-eEEeeCHHHHhhCCcCCCceEEEEeecCChHHhccccccchHHHHHHHhccHHHHHHHHHH
Confidence            996543221  1122222 11111111      11111122222222110                    1122334444


Q ss_pred             HHhc---CCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEc-CCCcCCCCCCCCC
Q 015158          273 YETL---AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITT-DLLARGIDVQQVS  348 (412)
Q Consensus       273 ~~~~---~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t-~~~~~G~d~~~~~  348 (412)
                      +...   ...+++|||+ .+.++.+++.|.+.+..+..+||+++..+|.++++.|.+|+.+|||+| +++++|+|+|+++
T Consensus       340 l~~~~~~~~~~~ivf~~-~~~~~~l~~~L~~~~~~v~~~~g~~~~~~r~~i~~~f~~g~~~vLv~T~~~~~~GiDip~v~  418 (510)
T 2oca_A          340 AIKLAQKDENAFVMFKH-VSHGKAIFDLIKNEYDKVYYVSGEVDTETRNIMKTLAENGKGIIIVASYGVFSTGISVKNLH  418 (510)
T ss_dssp             HHHHHTTTCEEEEEESS-HHHHHHHHHHHHTTCSSEEEESSSTTHHHHHHHHHHHHHCCSCEEEEEHHHHHHSCCCCSEE
T ss_pred             HHHHHhcCCCeEEEEec-HHHHHHHHHHHHHcCCCeEEEECCCCHHHHHHHHHHHhCCCCCEEEEEcChhhcccccccCc
Confidence            4443   2344555555 899999999999988899999999999999999999999999999999 9999999999999


Q ss_pred             EEEEccCCCChhhHHHhhhhcccCCCCceEEEEec
Q 015158          349 LVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVT  383 (412)
Q Consensus       349 ~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~  383 (412)
                      +||+++.|+|...|.|++||+||.|+.+.++++++
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            99999999999999999999999998875555554

>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=2.4e-40  Score=350.23  Aligned_cols=330  Identities=18%  Similarity=0.278  Sum_probs=244.2

Q ss_pred             CCCCChHHHHhhhhhhhc-CccEEEECCCCCCchhHhHHHHHHhhccC--------CCceeEEEEcCCHHHHHHHHHHHH
Q 015158           58 GFEKPSAIQQRGIVPFCK-GLDVIQQAQSGTGKTATFCSGILQQLDYG--------LVECQALVLAPTRELAQQIEKVMR  128 (412)
Q Consensus        58 ~~~~l~~~Q~~a~~~~~~-~~~~lv~~~tGsGKT~~~~~~~~~~~~~~--------~~~~~~lil~P~~~L~~q~~~~~~  128 (412)
                      ||..|++.|.++++.++. ++|+++++|||||||+++.++++..+...        ..+.+++|++|+++|+.|..+.+.
T Consensus        76 g~~~ln~iQs~~~~~al~~~~N~lv~APTGsGKTlva~l~il~~l~~~~~~~~~~~~~~~k~lyiaP~kALa~e~~~~l~  155 (1724)
T 4f92_B           76 GFKTLNRIQSKLYRAALETDENLLLCAPTGAGKTNVALMCMLREIGKHINMDGTINVDDFKIIYIAPMRSLVQEMVGSFG  155 (1724)
T ss_dssp             TCSBCCHHHHHTHHHHHTCCCCEEEECCTTSCCHHHHHHHHHHHHGGGCCTTSSCCTTSCEEEEECSSHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHcCCCcEEEEeCCcchHHHHHHHHHHHHHHhhccccccccCCCCEEEEECCHHHHHHHHHHHHH
Confidence            788999999999999774 78999999999999999999999887542        235689999999999999999999


Q ss_pred             HhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCC--CCCCceEEEEeCCchhhccCcHHHHHHHH
Q 015158          129 ALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSL--RPDNIRIFVLDEADEMLSRGFKDQIYDIF  206 (412)
Q Consensus       129 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~--~~~~~~~iiiDE~h~~~~~~~~~~~~~i~  206 (412)
                      +.....|+.+..++|+......   ...+++|+|+|||++..++.+...  .++.+++||+||+|.+.+ ..+..+..++
T Consensus       156 ~~~~~~gi~V~~~tGd~~~~~~---~~~~~~IlVtTpEkld~llr~~~~~~~l~~v~~vIiDEvH~l~d-~RG~~lE~~l  231 (1724)
T 4f92_B          156 KRLATYGITVAELTGDHQLCKE---EISATQIIVCTPEKWDIITRKGGERTYTQLVRLIILDEIHLLHD-DRGPVLEALV  231 (1724)
T ss_dssp             HHHTTTTCCEEECCSSCSSCCT---TGGGCSEEEECHHHHHHHTTSSTTHHHHTTEEEEEETTGGGGGS-TTHHHHHHHH
T ss_pred             HHHhhCCCEEEEEECCCCCCcc---ccCCCCEEEECHHHHHHHHcCCccchhhcCcCEEEEecchhcCC-ccHHHHHHHH
Confidence            9888889999999998765332   124579999999999766654332  246899999999997765 4454444433


Q ss_pred             -------HhCCCCceEEEEeecCChHHHHHHHHhcCCCe-EEEecCCccccCCceEEEEEeccch--hhH----HHHHHH
Q 015158          207 -------QLLPPKIQVGVFSATMPPEALEITRKFMNKPV-RILVKRDELTLEGIKQFHVNVEKEE--WKL----ETLCDL  272 (412)
Q Consensus       207 -------~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~--~~~----~~l~~~  272 (412)
                             ..++++.|+|++|||+++ ..+...++...+. ..........+..+...+.......  ...    ..+.+.
T Consensus       232 ~rl~~~~~~~~~~~riI~LSATl~N-~~dvA~wL~~~~~~~~~~~~~~~RPvpL~~~~~~~~~~~~~~~~~~~~~~~~~~  310 (1724)
T 4f92_B          232 ARAIRNIEMTQEDVRLIGLSATLPN-YEDVATFLRVDPAKGLFYFDNSFRPVPLEQTYVGITEKKAIKRFQIMNEIVYEK  310 (1724)
T ss_dssp             HHHHHHHHHHTCCCEEEEEECSCTT-HHHHHHHTTCCHHHHEEECCGGGCSSCEEEECCEECCCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCCCcEEEEecccCC-HHHHHHHhCCCCCCCeEEECCCCccCccEEEEeccCCcchhhhhHHHHHHHHHH
Confidence                   345678999999999975 3344443332211 1111222222333444443333221  111    222233


Q ss_pred             HHhc-CCCcEEEEEcchhHHHHHHHHHhcC-------------------------------------CCeeEEecCCCCH
Q 015158          273 YETL-AITQSVIFVNTRRKVDWLTDKMRSR-------------------------------------DHTVSATHGDMDQ  314 (412)
Q Consensus       273 ~~~~-~~~k~lif~~~~~~~~~~~~~L~~~-------------------------------------~~~~~~~~~~~~~  314 (412)
                      +... ..+++||||++++.|+.+++.|.+.                                     ...+.++||+++.
T Consensus       311 v~~~~~~~~~LVF~~sR~~~~~~A~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Gva~HHagL~~  390 (1724)
T 4f92_B          311 IMEHAGKNQVLVFVHSRKETGKTARAIRDMCLEKDTLGLFLREGSASTEVLRTEAEQCKNLELKDLLPYGFAIHHAGMTR  390 (1724)
T ss_dssp             HTTCCSSCCEEEECSSTTTTHHHHHHHHHHHHHTTSTTCCSSCCTTCSSHHHHTTSCCSTHHHHHHTTTTEEEECSSSCT
T ss_pred             HHHHhcCCcEEEECCCHHHHHHHHHHHHHHHhhccchhhhcccchhHHHHHHhhhcccccHHHHHHhhcCEEEEcCCCCH
Confidence            3332 4578999999999999888877531                                     2348899999999


Q ss_pred             HHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEE----cc------CCCChhhHHHhhhhcccCCC--CceEEEEe
Q 015158          315 NTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVIN----YD------LPTQPENYLHRIGRSGRFGR--KGVAINFV  382 (412)
Q Consensus       315 ~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~----~~------~~~s~~~~~Q~~GR~~R~g~--~g~~~~~~  382 (412)
                      .+|..+++.|++|.++|||||++++.|+|+|..++||.    ++      .|.+..+|.||+|||||.|.  .|.++++.
T Consensus       391 ~~R~~vE~~F~~G~i~vlvaTsTLa~GVNlPa~~vVI~~~~~~~~~~~~~~~ls~~~~~Qm~GRAGR~g~d~~G~~ii~~  470 (1724)
T 4f92_B          391 VDRTLVEDLFADKHIQVLVSTATLAWGVNLPAHTVIIKGTQVYSPEKGRWTELGALDILQMLGRAGRPQYDTKGEGILIT  470 (1724)
T ss_dssp             HHHHHHHHHHHTTCCCEEEECHHHHHHSCCCBSEEEEECCEEEETTTTEEEECCHHHHHHHHTTBSCTTTCSCEEEEEEE
T ss_pred             HHHHHHHHHHHCCCCeEEEEcchhHhhCCCCCceEEEeCCEEecCcCCCcccCCHHHHHHhhhhccCCCCCCccEEEEEe
Confidence            99999999999999999999999999999998888874    22      35689999999999999874  68999998


Q ss_pred             ccCcHHHHHH
Q 015158          383 TRDDERMLFD  392 (412)
Q Consensus       383 ~~~~~~~~~~  392 (412)
                      .+.+...+..
T Consensus       471 ~~~~~~~~~~  480 (1724)
T 4f92_B          471 SHGELQYYLS  480 (1724)
T ss_dssp             ESTTCCHHHH
T ss_pred             cchhHHHHHH
Confidence            8877655433

>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=2.2e-40  Score=316.05  Aligned_cols=292  Identities=19%  Similarity=0.256  Sum_probs=219.9

Q ss_pred             CChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcE-EE
Q 015158           61 KPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVK-VH  139 (412)
Q Consensus        61 ~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~-~~  139 (412)
                      +|+++|.++++.+.+++++++.+|||+|||++++.++...      +.++||+||+++|+.||.+++.++    +.. +.
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            4999999999999999999999999999999998887754      247999999999999999998884    667 77


Q ss_pred             EEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEe
Q 015158          140 ACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFS  219 (412)
Q Consensus       140 ~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~S  219 (412)
                      .++|+...         ..+|+|+|++.+.......   ..++++||+||+|++.+..+..    +...+ +..+++++|
T Consensus       163 ~~~g~~~~---------~~~Ivv~T~~~l~~~~~~~---~~~~~liIvDEaH~~~~~~~~~----~~~~~-~~~~~l~lS  225 (472)
T 2fwr_A          163 EFSGRIKE---------LKPLTVSTYDSAYVNAEKL---GNRFMLLIFDEVHHLPAESYVQ----IAQMS-IAPFRLGLT  225 (472)
T ss_dssp             EBSSSCBC---------CCSEEEEEHHHHHHTHHHH---TTTCSEEEEETGGGTTSTTTHH----HHHTC-CCSEEEEEE
T ss_pred             EECCCcCC---------cCCEEEEEcHHHHHHHHHh---cCCCCEEEEECCcCCCChHHHH----HHHhc-CCCeEEEEe
Confidence            77776542         4689999999987765421   2458999999999998877653    44444 467899999


Q ss_pred             ecCChHH--HHHHHHhcCCCeEEEecCCccc---cCCceE--EEEEe---------------------------------
Q 015158          220 ATMPPEA--LEITRKFMNKPVRILVKRDELT---LEGIKQ--FHVNV---------------------------------  259 (412)
Q Consensus       220 AT~~~~~--~~~~~~~~~~~~~~~~~~~~~~---~~~~~~--~~~~~---------------------------------  259 (412)
                      |||....  ...+..+++.. ..........   ......  .....                                 
T Consensus       226 ATp~~~~~~~~~l~~~~~~~-~~~~~~~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~  304 (472)
T 2fwr_A          226 ATFEREDGRHEILKEVVGGK-VFELFPDSLAGKHLAKYTIKRIFVPLAEDERVEYEKREKVYKQFLRARGITLRRAEDFN  304 (472)
T ss_dssp             SCCCCTTSGGGSHHHHTCCE-EEECCHHHHTSCCCCSEEECCEEECCCHHHHHHTTTTTHHHHSCSSSCCCTTTCCSSST
T ss_pred             cCccCCCCHHHHHHHHhCCe-EeecCHHHHhcCcCCCeEEEEEEcCCCHHHHHHHHHHHHHHHHHHHhcCccccchhhHH
Confidence            9997310  00111111111 0000000000   000000  00000                                 


Q ss_pred             --------------------------ccchhhHHHHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCC
Q 015158          260 --------------------------EKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMD  313 (412)
Q Consensus       260 --------------------------~~~~~~~~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~  313 (412)
                                                .....+...+.+++.....+++||||++.+.++.+++.|.     +..+||+++
T Consensus       305 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~k~lvF~~~~~~~~~l~~~l~-----~~~~~g~~~  379 (472)
T 2fwr_A          305 KIVMASGYDERAYEALRAWEEARRIAFNSKNKIRKLREILERHRKDKIIIFTRHNELVYRISKVFL-----IPAITHRTS  379 (472)
T ss_dssp             TTTTTTCCSSSSSTTTHHHHHHHHHHHSCSHHHHHHHHHHHHTSSSCBCCBCSCHHHHHHHHHHTT-----CCBCCSSSC
T ss_pred             HHHHHhccCHHHHHHHHHHHHHHHHhhcChHHHHHHHHHHHhCCCCcEEEEECCHHHHHHHHHHhC-----cceeeCCCC
Confidence                                      0122356777888888778999999999999999999984     667899999


Q ss_pred             HHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccCCCC-ceEEE--EeccC
Q 015158          314 QNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRK-GVAIN--FVTRD  385 (412)
Q Consensus       314 ~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~-g~~~~--~~~~~  385 (412)
                      ..+|.++++.|++|+.+|||+|+++++|+|+|++++||+++.|+|+..|.|++||+||.|+. +.+++  +++.+
T Consensus       380 ~~~R~~~~~~F~~g~~~vLv~T~~~~~Gldlp~~~~Vi~~~~~~s~~~~~Q~~GR~~R~g~~k~~~~i~~lv~~~  454 (472)
T 2fwr_A          380 REEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQRLGRILRPSKGKKEAVLYELISRG  454 (472)
T ss_dssp             SHHHHTHHHHHHHSSCSBCBCSSCCCSSSCSCCBSEEEEECCSSCCHHHHHHHHHSBCCCTTTCCEEEEEEEECS
T ss_pred             HHHHHHHHHHHhCCCCCEEEEcCchhcCcccccCcEEEEECCCCCHHHHHHHHhhccCCCCCCceEEEEEEEeCC
Confidence            99999999999999999999999999999999999999999999999999999999999865 44444  44443

>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=4.7e-39  Score=311.08  Aligned_cols=322  Identities=18%  Similarity=0.212  Sum_probs=240.8

Q ss_pred             HCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccC
Q 015158           56 AYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLG  135 (412)
Q Consensus        56 ~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~  135 (412)
                      ..|+ .|++.|..+++.+++|+  +..++||+|||++|.++++.....   +..++|++||+.|+.|.++++..++...+
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--IAEMKTGEGKTLTSTLPVYLNALT---GKGVHVVTVNEYLASRDAEQMGKIFEFLG  152 (844)
T ss_dssp             HHSC-CCCHHHHHHHHHHHTTS--EEECCTTSCHHHHHHHHHHHHHTT---SSCEEEEESSHHHHHHHHHHHHHHHHHTT
T ss_pred             HcCC-CCcHHHHHhhHHHhCCC--EEEccCCcHHHHHHHHHHHHHHHc---CCCEEEEeCCHHHHHHHHHHHHHHHhhcC
Confidence            4699 79999999999999998  899999999999999999843332   34799999999999999999999998889


Q ss_pred             cEEEEEEcCcchHHHHHHhcCCCcEEEeChHHH-HHHHHcC------CCCCCCceEEEEeCCchhh-ccC----------
Q 015158          136 VKVHACVGGTSVREDQRILSSGVHVVVGTPGRV-FDMLRRQ------SLRPDNIRIFVLDEADEML-SRG----------  197 (412)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l-~~~~~~~------~~~~~~~~~iiiDE~h~~~-~~~----------  197 (412)
                      +.+..+.|+.+....  ....+++|+|+||..| +.++...      ...++.+.++|+||||.++ +.+          
T Consensus       153 l~v~~i~gg~~~~~r--~~~~~~dIv~gTpgrlgfD~L~D~m~~~~~~l~lr~~~~lVlDEaD~mLiDea~tplIisg~~  230 (844)
T 1tf5_A          153 LTVGLNLNSMSKDEK--REAYAADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSILIDEARTPLIISGQA  230 (844)
T ss_dssp             CCEEECCTTSCHHHH--HHHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEEETHHHHHTTTTTCEEEEEEEE
T ss_pred             CeEEEEeCCCCHHHH--HHhcCCCEEEECchhhhHHHHHHhhhcchhhhcccCCCEEEECchhhhhhhccccchhhcCCc
Confidence            999999998765433  2334579999999999 5555432      3456789999999999987 543          


Q ss_pred             -----cHHHHHHHHHhCCC---------CceEE-----------------EEeecCCh---HHHHHH--HHhcCC-C-eE
Q 015158          198 -----FKDQIYDIFQLLPP---------KIQVG-----------------VFSATMPP---EALEIT--RKFMNK-P-VR  239 (412)
Q Consensus       198 -----~~~~~~~i~~~~~~---------~~~~i-----------------~~SAT~~~---~~~~~~--~~~~~~-~-~~  239 (412)
                           +...+..+...+++         ..++.                 ++|||.+.   .+...+  ..++.. . ..
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                 55777888887763         44454                 67888542   111111  111110 0 00


Q ss_pred             E------Ee-----------------------------cCC---------------------------------------
Q 015158          240 I------LV-----------------------------KRD---------------------------------------  245 (412)
Q Consensus       240 ~------~~-----------------------------~~~---------------------------------------  245 (412)
                      +      .+                             ...                                       
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      00                             000                                       


Q ss_pred             -----ccccCCce--EEEEEeccchhhHHHHHHHHHhc--CCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHH
Q 015158          246 -----ELTLEGIK--QFHVNVEKEEWKLETLCDLYETL--AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNT  316 (412)
Q Consensus       246 -----~~~~~~~~--~~~~~~~~~~~~~~~l~~~~~~~--~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~  316 (412)
                           ....+...  ...........+...+.+.+...  ...++||||+|++.++.+++.|++.|+.+..+||++...+
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                 00000010  01112223456777777766542  4568999999999999999999999999999999988777


Q ss_pred             HHHHHHHHhcCCCcEEEEcCCCcCCCCCC--------CCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcH
Q 015158          317 RDIIMREFRSGSSRVLITTDLLARGIDVQ--------QVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDE  387 (412)
Q Consensus       317 r~~~~~~f~~g~~~vlv~t~~~~~G~d~~--------~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~  387 (412)
                      +..+.+.++.  ..|+|||+++++|+|++        ++.+||.++.|.|...|.||+||+||.|.+|.++.|++..|.
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 AQIIEEAGQK--GAVTIATNMAGRGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGDPGITQFYLSMEDE  547 (844)
T ss_dssp             HHHHTTTTST--TCEEEEETTSSTTCCCCCCTTSGGGTSEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEETTSS
T ss_pred             HHHHHHcCCC--CeEEEeCCccccCcCccccchhhhcCCcEEEEecCCCCHHHHHhhcCccccCCCCCeEEEEecHHHH
Confidence            7655554444  46999999999999999        788999999999999999999999999999999999988764

>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=2e-40  Score=321.33  Aligned_cols=321  Identities=18%  Similarity=0.133  Sum_probs=232.4

Q ss_pred             CCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHH
Q 015158           44 MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQI  123 (412)
Q Consensus        44 ~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~  123 (412)
                      +++++.+.+.+... ...+.|.|..+++.+.+++++++.+|||||||++|+++++..+..  .+.++||++|+++|+.|+
T Consensus       155 l~~~~~~~~~l~~~-~~~~lpiq~~~i~~l~~g~dvlv~a~TGSGKT~~~~lpil~~l~~--~~~~vLvl~PtreLa~Qi  231 (618)
T 2whx_A          155 VTKSGDYVSAITQA-ERIGEPDYEVDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALK--RRLRTLILAPTRVVAAEM  231 (618)
T ss_dssp             -------CEECBCC-CCCCCCCCCCCGGGGSTTCEEEECCCTTSSTTTTHHHHHHHHHHH--TTCCEEEEESSHHHHHHH
T ss_pred             ccchHHHHHHHhhc-cccCCCccccCHHHHhcCCeEEEEcCCCCCHHHHHHHHHHHHHHh--CCCeEEEEcChHHHHHHH
Confidence            45666666655532 366788888889999999999999999999999998888877654  346899999999999999


Q ss_pred             HHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHH
Q 015158          124 EKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIY  203 (412)
Q Consensus       124 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~  203 (412)
                      .+.+..      ..+. +.+.. .   ......+..+.++|.+.+.+.+... ..+.++++||+||||++ +.++...+.
T Consensus       232 ~~~l~~------~~v~-~~~~~-l---~~~~tp~~~i~~~t~~~l~~~l~~~-~~l~~~~~iViDEah~~-~~~~~~~~~  298 (618)
T 2whx_A          232 EEALRG------LPIR-YQTPA-V---KSDHTGREIVDLMCHATFTTRLLSS-TRVPNYNLIVMDEAHFT-DPCSVAARG  298 (618)
T ss_dssp             HHHTTT------SCEE-ECCTT-S---SCCCCSSSCEEEEEHHHHHHHHHHC-SSCCCCSEEEEESTTCC-SHHHHHHHH
T ss_pred             HHHhcC------Ccee-Eeccc-c---eeccCCCceEEEEChHHHHHHHhcc-ccccCCeEEEEECCCCC-CccHHHHHH
Confidence            987763      2232 21111 0   0112234567788988887766554 34678999999999997 555666666


Q ss_pred             HHHHhCC-CCceEEEEeecCChHHHHHHHHhcC-CCeEEEecCCccccCCceEEEEEeccchhhHHHHHHHHHhcCCCcE
Q 015158          204 DIFQLLP-PKIQVGVFSATMPPEALEITRKFMN-KPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQS  281 (412)
Q Consensus       204 ~i~~~~~-~~~~~i~~SAT~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~  281 (412)
                      .+...++ ++.+++++|||++.....    +.. .+..+.....             .+.  .....+...+.. ..+++
T Consensus       299 ~i~~~l~~~~~q~il~SAT~~~~~~~----~~~~~~~~~~v~~~-------------~~~--~~~~~ll~~l~~-~~~~~  358 (618)
T 2whx_A          299 YISTRVEMGEAAAIFMTATPPGSTDP----FPQSNSPIEDIERE-------------IPE--RSWNTGFDWITD-YQGKT  358 (618)
T ss_dssp             HHHHHHHHTSCEEEEECSSCTTCCCS----SCCCSSCEEEEECC-------------CCS--SCCSSSCHHHHH-CCSCE
T ss_pred             HHHHHhcccCccEEEEECCCchhhhh----hhccCCceeeeccc-------------CCH--HHHHHHHHHHHh-CCCCE
Confidence            6666654 678999999999765321    211 2222221111             010  011112222333 25799


Q ss_pred             EEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEE-----------
Q 015158          282 VIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLV-----------  350 (412)
Q Consensus       282 lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~v-----------  350 (412)
                      ||||++++.++.+++.|++.+..+..+||+    +|.++++.|++|+.+|||||+++++|+|+| +++|           
T Consensus       359 LVF~~s~~~a~~l~~~L~~~g~~v~~lhg~----~R~~~l~~F~~g~~~VLVaTdv~~rGiDi~-v~~VId~g~~~~P~~  433 (618)
T 2whx_A          359 VWFVPSIKAGNDIANCLRKSGKRVIQLSRK----TFDTEYPKTKLTDWDFVVTTDISEMGANFR-AGRVIDPRRCLKPVI  433 (618)
T ss_dssp             EEECSSHHHHHHHHHHHHHTTCCEEEECTT----THHHHTTHHHHSCCSEEEECGGGGTTCCCC-CSEEEECCEEEEEEE
T ss_pred             EEEECChhHHHHHHHHHHHcCCcEEEEChH----HHHHHHHhhcCCCcEEEEECcHHHcCcccC-ceEEEECcceeccee
Confidence            999999999999999999999999999985    688899999999999999999999999997 8888           


Q ss_pred             ---------EEccCCCChhhHHHhhhhcccCCC-CceEEEEec---cCcHHHHHHHHHHhccccccCC
Q 015158          351 ---------INYDLPTQPENYLHRIGRSGRFGR-KGVAINFVT---RDDERMLFDIQKFYNVVIEELP  405 (412)
Q Consensus       351 ---------i~~~~~~s~~~~~Q~~GR~~R~g~-~g~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~  405 (412)
                               ++++.|.|..+|+||+||+||.|. .|.+++|++   +.+...+..+++.+......++
T Consensus       434 ~~~~~~~~~i~~d~P~s~~~yiQR~GRaGR~g~~~G~ai~l~~~~~~~d~~~l~~le~~i~l~~~~~~  501 (618)
T 2whx_A          434 LTDGPERVILAGPIPVTPASAAQRRGRIGRNPAQEDDQYVFSGDPLKNDEDHAHWTEAKMLLDNIYTP  501 (618)
T ss_dssp             ECSSSCEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECSCCCCCCTTCHHHHHHHHHHTTCCCT
T ss_pred             cccCCCceEEcccccCCHHHHHHhccccCCCCCCCCeEEEEccCCchhhHHHHHHHHhHhccccccCC
Confidence                     555668999999999999999965 899999997   7788888888887765444443

>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=1.3e-38  Score=316.22  Aligned_cols=336  Identities=16%  Similarity=0.212  Sum_probs=244.2

Q ss_pred             hhccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhc-CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEc
Q 015158           36 EVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCK-GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLA  114 (412)
Q Consensus        36 ~~~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~-~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~  114 (412)
                      .+..+|+++++++.+.+.+...+ ..|.+.|++++..++. ++++++.+|||+|||+.....+.........+.++++++
T Consensus        69 ~~~~~f~~~~l~~~~~~~l~~r~-~lP~~~q~~~i~~~l~~~~~vii~gpTGSGKTtllp~ll~~~~~~~~~g~~ilvl~  147 (773)
T 2xau_A           69 GKINPFTGREFTPKYVDILKIRR-ELPVHAQRDEFLKLYQNNQIMVFVGETGSGKTTQIPQFVLFDEMPHLENTQVACTQ  147 (773)
T ss_dssp             SSBCTTTCSBCCHHHHHHHHHHT-TSGGGGGHHHHHHHHHHCSEEEEECCTTSSHHHHHHHHHHHHHCGGGGTCEEEEEE
T ss_pred             CCCCCccccCCCHHHHHHHHHhh-cCChHHHHHHHHHHHhCCCeEEEECCCCCCHHHHHHHHHHHhccccCCCceEEecC
Confidence            34678999999999999999888 5588888888887665 578999999999999843333322221111245799999


Q ss_pred             CCHHHHHHHHHHHHHhhc-ccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCch-
Q 015158          115 PTRELAQQIEKVMRALGD-YLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADE-  192 (412)
Q Consensus       115 P~~~L~~q~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~-  192 (412)
                      |+++|+.|+.+.+..... ..+..+........      ......+|+++|++.+.+.+... ..+.++++||+||+|. 
T Consensus       148 P~r~La~q~~~~l~~~~~~~v~~~vG~~i~~~~------~~~~~~~I~v~T~G~l~r~l~~~-~~l~~~~~lIlDEah~R  220 (773)
T 2xau_A          148 PRRVAAMSVAQRVAEEMDVKLGEEVGYSIRFEN------KTSNKTILKYMTDGMLLREAMED-HDLSRYSCIILDEAHER  220 (773)
T ss_dssp             SCHHHHHHHHHHHHHHTTCCBTTTEEEEETTEE------ECCTTCSEEEEEHHHHHHHHHHS-TTCTTEEEEEECSGGGC
T ss_pred             chHHHHHHHHHHHHHHhCCchhheecceecccc------ccCCCCCEEEECHHHHHHHHhhC-ccccCCCEEEecCcccc
Confidence            999999999887765432 22223322211111      11245789999999999877654 3467899999999996 


Q ss_pred             hhccCc-HHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhh---HHH
Q 015158          193 MLSRGF-KDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWK---LET  268 (412)
Q Consensus       193 ~~~~~~-~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~  268 (412)
                      ..+.+. ...+..+.... ++.+++++|||++.+   .+..+++....+......   ..+...+.........   ...
T Consensus       221 ~ld~d~~~~~l~~l~~~~-~~~~iIl~SAT~~~~---~l~~~~~~~~vi~v~gr~---~pv~~~~~~~~~~~~~~~~l~~  293 (773)
T 2xau_A          221 TLATDILMGLLKQVVKRR-PDLKIIIMSATLDAE---KFQRYFNDAPLLAVPGRT---YPVELYYTPEFQRDYLDSAIRT  293 (773)
T ss_dssp             CHHHHHHHHHHHHHHHHC-TTCEEEEEESCSCCH---HHHHHTTSCCEEECCCCC---CCEEEECCSSCCSCHHHHHHHH
T ss_pred             ccchHHHHHHHHHHHHhC-CCceEEEEeccccHH---HHHHHhcCCCcccccCcc---cceEEEEecCCchhHHHHHHHH
Confidence            443322 23344444433 578999999999642   344455544444433222   2233333333222222   233


Q ss_pred             HHHHHHhcCCCcEEEEEcchhHHHHHHHHHhc-----------CCCeeEEecCCCCHHHHHHHHHHHh-----cCCCcEE
Q 015158          269 LCDLYETLAITQSVIFVNTRRKVDWLTDKMRS-----------RDHTVSATHGDMDQNTRDIIMREFR-----SGSSRVL  332 (412)
Q Consensus       269 l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~-----------~~~~~~~~~~~~~~~~r~~~~~~f~-----~g~~~vl  332 (412)
                      +..+......+++||||++++.++.+++.|.+           .+..+..+||+++..+|..+++.|.     +|+.+||
T Consensus       294 l~~~~~~~~~g~iLVF~~~~~~i~~l~~~L~~~~~~l~~~~~~~~~~v~~lhg~l~~~eR~~v~~~f~~~~~~~g~~kVl  373 (773)
T 2xau_A          294 VLQIHATEEAGDILLFLTGEDEIEDAVRKISLEGDQLVREEGCGPLSVYPLYGSLPPHQQQRIFEPAPESHNGRPGRKVV  373 (773)
T ss_dssp             HHHHHHHSCSCEEEEECSCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECTTCCHHHHGGGGSCCCCCSSSSCCEEEE
T ss_pred             HHHHHHhcCCCCEEEECCCHHHHHHHHHHHHHHHHhhcccccCCCeEEEEeCCCCCHHHHHHHHhhcccccCCCCceEEE
Confidence            34444444678999999999999999999975           5778999999999999999999999     9999999


Q ss_pred             EEcCCCcCCCCCCCCCEEEEccC------------------CCChhhHHHhhhhcccCCCCceEEEEeccCcH
Q 015158          333 ITTDLLARGIDVQQVSLVINYDL------------------PTQPENYLHRIGRSGRFGRKGVAINFVTRDDE  387 (412)
Q Consensus       333 v~t~~~~~G~d~~~~~~vi~~~~------------------~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~  387 (412)
                      |||+++++|+|+|++++||+++.                  |.|..+|.||+||+||. .+|.|+.++++.+.
T Consensus       374 VAT~iae~GidIp~v~~VId~g~~k~~~yd~~~g~~~L~~~p~S~~s~~QR~GRaGR~-~~G~~~~l~~~~~~  445 (773)
T 2xau_A          374 ISTNIAETSLTIDGIVYVVDPGFSKQKVYNPRIRVESLLVSPISKASAQQRAGRAGRT-RPGKCFRLYTEEAF  445 (773)
T ss_dssp             EECTHHHHTCCCTTEEEEEECSEEEEEEEETTTTEEEEEEEECCHHHHHHHHHGGGSS-SSEEEEESSCHHHH
T ss_pred             EeCcHHHhCcCcCCeEEEEeCCCccceeeccccCccccccccCCHHHHHhhccccCCC-CCCEEEEEecHHHh
Confidence            99999999999999999999887                  88999999999999999 78999999977654

>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=2e-38  Score=298.80  Aligned_cols=287  Identities=18%  Similarity=0.135  Sum_probs=208.3

Q ss_pred             CCCCChHHHHhhhhhhhcCccE-EEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCc
Q 015158           58 GFEKPSAIQQRGIVPFCKGLDV-IQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGV  136 (412)
Q Consensus        58 ~~~~l~~~Q~~a~~~~~~~~~~-lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~  136 (412)
                      |+.+++|.|+ +++.++++++. ++.+|||||||++++++++.....  .+.+++|++|+++|+.|+.+.+..      .
T Consensus         1 G~~q~~~iq~-~i~~~l~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~--~~~~~lvl~Ptr~La~Q~~~~l~g------~   71 (451)
T 2jlq_A            1 GSAMGEPDYE-VDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALL--RRLRTLILAPTRVVAAEMEEALRG------L   71 (451)
T ss_dssp             CCCCCSCCCC-CCGGGGSTTCEEEECCCTTSSCCTTHHHHHHHHHHH--TTCCEEEEESSHHHHHHHHHHTTT------S
T ss_pred             CCCCCCCcHH-HHHHHHhcCCeEEEECCCCCCHhhHHHHHHHHHHHh--cCCcEEEECCCHHHHHHHHHHhcC------c
Confidence            5677899985 78998888776 889999999999988888766543  236899999999999999987753      2


Q ss_pred             EEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHH-HhCCCCceE
Q 015158          137 KVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIF-QLLPPKIQV  215 (412)
Q Consensus       137 ~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~-~~~~~~~~~  215 (412)
                      .+.........     ....+..|.++|++.+.+.+.+. ..+.++++||+||||++ +..+...+..+. ...+++.++
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            33222211110     12234578999999998777654 34678999999999976 332222222222 223457899


Q ss_pred             EEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhHHHHHHHHHhcCCCcEEEEEcchhHHHHHH
Q 015158          216 GVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLT  295 (412)
Q Consensus       216 i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lif~~~~~~~~~~~  295 (412)
                      +++|||++.....   .....+..+......             +..  ....+...+.. ..+++||||++++.++.++
T Consensus       145 i~~SAT~~~~~~~---~~~~~~~~~~~~~~~-------------p~~--~~~~~~~~l~~-~~~~~lVF~~s~~~a~~l~  205 (451)
T 2jlq_A          145 IFMTATPPGSTDP---FPQSNSPIEDIEREI-------------PER--SWNTGFDWITD-YQGKTVWFVPSIKAGNDIA  205 (451)
T ss_dssp             EEECSSCTTCCCS---SCCCSSCEEEEECCC-------------CSS--CCSSSCHHHHH-CCSCEEEECSSHHHHHHHH
T ss_pred             EEEccCCCccchh---hhcCCCceEecCccC-------------Cch--hhHHHHHHHHh-CCCCEEEEcCCHHHHHHHH
Confidence            9999999763221   112222222221100             000  00011222333 2469999999999999999


Q ss_pred             HHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEcc--------------------C
Q 015158          296 DKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYD--------------------L  355 (412)
Q Consensus       296 ~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~--------------------~  355 (412)
                      +.|++.+..+..+|+++.    .++++.|++|+.+|||||+++++|+|+|+ ++||+++                    .
T Consensus       206 ~~L~~~g~~~~~lh~~~~----~~~~~~f~~g~~~vLVaT~v~~~GiDip~-~~VI~~~~~~~~~~d~~~~~~l~~~~~~  280 (451)
T 2jlq_A          206 NCLRKSGKRVIQLSRKTF----DTEYPKTKLTDWDFVVTTDISEMGANFRA-GRVIDPRRCLKPVILTDGPERVILAGPI  280 (451)
T ss_dssp             HHHHTTTCCEEEECTTTH----HHHGGGGGSSCCSEEEECGGGGSSCCCCC-SEEEECCEEEEEEEECSSSCEEEEEEEE
T ss_pred             HHHHHcCCeEEECCHHHH----HHHHHhhccCCceEEEECCHHHhCcCCCC-CEEEECCCcccccccccccceeeecccc
Confidence            999999999999999753    57899999999999999999999999999 9999988                    8


Q ss_pred             CCChhhHHHhhhhcccCCC-CceEEEEecc
Q 015158          356 PTQPENYLHRIGRSGRFGR-KGVAINFVTR  384 (412)
Q Consensus       356 ~~s~~~~~Q~~GR~~R~g~-~g~~~~~~~~  384 (412)
                      |.|..+|.||+||+||.|. +|.++++...
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            9999999999999999998 7888888744

>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=8.3e-39  Score=312.92  Aligned_cols=313  Identities=16%  Similarity=0.206  Sum_probs=198.3

Q ss_pred             CChHHHHhhhhhhhc-----CccEEEECCCCCCchhHhHHHHHHhhccC------CCceeEEEEcCCHHHHHHHH-HHHH
Q 015158           61 KPSAIQQRGIVPFCK-----GLDVIQQAQSGTGKTATFCSGILQQLDYG------LVECQALVLAPTRELAQQIE-KVMR  128 (412)
Q Consensus        61 ~l~~~Q~~a~~~~~~-----~~~~lv~~~tGsGKT~~~~~~~~~~~~~~------~~~~~~lil~P~~~L~~q~~-~~~~  128 (412)
                      .|+++|.++++.+.+     ++++++++|||+|||++++..+...+..+      ...+++||++|+++|+.|+. +.+.
T Consensus       178 ~lr~~Q~~ai~~~~~~~~~~~~~~ll~~~TGsGKT~~~~~~~~~l~~~~~~~~~~~~~~~vlil~P~~~L~~Q~~~~~~~  257 (590)
T 3h1t_A          178 SPRYYQQIAINRAVQSVLQGKKRSLITMATGTGKTVVAFQISWKLWSARWNRTGDYRKPRILFLADRNVLVDDPKDKTFT  257 (590)
T ss_dssp             -CCHHHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHHHHHHHHHTTCCSSCSSSCCCEEEEEC-----------CCT
T ss_pred             CchHHHHHHHHHHHHHHhcCCCceEEEecCCCChHHHHHHHHHHHHhcccccccccCCCeEEEEeCCHHHHHHHHHHHHH
Confidence            599999999999876     46789999999999999766655444332      14578999999999999999 7776


Q ss_pred             HhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHc----CCCCCCCceEEEEeCCchhhccCcHHHHHH
Q 015158          129 ALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRR----QSLRPDNIRIFVLDEADEMLSRGFKDQIYD  204 (412)
Q Consensus       129 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~----~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~  204 (412)
                      .+.    ..+..+.++.        ...+.+|+|+|+++|......    ..+....+++||+||||++.... ...+..
T Consensus       258 ~~~----~~~~~~~~~~--------~~~~~~I~v~T~~~l~~~~~~~~~~~~~~~~~~~lvIiDEaH~~~~~~-~~~~~~  324 (590)
T 3h1t_A          258 PFG----DARHKIEGGK--------VVKSREIYFAIYQSIASDERRPGLYKEFPQDFFDLIIIDECHRGSARD-NSNWRE  324 (590)
T ss_dssp             TTC----SSEEECCC----------CCSSCSEEEEEGGGC------CCGGGGSCTTSCSEEEESCCC----------CHH
T ss_pred             hcc----hhhhhhhccC--------CCCCCcEEEEEhhhhccccccccccccCCCCccCEEEEECCccccccc-hHHHHH
Confidence            653    2333333221        234679999999999876541    23445678999999999986542 245566


Q ss_pred             HHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccc---cCCceEEEEEec---------------------
Q 015158          205 IFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELT---LEGIKQFHVNVE---------------------  260 (412)
Q Consensus       205 i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~---------------------  260 (412)
                      ++..++ +.+++++||||..........+++.+...........   ............                     
T Consensus       325 il~~~~-~~~~l~lTATP~~~~~~~~~~~f~~~~~~~~~~~~i~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  403 (590)
T 3h1t_A          325 ILEYFE-PAFQIGMTATPLREDNRDTYRYFGNPIYTYSLRQGIDDGFLAPYRVHRVISEVDAAGWRPSKGDVDRFGREIP  403 (590)
T ss_dssp             HHHHST-TSEEEEEESSCSCTTTHHHHHHSCSCSEEECHHHHHHHTSSCCEEEEEEEETTCC------------------
T ss_pred             HHHhCC-cceEEEeccccccccchhHHHHcCCceEecCHHHHhhCCccCCcEEEEeeeeeeccccccccccccccccccc
Confidence            666665 4679999999986544445555554443321111000   000000000000                     


Q ss_pred             -------cc------hhh----HHHHHHHHHhc-CCCcEEEEEcchhHHHHHHHHHhcCCC--------eeEEecCCCCH
Q 015158          261 -------KE------EWK----LETLCDLYETL-AITQSVIFVNTRRKVDWLTDKMRSRDH--------TVSATHGDMDQ  314 (412)
Q Consensus       261 -------~~------~~~----~~~l~~~~~~~-~~~k~lif~~~~~~~~~~~~~L~~~~~--------~~~~~~~~~~~  314 (412)
                             ..      ...    ...+.+.+... ..+++||||+++++++.+++.|.+.+.        .+..+||.++ 
T Consensus       404 ~~~~~~~~~~~~~~~~~r~~~i~~~l~~~l~~~~~~~k~lVF~~~~~~a~~l~~~L~~~~~~~~~~~~~~~~~i~g~~~-  482 (590)
T 3h1t_A          404 DGEYQTKDFERVIALKARTDAFAKHLTDFMKRTDRFAKTIVFCVDQEHADEMRRALNNLNSDLSRKHPDYVARVTSEEG-  482 (590)
T ss_dssp             -----CCSHHHHHHHHHTHHHHHHHHHHHHHHHCTTSEEEEEESSHHHHHHHHHHHHHHTHHHHTTCTTSEEECSSTTH-
T ss_pred             cccCCHHHhhhHhcChHHHHHHHHHHHHHHHhcCCCccEEEEECCHHHHHHHHHHHHHhhhhhhccCCCeEEEEeCCCh-
Confidence                   00      001    12233334443 447999999999999999999987543        2677888865 


Q ss_pred             HHHHHHHHHHhcCCCc---EEEEcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccCCC--CceEEEEeccC-cHH
Q 015158          315 NTRDIIMREFRSGSSR---VLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGR--KGVAINFVTRD-DER  388 (412)
Q Consensus       315 ~~r~~~~~~f~~g~~~---vlv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~--~g~~~~~~~~~-~~~  388 (412)
                      ++|..++++|++|+.+   |+++|+++++|+|+|.+++||+++.++|...|.||+||++|.++  .+..+++++.. ...
T Consensus       483 ~~r~~~l~~F~~~~~~~~~ilvtt~~l~~GiDip~v~~Vi~~~~~~s~~~~~Q~iGR~~R~~~~~~k~~~~I~D~~g~~~  562 (590)
T 3h1t_A          483 KIGKGHLSRFQELETSTPVILTTSQLLTTGVDAPTCKNVVLARVVNSMSEFKQIVGRGTRLREDYGKLWFNIIDYTGSAT  562 (590)
T ss_dssp             HHHHHHHHHHHCTTCCCCCEEEESSTTTTTCCCTTEEEEEEESCCCCHHHHHHHHTTSCCCBGGGTBSCEEEEECSSSHH
T ss_pred             HHHHHHHHHHhCCCCCCCEEEEECChhhcCccchheeEEEEEecCCChHHHHHHHhhhcccCccCCCCEEEEEecCCcHH
Confidence            4799999999998765   88889999999999999999999999999999999999999875  34444444443 443

>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=1.8e-37  Score=299.16  Aligned_cols=322  Identities=18%  Similarity=0.209  Sum_probs=223.1

Q ss_pred             CCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCc
Q 015158           57 YGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGV  136 (412)
Q Consensus        57 ~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~  136 (412)
                      .|. .|++.|..+++.+++|+  +..++||+|||+++.++++.....   +..++|++||+.|+.|.++.+..++...++
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--IAEMRTGEGKTLTATLPAYLNALT---GKGVHVVTVNDYLAQRDAENNRPLFEFLGL  144 (853)
T ss_dssp             HSC-CCCHHHHHHHHHHHSSE--EEECCTTSCHHHHHHHHHHHHHTT---SSCCEEEESSHHHHHHHHHHHHHHHHHTTC
T ss_pred             cCC-CCChHHHhhcccccCCe--eeeecCCchHHHHHHHHHHHHHHc---CCcEEEEcCCHHHHHHHHHHHHHHHHhcCC
Confidence            466 49999999999999998  899999999999999999854433   347999999999999999999999998999


Q ss_pred             EEEEEEcCcchHHHHHHhcCCCcEEEeChHHH-HHHHHcC------CCCCCCceEEEEeCCchhh-ccC-----------
Q 015158          137 KVHACVGGTSVREDQRILSSGVHVVVGTPGRV-FDMLRRQ------SLRPDNIRIFVLDEADEML-SRG-----------  197 (412)
Q Consensus       137 ~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l-~~~~~~~------~~~~~~~~~iiiDE~h~~~-~~~-----------  197 (412)
                      ++..+.|+.+...  .....+++|+|+||..| +.++...      ....+++.++|+||||.++ +.+           
T Consensus       145 ~v~~i~GG~~~~~--r~~~~~~dIvvgTpgrl~fDyLrd~~~~~~~~~~~~~l~~lVlDEaD~mLiD~a~tpLIiSg~~~  222 (853)
T 2fsf_A          145 TVGINLPGMPAPA--KREAYAADITYGTNNEYGFDYLRDNMAFSPEERVQRKLHYALVDEVDSILIDEARTPLIISGPAE  222 (853)
T ss_dssp             CEEECCTTCCHHH--HHHHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCSCCEEEESCHHHHTTTTTTCEEEEEEC--
T ss_pred             eEEEEeCCCCHHH--HHHhcCCCEEEECCchhhHHHHHhhhhccHhHhcccCCcEEEECchHHHHHhcCcccccccCCCc
Confidence            9999999877543  23334589999999999 6666543      2456889999999999987 432           


Q ss_pred             ----cHHHHHHHHHhCCC--------------------CceEE------------------------EEeecCCh---HH
Q 015158          198 ----FKDQIYDIFQLLPP--------------------KIQVG------------------------VFSATMPP---EA  226 (412)
Q Consensus       198 ----~~~~~~~i~~~~~~--------------------~~~~i------------------------~~SAT~~~---~~  226 (412)
                          +...+..+...+++                    ..++.                        ++|||.+.   .+
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                45566677766653                    22332                        67888542   11


Q ss_pred             HHHH--HHhcCCC-------------------------------------eEEEecCCccccCCce--------------
Q 015158          227 LEIT--RKFMNKP-------------------------------------VRILVKRDELTLEGIK--------------  253 (412)
Q Consensus       227 ~~~~--~~~~~~~-------------------------------------~~~~~~~~~~~~~~~~--------------  253 (412)
                      ...+  ..++...                                     ..+.+.........+.              
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            1000  0011000                                     0011111110000000              


Q ss_pred             --------------------------------EEEEEeccchhhHHHHHHHHHh-c-CCCcEEEEEcchhHHHHHHHHHh
Q 015158          254 --------------------------------QFHVNVEKEEWKLETLCDLYET-L-AITQSVIFVNTRRKVDWLTDKMR  299 (412)
Q Consensus       254 --------------------------------~~~~~~~~~~~~~~~l~~~~~~-~-~~~k~lif~~~~~~~~~~~~~L~  299 (412)
                                                      ...........+...+.+.+.. + ...++||||+|++.++.+++.|+
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                                            0001122335577777777754 2 45789999999999999999999


Q ss_pred             cCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCC--------------------------------
Q 015158          300 SRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQV--------------------------------  347 (412)
Q Consensus       300 ~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~--------------------------------  347 (412)
                      +.|+.+.++||++...++..+.+.|+.|  .|+|+|+++++|+|++..                                
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            9999999999998888887788878776  699999999999999863                                


Q ss_pred             -----CEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHH
Q 015158          348 -----SLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDER  388 (412)
Q Consensus       348 -----~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~  388 (412)
                           .+||.++.|.|...|.|++||+||.|.+|.++.|++..|..
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                 59999999999999999999999999999999999887743

>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=1.9e-38  Score=309.17  Aligned_cols=307  Identities=21%  Similarity=0.183  Sum_probs=216.1

Q ss_pred             CChHHHH-----hhhhhhh------cCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHH
Q 015158           61 KPSAIQQ-----RGIVPFC------KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRA  129 (412)
Q Consensus        61 ~l~~~Q~-----~a~~~~~------~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~  129 (412)
                      .|++.|+     ++++.++      +++++++.+|||||||++|+++++..+..  .+.+++|++||++|+.|+.+.+..
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 YVSAIVQGERVEEPVPEAYNPEMLKKRQLTVLDLHPGAGKTRRILPQIIKDAIQ--KRLRTAVLAPTRVVAAEMAEALRG  292 (673)
T ss_dssp             EEEEEECC-------CCCCCGGGGSTTCEEEECCCTTTTTTTTHHHHHHHHHHH--TTCCEEEEESSHHHHHHHHHHTTT
T ss_pred             ccCceeeccccccchHHHhhHHHHhcCCeEEEEeCCCCCHHHHHHHHHHHHHHh--CCCcEEEEccHHHHHHHHHHHHhc
Confidence            7899999     9999888      89999999999999999999988877544  336899999999999999988875


Q ss_pred             hhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhC
Q 015158          130 LGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLL  209 (412)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~  209 (412)
                      +    ++.  ...+.     .......+.-+-+.+...+.+.+... ..+.++++||+||+|++ +..+...+..+...+
T Consensus       293 ~----~i~--~~~~~-----l~~v~tp~~ll~~l~~~~l~~~l~~~-~~l~~l~lvViDEaH~~-~~~~~~~~~~l~~~~  359 (673)
T 2wv9_A          293 L----PVR--YLTPA-----VQREHSGNEIVDVMCHATLTHRLMSP-LRVPNYNLFVMDEAHFT-DPASIAARGYIATRV  359 (673)
T ss_dssp             S----CCE--ECCC--------CCCCSCCCEEEEEHHHHHHHHHSS-SCCCCCSEEEEESTTCC-CHHHHHHHHHHHHHH
T ss_pred             C----Cee--eeccc-----ccccCCHHHHHHHHHhhhhHHHHhcc-cccccceEEEEeCCccc-CccHHHHHHHHHHhc
Confidence            4    222  11110     00011222345566777776665553 45678999999999997 222222333333333


Q ss_pred             -CCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhHHHHHHHHHhcCCCcEEEEEcch
Q 015158          210 -PPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTR  288 (412)
Q Consensus       210 -~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lif~~~~  288 (412)
                       +.+.++++||||+++....    +...            ...+......... ......+ ..+.. ..+++||||+++
T Consensus       360 ~~~~~~vl~~SAT~~~~i~~----~~~~------------~~~i~~v~~~~~~-~~~~~~l-~~l~~-~~~~~lVF~~s~  420 (673)
T 2wv9_A          360 EAGEAAAIFMTATPPGTSDP----FPDT------------NSPVHDVSSEIPD-RAWSSGF-EWITD-YAGKTVWFVASV  420 (673)
T ss_dssp             HTTSCEEEEECSSCTTCCCS----SCCC------------SSCEEEEECCCCS-SCCSSCC-HHHHS-CCSCEEEECSSH
T ss_pred             cccCCcEEEEcCCCChhhhh----hccc------------CCceEEEeeecCH-HHHHHHH-HHHHh-CCCCEEEEECCH
Confidence             2578999999999754211    1110            0011111111111 1111111 22222 457999999999


Q ss_pred             hHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEE----------------
Q 015158          289 RKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVIN----------------  352 (412)
Q Consensus       289 ~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~----------------  352 (412)
                      +.++.+++.|++.+..+..+||+    +|.++++.|++|+.+|||||+++++|+|+| +++||+                
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    789999999999999999999999999999 999997                


Q ss_pred             ----ccCCCChhhHHHhhhhcccC-CCCceEEEEe---ccCcHHHHHHHHHHhccccccCCh
Q 015158          353 ----YDLPTQPENYLHRIGRSGRF-GRKGVAINFV---TRDDERMLFDIQKFYNVVIEELPA  406 (412)
Q Consensus       353 ----~~~~~s~~~~~Q~~GR~~R~-g~~g~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~  406 (412)
                          ++.|.+..+|.||+||+||. |+.|.|++|+   ++.+...+..++..+......+++
T Consensus       496 ~~ll~d~P~s~~~y~Qr~GRaGR~~g~~G~ai~l~~~~~~~d~~~l~~ie~~~~l~~~~~~~  557 (673)
T 2wv9_A          496 VILSVPSAITSASAAQRRGRVGRNPSQIGDEYHYGGGTSEDDTMLAHWTEAKILLDNIHLPN  557 (673)
T ss_dssp             EEECCSEECCHHHHHHHHTTSSCCSSCCCEEEEECSCCCCCCTTBHHHHHHHHHHHTSCBTT
T ss_pred             ceecccCCCCHHHHHHHhhccCCCCCCCCEEEEEEecCChhHHHHHHHHHHHHhhhhccCCc
Confidence                45788999999999999999 7899999996   567777777777766443333333

>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=1.4e-38  Score=305.41  Aligned_cols=293  Identities=20%  Similarity=0.221  Sum_probs=217.4

Q ss_pred             CChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEE
Q 015158           61 KPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHA  140 (412)
Q Consensus        61 ~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~  140 (412)
                      .++++|+.++..+.+++++++.+|||||||.++.++++..      +.+++|++|+++|+.|+++.+.+..   +..+..
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            3677888888888899999999999999999998877752      3489999999999999998776654   445556


Q ss_pred             EEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCCCCce--EEEE
Q 015158          141 CVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQ--VGVF  218 (412)
Q Consensus       141 ~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~--~i~~  218 (412)
                      ..|+..       ...+.+|+|+||++|   +.+..+...++++||+||+|. .+.++...+..++..++...+  ++++
T Consensus       288 ~vG~~~-------~~~~~~IlV~TPGrL---l~~~~l~l~~l~~lVlDEAH~-l~~~~~~~l~~Il~~l~~~~~~llil~  356 (666)
T 3o8b_A          288 RTGVRT-------ITTGAPVTYSTYGKF---LADGGCSGGAYDIIICDECHS-TDSTTILGIGTVLDQAETAGARLVVLA  356 (666)
T ss_dssp             ECSSCE-------ECCCCSEEEEEHHHH---HHTTSCCTTSCSEEEETTTTC-CSHHHHHHHHHHHHHTTTTTCSEEEEE
T ss_pred             EECcEe-------ccCCCCEEEECcHHH---HhCCCcccCcccEEEEccchh-cCccHHHHHHHHHHhhhhcCCceEEEE
Confidence            666543       345679999999998   355667778899999999986 455567778888888876554  7888


Q ss_pred             eecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhHHHHHHHHHhcCCCcEEEEEcchhHHHHHHHHH
Q 015158          219 SATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKM  298 (412)
Q Consensus       219 SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L  298 (412)
                      |||++....      ...+.........   ......   ... ...       +.....+++||||++++.++.+++.|
T Consensus       357 SAT~~~~i~------~~~p~i~~v~~~~---~~~i~~---~~~-~~~-------l~~~~~~~vLVFv~Tr~~ae~la~~L  416 (666)
T 3o8b_A          357 TATPPGSVT------VPHPNIEEVALSN---TGEIPF---YGK-AIP-------IEAIRGGRHLIFCHSKKKCDELAAKL  416 (666)
T ss_dssp             ESSCTTCCC------CCCTTEEEEECBS---CSSEEE---TTE-EEC-------GGGSSSSEEEEECSCHHHHHHHHHHH
T ss_pred             CCCCCcccc------cCCcceEEEeecc---cchhHH---HHh-hhh-------hhhccCCcEEEEeCCHHHHHHHHHHH
Confidence            999986310      1111111110000   000000   000 000       12335689999999999999999999


Q ss_pred             hcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEE----------cc-----------CCC
Q 015158          299 RSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVIN----------YD-----------LPT  357 (412)
Q Consensus       299 ~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~----------~~-----------~~~  357 (412)
                      ++.++.+..+||++++.+       |.++..+|||+|+++++|+|++ +++||+          ++           .|.
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            999999999999998764       4556679999999999999997 999985          44           789


Q ss_pred             ChhhHHHhhhhcccCCCCceEEEEeccCcHHH--H--HHHHHHhcccccc
Q 015158          358 QPENYLHRIGRSGRFGRKGVAINFVTRDDERM--L--FDIQKFYNVVIEE  403 (412)
Q Consensus       358 s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~--~--~~~~~~~~~~~~~  403 (412)
                      |..+|+||+||+|| |.+|. +.|+++.+...  +  ..+++.++...++
T Consensus       489 s~~syiQRiGRtGR-g~~G~-i~lvt~~e~~~~~l~~~~i~~~~~~~~~~  536 (666)
T 3o8b_A          489 DAVSRSQRRGRTGR-GRRGI-YRFVTPGERPSGMFDSSVLCECYDAGCAW  536 (666)
T ss_dssp             BHHHHHHHHTTBCS-SSCEE-EEESCCCCBCSSBCCHHHHHHHHHHHHHT
T ss_pred             CHHHHHHHhccCCC-CCCCE-EEEEecchhhcccccHHHHHHHhcCCccc
Confidence            99999999999999 89999 88988876554  3  5555555544443

>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=3.7e-36  Score=290.44  Aligned_cols=323  Identities=20%  Similarity=0.268  Sum_probs=245.2

Q ss_pred             CCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCc
Q 015158           57 YGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGV  136 (412)
Q Consensus        57 ~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~  136 (412)
                      .|+ .|++.|..+++.+++|+  +..++||+|||+++.++++.....+   ..++|++||+.|+.|.++.+..++...++
T Consensus       108 lG~-rP~~VQ~~~ip~Ll~G~--Iaem~TGeGKTLa~~LP~~l~aL~g---~~v~VvTpTreLA~Qdae~m~~l~~~lGL  181 (922)
T 1nkt_A          108 LDQ-RPFDVQVMGAAALHLGN--VAEMKTGEGKTLTCVLPAYLNALAG---NGVHIVTVNDYLAKRDSEWMGRVHRFLGL  181 (922)
T ss_dssp             HSC-CCCHHHHHHHHHHHTTE--EEECCTTSCHHHHTHHHHHHHHTTT---SCEEEEESSHHHHHHHHHHHHHHHHHTTC
T ss_pred             cCC-CCCHHHHHHHHhHhcCC--EEEecCCCccHHHHHHHHHHHHHhC---CCeEEEeCCHHHHHHHHHHHHHHHhhcCC
Confidence            488 69999999999999998  9999999999999999996443333   47999999999999999999999999999


Q ss_pred             EEEEEEcCcchHHHHHHhcCCCcEEEeChHHH-HHHHHcC------CCCCCCceEEEEeCCchhh-cc------------
Q 015158          137 KVHACVGGTSVREDQRILSSGVHVVVGTPGRV-FDMLRRQ------SLRPDNIRIFVLDEADEML-SR------------  196 (412)
Q Consensus       137 ~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l-~~~~~~~------~~~~~~~~~iiiDE~h~~~-~~------------  196 (412)
                      ++.++.|+.+....  .....++|+|+||..| +.++...      ....+.+.++|+||||.++ +.            
T Consensus       182 sv~~i~gg~~~~~r--~~~y~~DIvygTpgrlgfDyLrD~m~~~~~~l~lr~l~~lIVDEaDsmLiDeartPLiiSg~~~  259 (922)
T 1nkt_A          182 QVGVILATMTPDER--RVAYNADITYGTNNEFGFDYLRDNMAHSLDDLVQRGHHYAIVDEVDSILIDEARTPLIISGPAD  259 (922)
T ss_dssp             CEEECCTTCCHHHH--HHHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEETTHHHHHTTGGGSCEEEEEECC
T ss_pred             eEEEEeCCCCHHHH--HHhcCCCEEEECchHhhHHHHHhhhhccHhhhccCCCCEEEEeChHHHHHhcCccceeecCCCC
Confidence            99999998774433  2333579999999998 6666543      3556789999999999987 42            


Q ss_pred             ---CcHHHHHHHHHhCC---------CCceEE-----------------EEeecCCh---HHHHHH--HHhcCCC-----
Q 015158          197 ---GFKDQIYDIFQLLP---------PKIQVG-----------------VFSATMPP---EALEIT--RKFMNKP-----  237 (412)
Q Consensus       197 ---~~~~~~~~i~~~~~---------~~~~~i-----------------~~SAT~~~---~~~~~~--~~~~~~~-----  237 (412)
                         ++...+..+...++         +..++.                 ++|||.+.   .+...+  ..++...     
T Consensus       260 ~~~~~y~~i~~iv~~L~~~~dy~vDek~rqv~Lte~G~~~~e~~l~i~~Lfsat~~~l~~~i~~aL~A~~l~~~d~dYiV  339 (922)
T 1nkt_A          260 GASNWYTEFARLAPLMEKDVHYEVDLRKRTVGVHEKGVEFVEDQLGIDNLYEAANSPLVSYLNNALKAKELFSRDKDYIV  339 (922)
T ss_dssp             CCHHHHHHHHHHHHHSCBTTTEEEETTTTEEEECHHHHHHHHHHHTCSSTTCSTTCCHHHHHHHHHHHHHHCCBTTTEEE
T ss_pred             cchhHHHHHHHHHHhCcccccceeccCcceEEecHhHHHHHHHHhCCccccCCcchhHHHHHHHHHHHHHHhhcccceee
Confidence               36678889999997         566777                 78899753   222211  1122111     


Q ss_pred             ---eEEEecC-----------------------------Cccc-------------------------------------
Q 015158          238 ---VRILVKR-----------------------------DELT-------------------------------------  248 (412)
Q Consensus       238 ---~~~~~~~-----------------------------~~~~-------------------------------------  248 (412)
                         ..+.+..                             ....                                     
T Consensus       340 ~dg~vviVDe~TGR~m~grr~sdGLHQaieaKe~V~I~~e~~TlatIt~Qnyfr~Y~kL~GMTGTa~te~~Ef~~iY~l~  419 (922)
T 1nkt_A          340 RDGEVLIVDEFTGRVLIGRRYNEGMHQAIEAKEHVEIKAENQTLATITLQNYFRLYDKLAGMTGTAQTEAAELHEIYKLG  419 (922)
T ss_dssp             CSSCEEEBCSSSCCBCTTCCCSTTHHHHHHHHTTCCCCCCEEEEEEECHHHHHTTSSEEEEEESCCGGGHHHHHHHHCCE
T ss_pred             ecCceEEEecccCcccCCccccchhhHHHhccccccccccccccceeehHHHHHhhhhhhccccCchhHHHHHHHHhCCC
Confidence               1111110                             0000                                     


Q ss_pred             -------cCCceE--EEEEeccchhhHHHHHHHHHhc--CCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHH
Q 015158          249 -------LEGIKQ--FHVNVEKEEWKLETLCDLYETL--AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTR  317 (412)
Q Consensus       249 -------~~~~~~--~~~~~~~~~~~~~~l~~~~~~~--~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r  317 (412)
                             .+....  ..........+...+...+...  .+.++||||+|++.++.+++.|++.|+.+.++||+....++
T Consensus       420 vv~IPtn~p~~R~d~~d~v~~t~~~K~~al~~~i~~~~~~gqpvLVft~Sie~sE~Ls~~L~~~Gi~~~vLnak~~~rEa  499 (922)
T 1nkt_A          420 VVSIPTNMPMIREDQSDLIYKTEEAKYIAVVDDVAERYAKGQPVLIGTTSVERSEYLSRQFTKRRIPHNVLNAKYHEQEA  499 (922)
T ss_dssp             EEECCCSSCCCCEECCCEEESCHHHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHTTCCCEEECSSCHHHHH
T ss_pred             eEEeCCCCCcccccCCcEEEeCHHHHHHHHHHHHHHHHhcCCcEEEEECCHHHHHHHHHHHHHCCCCEEEecCChhHHHH
Confidence                   000000  0011223355777777666542  45689999999999999999999999999999999877777


Q ss_pred             HHHHHHHhcCCCcEEEEcCCCcCCCCCCCC--------------------------------------------------
Q 015158          318 DIIMREFRSGSSRVLITTDLLARGIDVQQV--------------------------------------------------  347 (412)
Q Consensus       318 ~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~--------------------------------------------------  347 (412)
                      ..+.+.|+.|  .|+|+|+++++|+|++..                                                  
T Consensus       500 ~iia~agr~G--~VtIATnmAgRGtDI~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~  577 (922)
T 1nkt_A          500 TIIAVAGRRG--GVTVATNMAGRGTDIVLGGNVDFLTDQRLRERGLDPVETPEEYEAAWHSELPIVKEEASKEAKEVIEA  577 (922)
T ss_dssp             HHHHTTTSTT--CEEEEETTCSTTCCCCTTCCHHHHHHHHHHHTTCCTTTSHHHHHHHHHHHHHHHHHHTTHHHHHHHHT
T ss_pred             HHHHhcCCCC--eEEEecchhhcCccccCCCCHHHHHHHHHhhccccccccchhhHHHHHHHHHHHHHHHHHhhhHHHhc
Confidence            7777777666  699999999999999964                                                  


Q ss_pred             --CEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHHH
Q 015158          348 --SLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERM  389 (412)
Q Consensus       348 --~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~  389 (412)
                        .+||.++.|.|...|.|++||+||.|.+|.+..|++..|.-.
T Consensus       578 GGlhVI~te~pes~riy~qr~GRTGRqGdpG~s~fflSleD~l~  621 (922)
T 1nkt_A          578 GGLYVLGTERHESRRIDNQLRGRSGRQGDPGESRFYLSLGDELM  621 (922)
T ss_dssp             TSEEEEECSCCSSHHHHHHHHHTSSGGGCCEEEEEEEETTSHHH
T ss_pred             CCcEEEeccCCCCHHHHHHHhcccccCCCCeeEEEEechhHHHH
Confidence              499999999999999999999999999999999999877643

>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=7.2e-38  Score=293.61  Aligned_cols=296  Identities=18%  Similarity=0.176  Sum_probs=198.0

Q ss_pred             hhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHH
Q 015158           72 PFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQ  151 (412)
Q Consensus        72 ~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  151 (412)
                      .+.+|+++++.+|||||||++|+++++..+...  +.+++|++||++|+.|+.+.+..+    +  +....+...     
T Consensus         4 ~l~~g~~vlv~a~TGSGKT~~~l~~~l~~~~~~--~~~~lil~Ptr~La~Q~~~~l~~~----~--v~~~~~~~~-----   70 (440)
T 1yks_A            4 MLKKGMTTVLDFHPGAGKTRRFLPQILAECARR--RLRTLVLAPTRVVLSEMKEAFHGL----D--VKFHTQAFS-----   70 (440)
T ss_dssp             TTSTTCEEEECCCTTSSTTTTHHHHHHHHHHHT--TCCEEEEESSHHHHHHHHHHTTTS----C--EEEESSCCC-----
T ss_pred             HhhCCCCEEEEcCCCCCHHHHHHHHHHHHHHhc--CCeEEEEcchHHHHHHHHHHHhcC----C--eEEecccce-----
Confidence            467899999999999999999988888766542  358999999999999999888754    2  222111100     


Q ss_pred             HHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhC-CCCceEEEEeecCChHHHHHH
Q 015158          152 RILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLL-PPKIQVGVFSATMPPEALEIT  230 (412)
Q Consensus       152 ~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~-~~~~~~i~~SAT~~~~~~~~~  230 (412)
                      .....+.-+-..+...+...+.. ...+.++++||+||+|++ +..+...+..+.... +.+.+++++|||+++....  
T Consensus        71 ~v~Tp~~l~~~l~~~~l~~~~~~-~~~~~~l~~vViDEah~~-~~~~~~~~~~~~~~~~~~~~~~l~~SAT~~~~~~~--  146 (440)
T 1yks_A           71 AHGSGREVIDAMCHATLTYRMLE-PTRVVNWEVIIMDEAHFL-DPASIAARGWAAHRARANESATILMTATPPGTSDE--  146 (440)
T ss_dssp             CCCCSSCCEEEEEHHHHHHHHTS-SSCCCCCSEEEETTTTCC-SHHHHHHHHHHHHHHHTTSCEEEEECSSCTTCCCS--
T ss_pred             eccCCccceeeecccchhHhhhC-cccccCccEEEEECcccc-CcchHHHHHHHHHHhccCCceEEEEeCCCCchhhh--
Confidence            00111122333444444443332 334678999999999997 332222222222222 3578999999999764321  


Q ss_pred             HHhcCCCeEEEecCCccccCCceEEEEEeccchhhHHHHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecC
Q 015158          231 RKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHG  310 (412)
Q Consensus       231 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~  310 (412)
                        +....            ..+.......+. ..... +...+.. ..+++||||++++.++.+++.|++.+..+..+||
T Consensus       147 --~~~~~------------~~~~~~~~~~~~-~~~~~-~~~~l~~-~~~~~lVF~~s~~~a~~l~~~L~~~~~~v~~lhg  209 (440)
T 1yks_A          147 --FPHSN------------GEIEDVQTDIPS-EPWNT-GHDWILA-DKRPTAWFLPSIRAANVMAASLRKAGKSVVVLNR  209 (440)
T ss_dssp             --SCCCS------------SCEEEEECCCCS-SCCSS-SCHHHHH-CCSCEEEECSCHHHHHHHHHHHHHTTCCEEECCS
T ss_pred             --hhhcC------------CCeeEeeeccCh-HHHHH-HHHHHHh-cCCCEEEEeCCHHHHHHHHHHHHHcCCCEEEecc
Confidence              11110            001111111111 11111 1122222 2579999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEE-------------------ccCCCChhhHHHhhhhccc
Q 015158          311 DMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVIN-------------------YDLPTQPENYLHRIGRSGR  371 (412)
Q Consensus       311 ~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~-------------------~~~~~s~~~~~Q~~GR~~R  371 (412)
                          .+|.++++.|++|+.+|||||+++++|+|+| +++||+                   ++.|.+..+|.||+||+||
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                3588999999999999999999999999999 999986                   7789999999999999999


Q ss_pred             C-CCCceEEEEe---ccCcHHHHHHHHHHhccccccCCh
Q 015158          372 F-GRKGVAINFV---TRDDERMLFDIQKFYNVVIEELPA  406 (412)
Q Consensus       372 ~-g~~g~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~  406 (412)
                      . |.+|.|++++   ++.+.+.+..++..+.....+++.
T Consensus       285 ~g~~~g~~~~l~~~~~~~~~~~l~~l~~~~~~~~~~l~~  323 (440)
T 1yks_A          285 NPNRDGDSYYYSEPTSENNAHHVCWLEASMLLDNMEVRG  323 (440)
T ss_dssp             CTTCCCEEEEECSCCCCCCTTBHHHHHHHHHHTTSCCGG
T ss_pred             CCCCCceEEEEeccCChhhhhhhhhhhHHhccccccccc
Confidence            8 6899999996   677888888888877554444443

>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=2.3e-37  Score=315.26  Aligned_cols=332  Identities=17%  Similarity=0.135  Sum_probs=231.1

Q ss_pred             CChHHHHhhhhhhhcC--ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEE
Q 015158           61 KPSAIQQRGIVPFCKG--LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKV  138 (412)
Q Consensus        61 ~l~~~Q~~a~~~~~~~--~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~  138 (412)
                      .|+|||.+++..+...  .++++.++||+|||.+++..+...+..+ ...++|||||+ +|+.||.+++.+..   +..+
T Consensus       153 ~LrpyQ~eav~~~l~~~~~~~LLad~tGlGKTi~Ai~~i~~l~~~g-~~~rvLIVvP~-sLl~Qw~~E~~~~f---~l~v  227 (968)
T 3dmq_A          153 SLIPHQLNIAHDVGRRHAPRVLLADEVGLGKTIEAGMILHQQLLSG-AAERVLIIVPE-TLQHQWLVEMLRRF---NLRF  227 (968)
T ss_dssp             CCCHHHHHHHHHHHHSSSCEEEECCCTTSCHHHHHHHHHHHHHHTS-SCCCEEEECCT-TTHHHHHHHHHHHS---CCCC
T ss_pred             CCcHHHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHHhC-CCCeEEEEeCH-HHHHHHHHHHHHHh---CCCE
Confidence            5999999999988864  5889999999999999987777665544 34579999999 99999999997754   5566


Q ss_pred             EEEEcCcchHHHHH--HhcCCCcEEEeChHHHHHHHHc-CCCCCCCceEEEEeCCchhhccCcH--HHHHHHHHhCCCCc
Q 015158          139 HACVGGTSVREDQR--ILSSGVHVVVGTPGRVFDMLRR-QSLRPDNIRIFVLDEADEMLSRGFK--DQIYDIFQLLPPKI  213 (412)
Q Consensus       139 ~~~~~~~~~~~~~~--~~~~~~~iii~T~~~l~~~~~~-~~~~~~~~~~iiiDE~h~~~~~~~~--~~~~~i~~~~~~~~  213 (412)
                      ..++++........  .....++|+|+|++.+.+.... ..+...++++||+||||++.+....  .....+........
T Consensus       228 ~v~~~~~~~~~~~~~~~~~~~~dIvI~T~~~L~~~~~~~~~l~~~~~dlVIvDEAH~~kn~~~~~s~~~~~l~~L~~~~~  307 (968)
T 3dmq_A          228 ALFDDERYAEAQHDAYNPFDTEQLVICSLDFARRSKQRLEHLCEAEWDLLVVDEAHHLVWSEDAPSREYQAIEQLAEHVP  307 (968)
T ss_dssp             EECCHHHHHHHHHTTCSSSTTCSEEEECHHHHHTSTTTTHHHHTSCCCEEEECCSSCCCCBTTBCCHHHHHHHHHHTTCS
T ss_pred             EEEccchhhhhhhhcccccccCCEEEEcHHHHhhCHHHHHHhhhcCCCEEEehhhHhhcCCCCcchHHHHHHHHHhhcCC
Confidence            66655432221111  1123568999999988542111 0122347899999999998755421  11222222223455


Q ss_pred             eEEEEeecCChH----HHHHHHH----------------------------hcCC-------------------------
Q 015158          214 QVGVFSATMPPE----ALEITRK----------------------------FMNK-------------------------  236 (412)
Q Consensus       214 ~~i~~SAT~~~~----~~~~~~~----------------------------~~~~-------------------------  236 (412)
                      +++++||||..+    ....+..                            +...                         
T Consensus       308 ~~L~LTATPi~n~~~el~sll~~L~p~~~~~~~~f~~~~~~~~~i~~~~~~l~~~~~~~~~~~~~L~~~l~~~~~~~l~~  387 (968)
T 3dmq_A          308 GVLLLTATPEQLGMESHFARLRLLDPNRFHDFAQFVEEQKNYCPVADAVAMLLAGNKLSNDELNMLGEMIGEQDIEPLLQ  387 (968)
T ss_dssp             SEEESCSSCSSSCSSCTHHHHHHHCTTTCSSTHHHHHHHHHHHHHHHHHHTTTTSCCCCGGGTTSSTTTTCTTCSSTTGG
T ss_pred             cEEEEEcCCccCCHHHHHHHHHhcCccccCCHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHHHhcchhhHHHHh
Confidence            699999998521    1111000                            0000                         


Q ss_pred             ---------------------------CeEEEecCCcc---ccCCceEEEEE----------------------------
Q 015158          237 ---------------------------PVRILVKRDEL---TLEGIKQFHVN----------------------------  258 (412)
Q Consensus       237 ---------------------------~~~~~~~~~~~---~~~~~~~~~~~----------------------------  258 (412)
                                                 ...+...+...   ...........                            
T Consensus       388 ~~~~~~~~~~~~~~~~i~~lld~~g~~~~l~r~~r~~i~~~p~r~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  467 (968)
T 3dmq_A          388 AANSDSEDAQSARQELVSMLMDRHGTSRVLFRNTRNGVKGFPKRELHTIKLPLPTQYQTAIKVSGIMGARKSAEDRARDM  467 (968)
T ss_dssp             GTCCCSSCSTTTHHHHHHHHGGGCTTTTTEECCCTTTCCCCCCCCCCEEEECCCHHHHHHHHHHHHTTCCSSGGGGTHHH
T ss_pred             cccchhhhhHHHHHHHHHHHHHhhCcchhhhhhhhhhhcccChhheEeeecCCCHHHHHHHHHHhhhhhhhhhHHHHhhh
Confidence                                       00000000000   00000111111                            


Q ss_pred             ----------------eccchhhHHHHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhc-CCCeeEEecCCCCHHHHHHHH
Q 015158          259 ----------------VEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRS-RDHTVSATHGDMDQNTRDIIM  321 (412)
Q Consensus       259 ----------------~~~~~~~~~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~-~~~~~~~~~~~~~~~~r~~~~  321 (412)
                                      ......+...+.+++.....+++||||++++.++.+++.|.+ .|+.+..+||+++..+|..++
T Consensus       468 l~pe~~~~~l~~~~~~~~~~~~K~~~L~~ll~~~~~~k~iVF~~~~~~~~~l~~~L~~~~g~~~~~lhG~~~~~~R~~~l  547 (968)
T 3dmq_A          468 LYPERIYQEFEGDNATWWNFDPRVEWLMGYLTSHRSQKVLVICAKAATALQLEQVLREREGIRAAVFHEGMSIIERDRAA  547 (968)
T ss_dssp             HCSGGGTTTTTSSSCCTTTTSHHHHHHHHHHHHTSSSCCCEECSSTHHHHHHHHHHHTTTCCCEEEECTTSCTTHHHHHH
T ss_pred             cChHHHHHHhhhhhhcccCccHHHHHHHHHHHhCCCCCEEEEeCcHHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHH
Confidence                            111234677888888887789999999999999999999995 599999999999999999999


Q ss_pred             HHHhcCC--CcEEEEcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHHh
Q 015158          322 REFRSGS--SRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFY  397 (412)
Q Consensus       322 ~~f~~g~--~~vlv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~  397 (412)
                      +.|++|+  ++|||+|+++++|+|+|.+++||++++|+++..|.|++||++|.|+.+.++++...........+.+.+
T Consensus       548 ~~F~~g~~~~~vLvaT~v~~~GlDl~~~~~VI~~d~p~~~~~~~Q~~GR~~R~Gq~~~v~v~~~~~~~t~ee~i~~~~  625 (968)
T 3dmq_A          548 AWFAEEDTGAQVLLCSEIGSEGRNFQFASHMVMFDLPFNPDLLEQRIGRLDRIGQAHDIQIHVPYLEKTAQSVLVRWY  625 (968)
T ss_dssp             HHHHSTTSSCEEEECSCCTTCSSCCTTCCEEECSSCCSSHHHHHHHHHTTSCSSSCSCCEEEEEEETTSHHHHHHHHH
T ss_pred             HHHhCCCCcccEEEecchhhcCCCcccCcEEEEecCCCCHHHHHHHhhccccCCCCceEEEEEecCCChHHHHHHHHH
Confidence            9999998  999999999999999999999999999999999999999999999998777665554433334455555

>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=1.2e-36  Score=284.81  Aligned_cols=269  Identities=17%  Similarity=0.149  Sum_probs=188.4

Q ss_pred             cCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHh
Q 015158           75 KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL  154 (412)
Q Consensus        75 ~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  154 (412)
                      +|+++++++|||||||.+++++++..+..  .+.+++|++||++|+.|+.+.+.      +..+....+...     ...
T Consensus         1 kg~~~lv~a~TGsGKT~~~l~~~l~~~~~--~g~~~lvl~Pt~~La~Q~~~~~~------~~~v~~~~~~~~-----~~~   67 (431)
T 2v6i_A            1 KRELTVLDLHPGAGKTRRVLPQLVREAVK--KRLRTVILAPTRVVASEMYEALR------GEPIRYMTPAVQ-----SER   67 (431)
T ss_dssp             -CCEEEEECCTTSCTTTTHHHHHHHHHHH--TTCCEEEEESSHHHHHHHHHHTT------TSCEEEC-------------
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHHHh--CCCCEEEECcHHHHHHHHHHHhC------CCeEEEEecCcc-----ccC
Confidence            36899999999999999998888855433  23589999999999999987765      344544444321     112


Q ss_pred             cCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHh-CCCCceEEEEeecCChHHHHHHHHh
Q 015158          155 SSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQL-LPPKIQVGVFSATMPPEALEITRKF  233 (412)
Q Consensus       155 ~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~-~~~~~~~i~~SAT~~~~~~~~~~~~  233 (412)
                      ..+..+.++|.+.+.+.+.. ...+.++++||+||+|++ +..+......+... .+.+.+++++|||+++....    +
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            23456778888888776665 445678999999999996 33223333333333 25689999999999863111    1


Q ss_pred             cCCCeEEEecCCccccCCceEEEEEeccchhhHHHHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCC
Q 015158          234 MNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMD  313 (412)
Q Consensus       234 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~  313 (412)
                      ...            ...+.......+.  .....+.+.+... .+++||||++++.++.+++.|++.+..+..+||+  
T Consensus       142 ~~~------------~~~i~~~~~~~~~--~~~~~~~~~l~~~-~~~~lVF~~~~~~~~~l~~~L~~~~~~v~~lhg~--  204 (431)
T 2v6i_A          142 PPS------------NSPIIDEETRIPD--KAWNSGYEWITEF-DGRTVWFVHSIKQGAEIGTCLQKAGKKVLYLNRK--  204 (431)
T ss_dssp             CCC------------SSCCEEEECCCCS--SCCSSCCHHHHSC-SSCEEEECSSHHHHHHHHHHHHHTTCCEEEESTT--
T ss_pred             cCC------------CCceeeccccCCH--HHHHHHHHHHHcC-CCCEEEEeCCHHHHHHHHHHHHHcCCeEEEeCCc--
Confidence            100            0111111001111  1111222333333 5789999999999999999999999999999997  


Q ss_pred             HHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCE-----------------EEEccCCCChhhHHHhhhhcccCCCC-
Q 015158          314 QNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSL-----------------VINYDLPTQPENYLHRIGRSGRFGRK-  375 (412)
Q Consensus       314 ~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~-----------------vi~~~~~~s~~~~~Q~~GR~~R~g~~-  375 (412)
                        +|.++++.|++|+.+|||||+++++|+|+| +.+                 |++++.|.+..+|.||+||+||.|.. 
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              578899999999999999999999999999 655                 46677888999999999999999854 


Q ss_pred             ceEEEEe
Q 015158          376 GVAINFV  382 (412)
Q Consensus       376 g~~~~~~  382 (412)
                      |.++++.
T Consensus       282 ~~~~~~~  288 (431)
T 2v6i_A          282 GDIYAYS  288 (431)
T ss_dssp             CCEEEEC
T ss_pred             CeEEEEc
Confidence            4555554

>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=6.8e-36  Score=287.06  Aligned_cols=309  Identities=15%  Similarity=0.184  Sum_probs=215.3

Q ss_pred             CChHHHHhhhhhhh----cCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCc
Q 015158           61 KPSAIQQRGIVPFC----KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGV  136 (412)
Q Consensus        61 ~l~~~Q~~a~~~~~----~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~  136 (412)
                      .|+|||.+++..+.    .++++++.++||+|||.+++..+..... .....++||||| .+|+.||.+++.++..  +.
T Consensus        37 ~L~~~Q~~~v~~l~~~~~~~~~~ilad~~GlGKT~~ai~~i~~~~~-~~~~~~~LIv~P-~~l~~qw~~e~~~~~~--~~  112 (500)
T 1z63_A           37 NLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAVFSDAKK-ENELTPSLVICP-LSVLKNWEEELSKFAP--HL  112 (500)
T ss_dssp             CCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHHHHHHHHHH-TTCCSSEEEEEC-STTHHHHHHHHHHHCT--TS
T ss_pred             cchHHHHHHHHHHHHHhhCCCCEEEEeCCCCcHHHHHHHHHHHHHh-cCCCCCEEEEcc-HHHHHHHHHHHHHHCC--Cc
Confidence            49999999998763    5788999999999999998665554433 234457999999 5689999999999875  45


Q ss_pred             EEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEE
Q 015158          137 KVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVG  216 (412)
Q Consensus       137 ~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i  216 (412)
                      .+..++|+...     .....++|+|+||+.+.+...   +....+++||+||||++.+..  ......+..++ ..+++
T Consensus       113 ~v~~~~g~~~~-----~~~~~~~ivi~t~~~l~~~~~---l~~~~~~~vIvDEaH~~kn~~--~~~~~~l~~l~-~~~~l  181 (500)
T 1z63_A          113 RFAVFHEDRSK-----IKLEDYDIILTTYAVLLRDTR---LKEVEWKYIVIDEAQNIKNPQ--TKIFKAVKELK-SKYRI  181 (500)
T ss_dssp             CEEECSSSTTS-----CCGGGSSEEEEEHHHHTTCHH---HHTCCEEEEEEETGGGGSCTT--SHHHHHHHTSC-EEEEE
T ss_pred             eEEEEecCchh-----ccccCCcEEEeeHHHHhccch---hcCCCcCEEEEeCccccCCHh--HHHHHHHHhhc-cCcEE
Confidence            56666665421     122457899999999865432   223478999999999987654  23444444553 46789


Q ss_pred             EEeecCChHHHHH-------------------------------------HHHhcCCCeEEEecCCc----cccCCceEE
Q 015158          217 VFSATMPPEALEI-------------------------------------TRKFMNKPVRILVKRDE----LTLEGIKQF  255 (412)
Q Consensus       217 ~~SAT~~~~~~~~-------------------------------------~~~~~~~~~~~~~~~~~----~~~~~~~~~  255 (412)
                      ++||||..+....                                     +..++. +..+......    ...+.....
T Consensus       182 ~LTaTP~~n~~~el~~ll~~l~p~~~~~~~~f~~~~~~~~~~~~~~~~~~l~~~l~-~~~lrr~k~~~~~~~~lp~~~~~  260 (500)
T 1z63_A          182 ALTGTPIENKVDDLWSIMTFLNPGLLGSYSEFKSKFATPIKKGDNMAKEELKAIIS-PFILRRTKYDKAIINDLPDKIET  260 (500)
T ss_dssp             EECSSCSTTCHHHHHHHHHHHSTTTTCCHHHHHTTTHHHHHTTCHHHHHHHHHHHT-TTEECCCTTCHHHHTTSCSEEEE
T ss_pred             EEecCCCCCCHHHHHHHHHHhCCCcCCCHHHHHHHhccccccccHHHHHHHHHHHh-hHeeeecccccchhhcCCCCeEE
Confidence            9999995421111                                     111111 1111111110    011222222


Q ss_pred             EEEeccc--------------------------------------------------------hhhHHHHHHHHHhc--C
Q 015158          256 HVNVEKE--------------------------------------------------------EWKLETLCDLYETL--A  277 (412)
Q Consensus       256 ~~~~~~~--------------------------------------------------------~~~~~~l~~~~~~~--~  277 (412)
                      ...+...                                                        ..+...+.+++...  .
T Consensus       261 ~v~~~l~~~~~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~l~~lr~~~~~p~l~~~~~~~~~~s~K~~~l~~~l~~~~~~  340 (500)
T 1z63_A          261 NVYCNLTPEQAAMYKAEVENLFNNIDSVTGIKRKGMILSTLLKLKQIVDHPALLKGGEQSVRRSGKMIRTMEIIEEALDE  340 (500)
T ss_dssp             EEEECCCHHHHHHHHHHHHHHTTTTTTCCTHHHHHHHHHHHHHHHHHTTCTHHHHCSCCCSTTCHHHHHHHHHHHHHHTT
T ss_pred             EEEcCCCHHHHHHHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhCCHHHhcCccchhhcchhHHHHHHHHHHHHcc
Confidence            2222111                                                        12333444555443  4


Q ss_pred             CCcEEEEEcchhHHHHHHHHHhcC-CCeeEEecCCCCHHHHHHHHHHHhcC-CCc-EEEEcCCCcCCCCCCCCCEEEEcc
Q 015158          278 ITQSVIFVNTRRKVDWLTDKMRSR-DHTVSATHGDMDQNTRDIIMREFRSG-SSR-VLITTDLLARGIDVQQVSLVINYD  354 (412)
Q Consensus       278 ~~k~lif~~~~~~~~~~~~~L~~~-~~~~~~~~~~~~~~~r~~~~~~f~~g-~~~-vlv~t~~~~~G~d~~~~~~vi~~~  354 (412)
                      ++++||||++...++.+.+.|.+. +..+..+||+++..+|.+++++|+++ +.+ +|++|+++++|+|++.+++||+++
T Consensus       341 ~~k~lvF~~~~~~~~~l~~~l~~~~~~~~~~~~g~~~~~~R~~~~~~F~~~~~~~vil~st~~~~~Glnl~~~~~vi~~d  420 (500)
T 1z63_A          341 GDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVKAGGFGINLTSANRVIHFD  420 (500)
T ss_dssp             TCCEEEECSCHHHHHHHHHHHHHHHTCCCCEEETTSCHHHHHHHHHHHHHCTTCCCCEEECCCC-CCCCCTTCSEEEESS
T ss_pred             CCcEEEEEehHHHHHHHHHHHHHhhCCCeEEEECCCCHHHHHHHHHHhcCCCCCCEEEEecccccCCCchhhCCEEEEeC
Confidence            579999999999999999999885 89999999999999999999999998 555 788999999999999999999999


Q ss_pred             CCCChhhHHHhhhhcccCCCCceEE--EEeccC
Q 015158          355 LPTQPENYLHRIGRSGRFGRKGVAI--NFVTRD  385 (412)
Q Consensus       355 ~~~s~~~~~Q~~GR~~R~g~~g~~~--~~~~~~  385 (412)
                      +|||+..+.|++||++|.|+.+.+.  .++...
T Consensus       421 ~~~~~~~~~Q~~gR~~R~Gq~~~v~v~~lv~~~  453 (500)
T 1z63_A          421 RWWNPAVEDQATDRVYRIGQTRNVIVHKLISVG  453 (500)
T ss_dssp             CCSCC---CHHHHTTTTTTTTSCEEEEEEEETT
T ss_pred             CCCCcchHHHHHHHHHHcCCCCeeEEEEEEeCC
Confidence            9999999999999999999877654  444444

>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=3.9e-37  Score=290.44  Aligned_cols=276  Identities=20%  Similarity=0.207  Sum_probs=193.0

Q ss_pred             HhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcc
Q 015158           67 QRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTS  146 (412)
Q Consensus        67 ~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~  146 (412)
                      ......+.+++++++.+|||||||++|+++++..+..  .+.++||++|+++|+.|+.+.+..      ..+....+...
T Consensus        12 ~~~~~~l~~~~~vlv~a~TGsGKT~~~~l~il~~~~~--~~~~~lvl~Ptr~La~Q~~~~l~g------~~v~~~~~~~~   83 (459)
T 2z83_A           12 RGSPNMLRKRQMTVLDLHPGSGKTRKILPQIIKDAIQ--QRLRTAVLAPTRVVAAEMAEALRG------LPVRYQTSAVQ   83 (459)
T ss_dssp             ---CGGGSTTCEEEECCCTTSCTTTTHHHHHHHHHHH--TTCCEEEEECSHHHHHHHHHHTTT------SCEEECC----
T ss_pred             HHHHHHHhcCCcEEEECCCCCCHHHHHHHHHHHHHHh--CCCcEEEECchHHHHHHHHHHhcC------ceEeEEecccc
Confidence            3335556778999999999999999999998877653  236899999999999999988763      22222211111


Q ss_pred             hHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchh-----hccCcHHHHHHHHHhCCCCceEEEEeec
Q 015158          147 VREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEM-----LSRGFKDQIYDIFQLLPPKIQVGVFSAT  221 (412)
Q Consensus       147 ~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~-----~~~~~~~~~~~i~~~~~~~~~~i~~SAT  221 (412)
                           .....+..+.++|...+.+.+... ..+.++++||+||||+.     ...++...   .  ..+++.+++++|||
T Consensus        84 -----~~~t~~~~i~~~~~~~l~~~l~~~-~~l~~~~~iViDEaH~~~~~~~~~~~~~~~---~--~~~~~~~~il~SAT  152 (459)
T 2z83_A           84 -----REHQGNEIVDVMCHATLTHRLMSP-NRVPNYNLFVMDEAHFTDPASIAARGYIAT---K--VELGEAAAIFMTAT  152 (459)
T ss_dssp             ---------CCCSEEEEEHHHHHHHHHSC-C-CCCCSEEEESSTTCCSHHHHHHHHHHHH---H--HHTTSCEEEEECSS
T ss_pred             -----cCCCCCcEEEEEchHHHHHHhhcc-ccccCCcEEEEECCccCCchhhHHHHHHHH---H--hccCCccEEEEEcC
Confidence                 011234467788888887766654 44678999999999983     22222111   1  12357899999999


Q ss_pred             CChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhHHHHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcC
Q 015158          222 MPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSR  301 (412)
Q Consensus       222 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~  301 (412)
                      ++........  ...++....              ...+.  .....+...+... .+++||||++++.++.+++.|++.
T Consensus       153 ~~~~~~~~~~--~~~pi~~~~--------------~~~~~--~~~~~~~~~l~~~-~~~~LVF~~s~~~~~~l~~~L~~~  213 (459)
T 2z83_A          153 PPGTTDPFPD--SNAPIHDLQ--------------DEIPD--RAWSSGYEWITEY-AGKTVWFVASVKMGNEIAMCLQRA  213 (459)
T ss_dssp             CTTCCCSSCC--CSSCEEEEE--------------CCCCS--SCCSSCCHHHHHC-CSCEEEECSCHHHHHHHHHHHHHT
T ss_pred             CCcchhhhcc--CCCCeEEec--------------ccCCc--chhHHHHHHHHhc-CCCEEEEeCChHHHHHHHHHHHhc
Confidence            9754211100  011211110              00010  0011111223333 579999999999999999999999


Q ss_pred             CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEE--------------------ccCCCChhh
Q 015158          302 DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVIN--------------------YDLPTQPEN  361 (412)
Q Consensus       302 ~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~--------------------~~~~~s~~~  361 (412)
                      +..+..+|++    +|..+++.|++|+.+|||||+++++|+|+|+ ++||+                    ++.|.|..+
T Consensus       214 g~~v~~lh~~----~R~~~~~~f~~g~~~iLVaT~v~~~GiDip~-~~VI~~G~~~~~~~~~~~~~~~~~~~d~p~s~~~  288 (459)
T 2z83_A          214 GKKVIQLNRK----SYDTEYPKCKNGDWDFVITTDISEMGANFGA-SRVIDCRKSVKPTILEEGEGRVILGNPSPITSAS  288 (459)
T ss_dssp             TCCEEEESTT----CCCCCGGGSSSCCCSEEEESSCC---CCCSC-SEEEECCEECCEEEECSSSCEEEECSCEECCHHH
T ss_pred             CCcEEecCHH----HHHHHHhhccCCCceEEEECChHHhCeecCC-CEEEECCcccccccccccccccccccCCCCCHHH
Confidence            9999999985    6778999999999999999999999999999 99998                    559999999


Q ss_pred             HHHhhhhcccCCC-CceEEEEeccC
Q 015158          362 YLHRIGRSGRFGR-KGVAINFVTRD  385 (412)
Q Consensus       362 ~~Q~~GR~~R~g~-~g~~~~~~~~~  385 (412)
                      |.||+||+||.|. +|.+++|+.+.
T Consensus       289 ~~QR~GRaGR~g~~~G~~~~~~~~~  313 (459)
T 2z83_A          289 AAQRRGRVGRNPNQVGDEYHYGGAT  313 (459)
T ss_dssp             HHHHHTTSSCCTTCCCEEEEECSCC
T ss_pred             HHHhccccCCCCCCCCeEEEEEccc
Confidence            9999999999997 89999999875

>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=5.9e-35  Score=253.55  Aligned_cols=226  Identities=31%  Similarity=0.469  Sum_probs=192.2

Q ss_pred             hhhhcccCCCCCCCCCChhhhccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHH
Q 015158           17 ARMNDLLGSDGQDFFTSYDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSG   96 (412)
Q Consensus        17 ~~~~~~~~~~~~~~~~~~~~~~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~   96 (412)
                      +.+++..................+|+++++++.+.+.+..+|+..|+++|.++++.+++++++++.+|||+|||++|+++
T Consensus        21 ~~~~~~~~~~~~~~~~~~~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~~~  100 (249)
T 3ber_A           21 QSMEEHDSPTEASQPIVEEEETKTFKDLGVTDVLCEACDQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALP  100 (249)
T ss_dssp             ---------CBCCCCCHHHHHHCCTGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHH
T ss_pred             cccccccCcccccCCcCcccccCCHHHcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEEcCCCCCchhHhHHH
Confidence            33444333333334444556778999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHc-C
Q 015158           97 ILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRR-Q  175 (412)
Q Consensus        97 ~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~-~  175 (412)
                      ++..+.....+.++||++|+++|+.|+.+.++++....++.+..+.|+............+++|+|+||+++...+.+ .
T Consensus       101 il~~l~~~~~~~~~lil~Ptr~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~  180 (249)
T 3ber_A          101 ILNALLETPQRLFALVLTPTRELAFQISEQFEALGSSIGVQSAVIVGGIDSMSQSLALAKKPHIIIATPGRLIDHLENTK  180 (249)
T ss_dssp             HHHHHHHSCCSSCEEEECSSHHHHHHHHHHHHHHHGGGTCCEEEECTTSCHHHHHHHHHTCCSEEEECHHHHHHHHHHST
T ss_pred             HHHHHhcCCCCceEEEEeCCHHHHHHHHHHHHHHhccCCeeEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHHcCC
Confidence            998877665567899999999999999999999988888899999998876666666667889999999999988876 4


Q ss_pred             CCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEe
Q 015158          176 SLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILV  242 (412)
Q Consensus       176 ~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~  242 (412)
                      .+...++++||+||||++.++++...+..++..++++.+++++|||++.........++.+|..+..
T Consensus       181 ~~~l~~~~~lViDEah~l~~~~~~~~l~~i~~~~~~~~~~l~~SAT~~~~v~~~~~~~l~~p~~i~v  247 (249)
T 3ber_A          181 GFNLRALKYLVMDEADRILNMDFETEVDKILKVIPRDRKTFLFSATMTKKVQKLQRAALKNPVKCAV  247 (249)
T ss_dssp             TCCCTTCCEEEECSHHHHHHTTCHHHHHHHHHSSCSSSEEEEEESSCCHHHHHHHHHHCSSCEEEEC
T ss_pred             CcCccccCEEEEcChhhhhccChHHHHHHHHHhCCCCCeEEEEeccCCHHHHHHHHHHCCCCEEEEe
Confidence            4567889999999999999999999999999999989999999999999999999999999887654

>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=2.4e-34  Score=243.33  Aligned_cols=202  Identities=37%  Similarity=0.635  Sum_probs=183.1

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHH
Q 015158           39 DTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRE  118 (412)
Q Consensus        39 ~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  118 (412)
                      .+|+++++++.+.+.+..+||..|+++|.++++.+++++++++.+|||+|||.+++++++..+.....+.+++|++|+++
T Consensus         3 ~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~~~~~~~~lil~Pt~~   82 (206)
T 1vec_A            3 NEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRE   82 (206)
T ss_dssp             SSGGGSCCCHHHHHHHHTTTCCSCCHHHHHHHHHHHTTCCEEEECCSSSTTHHHHHHHHHHHCCTTSCSCCEEEECSCHH
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHccCCCEEEECCCCCchHHHHHHHHHHHhcccCCCeeEEEEeCcHH
Confidence            46999999999999999999999999999999999999999999999999999999999988766556678999999999


Q ss_pred             HHHHHHHHHHHhhccc-CcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccC
Q 015158          119 LAQQIEKVMRALGDYL-GVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRG  197 (412)
Q Consensus       119 L~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~  197 (412)
                      |+.|+.+.+..+.... +..+...+|+............+++|+|+||+++.+.+.+......+++++|+||||++.+.+
T Consensus        83 L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~lViDEah~~~~~~  162 (206)
T 1vec_A           83 LALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQD  162 (206)
T ss_dssp             HHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEEETHHHHTSTT
T ss_pred             HHHHHHHHHHHHHhhcCCceEEEEeCCccHHHHHHhcCCCCCEEEeCHHHHHHHHHcCCcCcccCCEEEEEChHHhHhhC
Confidence            9999999999987666 678888888887766666666788999999999999998877778899999999999999989


Q ss_pred             cHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEE
Q 015158          198 FKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRI  240 (412)
Q Consensus       198 ~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~  240 (412)
                      +...+..+...++++.+++++|||+++.....+..++.+|..+
T Consensus       163 ~~~~l~~i~~~~~~~~~~l~~SAT~~~~~~~~~~~~l~~p~~i  205 (206)
T 1vec_A          163 FVQIMEDIILTLPKNRQILLYSATFPLSVQKFMNSHLEKPYEI  205 (206)
T ss_dssp             THHHHHHHHHHSCTTCEEEEEESCCCHHHHHHHHHHCSSCEEE
T ss_pred             cHHHHHHHHHhCCccceEEEEEeeCCHHHHHHHHHHcCCCeEe
Confidence            9999999999999899999999999999999999998887654

>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=8.2e-35  Score=252.19  Aligned_cols=210  Identities=31%  Similarity=0.429  Sum_probs=190.5

Q ss_pred             hhccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccC-----CCceeE
Q 015158           36 EVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYG-----LVECQA  110 (412)
Q Consensus        36 ~~~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~-----~~~~~~  110 (412)
                      .+..+|+++++++.+.+.+...||..|+++|.++++.+++|+++++.+|||+|||++|+++++..+...     ..++++
T Consensus        26 ~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~g~~~l~~apTGsGKT~~~~l~~l~~l~~~~~~~~~~~~~~  105 (242)
T 3fe2_A           26 KPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPFLERGDGPIC  105 (242)
T ss_dssp             CCCSSTTTTTCCHHHHHHHHTTTCCSCCHHHHHHHHHHHHTCCEEEEECTTSCHHHHHHHHHHHHHHTSCCCCTTCCCSE
T ss_pred             CccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCcCHHHHHHHHHHHHHHHhccccccCCCCEE
Confidence            456789999999999999999999999999999999999999999999999999999999999876532     245689


Q ss_pred             EEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCC
Q 015158          111 LVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEA  190 (412)
Q Consensus       111 lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~  190 (412)
                      +|++|+++|+.|+.+.++.+....++.+..++|+............+++|+|+||+++...+.+....+.+++++|+|||
T Consensus       106 lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~~~~~~lViDEa  185 (242)
T 3fe2_A          106 LVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLECGKTNLRRTTYLVLDEA  185 (242)
T ss_dssp             EEECSSHHHHHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHHTSCCCTTCCEEEETTH
T ss_pred             EEEeCcHHHHHHHHHHHHHHHhhcCceEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHHcCCCCcccccEEEEeCH
Confidence            99999999999999999999888889999999998877776666777899999999999999888888889999999999


Q ss_pred             chhhccCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCC
Q 015158          191 DEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRD  245 (412)
Q Consensus       191 h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~  245 (412)
                      |++.+++|...+..++..++++.+++++|||+++........++.++..+.....
T Consensus       186 h~l~~~~~~~~~~~i~~~~~~~~q~~~~SAT~~~~~~~~~~~~l~~~~~i~~~~~  240 (242)
T 3fe2_A          186 DRMLDMGFEPQIRKIVDQIRPDRQTLMWSATWPKEVRQLAEDFLKDYIHINIGAL  240 (242)
T ss_dssp             HHHHHTTCHHHHHHHHTTSCSSCEEEEEESCCCHHHHHHHHHHCSSCEEEEECC-
T ss_pred             HHHhhhCcHHHHHHHHHhCCccceEEEEEeecCHHHHHHHHHHCCCCEEEEecCC
Confidence            9999999999999999999999999999999999999999999999988877654

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A

Probab=100.00  E-value=1.1e-34  Score=248.65  Aligned_cols=214  Identities=61%  Similarity=0.945  Sum_probs=181.4

Q ss_pred             CCChhhhccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeE
Q 015158           31 FTSYDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQA  110 (412)
Q Consensus        31 ~~~~~~~~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~  110 (412)
                      ...+..+..+|+++++++.+.+.+..+|+..|+++|.++++.+.+++++++.+|||+|||.+++++++..+.....+.++
T Consensus         6 ~~~~~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~~pTGsGKT~~~~~~~l~~l~~~~~~~~~   85 (224)
T 1qde_A            6 QTNYDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQA   85 (224)
T ss_dssp             CBSCCCCCCCGGGGTCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCE
T ss_pred             ccccCcccCChhhcCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHhccCCCceE
Confidence            34455566789999999999999999999999999999999999999999999999999999999999888766566799


Q ss_pred             EEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCC
Q 015158          111 LVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEA  190 (412)
Q Consensus       111 lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~  190 (412)
                      +|++|+++|+.|+.+.+..+....+..+..++|+........... .++|+|+||+++...+.+......++++||+|||
T Consensus        86 lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~-~~~iiv~Tp~~l~~~~~~~~~~~~~~~~iViDEa  164 (224)
T 1qde_A           86 LMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLR-DAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEA  164 (224)
T ss_dssp             EEECSSHHHHHHHHHHHHHHTTTSCCCEEEECC----------CT-TCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETH
T ss_pred             EEEECCHHHHHHHHHHHHHHhcccCceEEEEeCCcchHHHHhcCC-CCCEEEECHHHHHHHHHhCCcchhhCcEEEEcCh
Confidence            999999999999999999998777888888888876554443333 3799999999999998887777889999999999


Q ss_pred             chhhccCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCC
Q 015158          191 DEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRD  245 (412)
Q Consensus       191 h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~  245 (412)
                      |++.++++...+..+...++++.+++++|||++++.......++..+..+.....
T Consensus       165 h~~~~~~~~~~l~~i~~~~~~~~~~i~lSAT~~~~~~~~~~~~~~~p~~i~~~~~  219 (224)
T 1qde_A          165 DEMLSSGFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKD  219 (224)
T ss_dssp             HHHHHTTCHHHHHHHHHHSCTTCEEEEEESSCCHHHHHHHHHHCSSCEEEC----
T ss_pred             hHHhhhhhHHHHHHHHHhCCccCeEEEEEeecCHHHHHHHHHHCCCCEEEEecCC
Confidence            9999999999999999999999999999999999999999999998887765443

>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=1.3e-34  Score=281.33  Aligned_cols=286  Identities=17%  Similarity=0.182  Sum_probs=209.1

Q ss_pred             hhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHH
Q 015158           71 VPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVRED  150 (412)
Q Consensus        71 ~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~  150 (412)
                      ...++++++++++|||||||..++..+...       +..+|++|+++|+.|+++.+.+.    +..+..++|+......
T Consensus       150 ar~l~rk~vlv~apTGSGKT~~al~~l~~~-------~~gl~l~PtR~LA~Qi~~~l~~~----g~~v~lltG~~~~iv~  218 (677)
T 3rc3_A          150 ARAMQRKIIFHSGPTNSGKTYHAIQKYFSA-------KSGVYCGPLKLLAHEIFEKSNAA----GVPCDLVTGEERVTVQ  218 (677)
T ss_dssp             HHTSCCEEEEEECCTTSSHHHHHHHHHHHS-------SSEEEEESSHHHHHHHHHHHHHT----TCCEEEECSSCEECCS
T ss_pred             HHhcCCCEEEEEcCCCCCHHHHHHHHHHhc-------CCeEEEeCHHHHHHHHHHHHHhc----CCcEEEEECCeeEEec
Confidence            345678999999999999998554444332       24589999999999999998886    6778888887654110


Q ss_pred             HHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCC-CCceEEEEeecCChHHHHH
Q 015158          151 QRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLP-PKIQVGVFSATMPPEALEI  229 (412)
Q Consensus       151 ~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~-~~~~~i~~SAT~~~~~~~~  229 (412)
                        ......+++++|++.+.        ....++++|+||+|++.+.++...+..++..++ ...+++++|||. +.. ..
T Consensus       219 --TpGr~~~il~~T~e~~~--------l~~~v~lvVIDEaH~l~d~~~g~~~~~~l~~l~~~~i~il~~SAT~-~~i-~~  286 (677)
T 3rc3_A          219 --PNGKQASHVSCTVEMCS--------VTTPYEVAVIDEIQMIRDPARGWAWTRALLGLCAEEVHLCGEPAAI-DLV-ME  286 (677)
T ss_dssp             --TTCCCCSEEEEEGGGCC--------SSSCEEEEEECSGGGGGCTTTHHHHHHHHHHCCEEEEEEEECGGGH-HHH-HH
T ss_pred             --CCCcccceeEecHhHhh--------hcccCCEEEEecceecCCccchHHHHHHHHccCccceEEEeccchH-HHH-HH
Confidence              00113678999976642        235789999999999998888999998888887 678899999994 222 33


Q ss_pred             HHHhcCCCeEEEecCCccccCCceEEEEEeccchhhHHHHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEec
Q 015158          230 TRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATH  309 (412)
Q Consensus       230 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~  309 (412)
                      +....+....+......   ...   ......    .    ..+... .+..+|||++++.++.+++.|++.+..+..+|
T Consensus       287 l~~~~~~~~~v~~~~r~---~~l---~~~~~~----l----~~l~~~-~~g~iIf~~s~~~ie~la~~L~~~g~~v~~lH  351 (677)
T 3rc3_A          287 LMYTTGEEVEVRDYKRL---TPI---SVLDHA----L----ESLDNL-RPGDCIVCFSKNDIYSVSRQIEIRGLESAVIY  351 (677)
T ss_dssp             HHHHHTCCEEEEECCCS---SCE---EECSSC----C----CSGGGC-CTTEEEECSSHHHHHHHHHHHHHTTCCCEEEC
T ss_pred             HHHhcCCceEEEEeeec---chH---HHHHHH----H----HHHHhc-CCCCEEEEcCHHHHHHHHHHHHhcCCCeeeee
Confidence            33333444433222110   000   000000    0    011122 24568999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHhc--CCCcEEEEcCCCcCCCCCCCCCEEEEccC--------------CCChhhHHHhhhhcccCC
Q 015158          310 GDMDQNTRDIIMREFRS--GSSRVLITTDLLARGIDVQQVSLVINYDL--------------PTQPENYLHRIGRSGRFG  373 (412)
Q Consensus       310 ~~~~~~~r~~~~~~f~~--g~~~vlv~t~~~~~G~d~~~~~~vi~~~~--------------~~s~~~~~Q~~GR~~R~g  373 (412)
                      |++++.+|..+++.|++  |+.+|||||+++++|+|+ ++++||+++.              |.|..+|.||+||+||.|
T Consensus       352 G~L~~~~R~~~~~~F~~~~g~~~VLVATdi~e~GlDi-~v~~VI~~~~~k~~~~~~G~~~~~p~s~~~~~QR~GRAGR~g  430 (677)
T 3rc3_A          352 GSLPPGTKLAQAKKFNDPNDPCKILVATDAIGMGLNL-SIRRIIFYSLIKPSINEKGERELEPITTSQALQIAGRAGRFS  430 (677)
T ss_dssp             TTSCHHHHHHHHHHHHCTTSSCCEEEECGGGGSSCCC-CBSEEEESCSBC-----------CBCCHHHHHHHHTTBTCTT
T ss_pred             ccCCHHHHHHHHHHHHccCCCeEEEEeCcHHHCCcCc-CccEEEECCccccccccCCccccccCCHHHHHHHhcCCCCCC
Confidence            99999999999999999  889999999999999999 8999999998              789999999999999998


Q ss_pred             CC---ceEEEEeccCcHHHHHHHHHH
Q 015158          374 RK---GVAINFVTRDDERMLFDIQKF  396 (412)
Q Consensus       374 ~~---g~~~~~~~~~~~~~~~~~~~~  396 (412)
                      ..   |.|+.+ ...+...++.+...
T Consensus       431 ~~g~~G~v~~l-~~~d~~~~~~~~~~  455 (677)
T 3rc3_A          431 SRFKEGEVTTM-NHEDLSLLKEILKR  455 (677)
T ss_dssp             SSCSSEEEEES-STTHHHHHHHHHHS
T ss_pred             CCCCCEEEEEE-ecchHHHHHHHHhc
Confidence            65   555544 34444444444433

>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=1e-34  Score=250.65  Aligned_cols=215  Identities=66%  Similarity=1.019  Sum_probs=177.8

Q ss_pred             CCCCCChhhhccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCc
Q 015158           28 QDFFTSYDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVE  107 (412)
Q Consensus        28 ~~~~~~~~~~~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~  107 (412)
                      +.....+..+..+|+++++++.+.+.+..+||..|+++|.++++.+++++++++.+|||+|||++|+++++..+.....+
T Consensus        19 ~~~~~~~~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~ai~~i~~~~~~li~apTGsGKT~~~~l~~l~~l~~~~~~   98 (237)
T 3bor_A           19 GVIESNWNEIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQLEIEFKE   98 (237)
T ss_dssp             --------CCCCSGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEECCCSSHHHHHHHHHHHHHHCCTTSCS
T ss_pred             CcccCCCCCccCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhcCCC
Confidence            33444455667889999999999999999999999999999999999999999999999999999999999887655556


Q ss_pred             eeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhc-CCCcEEEeChHHHHHHHHcCCCCCCCceEEE
Q 015158          108 CQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILS-SGVHVVVGTPGRVFDMLRRQSLRPDNIRIFV  186 (412)
Q Consensus       108 ~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~iii~T~~~l~~~~~~~~~~~~~~~~ii  186 (412)
                      .++||++|+++|+.|+.+.+..+....+..+....|+........... ..++|+|+||+++...+.+......++++||
T Consensus        99 ~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~~~~lV  178 (237)
T 3bor_A           99 TQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFV  178 (237)
T ss_dssp             CCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECC-------------CCCSEEEECHHHHHHHHHTTSSCSTTCCEEE
T ss_pred             ceEEEEECcHHHHHHHHHHHHHHhhhcCceEEEEECCCchHHHHHHHhcCCCCEEEECHHHHHHHHHhCCcCcccCcEEE
Confidence            789999999999999999999998777788888888776554433333 3489999999999999988777788899999


Q ss_pred             EeCCchhhccCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEe
Q 015158          187 LDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILV  242 (412)
Q Consensus       187 iDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~  242 (412)
                      +||||++.++++...+..++..++...+++++|||++++....+..++.++..+..
T Consensus       179 iDEah~~~~~~~~~~l~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~l~~p~~i~v  234 (237)
T 3bor_A          179 LDEADEMLSRGFKDQIYEIFQKLNTSIQVVLLSATMPTDVLEVTKKFMRDPIRILV  234 (237)
T ss_dssp             EESHHHHHHTTCHHHHHHHHHHSCTTCEEEEECSSCCHHHHHHHHHHCSSCEEEC-
T ss_pred             ECCchHhhccCcHHHHHHHHHhCCCCCeEEEEEEecCHHHHHHHHHHCCCCEEEEe
Confidence            99999999999999999999999999999999999999999999999988877654

>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=2.2e-33  Score=275.33  Aligned_cols=318  Identities=17%  Similarity=0.160  Sum_probs=218.0

Q ss_pred             CChHHHHhhhhhhh---------cCccEEEECCCCCCchhHhHHHHHHhhccCC----CceeEEEEcCCHHHHHHHHHHH
Q 015158           61 KPSAIQQRGIVPFC---------KGLDVIQQAQSGTGKTATFCSGILQQLDYGL----VECQALVLAPTRELAQQIEKVM  127 (412)
Q Consensus        61 ~l~~~Q~~a~~~~~---------~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~----~~~~~lil~P~~~L~~q~~~~~  127 (412)
                      .|+|||.+++..+.         .+.++++..+||+|||.+++..+...+....    ...++|||||+ +|+.||.+++
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            49999999999874         3567899999999999998777766554332    23469999996 8899999999


Q ss_pred             HHhhcccCcEEEEEEcCcchHHHHH---Hhc-----CCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcH
Q 015158          128 RALGDYLGVKVHACVGGTSVREDQR---ILS-----SGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFK  199 (412)
Q Consensus       128 ~~~~~~~~~~~~~~~~~~~~~~~~~---~~~-----~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~  199 (412)
                      .++... ...+..++++........   ...     ..++|+|+||+.+.....  .+....+++||+||||++.+..  
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            998754 455555665543322111   111     146899999999976542  3444678999999999987654  


Q ss_pred             HHHHHHHHhCCCCceEEEEeecCChHHH-------HH-----------HHHhcC--------------------------
Q 015158          200 DQIYDIFQLLPPKIQVGVFSATMPPEAL-------EI-----------TRKFMN--------------------------  235 (412)
Q Consensus       200 ~~~~~i~~~~~~~~~~i~~SAT~~~~~~-------~~-----------~~~~~~--------------------------  235 (412)
                      ......+..++ ..+.+++||||-.+..       .+           +...+.                          
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            22333333343 4578999999853210       00           000000                          


Q ss_pred             ----CCeEEEecCCcc--ccCCceEEEEEecc------------------------------------------------
Q 015158          236 ----KPVRILVKRDEL--TLEGIKQFHVNVEK------------------------------------------------  261 (412)
Q Consensus       236 ----~~~~~~~~~~~~--~~~~~~~~~~~~~~------------------------------------------------  261 (412)
                          .+..........  ..+........+..                                                
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                000000000000  01111111111000                                                


Q ss_pred             -----------------------------chhhHHHHHHHHHh---cCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEec
Q 015158          262 -----------------------------EEWKLETLCDLYET---LAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATH  309 (412)
Q Consensus       262 -----------------------------~~~~~~~l~~~~~~---~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~  309 (412)
                                                   ...+...+..++..   ..++|+||||++...++.+.+.|...++.+..+|
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                                         01222333333333   3468999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHhcCCCc---EEEEcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccCCCCceE--EEEecc
Q 015158          310 GDMDQNTRDIIMREFRSGSSR---VLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVA--INFVTR  384 (412)
Q Consensus       310 ~~~~~~~r~~~~~~f~~g~~~---vlv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~--~~~~~~  384 (412)
                      |+++..+|.+++++|++++..   +|++|.++++|+|++.+++||++++||++..+.|++||++|.|+...+  +.++..
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            999999999999999998654   889999999999999999999999999999999999999999987654  445555


Q ss_pred             C
Q 015158          385 D  385 (412)
Q Consensus       385 ~  385 (412)
                      .
T Consensus       528 ~  528 (644)
T 1z3i_X          528 G  528 (644)
T ss_dssp             T
T ss_pred             C
Confidence            4

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=100.00  E-value=2.9e-34  Score=288.42  Aligned_cols=330  Identities=19%  Similarity=0.220  Sum_probs=231.9

Q ss_pred             CChHHHHhhhhhhh----cCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCc
Q 015158           61 KPSAIQQRGIVPFC----KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGV  136 (412)
Q Consensus        61 ~l~~~Q~~a~~~~~----~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~  136 (412)
                      .|+|||.+++..+.    .++++++..+||+|||++++..+...........++||||| .+|+.||.+++.++..  +.
T Consensus       236 ~Lr~yQ~egv~~l~~~~~~~~~~ILademGlGKT~~ai~~i~~l~~~~~~~~~~LIV~P-~sll~qW~~E~~~~~p--~~  312 (800)
T 3mwy_W          236 ELRDFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFISWLIFARRQNGPHIIVVP-LSTMPAWLDTFEKWAP--DL  312 (800)
T ss_dssp             CCCTHHHHHHHHHHHHHTTTCCEEECCCTTSSTTHHHHHHHHHHHHHHSCCSCEEEECC-TTTHHHHHHHHHHHST--TC
T ss_pred             CcCHHHHHHHHHHHHHhhcCCCEEEEeCCCcchHHHHHHHHHHHHHhcCCCCCEEEEEC-chHHHHHHHHHHHHCC--Cc
Confidence            59999999998766    68899999999999999887766655443344557999999 6788999999999875  56


Q ss_pred             EEEEEEcCcchHHHHH------------HhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHH
Q 015158          137 KVHACVGGTSVREDQR------------ILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYD  204 (412)
Q Consensus       137 ~~~~~~~~~~~~~~~~------------~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~  204 (412)
                      .+..++|+........            .....++|+|+||+.+......  +....+++||+||||++.+..  .....
T Consensus       313 ~v~~~~g~~~~r~~~~~~~~~~~~~~~~~~~~~~dvvitTy~~l~~~~~~--l~~~~w~~vIvDEaH~lkn~~--s~~~~  388 (800)
T 3mwy_W          313 NCICYMGNQKSRDTIREYEFYTNPRAKGKKTMKFNVLLTTYEYILKDRAE--LGSIKWQFMAVDEAHRLKNAE--SSLYE  388 (800)
T ss_dssp             CEEECCCSSHHHHHHHHHHSCSCC-----CCCCCSEEEECTTHHHHTHHH--HHTSEEEEEEETTGGGGCCSS--SHHHH
T ss_pred             eEEEEeCCHHHHHHHHHHHhhccccccccccccCCEEEecHHHHHhhHHH--HhcCCcceeehhhhhhhcCch--hHHHH
Confidence            6777777665433221            1234578999999999764332  122368999999999986554  34444


Q ss_pred             HHHhCCCCceEEEEeecCCh----HHHHHHHHhcC-----------------------------CCeEEEecCCcc--cc
Q 015158          205 IFQLLPPKIQVGVFSATMPP----EALEITRKFMN-----------------------------KPVRILVKRDEL--TL  249 (412)
Q Consensus       205 i~~~~~~~~~~i~~SAT~~~----~~~~~~~~~~~-----------------------------~~~~~~~~~~~~--~~  249 (412)
                      .+..++ ....+++||||..    ++...+..+..                             .+..........  ..
T Consensus       389 ~l~~l~-~~~rl~LTgTPiqN~l~el~~ll~fL~p~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~p~~lRR~k~dv~~~L  467 (800)
T 3mwy_W          389 SLNSFK-VANRMLITGTPLQNNIKELAALVNFLMPGRFTIDQEIDFENQDEEQEEYIHDLHRRIQPFILRRLKKDVEKSL  467 (800)
T ss_dssp             HHTTSE-EEEEEEECSCCCSSCSHHHHHHHHHHCSCCC---------CCTTHHHHHHHHHHHTTGGGEEECCGGGGTTTS
T ss_pred             HHHHhh-hccEEEeeCCcCCCCHHHHHHHHHHhCccccCchhhhcccccchhHHHHHHHHHHHHhHHHhhhhHHhhhhcc
Confidence            555553 4567999999942    12111111111                             011111110000  01


Q ss_pred             CCceEEEEEecc--------------------------------------------------------------------
Q 015158          250 EGIKQFHVNVEK--------------------------------------------------------------------  261 (412)
Q Consensus       250 ~~~~~~~~~~~~--------------------------------------------------------------------  261 (412)
                      +........+..                                                                    
T Consensus       468 P~k~~~~v~v~ls~~q~~~Y~~i~~~~~~~l~~~~~~~~~~~l~~l~~Lrk~~~hp~l~~~~~~~~~~~~~~~~~~~~~~  547 (800)
T 3mwy_W          468 PSKTERILRVELSDVQTEYYKNILTKNYSALTAGAKGGHFSLLNIMNELKKASNHPYLFDNAEERVLQKFGDGKMTRENV  547 (800)
T ss_dssp             CCEEEEEEEECCCHHHHHHHHHHHHHCCC----------CTHHHHHHHHHHHHHCGGGSSSHHHHHCCCC----CCSHHH
T ss_pred             CCcEEEEEEeCCCHHHHHHHHHHHHHHHHHHhhccccchhhHHHHHHHHHHHhcChhhhcchHHHHHHhcccccccHHHH
Confidence            111111111111                                                                    


Q ss_pred             ------chhhHHHHHHHHHhc--CCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCC---c
Q 015158          262 ------EEWKLETLCDLYETL--AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSS---R  330 (412)
Q Consensus       262 ------~~~~~~~l~~~~~~~--~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~---~  330 (412)
                            ...+...+.+++...  .+.++||||+....++.+.++|...|+.+..++|+++..+|..++++|+++..   .
T Consensus       548 ~~~l~~~s~K~~~L~~lL~~~~~~g~kvLIFsq~~~~ld~L~~~L~~~g~~~~~i~G~~~~~eR~~~i~~F~~~~~~~~v  627 (800)
T 3mwy_W          548 LRGLIMSSGKMVLLDQLLTRLKKDGHRVLIFSQMVRMLDILGDYLSIKGINFQRLDGTVPSAQRRISIDHFNSPDSNDFV  627 (800)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHTTTTCCEEEEESCHHHHHHHHHHHHHHTCCCEEESTTSCHHHHHHHHHTTSSTTCSCCC
T ss_pred             HHHhhhcChHHHHHHHHHHHHhhCCCeEEEEechHHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHhhCCCCCceE
Confidence                  122444555666554  34799999999999999999999999999999999999999999999998654   4


Q ss_pred             EEEEcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccCCCCceE--EEEeccC--cHHHHHHHHHHhc
Q 015158          331 VLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVA--INFVTRD--DERMLFDIQKFYN  398 (412)
Q Consensus       331 vlv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~--~~~~~~~--~~~~~~~~~~~~~  398 (412)
                      +|++|.++++|+|++.+++||+++++||+..+.|++||++|.|+...+  +.+++..  +.+.+....+.+.
T Consensus       628 ~LlSt~agg~GlNL~~a~~VI~~D~~wnp~~~~Qa~gR~~RiGQ~k~V~Vyrlv~~~TiEe~i~~~~~~K~~  699 (800)
T 3mwy_W          628 FLLSTRAGGLGINLMTADTVVIFDSDWNPQADLQAMARAHRIGQKNHVMVYRLVSKDTVEEEVLERARKKMI  699 (800)
T ss_dssp             EEEEHHHHTTTCCCTTCCEEEESSCCSCSHHHHHHHTTTSCSSCCSCEEEEEEEETTSHHHHHHHHHHHHTT
T ss_pred             EEEecccccCCCCccccceEEEecCCCChhhHHHHHHHHHhcCCCceEEEEEEecCCCHHHHHHHHHHHHHH
Confidence            899999999999999999999999999999999999999999976554  4455554  4555555554443

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=100.00  E-value=1.8e-34  Score=246.28  Aligned_cols=207  Identities=33%  Similarity=0.503  Sum_probs=182.4

Q ss_pred             ccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCH
Q 015158           38 YDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTR  117 (412)
Q Consensus        38 ~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~  117 (412)
                      ..+|+++++++.+.+.+...|+..|+++|.++++.+++++++++.+|||+|||.+|+++++..+.....+.+++|++|++
T Consensus         3 ~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~   82 (219)
T 1q0u_A            3 ETQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPERAEVQAVITAPTR   82 (219)
T ss_dssp             -CCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCTTSCSCCEEEECSSH
T ss_pred             CCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhCcCCceEEEEcCcH
Confidence            35799999999999999999999999999999999999999999999999999999999998877655567899999999


Q ss_pred             HHHHHHHHHHHHhhccc----CcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchh
Q 015158          118 ELAQQIEKVMRALGDYL----GVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEM  193 (412)
Q Consensus       118 ~L~~q~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~  193 (412)
                      +|+.|+.+.+.++....    +..+..+.|+............+++|+|+||+++...+.+......+++++|+||||++
T Consensus        83 ~L~~q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~l~~~~~~~~~~~~lViDEah~~  162 (219)
T 1q0u_A           83 ELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLNVQPHIVIGTPGRINDFIREQALDVHTAHILVVDEADLM  162 (219)
T ss_dssp             HHHHHHHHHHHHHHTTSCGGGCCCEEEECCCSHHHHTTCCCSSCCSEEEECHHHHHHHHHTTCCCGGGCCEEEECSHHHH
T ss_pred             HHHHHHHHHHHHHhhhcccccceEEEEEeCCCCHHHHHHHcCCCCCEEEeCHHHHHHHHHcCCCCcCcceEEEEcCchHH
Confidence            99999999999987655    67788888877654443334457899999999999998887777788999999999999


Q ss_pred             hccCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecC
Q 015158          194 LSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKR  244 (412)
Q Consensus       194 ~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~  244 (412)
                      .++++...+..+...++++.+++++|||++.+..+.+..++.+|..+....
T Consensus       163 ~~~~~~~~l~~i~~~~~~~~~~l~~SAT~~~~~~~~~~~~~~~p~~~~~~~  213 (219)
T 1q0u_A          163 LDMGFITDVDQIAARMPKDLQMLVFSATIPEKLKPFLKKYMENPTFVHVLE  213 (219)
T ss_dssp             HHTTCHHHHHHHHHTSCTTCEEEEEESCCCGGGHHHHHHHCSSCEEEECC-
T ss_pred             hhhChHHHHHHHHHhCCcccEEEEEecCCCHHHHHHHHHHcCCCeEEEeec
Confidence            999999999999999998999999999999999999999999988765443

>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=7.5e-34  Score=244.17  Aligned_cols=205  Identities=39%  Similarity=0.610  Sum_probs=179.9

Q ss_pred             hhccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcC
Q 015158           36 EVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAP  115 (412)
Q Consensus        36 ~~~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P  115 (412)
                      .+..+|+++++++.+.+.+...||..|+++|.++++.+.+|+++++.+|||+|||++|+++++..+.....+.++||++|
T Consensus        21 ~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~~~~~~~~lil~P  100 (230)
T 2oxc_A           21 AEPADFESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDSLVLENLSTQILILAP  100 (230)
T ss_dssp             ---CCGGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTSCSCCEEEECS
T ss_pred             CCCCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhcCCCceEEEEeC
Confidence            34467999999999999999999999999999999999999999999999999999999999888765555678999999


Q ss_pred             CHHHHHHHHHHHHHhhccc-CcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhh
Q 015158          116 TRELAQQIEKVMRALGDYL-GVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEML  194 (412)
Q Consensus       116 ~~~L~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~  194 (412)
                      +++|+.|+.+.+..+.... ++.+..++|+.....+.... .+++|+|+||+++.+.+....+...+++++|+||||++.
T Consensus       101 t~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~-~~~~Iiv~Tp~~l~~~~~~~~~~~~~~~~lViDEah~~~  179 (230)
T 2oxc_A          101 TREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRL-KKCHIAVGSPGRIKQLIELDYLNPGSIRLFILDEADKLL  179 (230)
T ss_dssp             SHHHHHHHHHHHHHHTTTSTTCCEEEECTTSCHHHHHHHT-TSCSEEEECHHHHHHHHHTTSSCGGGCCEEEESSHHHHH
T ss_pred             CHHHHHHHHHHHHHHhcccCCceEEEEeCCCCHHHHHHhc-cCCCEEEECHHHHHHHHhcCCcccccCCEEEeCCchHhh
Confidence            9999999999999987654 78888888887765554444 467999999999999988777777889999999999999


Q ss_pred             ccC-cHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEE
Q 015158          195 SRG-FKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRIL  241 (412)
Q Consensus       195 ~~~-~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~  241 (412)
                      +++ |...+..++..++...+++++|||+++.....+..+++++..+.
T Consensus       180 ~~~~~~~~~~~i~~~~~~~~~~l~lSAT~~~~~~~~~~~~~~~p~~i~  227 (230)
T 2oxc_A          180 EEGSFQEQINWIYSSLPASKQMLAVSATYPEFLANALTKYMRDPTFVR  227 (230)
T ss_dssp             STTSSHHHHHHHHHHSCSSCEEEEEESCCCHHHHHHHTTTCSSCEEEC
T ss_pred             cCcchHHHHHHHHHhCCCCCeEEEEEeccCHHHHHHHHHHcCCCeEEE
Confidence            887 89999999999998999999999999988888888888887654

>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=9.5e-34  Score=243.46  Aligned_cols=206  Identities=31%  Similarity=0.438  Sum_probs=177.1

Q ss_pred             hhhcccccc-CCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccC------CCc
Q 015158           35 DEVYDTFDA-MGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYG------LVE  107 (412)
Q Consensus        35 ~~~~~~f~~-~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~------~~~  107 (412)
                      ..+..+|++ +++++.+.+.+...||..|+++|.++++.+++|+++++.+|||+|||++|+++++..+...      ..+
T Consensus        15 p~p~~~f~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~apTGsGKT~~~~l~~~~~l~~~~~~~~~~~~   94 (228)
T 3iuy_A           15 PKPTCRFKDAFQQYPDLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIHLDSQPISREQRNG   94 (228)
T ss_dssp             CCCCCSHHHHHTTCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHC---------CC
T ss_pred             CCChhhHhhhhccCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhccchhhccCC
Confidence            344567777 6899999999999999999999999999999999999999999999999999988776432      245


Q ss_pred             eeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEE
Q 015158          108 CQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVL  187 (412)
Q Consensus       108 ~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iii  187 (412)
                      ++++|++|+++|+.|+.+.+..+. ..+..+..++|+............+++|+|+||+++.+.+......+.++++||+
T Consensus        95 ~~~lil~Pt~~L~~q~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~Tp~~l~~~~~~~~~~~~~~~~lVi  173 (228)
T 3iuy_A           95 PGMLVLTPTRELALHVEAECSKYS-YKGLKSICIYGGRNRNGQIEDISKGVDIIIATPGRLNDLQMNNSVNLRSITYLVI  173 (228)
T ss_dssp             CSEEEECSSHHHHHHHHHHHHHHC-CTTCCEEEECC------CHHHHHSCCSEEEECHHHHHHHHHTTCCCCTTCCEEEE
T ss_pred             CcEEEEeCCHHHHHHHHHHHHHhc-ccCceEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHHcCCcCcccceEEEE
Confidence            689999999999999999999985 3477888888887766666666777899999999999998888888889999999


Q ss_pred             eCCchhhccCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEE
Q 015158          188 DEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRIL  241 (412)
Q Consensus       188 DE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~  241 (412)
                      ||||++.++++...+..++..++++.+++++|||+++........++.+|..+.
T Consensus       174 DEah~~~~~~~~~~~~~i~~~~~~~~~~l~~SAT~~~~~~~~~~~~l~~p~~i~  227 (228)
T 3iuy_A          174 DEADKMLDMEFEPQIRKILLDVRPDRQTVMTSATWPDTVRQLALSYLKDPMIVY  227 (228)
T ss_dssp             CCHHHHHHTTCHHHHHHHHHHSCSSCEEEEEESCCCHHHHHHHHTTCSSCEEEE
T ss_pred             ECHHHHhccchHHHHHHHHHhCCcCCeEEEEEeeCCHHHHHHHHHHCCCCEEEe
Confidence            999999999999999999999999999999999999999999999998887664

>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=6.3e-34  Score=248.51  Aligned_cols=217  Identities=32%  Similarity=0.474  Sum_probs=184.3

Q ss_pred             hccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCC---------Cc
Q 015158           37 VYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGL---------VE  107 (412)
Q Consensus        37 ~~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~---------~~  107 (412)
                      +..+|+++++++.+.+.|...||..|+++|.++++.+++++++++.+|||+|||++|+++++..+....         .+
T Consensus        21 ~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~l~~a~TGsGKT~~~~~~~l~~l~~~~~~~~~~~~~~~  100 (253)
T 1wrb_A           21 VIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAY  100 (253)
T ss_dssp             CCCSSGGGSCCCSTTTTTTTTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHTTCC------CCBC
T ss_pred             ccCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhhccccccccccCC
Confidence            556899999999999999999999999999999999999999999999999999999999998765432         23


Q ss_pred             eeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEE
Q 015158          108 CQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVL  187 (412)
Q Consensus       108 ~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iii  187 (412)
                      +++||++|+++|+.|+.+.+..+....++.+..+.|+............+++|+|+||+++...+........+++++|+
T Consensus       101 ~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~~lVi  180 (253)
T 1wrb_A          101 PKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEKNKISLEFCKYIVL  180 (253)
T ss_dssp             CSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCSHHHHHHHSSCCSEEEECHHHHHHHHHTTSBCCTTCCEEEE
T ss_pred             ceEEEEECCHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHhCCCCCEEEECHHHHHHHHHcCCCChhhCCEEEE
Confidence            58999999999999999999999877788888899888777666666778899999999999999887777889999999


Q ss_pred             eCCchhhccCcHHHHHHHHHhC--CC--CceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCce
Q 015158          188 DEADEMLSRGFKDQIYDIFQLL--PP--KIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIK  253 (412)
Q Consensus       188 DE~h~~~~~~~~~~~~~i~~~~--~~--~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  253 (412)
                      ||||++.+++|...+..++..+  +.  +.+++++|||++++.......++.++..+.........++++
T Consensus       181 DEah~~~~~~~~~~~~~i~~~~~~~~~~~~q~l~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~i~  250 (253)
T 1wrb_A          181 DEADRMLDMGFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTVGRVGSTSDSIK  250 (253)
T ss_dssp             ETHHHHHHTTCHHHHHHHHHSSCCCCGGGCEEEEEESSCCHHHHHHHHHHCSSCEEEEEC----------
T ss_pred             eCHHHHHhCchHHHHHHHHhhccCCCCCCcEEEEEEEeCCHHHHHHHHHHcCCCEEEEECCCCCCcCCce
Confidence            9999999999999999998853  33  678999999999999999999999998887766555444443

>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=4.3e-33  Score=235.90  Aligned_cols=201  Identities=38%  Similarity=0.563  Sum_probs=178.8

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccC---CCceeEEEEcCC
Q 015158           40 TFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYG---LVECQALVLAPT  116 (412)
Q Consensus        40 ~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~---~~~~~~lil~P~  116 (412)
                      +|+++++++.+.+.+...|+..|+++|.++++.+.+++++++.+|||+|||.+++++++..+...   ..+++++|++|+
T Consensus         2 ~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~l~~~~~~~~~~~~lil~P~   81 (207)
T 2gxq_A            2 EFKDFPLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAERLAPSQERGRKPRALVLTPT   81 (207)
T ss_dssp             CGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCCCTTCCCSEEEECSS
T ss_pred             ChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHcCCCCEEEECCCCChHHHHHHHHHHHHHhhccccCCCCcEEEEECC
Confidence            58899999999999999999999999999999999999999999999999999999998877532   245689999999


Q ss_pred             HHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhcc
Q 015158          117 RELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSR  196 (412)
Q Consensus       117 ~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~  196 (412)
                      ++|+.|+.+.+..+...  ..+..++|+............+++|+|+||+.+.+.+.+......+++++|+||||++.+.
T Consensus        82 ~~L~~q~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~iViDEah~~~~~  159 (207)
T 2gxq_A           82 RELALQVASELTAVAPH--LKVVAVYGGTGYGKQKEALLRGADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSM  159 (207)
T ss_dssp             HHHHHHHHHHHHHHCTT--SCEEEECSSSCSHHHHHHHHHCCSEEEECHHHHHHHHHHTSSCCTTCSEEEEESHHHHHHT
T ss_pred             HHHHHHHHHHHHHHhhc--ceEEEEECCCChHHHHHHhhCCCCEEEECHHHHHHHHHcCCcchhhceEEEEEChhHhhcc
Confidence            99999999999998653  6677788887766665556667899999999999998887777889999999999999999


Q ss_pred             CcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEe
Q 015158          197 GFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILV  242 (412)
Q Consensus       197 ~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~  242 (412)
                      ++...+..++..++++.+++++|||+++........++.+|..+..
T Consensus       160 ~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~p~~i~~  205 (207)
T 2gxq_A          160 GFEEEVEALLSATPPSRQTLLFSATLPSWAKRLAERYMKNPVLINV  205 (207)
T ss_dssp             TCHHHHHHHHHTSCTTSEEEEECSSCCHHHHHHHHHHCSSCEEEEC
T ss_pred             chHHHHHHHHHhCCccCeEEEEEEecCHHHHHHHHHHcCCCeEEEc
Confidence            9999999999999989999999999999999999999998887653

>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=4.6e-33  Score=281.40  Aligned_cols=319  Identities=13%  Similarity=0.088  Sum_probs=208.6

Q ss_pred             CChHHHHhhhhhhhc--------------CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHH
Q 015158           61 KPSAIQQRGIVPFCK--------------GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKV  126 (412)
Q Consensus        61 ~l~~~Q~~a~~~~~~--------------~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~  126 (412)
                      .|||+|.+|++.++.              +++++++++||||||.++ ++++..+.......++||+||+++|+.|+.+.
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            499999999999875              368999999999999997 44455544333346899999999999999999


Q ss_pred             HHHhhcccCcEEEEEEcCcchHHHHHHh-cCCCcEEEeChHHHHHHHHcCC-C-CCCCceEEEEeCCchhhccCcHHHHH
Q 015158          127 MRALGDYLGVKVHACVGGTSVREDQRIL-SSGVHVVVGTPGRVFDMLRRQS-L-RPDNIRIFVLDEADEMLSRGFKDQIY  203 (412)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~iii~T~~~l~~~~~~~~-~-~~~~~~~iiiDE~h~~~~~~~~~~~~  203 (412)
                      +..+....      ..++.+.......+ ..+.+|+|+|+++|...+.... . ....+.+||+||||+....   ....
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            98875421      11233333333333 3568999999999998775432 1 2346789999999996532   3355


Q ss_pred             HHHHhCCCCceEEEEeecCChHHH----HHHHHhcCCCeEEEecCCccccC---CceEEEEEe-----------c-----
Q 015158          204 DIFQLLPPKIQVGVFSATMPPEAL----EITRKFMNKPVRILVKRDELTLE---GIKQFHVNV-----------E-----  260 (412)
Q Consensus       204 ~i~~~~~~~~~~i~~SAT~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~-----------~-----  260 (412)
                      .+...++ +.+++++||||.....    .....+++.++..+.........   .+...+...           .     
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            6666665 5789999999974321    12333444433222110000000   000000000           0     


Q ss_pred             --------cchhhHHHHH-HHHHh---c--------CCCcEEEEEcchhHHHHHHHHHhcCC------------Cee-EE
Q 015158          261 --------KEEWKLETLC-DLYET---L--------AITQSVIFVNTRRKVDWLTDKMRSRD------------HTV-SA  307 (412)
Q Consensus       261 --------~~~~~~~~l~-~~~~~---~--------~~~k~lif~~~~~~~~~~~~~L~~~~------------~~~-~~  307 (412)
                              ....+...+. .++..   .        ...++||||+|+++|..+++.|.+.+            ..+ .+
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                    0111122222 22221   1        23589999999999999999997643            344 44


Q ss_pred             ecCC----------C----------CH-----------------------------HHHHHHHHHHhcCCCcEEEEcCCC
Q 015158          308 THGD----------M----------DQ-----------------------------NTRDIIMREFRSGSSRVLITTDLL  338 (412)
Q Consensus       308 ~~~~----------~----------~~-----------------------------~~r~~~~~~f~~g~~~vlv~t~~~  338 (412)
                      +|++          +          +.                             ..|..++++|++|++++||+|+++
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            5542          1          21                             147889999999999999999999


Q ss_pred             cCCCCCCCCCEEEEccCCCChhhHHHhhhhcccCCCC--ceEEEEeccCcHHHHH
Q 015158          339 ARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRK--GVAINFVTRDDERMLF  391 (412)
Q Consensus       339 ~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~--g~~~~~~~~~~~~~~~  391 (412)
                      .+|+|+|.+ +++.++.|.+...++|++||++|.++.  ..++++......+.+.
T Consensus       660 ltGfDiP~l-~tlylDkpl~~~~liQaIGRtnR~~~~~K~~G~IVdf~~~~~~l~  713 (1038)
T 2w00_A          660 LTGFDAPTL-NTLFVDKNLRYHGLMQAFSRTNRIYDATKTFGNIVTFRDLERSTI  713 (1038)
T ss_dssp             SSSCCCTTE-EEEEEESCCCHHHHHHHHHTTCCCCCTTCCSEEEEESSCCHHHHH
T ss_pred             HhCcCcccc-cEEEEccCCCccceeehhhccCcCCCCCCCcEEEEEccccHHHHH
Confidence            999999999 566788999999999999999998753  2344444444444443

>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-33  Score=238.47  Aligned_cols=204  Identities=41%  Similarity=0.635  Sum_probs=178.7

Q ss_pred             ccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCH
Q 015158           38 YDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTR  117 (412)
Q Consensus        38 ~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~  117 (412)
                      ..+|+++++++.+.+.+...|+..|+++|.++++.+++++++++.+|||+|||.+++++++..+.......+++|++|++
T Consensus        13 ~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~Pt~   92 (220)
T 1t6n_A           13 SSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTR   92 (220)
T ss_dssp             -CCSTTSCCCHHHHHHHHHTTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCTTCCCEEEECSCH
T ss_pred             CCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCchhhhhhHHHHHhhhccCCCEEEEEEeCCH
Confidence            35799999999999999999999999999999999999999999999999999999999998876655556899999999


Q ss_pred             HHHHHHHHHHHHhhccc-CcEEEEEEcCcchHHHHHHh-cCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhc
Q 015158          118 ELAQQIEKVMRALGDYL-GVKVHACVGGTSVREDQRIL-SSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLS  195 (412)
Q Consensus       118 ~L~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~-~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~  195 (412)
                      +|+.|+.+.++++.... +..+..++|+.....+.... ...++|+|+||+.+...+........+++++|+||||++.+
T Consensus        93 ~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~lViDEah~~~~  172 (220)
T 1t6n_A           93 ELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLE  172 (220)
T ss_dssp             HHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEESHHHHHS
T ss_pred             HHHHHHHHHHHHHHhhCCCceEEEEeCCCChHHHHHHHhcCCCCEEEeCHHHHHHHHHhCCCCcccCCEEEEcCHHHHhc
Confidence            99999999999987665 78888888887765554433 34579999999999999888777788999999999999886


Q ss_pred             -cCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEE
Q 015158          196 -RGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRIL  241 (412)
Q Consensus       196 -~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~  241 (412)
                       .++...+..+...++++.+++++|||+++........++.+|..+.
T Consensus       173 ~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~p~~i~  219 (220)
T 1t6n_A          173 QLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIF  219 (220)
T ss_dssp             SHHHHHHHHHHHHTSCSSSEEEEEESCCCTTTHHHHHTTCSSCEEEE
T ss_pred             ccCcHHHHHHHHHhCCCcCeEEEEEeecCHHHHHHHHHHcCCCeEEe
Confidence             4677888889998888999999999999998888888888887653

>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=1.1e-32  Score=238.20  Aligned_cols=207  Identities=28%  Similarity=0.465  Sum_probs=179.4

Q ss_pred             hhccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccC----CCceeEE
Q 015158           36 EVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYG----LVECQAL  111 (412)
Q Consensus        36 ~~~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~----~~~~~~l  111 (412)
                      ....+|+++++++.+.+.|...++..|+++|.++++.+++++++++.+|||+|||++++++++..+...    ..+.+++
T Consensus        22 ~~~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~li~a~TGsGKT~~~~~~~l~~l~~~~~~~~~~~~~l  101 (236)
T 2pl3_A           22 NEITRFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEALYRLQWTSTDGLGVL  101 (236)
T ss_dssp             GGCSBGGGSCCCHHHHHHHHHTTCCBCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHTTCCGGGCCCEE
T ss_pred             cccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEEeCCCCcHHHHHHHHHHHHHHhhcccccCCceEE
Confidence            345689999999999999999999999999999999999999999999999999999999988776431    2356899


Q ss_pred             EEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcC-CCCCCCceEEEEeCC
Q 015158          112 VLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQ-SLRPDNIRIFVLDEA  190 (412)
Q Consensus       112 il~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~-~~~~~~~~~iiiDE~  190 (412)
                      |++|+++|+.|+.+.+..+....++.+..++|+.......... .+++|+|+||+++.+.+... .+...+++++|+|||
T Consensus       102 il~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~-~~~~iiv~Tp~~l~~~l~~~~~~~~~~~~~lViDEa  180 (236)
T 2pl3_A          102 IISPTRELAYQTFEVLRKVGKNHDFSAGLIIGGKDLKHEAERI-NNINILVCTPGRLLQHMDETVSFHATDLQMLVLDEA  180 (236)
T ss_dssp             EECSSHHHHHHHHHHHHHHTTTSSCCEEEECCC--CHHHHHHH-TTCSEEEECHHHHHHHHHHCSSCCCTTCCEEEETTH
T ss_pred             EEeCCHHHHHHHHHHHHHHhCCCCeeEEEEECCCCHHHHHHhC-CCCCEEEECHHHHHHHHHhcCCcccccccEEEEeCh
Confidence            9999999999999999999877778888888887765544433 46799999999998887654 456788999999999


Q ss_pred             chhhccCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEec
Q 015158          191 DEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVK  243 (412)
Q Consensus       191 h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~  243 (412)
                      |++.++++...+..++..+++..+++++|||+++........++.+|..+...
T Consensus       181 h~~~~~~~~~~~~~i~~~~~~~~~~l~~SAT~~~~~~~~~~~~~~~p~~i~~~  233 (236)
T 2pl3_A          181 DRILDMGFADTMNAVIENLPKKRQTLLFSATQTKSVKDLARLSLKNPEYVWVH  233 (236)
T ss_dssp             HHHHHTTTHHHHHHHHHTSCTTSEEEEEESSCCHHHHHHHHHSCSSCEEEECC
T ss_pred             HHHhcCCcHHHHHHHHHhCCCCCeEEEEEeeCCHHHHHHHHHhCCCCEEEEeC
Confidence            99999999999999999999999999999999999989888888888877643

>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=1.6e-32  Score=240.11  Aligned_cols=200  Identities=30%  Similarity=0.494  Sum_probs=173.5

Q ss_pred             cccccCC--CCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccC----CCceeEEE
Q 015158           39 DTFDAMG--LQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYG----LVECQALV  112 (412)
Q Consensus        39 ~~f~~~~--l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~----~~~~~~li  112 (412)
                      .+|+.++  +++.+.+.+..+||..|+++|.++++.++.++++++++|||+|||++|+++++..+...    ..+.+++|
T Consensus        52 ~~f~~l~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~l~~l~~l~~~~~~~~~~~~~li  131 (262)
T 3ly5_A           52 TSFASLCNLVNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRFMPRNGTGVLI  131 (262)
T ss_dssp             GCC-----CCCHHHHHHHHHTTCCBCCHHHHHHHHHHHHTCCCEECCCTTSCHHHHHHHHHHHHHHHTTCCGGGCCCEEE
T ss_pred             CChhHhccccCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCcEEEEccCCCCchHHHHHHHHHHHHhccccccCCceEEE
Confidence            3566665  89999999999999999999999999999999999999999999999999999876532    13568999


Q ss_pred             EcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCC-CCCCCceEEEEeCCc
Q 015158          113 LAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQS-LRPDNIRIFVLDEAD  191 (412)
Q Consensus       113 l~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~-~~~~~~~~iiiDE~h  191 (412)
                      ++|+++|+.|+.+.++++....+..+..+.|+............+++|+|+||+++...+.... ....++++||+||||
T Consensus       132 l~Pt~~La~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~~~~~~~~~~~~l~~lViDEah  211 (262)
T 3ly5_A          132 LSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQKLGNGINIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEAD  211 (262)
T ss_dssp             ECSSHHHHHHHHHHHHHHTTTCCSCEEEECSSSCHHHHHHHHHHCCSEEEECHHHHHHHHHHCTTCCCTTCCEEEECSHH
T ss_pred             EeCCHHHHHHHHHHHHHHHhhcCceEEEEECCCCHHHHHHHhcCCCCEEEEcHHHHHHHHHccCCcccccCCEEEEcChH
Confidence            9999999999999999998888888999999888776666666678999999999998877653 567889999999999


Q ss_pred             hhhccCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCe
Q 015158          192 EMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPV  238 (412)
Q Consensus       192 ~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~  238 (412)
                      ++.+++|...+..++..++...+++++|||+++....+....+..+.
T Consensus       212 ~l~~~~~~~~l~~i~~~~~~~~q~l~~SAT~~~~v~~~~~~~l~~~~  258 (262)
T 3ly5_A          212 RILDVGFEEELKQIIKLLPTRRQTMLFSATQTRKVEDLARISLKKEP  258 (262)
T ss_dssp             HHHHTTCHHHHHHHHHHSCSSSEEEEECSSCCHHHHHHHHHHCSSCC
T ss_pred             HHhhhhHHHHHHHHHHhCCCCCeEEEEEecCCHHHHHHHHHHcCCCC
Confidence            99999999999999999999999999999999999888887776543

>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=1.8e-32  Score=243.94  Aligned_cols=205  Identities=36%  Similarity=0.587  Sum_probs=179.9

Q ss_pred             hccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcC--ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEc
Q 015158           37 VYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKG--LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLA  114 (412)
Q Consensus        37 ~~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~--~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~  114 (412)
                      ...+|+.+++++.+.+.|..+||..|+++|.++++.++.+  +++++.+|||||||++|+++++..+.....++++||++
T Consensus        90 ~~~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~ai~~il~~~~~~~l~~a~TGsGKT~a~~lp~l~~l~~~~~~~~~lil~  169 (300)
T 3fmo_B           90 SVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLS  169 (300)
T ss_dssp             CCCCSGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHTSSSCCCEEEECCTTSSHHHHHHHHHHHHCCTTSCSCCEEEEC
T ss_pred             CcCCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCCccHHHHHHHHHhhhccCCCceEEEEc
Confidence            4568999999999999999999999999999999999987  99999999999999999999999887766677899999


Q ss_pred             CCHHHHHHHHHHHHHhhccc-CcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHc-CCCCCCCceEEEEeCCch
Q 015158          115 PTRELAQQIEKVMRALGDYL-GVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRR-QSLRPDNIRIFVLDEADE  192 (412)
Q Consensus       115 P~~~L~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~-~~~~~~~~~~iiiDE~h~  192 (412)
                      |+++|+.|+.+.+..+.... ++.+....|+......   ...+++|+|+||++|..++.+ ..+.+.++++||+||||+
T Consensus       170 PtreLa~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~---~~~~~~IlV~TP~~l~~~l~~~~~~~l~~l~~lVlDEad~  246 (300)
T 3fmo_B          170 PTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERG---QKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADV  246 (300)
T ss_dssp             SSHHHHHHHHHHHHHHTTTSTTCCEEEESTTCCCCTT---CCCCCSEEEECHHHHHHHHTTTCCCCGGGCSEEEETTHHH
T ss_pred             CcHHHHHHHHHHHHHHHhhCCCcEEEEEeCCccHhhh---hcCCCCEEEECHHHHHHHHHhcCCCChhhceEEEEeCHHH
Confidence            99999999999999987654 5777777776654322   135678999999999998866 455678899999999999


Q ss_pred             hhc-cCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEecC
Q 015158          193 MLS-RGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKR  244 (412)
Q Consensus       193 ~~~-~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~  244 (412)
                      +.+ .++...+..+...++++.|++++|||++.........++.+|..+....
T Consensus       247 l~~~~~~~~~~~~i~~~~~~~~q~i~~SAT~~~~v~~~a~~~l~~p~~i~~~~  299 (300)
T 3fmo_B          247 MIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKR  299 (300)
T ss_dssp             HHHSTTHHHHHHHHHTTSCTTCEEEEEESCCCHHHHHHHHHHSSSCEEEEECC
T ss_pred             HhhccCcHHHHHHHHHhCCCCCEEEEEeccCCHHHHHHHHHHCCCCeEEEecC
Confidence            987 6788999999999999999999999999999999999999998877643

>3jux_A Protein translocase subunit SECA; protein translocation, ATPase, conformational change, peptide binding, ATP-binding, cell inner membrane; HET: ADP; 3.10A {Thermotoga maritima} PDB: 3din_A*

Probab=99.98  E-value=6e-30  Score=242.14  Aligned_cols=321  Identities=18%  Similarity=0.190  Sum_probs=230.4

Q ss_pred             CCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCc
Q 015158           57 YGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGV  136 (412)
Q Consensus        57 ~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~  136 (412)
                      .|+. |++.|.-..-.+.+|+  +..+.||+|||+++.++++-....+   ..+.|++|+..|+.|-++++..+...+|+
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 LGMR-PFDVQVMGGIALHEGK--VAEMKTGEGKTLAATMPIYLNALIG---KGVHLVTVNDYLARRDALWMGPVYLFLGL  145 (822)
T ss_dssp             TSCC-CCHHHHHHHHHHHTTC--EEECCTTSCHHHHTHHHHHHHHTTS---SCEEEEESSHHHHHHHHHHHHHHHHHTTC
T ss_pred             hCCC-CcHHHHHHHHHHhCCC--hhhccCCCCccHHHHHHHHHHHhcC---CceEEEeccHHHHHhHHHHHHHHHHHhCC
Confidence            3666 9999999998888887  8999999999999998887443333   47999999999999999999999999999


Q ss_pred             EEEEEEcCc------------------------------------------------chHHHHHHhcCCCcEEEeChHHH
Q 015158          137 KVHACVGGT------------------------------------------------SVREDQRILSSGVHVVVGTPGRV  168 (412)
Q Consensus       137 ~~~~~~~~~------------------------------------------------~~~~~~~~~~~~~~iii~T~~~l  168 (412)
                      ++.++....                                                ......+...-.++|+++|...|
T Consensus       146 svg~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~err~aY~~DItYgTn~Ef  225 (822)
T 3jux_A          146 RVGVINSLGKSYEVVWKNPDLARKAIEENWSVWPDGFNGEVLKEESMNKEAVEAFQVELKEITRKEAYLCDVTYGTNNEF  225 (822)
T ss_dssp             CEEEEETTTEEEEEEESSHHHHHHHHHTTCCSSCTTCCSSSCCGGGSCHHHHTTTCEECCBCCHHHHHHSSEEEEEHHHH
T ss_pred             EEEEEcCCCcccccccccchhhhhhhcccccccccccccccccccccccccchhccccCCHHHHHHHhcCCCEEccCcch
Confidence            999988721                                                00001111122368999999887


Q ss_pred             HH-HHHc------CCCCCCCceEEEEeCCchhh-ccC---------------cHHHHHHHHHhC----------------
Q 015158          169 FD-MLRR------QSLRPDNIRIFVLDEADEML-SRG---------------FKDQIYDIFQLL----------------  209 (412)
Q Consensus       169 ~~-~~~~------~~~~~~~~~~iiiDE~h~~~-~~~---------------~~~~~~~i~~~~----------------  209 (412)
                      -- .+..      .....+.+.+.|+||++.++ +..               ....+..+...+                
T Consensus       226 gFDYLRDnm~~~~~~~vqR~~~~aIVDEvDSiLIDeArtPLiISg~~~~~~~~y~~~~~~v~~l~~~~dy~vdek~~~v~  305 (822)
T 3jux_A          226 GFDYLRDNLVLDYNDKVQRGHFYAIVDEADSVLIDEARTPLIISGPSKESPSVYRRFAQIAKKFVKDKDFTVDEKARTII  305 (822)
T ss_dssp             HHHHHHHTSCSSTTSCCCCCCCEEEEETHHHHHTTGGGSCEEEECCCCSCHHHHHHHHHHTTSSCBTTTEEECCSSSCEE
T ss_pred             hhHhHHhhccCCHHHhccCCCCeEEEecccceeecCCCCCceeeCCCCCccHHHHHHHHHHHhcCcCCcEEEEcccCeEE
Confidence            43 3332      12234678899999999754 110               000111111100                


Q ss_pred             ----------------------------------------C---------------------------------------
Q 015158          210 ----------------------------------------P---------------------------------------  210 (412)
Q Consensus       210 ----------------------------------------~---------------------------------------  210 (412)
                                                              .                                       
T Consensus       306 lTe~G~~~~E~~l~i~nly~~~n~~l~~~i~~AL~A~~l~~~d~dYiV~dg~V~iVDe~TGR~m~grr~s~GLHQaiEaK  385 (822)
T 3jux_A          306 LTEEGVAKAEKIIGVENLYDPGNVSLLYHLINALKALHLFKKDVDYVVMNGEVIIVDEFTGRLLPGRRYSGGLHQAIEAK  385 (822)
T ss_dssp             ECHHHHHHHHHHHTCSCTTSGGGHHHHHHHHHHHHHHHHSTTTSSEEEETTEEEECSSSSCSCCCSCCCGGGHHHHHHHH
T ss_pred             ECHHHHHHHHHHhCCccccchhhhHHHHHHHHHHHHHHHHcCCCcEEEECCEEEEEECCCCcCCCCCcCchHHHHHHHHH
Confidence                                                    0                                       


Q ss_pred             ----------------------CCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhHHH
Q 015158          211 ----------------------PKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLET  268 (412)
Q Consensus       211 ----------------------~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  268 (412)
                                            --.++.|||||......+ +...++-.+. .+ +....................+...
T Consensus       386 Egv~i~~e~~tla~IT~Qn~Fr~Y~kL~GMTGTa~te~~E-f~~iY~l~vv-~I-Ptnkp~~R~d~~d~vy~t~~eK~~a  462 (822)
T 3jux_A          386 EGVPIKEESITYATITFQNYFRMYEKLAGMTGTAKTEESE-FVQVYGMEVV-VI-PTHKPMIRKDHDDLVFRTQKEKYEK  462 (822)
T ss_dssp             HSSCCCCCCCEEEEECHHHHHTTSSEEEEEESSCGGGHHH-HHHHSCCCEE-EC-CCSSCCCCEECCCEEESSHHHHHHH
T ss_pred             cCCCCCCCcchhHHHHHHHHHHHhhHHeEECCCCchHHHH-HHHHhCCeEE-EE-CCCCCcceeecCcEEEecHHHHHHH
Confidence                                  124799999999876554 4555554432 22 2221111122211223344567777


Q ss_pred             HHHHHHhc--CCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCC-
Q 015158          269 LCDLYETL--AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQ-  345 (412)
Q Consensus       269 l~~~~~~~--~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~-  345 (412)
                      +.+.+...  .+.++||||+|++.++.+++.|++.|+.+..+||+....++..+.+.++.|  .|+|||+++++|+|++ 
T Consensus       463 l~~~I~~~~~~gqpVLVFt~S~e~sE~Ls~~L~~~Gi~~~vLhgkq~~rE~~ii~~ag~~g--~VtVATdmAgRGtDI~l  540 (822)
T 3jux_A          463 IVEEIEKRYKKGQPVLVGTTSIEKSELLSSMLKKKGIPHQVLNAKYHEKEAEIVAKAGQKG--MVTIATNMAGRGTDIKL  540 (822)
T ss_dssp             HHHHHHHHHHHTCCEEEEESSHHHHHHHHHHHHTTTCCCEEECSCHHHHHHHHHHHHHSTT--CEEEEETTTTTTCCCCC
T ss_pred             HHHHHHHHhhCCCCEEEEECCHHHHHHHHHHHHHCCCCEEEeeCCchHHHHHHHHhCCCCC--eEEEEcchhhCCcCccC
Confidence            77776653  457999999999999999999999999999999986555555555555544  6999999999999998 


Q ss_pred             -------CCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHH
Q 015158          346 -------QVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDER  388 (412)
Q Consensus       346 -------~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~  388 (412)
                             +..+||.++.|.|...|.|++||+||.|.+|.+++|++..|.-
T Consensus       541 g~~V~~~GglhVInte~Pes~r~y~qriGRTGRqG~~G~a~~fvsleD~l  590 (822)
T 3jux_A          541 GPGVAELGGLCIIGTERHESRRIDNQLRGRAGRQGDPGESIFFLSLEDDL  590 (822)
T ss_dssp             CTTTTTTTSCEEEESSCCSSHHHHHHHHTTSSCSSCCCEEEEEEETTSHH
T ss_pred             CcchhhcCCCEEEecCCCCCHHHHHHhhCccccCCCCeeEEEEechhHHH
Confidence                   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=99.98  E-value=1.3e-31  Score=232.72  Aligned_cols=208  Identities=26%  Similarity=0.454  Sum_probs=172.2

Q ss_pred             ccccccC----CCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccC-CCceeEEE
Q 015158           38 YDTFDAM----GLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYG-LVECQALV  112 (412)
Q Consensus        38 ~~~f~~~----~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~-~~~~~~li  112 (412)
                      ..+|+.+    ++++.+.+.+...||..|+++|.++++.+++++++++.+|||+|||++|+++++..+... ..+.+++|
T Consensus        24 ~~~f~~l~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~~~~~~~~~li  103 (245)
T 3dkp_A           24 IATFQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMQLKQPANKGFRALI  103 (245)
T ss_dssp             CSSHHHHHHHHCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHCSCCSSSCCEEE
T ss_pred             ccCHHHhhhccCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHhhcccCCceEEE
Confidence            3455554    899999999999999999999999999999999999999999999999999999887542 34568999


Q ss_pred             EcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHH-HHHhcCCCcEEEeChHHHHHHHHcC--CCCCCCceEEEEeC
Q 015158          113 LAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVRED-QRILSSGVHVVVGTPGRVFDMLRRQ--SLRPDNIRIFVLDE  189 (412)
Q Consensus       113 l~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~iii~T~~~l~~~~~~~--~~~~~~~~~iiiDE  189 (412)
                      ++|+++|+.|+.+.+.++....+..+..++++...... ......+++|+|+||+++...+...  ...+.+++++|+||
T Consensus       104 l~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~~~~~~~~lViDE  183 (245)
T 3dkp_A          104 ISPTRELASQIHRELIKISEGTGFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPPGIDLASVEWLVVDE  183 (245)
T ss_dssp             ECSSHHHHHHHHHHHHHHTTTSCCCEECCCHHHHHHTTTSTTSCCCCCEEEECHHHHHHHHHSSSCSCCCTTCCEEEESS
T ss_pred             EeCCHHHHHHHHHHHHHHhcccCceEEEEecCccHHHHhhhhhcCCCCEEEECHHHHHHHHHhCCCCcccccCcEEEEeC
Confidence            99999999999999999988777777777665432221 1122456799999999999988776  45678899999999


Q ss_pred             Cchhhc---cCcHHHHHHHHHhC-CCCceEEEEeecCChHHHHHHHHhcCCCeEEEecCC
Q 015158          190 ADEMLS---RGFKDQIYDIFQLL-PPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRD  245 (412)
Q Consensus       190 ~h~~~~---~~~~~~~~~i~~~~-~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~  245 (412)
                      ||++.+   .++...+..++..+ +.+.+++++|||++++.......++.++..+.....
T Consensus       184 ah~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~SAT~~~~v~~~~~~~l~~p~~i~~~~~  243 (245)
T 3dkp_A          184 SDKLFEDGKTGFRDQLASIFLACTSHKVRRAMFSATFAYDVEQWCKLNLDNVISVSIGAR  243 (245)
T ss_dssp             HHHHHHHC--CHHHHHHHHHHHCCCTTCEEEEEESSCCHHHHHHHHHHSSSCEEEEECC-
T ss_pred             hHHhcccccccHHHHHHHHHHhcCCCCcEEEEEeccCCHHHHHHHHHhCCCCEEEEeCCC
Confidence            999987   46778888887665 457899999999999999999999999988877553

>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=3.3e-28  Score=197.36  Aligned_cols=162  Identities=67%  Similarity=1.026  Sum_probs=147.3

Q ss_pred             CceEEEEEeccchhhHHHHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCc
Q 015158          251 GIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSR  330 (412)
Q Consensus       251 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~  330 (412)
                      ++.+.+..++....+...+.+++.....+++||||++++.++.+++.|.+.+..+..+||+++..+|..+++.|++|+.+
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            56777777777666999999999998889999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHHhccccccCChhhhh
Q 015158          331 VLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVAD  410 (412)
Q Consensus       331 vlv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  410 (412)
                      |||+|+++++|+|+|++++||+++.|++...|.||+||+||.|++|.+++++++.+...+..++++++..+++++.++.+
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            99999999999999999999999999999999999999999999999999999999999999999999999999988766


Q ss_pred             cC
Q 015158          411 LL  412 (412)
Q Consensus       411 l~  412 (412)
                      ++
T Consensus       163 ~~  164 (165)
T 1fuk_A          163 LL  164 (165)
T ss_dssp             TT
T ss_pred             hc
Confidence            53

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}

Probab=99.96  E-value=2.9e-27  Score=191.34  Aligned_cols=158  Identities=41%  Similarity=0.634  Sum_probs=146.7

Q ss_pred             cccCCceEEEEEeccchhhHHHHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhc
Q 015158          247 LTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRS  326 (412)
Q Consensus       247 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~  326 (412)
                      ..++++.+.+..+.. ..+...+.+++.....+++||||++++.++.+++.|.+.+..+..+||+++..+|..+++.|++
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            345667888777765 6688999999998888899999999999999999999999999999999999999999999999


Q ss_pred             CCCcEEEEcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHHhccccccCC
Q 015158          327 GSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELP  405 (412)
Q Consensus       327 g~~~vlv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  405 (412)
                      |+.+|||+|+++++|+|+|++++||+++.|+++..|.||+||+||.|++|.+++++++.+...+..++++++..+++++
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            9999999999999999999999999999999999999999999999999999999999999999999999998877654

>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=2.9e-27  Score=193.82  Aligned_cols=160  Identities=45%  Similarity=0.796  Sum_probs=146.7

Q ss_pred             ccCCceEEEEEeccchhhHHHHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcC
Q 015158          248 TLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSG  327 (412)
Q Consensus       248 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g  327 (412)
                      .+.++.+.+..++....+...+.++++....+++||||++++.++.+++.|.+.+..+..+||+++..+|..+++.|++|
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            45678888888887677999999999988889999999999999999999999999999999999999999999999999


Q ss_pred             CCcEEEEcCCCcCCCCCCCCCEEEEccCC------CChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHHhcccc
Q 015158          328 SSRVLITTDLLARGIDVQQVSLVINYDLP------TQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVI  401 (412)
Q Consensus       328 ~~~vlv~t~~~~~G~d~~~~~~vi~~~~~------~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~  401 (412)
                      +.+|||+|+++++|+|+|.+++||+++.|      .+...|.||+||+||.|+.|.+++++++.+...+..+++.++..+
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      899999999999999999999999999999999999999999988


Q ss_pred             ccCChh
Q 015158          402 EELPAN  407 (412)
Q Consensus       402 ~~~~~~  407 (412)
                      ++++..
T Consensus       164 ~~~~~~  169 (175)
T 2rb4_A          164 KQLNAE  169 (175)
T ss_dssp             EEECSS
T ss_pred             cccCCc
Confidence            877754

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}

Probab=99.95  E-value=1.9e-27  Score=196.74  Aligned_cols=179  Identities=27%  Similarity=0.446  Sum_probs=145.4

Q ss_pred             HHhcCCCeEEEecCCccccCCceEEEEEeccchhhHHHHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecC
Q 015158          231 RKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHG  310 (412)
Q Consensus       231 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~  310 (412)
                      ..++.+|..+.+........++.+.+..++. ..+...+.+++.... +++||||++++.++.+++.|+..++.+..+||
T Consensus         9 ~~~~~~p~~i~v~~~~~~~~~i~q~~~~~~~-~~K~~~L~~~l~~~~-~~~lVF~~~~~~~~~l~~~L~~~g~~~~~lhg   86 (191)
T 2p6n_A            9 SGVDLGTENLYFQSMGAASLDVIQEVEYVKE-EAKMVYLLECLQKTP-PPVLIFAEKKADVDAIHEYLLLKGVEAVAIHG   86 (191)
T ss_dssp             -------------------CCSEEEEEECCG-GGHHHHHHHHHTTSC-SCEEEECSCHHHHHHHHHHHHHHTCCEEEECT
T ss_pred             ccccCCCEEEEECCCCCCCcCceEEEEEcCh-HHHHHHHHHHHHhCC-CCEEEEECCHHHHHHHHHHHHHcCCcEEEEeC
Confidence            3455667677666666667788888887765 568888888887754 68999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccC-cHHH
Q 015158          311 DMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRD-DERM  389 (412)
Q Consensus       311 ~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~-~~~~  389 (412)
                      +++..+|..+++.|++|+.+|||+|+++++|+|+|++++||++++|+++..|.||+||+||.|+.|.+++|+++. +...
T Consensus        87 ~~~~~~R~~~l~~F~~g~~~vLvaT~~~~~Gldi~~v~~VI~~d~p~~~~~~~qr~GR~gR~g~~g~~i~l~~~~~~~~~  166 (191)
T 2p6n_A           87 GKDQEERTKAIEAFREGKKDVLVATDVASKGLDFPAIQHVINYDMPEEIENYVHRIGRTGCSGNTGIATTFINKACDESV  166 (191)
T ss_dssp             TSCHHHHHHHHHHHHHTSCSEEEECHHHHTTCCCCCCSEEEESSCCSSHHHHHHHHTTSCC---CCEEEEEECTTSCHHH
T ss_pred             CCCHHHHHHHHHHHhcCCCEEEEEcCchhcCCCcccCCEEEEeCCCCCHHHHHHHhCccccCCCCcEEEEEEcCchhHHH
Confidence            999999999999999999999999999999999999999999999999999999999999999999999999986 7888


Q ss_pred             HHHHHHHhccccccCChhhhhc
Q 015158          390 LFDIQKFYNVVIEELPANVADL  411 (412)
Q Consensus       390 ~~~~~~~~~~~~~~~~~~~~~l  411 (412)
                      +..+++.++...+.+|.++.++
T Consensus       167 ~~~l~~~l~~~~~~~p~~l~~~  188 (191)
T 2p6n_A          167 LMDLKALLLEAKQKVPPVLQVL  188 (191)
T ss_dssp             HHHHHHHHHHTTCCCCHHHHST
T ss_pred             HHHHHHHHHHccCcCCHHHHhh
Confidence            9999999999999999988764

>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=8.6e-26  Score=221.23  Aligned_cols=117  Identities=26%  Similarity=0.363  Sum_probs=108.1

Q ss_pred             CCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccC-
Q 015158          277 AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDL-  355 (412)
Q Consensus       277 ~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~-  355 (412)
                      .+.++||||+++..++.+++.|.+.|+.+..+||+++..+|..+++.|++|+.+|||+|+++++|+|+|++++||+++. 
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             ----CCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHH
Q 015158          356 ----PTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQ  394 (412)
Q Consensus       356 ----~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~  394 (412)
                          |.|...|+||+||+||.+ .|.+++++++.+....+.+.
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                889999999999999995 79999999887665544443

>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=4.7e-27  Score=191.55  Aligned_cols=158  Identities=35%  Similarity=0.660  Sum_probs=144.8

Q ss_pred             CCceEEEEEeccchhhHHHHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCC
Q 015158          250 EGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSS  329 (412)
Q Consensus       250 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~  329 (412)
                      ..+.+.+..+.. ..+...+.++++....+++||||++++.++.+++.|.+.+..+..+||+++..+|..+++.|++|+.
T Consensus         4 ~~i~q~~~~~~~-~~K~~~L~~ll~~~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~hg~~~~~~r~~~~~~f~~g~~   82 (172)
T 1t5i_A            4 HGLQQYYVKLKD-NEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQR   82 (172)
T ss_dssp             -CCEEEEEECCG-GGHHHHHHHHHHHSCCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSC
T ss_pred             CCeEEEEEECCh-HHHHHHHHHHHHhCCCCcEEEEECCHHHHHHHHHHHHhcCCCEEEEECCCCHHHHHHHHHHHHCCCC
Confidence            457777777765 6688999999998888999999999999999999999999999999999999999999999999999


Q ss_pred             cEEEEcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccC-cHHHHHHHHHHhccccccCChhh
Q 015158          330 RVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRD-DERMLFDIQKFYNVVIEELPANV  408 (412)
Q Consensus       330 ~vlv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~  408 (412)
                      +|||+|+++++|+|+|++++||+++.|+|+..|.||+||+||.|+.|.+++++++. +.+.++.+++.+...++++|.++
T Consensus        83 ~vLvaT~~~~~Gldi~~~~~Vi~~d~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~  162 (172)
T 1t5i_A           83 RILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEI  162 (172)
T ss_dssp             SEEEESSCCSTTCCGGGCSEEEESSCCSSHHHHHHHHHHHTGGGCCCEEEEEECSHHHHHHHHHHHHHHCCCEEECC---
T ss_pred             cEEEECCchhcCcchhhCCEEEEECCCCCHHHHHHHhcccccCCCCcEEEEEEcChhHHHHHHHHHHHHhcchhhCChhh
Confidence            99999999999999999999999999999999999999999999999999999875 56788999999999999998765

>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=3.3e-27  Score=194.62  Aligned_cols=164  Identities=34%  Similarity=0.538  Sum_probs=138.0

Q ss_pred             cccCCceEEEEEeccchhhHHHHHHHHHhc-CCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHh
Q 015158          247 LTLEGIKQFHVNVEKEEWKLETLCDLYETL-AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFR  325 (412)
Q Consensus       247 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~  325 (412)
                      ...+++.+.+..+.. ..+...+.+++... ..+++||||+++..++.+++.|+..++.+..+||+++..+|..+++.|+
T Consensus        15 ~~~~~i~q~~~~v~~-~~K~~~L~~ll~~~~~~~k~lVF~~~~~~~~~l~~~L~~~g~~~~~lhg~~~~~~r~~~~~~f~   93 (185)
T 2jgn_A           15 STSENITQKVVWVEE-SDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFR   93 (185)
T ss_dssp             -CCTTEEEEEEECCG-GGHHHHHHHHHHHC-CCSCEEEEESCHHHHHHHHHHHHHTTCCEEEEC--------CHHHHHHH
T ss_pred             CCCCCceEEEEEeCc-HHHHHHHHHHHHhcCCCCeEEEEECCHHHHHHHHHHHHHcCCceEEEeCCCCHHHHHHHHHHHH
Confidence            445678888887765 56888899998886 5689999999999999999999999999999999999999999999999


Q ss_pred             cCCCcEEEEcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHHhccccccCC
Q 015158          326 SGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELP  405 (412)
Q Consensus       326 ~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  405 (412)
                      +|+.+|||+|+++++|+|+|++++||+++.|+|+..|.||+||+||.|+.|.+++++++.+...++.++++++...+.+|
T Consensus        94 ~g~~~vLvaT~~~~~Gldi~~~~~VI~~d~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~l~~~l~~~~~~~~  173 (185)
T 2jgn_A           94 SGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINITKDLLDLLVEAKQEVP  173 (185)
T ss_dssp             HTSSSEEEEEC------CCCSBSEEEESSCCSSHHHHHHHHTTBCCTTSCEEEEEEECGGGGGGHHHHHHHHHHTTCCCC
T ss_pred             cCCCeEEEEcChhhcCCCcccCCEEEEeCCCCCHHHHHHHccccCCCCCCcEEEEEEchhhHHHHHHHHHHHHhccCCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhhc
Q 015158          406 ANVADL  411 (412)
Q Consensus       406 ~~~~~l  411 (412)
                      .++.++
T Consensus       174 ~~l~~~  179 (185)
T 2jgn_A          174 SWLENM  179 (185)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            887654

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=99.95  E-value=1.3e-25  Score=216.59  Aligned_cols=317  Identities=19%  Similarity=0.186  Sum_probs=227.8

Q ss_pred             CCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCc
Q 015158           57 YGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGV  136 (412)
Q Consensus        57 ~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~  136 (412)
                      .|+ .|++.|..+++.+++|+  +..+.||+|||+++.++++.....+   ..++|++||+.|+.|.++.+..++..+++
T Consensus        76 lG~-~Pt~VQ~~~ip~LlqG~--IaeakTGeGKTLvf~Lp~~L~aL~G---~qv~VvTPTreLA~Qdae~m~~l~~~lGL  149 (997)
T 2ipc_A           76 LGM-RHFDVQLIGGAVLHEGK--IAEMKTGEGKTLVATLAVALNALTG---KGVHVVTVNDYLARRDAEWMGPVYRGLGL  149 (997)
T ss_dssp             TCC-CCCHHHHHHHHHHHTTS--EEECCSTHHHHHHHHHHHHHHHTTC---SCCEEEESSHHHHHHHHHHHHHHHHTTTC
T ss_pred             hCC-CCcHHHHhhcccccCCc--eeeccCCCchHHHHHHHHHHHHHhC---CCEEEEeCCHHHHHHHHHHHHHHHHhcCC
Confidence            588 69999999999999998  8999999999999999996443333   47999999999999999999999999999


Q ss_pred             EEEEEEcCcchHHHHHHhcCCCcEEEeChHHH-HHHHHcC------CCCCC---CceEEEEeCCchhh-ccCc-------
Q 015158          137 KVHACVGGTSVREDQRILSSGVHVVVGTPGRV-FDMLRRQ------SLRPD---NIRIFVLDEADEML-SRGF-------  198 (412)
Q Consensus       137 ~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l-~~~~~~~------~~~~~---~~~~iiiDE~h~~~-~~~~-------  198 (412)
                      ++..+.|+.+....  .....++|+|+||..| +.++...      ...++   ++.++|+||+|.++ +.+.       
T Consensus       150 sv~~i~Gg~~~~~r--~~ay~~DIvyGTpgrlgfDyLrd~m~~~~~~l~~r~d~~l~~lIIDEaDsmLiDeartPLIISg  227 (997)
T 2ipc_A          150 SVGVIQHASTPAER--RKAYLADVTYVTNSELGFDYLRDNMAISPDQLVLRHDHPLHYAIIDEVDSILIDEARTPLIISG  227 (997)
T ss_dssp             CEEECCTTCCHHHH--HHHHTSSEEEEEHHHHHHHHHHHTSCSSTTTCCSCSSSSSCEEEETTHHHHTTSSTTSCEEEEE
T ss_pred             eEEEEeCCCCHHHH--HHHcCCCEEEECchhhhhHHHHHhhhcchhhcccccCCCcceEEEechHHHHHhCCCCCeeeeC
Confidence            99999998774333  3334689999999999 6666654      24456   89999999999875 2110       


Q ss_pred             --------HHHHHHHHHhCC------------------------------------------------------------
Q 015158          199 --------KDQIYDIFQLLP------------------------------------------------------------  210 (412)
Q Consensus       199 --------~~~~~~i~~~~~------------------------------------------------------------  210 (412)
                              ...+..+...++                                                            
T Consensus       228 p~~~~~~lY~~~~~~i~~L~~~~~~~~~~~~~~~~dy~vdek~r~v~LTe~G~~~~E~~l~i~~Ly~~~n~~l~~~i~~A  307 (997)
T 2ipc_A          228 PAEKATDLYYKMAEIAKKLERGLPAEPGVRKEPTGDYTVEEKNRSVHLTLQGIAKAEKLLGIEGLFSPENMELAHMLIQA  307 (997)
T ss_dssp             SCSSCHHHHHHHHHHHHHSCCCCCCCSSSCCCSSCCCCCTTSCCCCCCCHHHHHHHHHHHSCHHHHTTTCHHHHHHHHHH
T ss_pred             CCccchHHHHHHHHHHHHhhhccccccccccCCCCCeEEecCcceEEEchHHHHHHHHHcCCccccCchhHHHHHHHHHH
Confidence                    011111111110                                                            


Q ss_pred             ---------------------------------------------------------------------CCceEEEEeec
Q 015158          211 ---------------------------------------------------------------------PKIQVGVFSAT  221 (412)
Q Consensus       211 ---------------------------------------------------------------------~~~~~i~~SAT  221 (412)
                                                                                           --.++.|||+|
T Consensus       308 LrA~~lf~rd~dYiV~dgeV~IVDe~TGR~m~grrwsdGLHQAiEAKEgv~I~~e~~TlAsIT~QnyFr~Y~kLsGMTGT  387 (997)
T 2ipc_A          308 IRAKELYHRDRDYIVQDGQVIIVDEFTGRLMPGRRYGEGLHQAIEAKEGVRIERENQTLATITYQNFFRLYEKRAGMTGT  387 (997)
T ss_dssp             HHHHHSSCHHHHEEECSSCEEEEETTTTEECTTCCCGGGHHHHHHHHTTCCCCCSCEEEEEECHHHHHTTSSEEEEEESS
T ss_pred             HHHHHHHhcCCCeEEECCEEEEEECCCCeeCCCCcccHHHHHHHHHHhCCCCCCCceeeeeeeHHHHHHhChHheecCCC
Confidence                                                                                 12478999999


Q ss_pred             CChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhHHHHHHHHH-hc-CCCcEEEEEcchhHHHHHHHHHh
Q 015158          222 MPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYE-TL-AITQSVIFVNTRRKVDWLTDKMR  299 (412)
Q Consensus       222 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~-~~-~~~k~lif~~~~~~~~~~~~~L~  299 (412)
                      ...+..+ +...++-.+.. +.. .....-....-........+...+.+-+. .+ .+.++||.|.|++..+.+++.|+
T Consensus       388 A~tE~~E-f~~iY~l~Vv~-IPT-n~p~~R~D~~d~vy~t~~~K~~AIv~eI~~~~~~GqPVLVgT~SIe~SE~LS~~L~  464 (997)
T 2ipc_A          388 AKTEEKE-FQEIYGMDVVV-VPT-NRPVIRKDFPDVVYRTEKGKFYAVVEEIAEKYERGQPVLVGTISIEKSERLSQMLK  464 (997)
T ss_dssp             CGGGHHH-HHHHHCCCEEE-CCC-SSCCCCEEEEEEEESSHHHHHHHHHHHHHHHHHHTCCEEEECSSHHHHHHHHHHHH
T ss_pred             chHHHHH-HHHHhCCCEEE-cCC-CCCcccccCCCeEEcCHHHHHHHHHHHHHHHHHCCCCEEEEeCCHHHHHHHHHHHh
Confidence            9776544 44455544422 222 11111122222333444555555544433 33 45799999999999999999998


Q ss_pred             ----------------------------------------------------------------------------cCCC
Q 015158          300 ----------------------------------------------------------------------------SRDH  303 (412)
Q Consensus       300 ----------------------------------------------------------------------------~~~~  303 (412)
                                                                                                  +.|+
T Consensus       465 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gI  544 (997)
T 2ipc_A          465 EPRLYLPRLEMRLELFKKASQKQQGPEWERLRKLLERPAQLKDEDLAPFEGLIPPKGNLRTAWEGLKRAVHTLAVLRQGI  544 (997)
T ss_dssp             CGGGGHHHHHHHHHHHHHHHTTCCSHHHHHHHHHTSSSTTCSHHHHSGGGGGCCSSHHHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             hccccchhhhhhhhhhhhhhhhccccchhhhhhhhhccccccccccccccccccccccccccccccchhhhhhHHHHcCC
Confidence                                                                                        4566


Q ss_pred             eeEEecCCCCHHHHHHHHHHHhcC-CCcEEEEcCCCcCCCCCCCC-------------------C---------------
Q 015158          304 TVSATHGDMDQNTRDIIMREFRSG-SSRVLITTDLLARGIDVQQV-------------------S---------------  348 (412)
Q Consensus       304 ~~~~~~~~~~~~~r~~~~~~f~~g-~~~vlv~t~~~~~G~d~~~~-------------------~---------------  348 (412)
                      ...++++.....+ .+|+.  +.| ...|.|+|+++++|.|+.--                   .               
T Consensus       545 ~H~VLNAK~he~E-AeIIA--qAG~~GaVTIATNMAGRGTDIkLggn~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  621 (997)
T 2ipc_A          545 PHQVLNAKHHARE-AEIVA--QAGRSKTVTIATNMAGRGTDIKLGGNPEYLAAALLEKEGFDRYEWKVELFIKKMVAGKE  621 (997)
T ss_dssp             CCCEECSSSHHHH-HHHHH--TTTSTTCEEEECSSTTTTSCCCSSCCHHHHHHHTTSSSCSSTTHHHHHHHHHHHHHTCH
T ss_pred             CeeeccccchHHH-HHHHH--hcCCCCeEEEEecccCCCcCeecCCCHHHHHHHHHHhhcccccccccccccccccccch
Confidence            7777776643222 23333  345 44599999999999998632                   1               


Q ss_pred             ----------------------------------------EEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcH
Q 015158          349 ----------------------------------------LVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDE  387 (412)
Q Consensus       349 ----------------------------------------~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~  387 (412)
                                                              +||....+.|...-.|..||+||-|.+|.+-.|++-.|.
T Consensus       622 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~V~e~GGLhVIGTeRhESrRIDnQLRGRaGRQGDPGsSrF~LSLeDd  700 (997)
T 2ipc_A          622 EEARALAQELGIREELLERIREIREECKQDEERVRALGGLFIIGTERHESRRIDNQLRGRAGRQGDPGGSRFYVSFDDD  700 (997)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHTTTCCCCEEESSCCSSHHHHHHHHHTSSCSSCCCEEEEEEESSSH
T ss_pred             hhccccchhhhhhhhHHHHHHHhhhhhhhhhhHHHhcCCeEEEeccCCchHHHHHHHhcccccCCCCCCeEEEEECChH
Confidence                                                    788899999999999999999999999999989887765

>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=99.94  E-value=1.9e-25  Score=218.73  Aligned_cols=172  Identities=23%  Similarity=0.299  Sum_probs=129.4

Q ss_pred             CCceEEEEeecCChHHHHHHHHhcCCCeEEEecCCccccCCceEEEEEeccchhhHHHHHHHHHh-c-CCCcEEEEEcch
Q 015158          211 PKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYET-L-AITQSVIFVNTR  288 (412)
Q Consensus       211 ~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~-~~~k~lif~~~~  288 (412)
                      ...+++++|||+++.....    ................+.     ..+.........+...+.. . .+.++||||+++
T Consensus       385 ~~~q~i~~SAT~~~~~~~~----~~~~~~~~~r~~~l~~p~-----i~v~~~~~~~~~Ll~~l~~~~~~~~~vlVf~~t~  455 (661)
T 2d7d_A          385 HMHNIVYVSATPGPYEIEH----TDEMVEQIIRPTGLLDPL-----IDVRPIEGQIDDLIGEIQARIERNERVLVTTLTK  455 (661)
T ss_dssp             TCSEEEEECSSCCHHHHHH----CSSCEEECCCTTCCCCCE-----EEEECSTTHHHHHHHHHHHHHTTTCEEEEECSSH
T ss_pred             cCCCEEEEecCCChhHHHh----hhCeeeeeecccCCCCCe-----EEEecccchHHHHHHHHHHHHhcCCeEEEEECCH
Confidence            3578899999997543221    111111111111111111     1122222333434333333 2 457999999999


Q ss_pred             hHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccC-----CCChhhHH
Q 015158          289 RKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDL-----PTQPENYL  363 (412)
Q Consensus       289 ~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~-----~~s~~~~~  363 (412)
                      ..++.+++.|++.|+.+..+||+++..+|..+++.|++|+.+|||+|+.+++|+|+|++++||+++.     |.|...|+
T Consensus       456 ~~ae~L~~~L~~~gi~~~~lh~~~~~~~R~~~l~~f~~g~~~VLVaT~~l~~GlDip~v~lVi~~d~d~~G~p~s~~~~i  535 (661)
T 2d7d_A          456 KMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLI  535 (661)
T ss_dssp             HHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHHTSCSEEEESCCCSTTCCCTTEEEEEETTTTCCTTTTSHHHHH
T ss_pred             HHHHHHHHHHHhcCCCeEEEeCCCCHHHHHHHHHHHhcCCeEEEEecchhhCCcccCCCCEEEEeCcccccCCCCHHHHH
Confidence            9999999999999999999999999999999999999999999999999999999999999999997     89999999


Q ss_pred             HhhhhcccCCCCceEEEEeccCcHHHHHH
Q 015158          364 HRIGRSGRFGRKGVAINFVTRDDERMLFD  392 (412)
Q Consensus       364 Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~  392 (412)
                      ||+||+||. ..|.+++++++.+......
T Consensus       536 Qr~GRagR~-~~G~~i~~~~~~~~~~~~~  563 (661)
T 2d7d_A          536 QTIGRAARN-AEGRVIMYADKITKSMEIA  563 (661)
T ss_dssp             HHHHTTTTS-TTCEEEEECSSCCHHHHHH
T ss_pred             HHhCcccCC-CCCEEEEEEeCCCHHHHHH
Confidence            999999998 6899999999876654443

>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=1.2e-25  Score=189.70  Aligned_cols=145  Identities=31%  Similarity=0.549  Sum_probs=136.3

Q ss_pred             chhhHHHHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCC
Q 015158          262 EEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARG  341 (412)
Q Consensus       262 ~~~~~~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G  341 (412)
                      ...+...+.+++.....+++||||++++.++.+++.|.+.++.+..+||+++..+|..+++.|++|+.+|||+|+++++|
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            36789999999998888999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHHhccccccCCh
Q 015158          342 IDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPA  406 (412)
Q Consensus       342 ~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  406 (412)
                      +|+|++++||+++.|+|...|.||+||+||.|++|.|++++++.+...+..+++.++..++.++.
T Consensus        95 idi~~v~~Vi~~~~p~~~~~~~qr~GR~gR~g~~g~~~~l~~~~~~~~~~~i~~~~~~~~~~~~~  159 (212)
T 3eaq_A           95 LDIPQVDLVVHYRLPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRERRDVEALERAVGRRFKRVNP  159 (212)
T ss_dssp             SSCCCBSEEEESSCCSSHHHHHHHHTTBCCCC--BEEEEEECGGGHHHHHHHHHHHSSCCEECCC
T ss_pred             CCCccCcEEEECCCCcCHHHHHHHhcccCCCCCCCeEEEEEchhHHHHHHHHHHHhcCcCeecCC
Confidence            99999999999999999999999999999999999999999999999999999999987776653

>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=8.8e-25  Score=192.69  Aligned_cols=154  Identities=31%  Similarity=0.520  Sum_probs=138.5

Q ss_pred             ceEEEEEeccchhhHHHHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcE
Q 015158          252 IKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRV  331 (412)
Q Consensus       252 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~v  331 (412)
                      +.+.+..... ..+...+.+++.....+++||||++++.++.+++.|.+.++.+..+||++++.+|..+++.|++|+.+|
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            4555665555 668999999999888899999999999999999999999999999999999999999999999999999


Q ss_pred             EEEcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHHhccccccCCh
Q 015158          332 LITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPA  406 (412)
Q Consensus       332 lv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  406 (412)
                      ||+|+++++|+|+|++++||+++.|++...|.||+||+||.|++|.|++|+++.+...+..+++.++..++.++.
T Consensus        82 LVaT~va~~Gidi~~v~~VI~~d~p~s~~~y~Qr~GRagR~g~~G~~i~l~~~~e~~~~~~ie~~~~~~~~~~~~  156 (300)
T 3i32_A           82 LVATDVAARGLDIPQVDLVVHYRMPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRERRDVEALERAVGRRFKRVNP  156 (300)
T ss_dssp             EEECSTTTCSTTCCCCSEEEESSCCSSTTHHHHHHTCCC-----CEEEEEECSSTHHHHHHHHHHHTCCCEECCC
T ss_pred             EEEechhhcCccccceeEEEEcCCCCCHHHHHHHccCcCcCCCCceEEEEeChHHHHHHHHHHHHhCCcceEeCC
Confidence            999999999999999999999999999999999999999999999999999999999999999999987776653

>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=99.86  E-value=7.2e-27  Score=190.36  Aligned_cols=155  Identities=34%  Similarity=0.536  Sum_probs=140.8

Q ss_pred             CceEEEEEeccchhhHHHHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCc
Q 015158          251 GIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSR  330 (412)
Q Consensus       251 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~  330 (412)
                      ++.+.+...+....+...+.++++....+++||||++++.++.+++.|++.+..+..+||+++..+|..+++.|++|+.+
T Consensus         3 ~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~iVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~r~~~~~~f~~g~~~   82 (170)
T 2yjt_D            3 KIHQWYYRADDLEHKTALLVHLLKQPEATRSIVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGRVN   82 (170)
Confidence            34455555554456788888888887778999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHHhccccccCC
Q 015158          331 VLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELP  405 (412)
Q Consensus       331 vlv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  405 (412)
                      |||+|+++++|+|+|++++||+++.|+|...|.||+||+||.|+.|.+++++++.+...+..++++++..++...
T Consensus        83 vLvaT~~~~~Gid~~~~~~Vi~~~~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  157 (170)
T 2yjt_D           83 VLVATDVAARGIDIPDVSHVFNFDMPRSGDTYLHRIGRTARAGRKGTAISLVEAHDHLLLGKVGRYIEEPIKARV  157 (170)
Confidence            999999999999999999999999999999999999999999999999999999999999999999988776554

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=99.91  E-value=5.7e-24  Score=204.35  Aligned_cols=103  Identities=11%  Similarity=0.173  Sum_probs=67.8

Q ss_pred             CCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEE--EcCCCcCCCCCCC----CCEE
Q 015158          277 AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLI--TTDLLARGIDVQQ----VSLV  350 (412)
Q Consensus       277 ~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv--~t~~~~~G~d~~~----~~~v  350 (412)
                      ..+++|||++|...++.+++.+..  .. ...++..  .++.+++++|+++. .|++  +|..+.+|+|+|+    +++|
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            457899999999999999998875  22 3445443  46888999999864 5777  7799999999997    7899


Q ss_pred             EEccCCCCh------------------------------hhHHHhhhhcccCCCCceEEEEeccC
Q 015158          351 INYDLPTQP------------------------------ENYLHRIGRSGRFGRKGVAINFVTRD  385 (412)
Q Consensus       351 i~~~~~~s~------------------------------~~~~Q~~GR~~R~g~~g~~~~~~~~~  385 (412)
                      |+++.|...                              ..+.|.+||+.|...+-.++++++..
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            999988431                              34679999999986655556566554

>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=99.91  E-value=9.4e-25  Score=185.85  Aligned_cols=164  Identities=16%  Similarity=0.133  Sum_probs=116.4

Q ss_pred             CCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccC---CCceeEEEEcCCHHHHHH-HHHHHHHhhc
Q 015158           57 YGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYG---LVECQALVLAPTRELAQQ-IEKVMRALGD  132 (412)
Q Consensus        57 ~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~---~~~~~~lil~P~~~L~~q-~~~~~~~~~~  132 (412)
                      .....|+++|.++++.+.+++++++.+|||+|||++++.++...+...   ..+.+++|++|+++|+.| +.+.+..+..
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            344469999999999999999999999999999999998888765432   124589999999999999 7788888765


Q ss_pred             ccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCC------CCCCCceEEEEeCCchhhccCcHHHH-HHH
Q 015158          133 YLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQS------LRPDNIRIFVLDEADEMLSRGFKDQI-YDI  205 (412)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~------~~~~~~~~iiiDE~h~~~~~~~~~~~-~~i  205 (412)
                      . +..+..+.|+............+++|+|+||+.|.+.+....      ....++++||+||||++.+.++...+ ..+
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 567777777665443333333457999999999998887643      44678899999999998766544443 333


Q ss_pred             HHhC-------------CCCceEEEEeec
Q 015158          206 FQLL-------------PPKIQVGVFSAT  221 (412)
Q Consensus       206 ~~~~-------------~~~~~~i~~SAT  221 (412)
                      ....             .+..+++++|||
T Consensus       188 ~~~~~~~~~~~~~~~~~~~~~~~l~lSAT  216 (216)
T 3b6e_A          188 LMQKLKNNRLKKENKPVIPLPQILGLTAS  216 (216)
T ss_dssp             HHHHHHHHHHHHTTCCCCCCCEEEEEECC
T ss_pred             HHHhcccccccccccCCCCcceEEEeecC
Confidence            2221             157889999998

>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=8e-22  Score=190.22  Aligned_cols=311  Identities=17%  Similarity=0.126  Sum_probs=197.6

Q ss_pred             CChHHHHhhhhhh----hcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCc
Q 015158           61 KPSAIQQRGIVPF----CKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGV  136 (412)
Q Consensus        61 ~l~~~Q~~a~~~~----~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~  136 (412)
                      ++||+|.+.+..+    ..++++++.+|||+|||++|+++++.      .+.+++|++||++|+.|+.+++..+....++
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------VKPKVLFVVRTHNEFYPIYRDLTKIREKRNI   76 (551)
T ss_dssp             SCCHHHHHHHHHHHHHHHTTCEEEEECCTTSSHHHHHHHHHHH------HCSEEEEEESSGGGHHHHHHHHTTCCCSSCC
T ss_pred             CCCHHHHHHHHHHHHHHHcCCcEEEECCCCccHHHHHHHHHHh------CCCeEEEEcCCHHHHHHHHHHHHHHhhhcCc
Confidence            3999999977754    46899999999999999999999887      2358999999999999999999888666677


Q ss_pred             EEEEEEcCcch---------------------------------HHHH------------------HHhcCCCcEEEeCh
Q 015158          137 KVHACVGGTSV---------------------------------REDQ------------------RILSSGVHVVVGTP  165 (412)
Q Consensus       137 ~~~~~~~~~~~---------------------------------~~~~------------------~~~~~~~~iii~T~  165 (412)
                      ++..+.|..+.                                 ....                  ......++|||+||
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            77776664321                                 0000                  11234679999999


Q ss_pred             HHHHHHHHcCCCCC-CCceEEEEeCCchhhccCc----------------------------------------------
Q 015158          166 GRVFDMLRRQSLRP-DNIRIFVLDEADEMLSRGF----------------------------------------------  198 (412)
Q Consensus       166 ~~l~~~~~~~~~~~-~~~~~iiiDE~h~~~~~~~----------------------------------------------  198 (412)
                      ..|+....+..+.. ....++|+||||++.+ ..                                              
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            99988755443322 3567999999998765 20                                              


Q ss_pred             ---------HHHHH----------------------------HHHH----------------------------hCCCC-
Q 015158          199 ---------KDQIY----------------------------DIFQ----------------------------LLPPK-  212 (412)
Q Consensus       199 ---------~~~~~----------------------------~i~~----------------------------~~~~~-  212 (412)
                               ...+.                            .++.                            .+... 
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                            0000                            01122 


Q ss_pred             ceEEEEeecCChHHHHHHHHhcCCC-eEE----EecCCccccCCceEEEEEe--cc--c---hhhHHHHHHHHHh---cC
Q 015158          213 IQVGVFSATMPPEALEITRKFMNKP-VRI----LVKRDELTLEGIKQFHVNV--EK--E---EWKLETLCDLYET---LA  277 (412)
Q Consensus       213 ~~~i~~SAT~~~~~~~~~~~~~~~~-~~~----~~~~~~~~~~~~~~~~~~~--~~--~---~~~~~~l~~~~~~---~~  277 (412)
                      ..+|++|||+.+  .......++-+ ...    ...-.... ..-...+...  +.  .   ......+.+.+..   ..
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            578999999986  34444455543 111    00111111 1112222221  11  0   1112333333322   24


Q ss_pred             CCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEc--CCCcCCCCCC-----CCCEE
Q 015158          278 ITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITT--DLLARGIDVQ-----QVSLV  350 (412)
Q Consensus       278 ~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t--~~~~~G~d~~-----~~~~v  350 (412)
                      .+.++||++|....+.+++.   .+..+..-..+++   +..+++.|+.++..|++++  ..+.+|+|+|     .++.|
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            57899999999999999873   3444443333444   4557778854444799998  5999999999     37889


Q ss_pred             EEccCCCC------------------------------hhhHHHhhhhcccCCCCceEEEEeccCcH
Q 015158          351 INYDLPTQ------------------------------PENYLHRIGRSGRFGRKGVAINFVTRDDE  387 (412)
Q Consensus       351 i~~~~~~s------------------------------~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~  387 (412)
                      |+.+.|+.                              ...+.|.+||+.|...+.-++++++..-.
T Consensus       467 iI~~lPfp~~dp~~~ar~~~~~~~~g~~~~~~~y~~pa~~~l~Qa~GRlIR~~~D~G~v~llD~R~~  533 (551)
T 3crv_A          467 VIVGIPYPPPDDYLKILAQRVSLKMNRENEEFLFKIPALVTIKQAIGRAIRDVNDKCNVWLLDKRFE  533 (551)
T ss_dssp             EEESCCCCCCSHHHHHHHHHTTCCSSTTTHHHHTHHHHHHHHHHHHHTTCCSTTCEEEEEEESGGGG
T ss_pred             EEEcCCCCCCCHHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHHHhccCccCCCccEEEEEeehhcc
Confidence            98887641                              11246999999998766666666666433

>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=99.88  E-value=1.2e-22  Score=179.78  Aligned_cols=153  Identities=17%  Similarity=0.112  Sum_probs=120.6

Q ss_pred             CChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEE
Q 015158           61 KPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHA  140 (412)
Q Consensus        61 ~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~  140 (412)
                      .|+++|.++++.++.+++.++++|||+|||.+++.++...+..+  ..++||++|+++|+.||.+++.++....+..+..
T Consensus       113 ~l~~~Q~~ai~~~l~~~~~ll~~~tGsGKT~~~~~~~~~~~~~~--~~~~lil~Pt~~L~~q~~~~l~~~~~~~~~~~~~  190 (282)
T 1rif_A          113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENY--EGKILIIVPTTALTTQMADDFVDYRLFSHAMIKK  190 (282)
T ss_dssp             CCCHHHHHHHHHHHHHSEEEECCCTTSCHHHHHHHHHHHHHHHC--SSEEEEECSSHHHHHHHHHHHHHHTSCCGGGEEE
T ss_pred             CccHHHHHHHHHHHhcCCeEEEcCCCCCcHHHHHHHHHHHHHcC--CCeEEEEECCHHHHHHHHHHHHHhcccccceEEE
Confidence            59999999999999888899999999999999987777655432  2479999999999999999999986655566666


Q ss_pred             EEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEee
Q 015158          141 CVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSA  220 (412)
Q Consensus       141 ~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SA  220 (412)
                      +.++.....   ......+|+|+|++.+.+..   .....++++||+||||++.+    ..+..++..+....+++++||
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   12245799999999875432   22346789999999999763    366777787777899999999


Q ss_pred             cCChH
Q 015158          221 TMPPE  225 (412)
Q Consensus       221 T~~~~  225 (412)
                      ||++.
T Consensus       261 Tp~~~  265 (282)
T 1rif_A          261 SLRDG  265 (282)
T ss_dssp             SCCTT
T ss_pred             CCCCc
Confidence            99764

>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=99.85  E-value=1.2e-20  Score=162.13  Aligned_cols=171  Identities=19%  Similarity=0.207  Sum_probs=122.6

Q ss_pred             CHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCC--CceeEEEEcCCHHHHHHHH
Q 015158           47 QENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGL--VECQALVLAPTRELAQQIE  124 (412)
Q Consensus        47 ~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~--~~~~~lil~P~~~L~~q~~  124 (412)
                      ++.+.+.+.......++++|.++++.+.+|+++++.+|||||||+++..+++.......  ...++++++|+++++.|+.
T Consensus        47 ~~~~~~~~~~~~~~p~~~~q~~~i~~i~~g~~~~i~g~TGsGKTt~~~~~~~~~~~~~~~~~~~~~l~~~p~~~la~q~~  126 (235)
T 3llm_A           47 DHDLQAILQERELLPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDDFIQNDRAAECNIVVTQPRRISAVSVA  126 (235)
T ss_dssp             CHHHHHHHHHHHTSGGGGGHHHHHHHHHHCSEEEEECCTTSSHHHHHHHHHHHHHHHTTCGGGCEEEEEESSHHHHHHHH
T ss_pred             CHHHHHHHHHHhcCChHHHHHHHHHHHhcCCEEEEEeCCCCCcHHhHHHHHhcchhhcCCCCceEEEEeccchHHHHHHH
Confidence            33444444443444589999999999999999999999999999888777776554332  2458999999999999998


Q ss_pred             HHHHHhhc-ccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchh-hccCcH-HH
Q 015158          125 KVMRALGD-YLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEM-LSRGFK-DQ  201 (412)
Q Consensus       125 ~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~-~~~~~~-~~  201 (412)
                      +.+..... ..+..+.........     ......+|+|+||+++.+.+..   .++++++||+||+|+. .+.++. ..
T Consensus       127 ~~~~~~~~~~~~~~~g~~~~~~~~-----~~~~~~~Ivv~Tpg~l~~~l~~---~l~~~~~lVlDEah~~~~~~~~~~~~  198 (235)
T 3llm_A          127 ERVAFERGEEPGKSCGYSVRFESI-----LPRPHASIMFCTVGVLLRKLEA---GIRGISHVIVDEIHERDINTDFLLVV  198 (235)
T ss_dssp             HHHHHTTTCCTTSSEEEEETTEEE-----CCCSSSEEEEEEHHHHHHHHHH---CCTTCCEEEECCTTSCCHHHHHHHHH
T ss_pred             HHHHHHhccccCceEEEeechhhc-----cCCCCCeEEEECHHHHHHHHHh---hhcCCcEEEEECCccCCcchHHHHHH
Confidence            88876432 223333332221110     0114578999999999998876   3678999999999984 555555 35


Q ss_pred             HHHHHHhCCCCceEEEEeecCChHH
Q 015158          202 IYDIFQLLPPKIQVGVFSATMPPEA  226 (412)
Q Consensus       202 ~~~i~~~~~~~~~~i~~SAT~~~~~  226 (412)
                      +..+.... ++.+++++|||++.+.
T Consensus       199 l~~i~~~~-~~~~~il~SAT~~~~~  222 (235)
T 3llm_A          199 LRDVVQAY-PEVRIVLMSATIDTSM  222 (235)
T ss_dssp             HHHHHHHC-TTSEEEEEECSSCCHH
T ss_pred             HHHHHhhC-CCCeEEEEecCCCHHH
Confidence            55666555 4789999999998754

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=99.84  E-value=2.1e-19  Score=174.57  Aligned_cols=111  Identities=15%  Similarity=0.261  Sum_probs=76.3

Q ss_pred             HHHHHhcCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcC--CCcCCCCCCC-
Q 015158          270 CDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTD--LLARGIDVQQ-  346 (412)
Q Consensus       270 ~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~--~~~~G~d~~~-  346 (412)
                      .+++... .+.++||++|....+.+++.|+.  .... ...+++..++..++++|. ++..||+++.  .+.+|+|+|+ 
T Consensus       441 ~~l~~~~-~g~~lvlF~Sy~~l~~v~~~l~~--~~~~-~~q~~~~~~~~~ll~~f~-~~~~vL~~v~~gsf~EGiD~~g~  515 (620)
T 4a15_A          441 EDIILKV-KKNTIVYFPSYSLMDRVENRVSF--EHMK-EYRGIDQKELYSMLKKFR-RDHGTIFAVSGGRLSEGINFPGN  515 (620)
T ss_dssp             HHHHHHH-CSCEEEEESCHHHHHHHTSSCCS--CCEE-CCTTCCSHHHHHHHHHHT-TSCCEEEEETTSCC--------C
T ss_pred             HHHHHhC-CCCEEEEeCCHHHHHHHHHHHHh--cchh-ccCCCChhHHHHHHHHhc-cCCcEEEEEecCceeccccCCCC
Confidence            3344433 47899999999999999998873  2222 444555678999999999 8888999974  8999999995 


Q ss_pred             -CCEEEEccCCCCh-----------------------------hhHHHhhhhcccCCCCceEEEEeccC
Q 015158          347 -VSLVINYDLPTQP-----------------------------ENYLHRIGRSGRFGRKGVAINFVTRD  385 (412)
Q Consensus       347 -~~~vi~~~~~~s~-----------------------------~~~~Q~~GR~~R~g~~g~~~~~~~~~  385 (412)
                       ++.||+.+.|+..                             ..+.|.+||+.|...+-.++++++..
T Consensus       516 ~l~~viI~~lPfp~~~p~~~ar~~~~~~~~g~~~~~~y~~pa~~~l~Qa~GRlIR~~~D~G~v~llD~R  584 (620)
T 4a15_A          516 ELEMIILAGLPFPRPDAINRSLFDYYERKYGKGWEYSVVYPTAIKIRQEIGRLIRSAEDTGACVILDKR  584 (620)
T ss_dssp             CCCEEEESSCCCCCCCHHHHHHHHHHHHHHSCHHHHHTHHHHHHHHHHHHHTTCCSTTCCEEEEEECGG
T ss_pred             ceEEEEEEcCCCCCCCHHHHHHHHHHHHhhCCCchHHhHHHHHHHHHHHhCccccCCCceEEEEEEccc
Confidence             7899999887531                             22479999999987665566666554

>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=99.83  E-value=3e-20  Score=159.25  Aligned_cols=138  Identities=17%  Similarity=0.190  Sum_probs=109.2

Q ss_pred             CChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcE-EE
Q 015158           61 KPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVK-VH  139 (412)
Q Consensus        61 ~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~-~~  139 (412)
                      .|+++|.+++..+.+++++++++|||+|||.+++.++...      +.+++|++|+++|+.||.+.+.++    +.. +.
T Consensus        93 ~l~~~Q~~ai~~~~~~~~~ll~~~tG~GKT~~a~~~~~~~------~~~~liv~P~~~L~~q~~~~~~~~----~~~~v~  162 (237)
T 2fz4_A           93 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINEL------STPTLIVVPTLALAEQWKERLGIF----GEEYVG  162 (237)
T ss_dssp             CCCHHHHHHHHHHTTTSEEEEEESSSTTHHHHHHHHHHHS------CSCEEEEESSHHHHHHHHHHHGGG----CGGGEE
T ss_pred             CcCHHHHHHHHHHHhCCCEEEEeCCCCCHHHHHHHHHHHc------CCCEEEEeCCHHHHHHHHHHHHhC----CCCeEE
Confidence            5999999999999999899999999999999987766653      247999999999999999988884    566 77


Q ss_pred             EEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEe
Q 015158          140 ACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFS  219 (412)
Q Consensus       140 ~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~S  219 (412)
                      .+.|+..         ...+|+|+|++.+.......   ...+++||+||+|++.+..+.    .+...++ ..+++++|
T Consensus       163 ~~~g~~~---------~~~~i~v~T~~~l~~~~~~~---~~~~~llIiDEaH~l~~~~~~----~i~~~~~-~~~~l~LS  225 (237)
T 2fz4_A          163 EFSGRIK---------ELKPLTVSTYDSAYVNAEKL---GNRFMLLIFDEVHHLPAESYV----QIAQMSI-APFRLGLT  225 (237)
T ss_dssp             EESSSCB---------CCCSEEEEEHHHHHHTHHHH---TTTCSEEEEECSSCCCTTTHH----HHHHTCC-CSEEEEEE
T ss_pred             EEeCCCC---------CcCCEEEEeHHHHHhhHHHh---cccCCEEEEECCccCCChHHH----HHHHhcc-CCEEEEEe
Confidence            7776654         24689999999987655421   245899999999998766543    3445454 67789999


Q ss_pred             ecCChH
Q 015158          220 ATMPPE  225 (412)
Q Consensus       220 AT~~~~  225 (412)
                      |||...
T Consensus       226 ATp~r~  231 (237)
T 2fz4_A          226 ATFERE  231 (237)
T ss_dssp             ESCC--
T ss_pred             cCCCCC
Confidence            999753

>1z5z_A Helicase of the SNF2/RAD54 family; hydrolase, recombination, hydrolase-recombination complex; 2.00A {Sulfolobus solfataricus} SCOP: c.37.1.19

Probab=99.77  E-value=2.4e-18  Score=149.91  Aligned_cols=125  Identities=16%  Similarity=0.235  Sum_probs=98.1

Q ss_pred             cchhhHHHHHHHHHhc--CCCcEEEEEcchhHHHHHHHHHhcC-CCeeEEecCCCCHHHHHHHHHHHhcC-CCc-EEEEc
Q 015158          261 KEEWKLETLCDLYETL--AITQSVIFVNTRRKVDWLTDKMRSR-DHTVSATHGDMDQNTRDIIMREFRSG-SSR-VLITT  335 (412)
Q Consensus       261 ~~~~~~~~l~~~~~~~--~~~k~lif~~~~~~~~~~~~~L~~~-~~~~~~~~~~~~~~~r~~~~~~f~~g-~~~-vlv~t  335 (412)
                      ....|...+.+++...  .+.++||||++...++.+.+.|.+. |+.+..+||+++..+|..++++|+++ +.+ +|++|
T Consensus        93 ~~s~K~~~L~~ll~~~~~~~~kvlIFs~~~~~~~~l~~~L~~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~v~L~st  172 (271)
T 1z5z_A           93 RRSGKMIRTMEIIEEALDEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSV  172 (271)
T ss_dssp             TTCHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHHHCSCCCEECTTSCHHHHHHHHHHHHHCTTCCEEEEEC
T ss_pred             ccCHHHHHHHHHHHHHHhCCCeEEEEeccHHHHHHHHHHHHHhcCCcEEEEECCCCHHHHHHHHHHhcCCCCCCEEEEeh
Confidence            3456888888888776  6789999999999999999999885 99999999999999999999999998 677 78899


Q ss_pred             CCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccCCCCceE--EEEeccC
Q 015158          336 DLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVA--INFVTRD  385 (412)
Q Consensus       336 ~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~--~~~~~~~  385 (412)
                      +++++|+|++.+++||++++||++..+.|++||++|.|+.+.+  +.++...
T Consensus       173 ~~~g~Glnl~~a~~VI~~d~~wnp~~~~Q~~gR~~R~Gq~~~v~v~~li~~~  224 (271)
T 1z5z_A          173 KAGGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVG  224 (271)
T ss_dssp             CTTCCCCCCTTCSEEEECSCCSCTTTC--------------CCEEEEEEETT
T ss_pred             hhhcCCcCcccCCEEEEECCCCChhHHHHHHHhccccCCCCceEEEEEeeCC
Confidence            9999999999999999999999999999999999999987765  4455554

>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=98.79  E-value=1.1e-08  Score=99.51  Aligned_cols=146  Identities=21%  Similarity=0.201  Sum_probs=87.4

Q ss_pred             hHHHHhhhhhhhcCccEEEECCCCCCchhH--hHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEE
Q 015158           63 SAIQQRGIVPFCKGLDVIQQAQSGTGKTAT--FCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHA  140 (412)
Q Consensus        63 ~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~--~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~  140 (412)
                      .+.|+.|+..++.++.+++.|++|||||.+  +++..+..... ..+.++++++||...+.++.+.+.......++....
T Consensus       151 ~~~Q~~Ai~~~l~~~~~vi~G~pGTGKTt~l~~ll~~l~~~~~-~~~~~vll~APTg~AA~~L~e~~~~~~~~l~l~~~~  229 (608)
T 1w36_D          151 INWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQMAD-GERCRIRLAAPTGKAAARLTESLGKALRQLPLTDEQ  229 (608)
T ss_dssp             CCHHHHHHHHHHTBSEEEEECCTTSTHHHHHHHHHHHHHHTCS-SCCCCEEEEBSSHHHHHHHHHHHTHHHHHSSCCSCC
T ss_pred             CHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHHHhhh-cCCCeEEEEeCChhHHHHHHHHHHHHHhcCCCCHHH
Confidence            688999999999999999999999999944  44444443321 234589999999999999888776654333321100


Q ss_pred             EEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEee
Q 015158          141 CVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSA  220 (412)
Q Consensus       141 ~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SA  220 (412)
                      ..+ ..  ..   ...-+.++-.++...  .+.........++++|+||++.+ +   ...+..++..++.+.+++++.-
T Consensus       230 ~~~-~~--~~---~~Tih~ll~~~~~~~--~~~~~~~~~l~~d~lIIDEAsml-~---~~~~~~Ll~~l~~~~~liLvGD  297 (608)
T 1w36_D          230 KKR-IP--ED---ASTLHRLLGAQPGSQ--RLRHHAGNPLHLDVLVVDEASMI-D---LPMMSRLIDALPDHARVIFLGD  297 (608)
T ss_dssp             CCS-CS--CC---CBTTTSCC-------------CTTSCCSCSEEEECSGGGC-B---HHHHHHHHHTCCTTCEEEEEEC
T ss_pred             Hhc-cc--hh---hhhhHhhhccCCCch--HHHhccCCCCCCCEEEEechhhC-C---HHHHHHHHHhCCCCCEEEEEcc
Confidence            000 00  00   000011111222211  01111122236899999999954 3   3567788888888888888776


Q ss_pred             c
Q 015158          221 T  221 (412)
Q Consensus       221 T  221 (412)
                      .
T Consensus       298 ~  298 (608)
T 1w36_D          298 R  298 (608)
T ss_dssp             T
T ss_pred             h
Confidence            5

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=98.63  E-value=3.6e-08  Score=96.85  Aligned_cols=67  Identities=22%  Similarity=0.218  Sum_probs=55.1

Q ss_pred             CChHHHHhhhhhhhcCc-cEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 015158           61 KPSAIQQRGIVPFCKGL-DVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRAL  130 (412)
Q Consensus        61 ~l~~~Q~~a~~~~~~~~-~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~  130 (412)
                      .|++.|++|+..++..+ -.+|+||+|||||.+..-.+...+..+   .++|+++||..-++++.+.+...
T Consensus       189 ~LN~~Q~~AV~~al~~~~~~lI~GPPGTGKT~ti~~~I~~l~~~~---~~ILv~a~TN~AvD~i~erL~~~  256 (646)
T 4b3f_X          189 CLDTSQKEAVLFALSQKELAIIHGPPGTGKTTTVVEIILQAVKQG---LKVLCCAPSNIAVDNLVERLALC  256 (646)
T ss_dssp             TCCHHHHHHHHHHHHCSSEEEEECCTTSCHHHHHHHHHHHHHHTT---CCEEEEESSHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHhcCCCceEEECCCCCCHHHHHHHHHHHHHhCC---CeEEEEcCchHHHHHHHHHHHhc
Confidence            48999999999987654 578999999999988776666655543   58999999999999998887654

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=98.56  E-value=5.7e-07  Score=89.79  Aligned_cols=70  Identities=21%  Similarity=0.248  Sum_probs=55.7

Q ss_pred             CCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 015158           59 FEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRAL  130 (412)
Q Consensus        59 ~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~  130 (412)
                      +..+++.|++|+..++.+...+|.||+|||||.+....+......  .+.++++++||...++++.+.+.+.
T Consensus       358 ~~~Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~~i~~~i~~l~~~--~~~~ILv~a~tn~A~d~l~~rL~~~  427 (802)
T 2xzl_A          358 FAQLNSSQSNAVSHVLQRPLSLIQGPPGTGKTVTSATIVYHLSKI--HKDRILVCAPSNVAVDHLAAKLRDL  427 (802)
T ss_dssp             SCCCCHHHHHHHHHHTTCSEEEEECSTTSSHHHHHHHHHHHHHHH--HCCCEEEEESSHHHHHHHHHHHHHT
T ss_pred             cccCCHHHHHHHHHHhcCCCEEEECCCCCCHHHHHHHHHHHHHhC--CCCeEEEEcCcHHHHHHHHHHHHhh
Confidence            345889999999999888788999999999998765444333321  2358999999999999999888765

>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=98.54  E-value=3.4e-07  Score=89.43  Aligned_cols=70  Identities=19%  Similarity=0.147  Sum_probs=55.2

Q ss_pred             CCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 015158           59 FEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRAL  130 (412)
Q Consensus        59 ~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~  130 (412)
                      ...+++.|.+|+..++.+...+|.||+|+|||.+....+......  .+.++++++|+...++++.+.+.+.
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            345899999999998888888999999999998765444333321  3458999999999999988877654

>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=98.51  E-value=7.4e-07  Score=85.70  Aligned_cols=126  Identities=20%  Similarity=0.236  Sum_probs=79.7

Q ss_pred             ChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEE
Q 015158           62 PSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHAC  141 (412)
Q Consensus        62 l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~  141 (412)
                      +++.|++++..+..++.+++.|++|+|||.+... ++..+..  .+.++++++||...+..+.+..       +.....+
T Consensus       190 L~~~Q~~Av~~~~~~~~~~I~G~pGTGKTt~i~~-l~~~l~~--~g~~Vl~~ApT~~Aa~~L~e~~-------~~~a~Ti  259 (574)
T 3e1s_A          190 LSEEQASVLDQLAGHRLVVLTGGPGTGKSTTTKA-VADLAES--LGLEVGLCAPTGKAARRLGEVT-------GRTASTV  259 (574)
T ss_dssp             CCHHHHHHHHHHTTCSEEEEECCTTSCHHHHHHH-HHHHHHH--TTCCEEEEESSHHHHHHHHHHH-------TSCEEEH
T ss_pred             CCHHHHHHHHHHHhCCEEEEEcCCCCCHHHHHHH-HHHHHHh--cCCeEEEecCcHHHHHHhHhhh-------cccHHHH
Confidence            8999999999999999999999999999976533 3333322  2358999999998877665532       1111111


Q ss_pred             EcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEeec
Q 015158          142 VGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSAT  221 (412)
Q Consensus       142 ~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT  221 (412)
                      +      ..   +.    ... +      .+.........+++||+||++.+.    ...+..++..++...+++++.-.
T Consensus       260 h------~l---l~----~~~-~------~~~~~~~~~~~~dvlIIDEasml~----~~~~~~Ll~~~~~~~~lilvGD~  315 (574)
T 3e1s_A          260 H------RL---LG----YGP-Q------GFRHNHLEPAPYDLLIVDEVSMMG----DALMLSLLAAVPPGARVLLVGDT  315 (574)
T ss_dssp             H------HH---TT----EET-T------EESCSSSSCCSCSEEEECCGGGCC----HHHHHHHHTTSCTTCEEEEEECT
T ss_pred             H------HH---Hc----CCc-c------hhhhhhcccccCCEEEEcCccCCC----HHHHHHHHHhCcCCCEEEEEecc
Confidence            0      00   00    000 0      011111223467899999999753    34566777778777777776554

>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=98.50  E-value=6.5e-07  Score=84.23  Aligned_cols=137  Identities=16%  Similarity=0.138  Sum_probs=79.8

Q ss_pred             HCCCCCChHHHHhhhhhhhcC-----ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 015158           56 AYGFEKPSAIQQRGIVPFCKG-----LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRAL  130 (412)
Q Consensus        56 ~~~~~~l~~~Q~~a~~~~~~~-----~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~  130 (412)
                      ...|..|++-|++|+..+...     ..++|.|+.|||||.+.. .++..+.... ...+++++||...+..+.+.+   
T Consensus        20 p~~~~~Ln~~Q~~av~~~~~~i~~~~~~~li~G~aGTGKT~ll~-~~~~~l~~~~-~~~il~~a~T~~Aa~~l~~~~---   94 (459)
T 3upu_A           20 HMTFDDLTEGQKNAFNIVMKAIKEKKHHVTINGPAGTGATTLTK-FIIEALISTG-ETGIILAAPTHAAKKILSKLS---   94 (459)
T ss_dssp             -CCSSCCCHHHHHHHHHHHHHHHSSSCEEEEECCTTSCHHHHHH-HHHHHHHHTT-CCCEEEEESSHHHHHHHHHHH---
T ss_pred             CCccccCCHHHHHHHHHHHHHHhcCCCEEEEEeCCCCCHHHHHH-HHHHHHHhcC-CceEEEecCcHHHHHHHHhhh---
Confidence            457788999999999987542     389999999999997654 3333433321 146999999988776665443   


Q ss_pred             hcccCcEEEEEEcCcchHHHHHHh---cCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHH
Q 015158          131 GDYLGVKVHACVGGTSVREDQRIL---SSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQ  207 (412)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~  207 (412)
                          +.....++      ......   ......+..          ........++++|+||+|.+.    ...+..+..
T Consensus        95 ----~~~~~T~h------~~~~~~~~~~~~~~~~~~----------~~~~~~~~~~~iiiDE~~~~~----~~~~~~l~~  150 (459)
T 3upu_A           95 ----GKEASTIH------SILKINPVTYEENVLFEQ----------KEVPDLAKCRVLICDEVSMYD----RKLFKILLS  150 (459)
T ss_dssp             ----SSCEEEHH------HHHTEEEEECSSCEEEEE----------CSCCCCSSCSEEEESCGGGCC----HHHHHHHHH
T ss_pred             ----ccchhhHH------HHhccCcccccccchhcc----------cccccccCCCEEEEECchhCC----HHHHHHHHH
Confidence                11111111      000000   000011111          112234568999999999753    345556666


Q ss_pred             hCCCCceEEEEeec
Q 015158          208 LLPPKIQVGVFSAT  221 (412)
Q Consensus       208 ~~~~~~~~i~~SAT  221 (412)
                      .++...+++++.-.
T Consensus       151 ~~~~~~~~~~vGD~  164 (459)
T 3upu_A          151 TIPPWCTIIGIGDN  164 (459)
T ss_dssp             HSCTTCEEEEEECT
T ss_pred             hccCCCEEEEECCH
Confidence            66666666666544

>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=98.48  E-value=9e-07  Score=88.27  Aligned_cols=69  Identities=20%  Similarity=0.167  Sum_probs=54.3

Q ss_pred             CCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHh
Q 015158           60 EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRAL  130 (412)
Q Consensus        60 ~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~  130 (412)
                      ..+++.|++|+..++.+...+|.||+|+|||.+....+. .+... .+.++++++||..-++++.+.+...
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            458999999999998888889999999999987654443 33221 3458999999999999888877654

>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=98.34  E-value=6.5e-05  Score=74.01  Aligned_cols=70  Identities=14%  Similarity=0.189  Sum_probs=56.7

Q ss_pred             CCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhcc-CCCceeEEEEcCCHHHHHHHHHHHHHhh
Q 015158           60 EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY-GLVECQALVLAPTRELAQQIEKVMRALG  131 (412)
Q Consensus        60 ~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~-~~~~~~~lil~P~~~L~~q~~~~~~~~~  131 (412)
                      ..+++-|++|+..  .+..++|.|+.|||||.+...-+...+.. +....+++++++|+..+.++.+.+.+..
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            3589999999984  35678999999999999887766666554 2344589999999999999999988764

>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=98.05  E-value=7.5e-05  Score=65.16  Aligned_cols=123  Identities=14%  Similarity=0.100  Sum_probs=89.9

Q ss_pred             chhhHHHHHHHHHhc--CCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCc
Q 015158          262 EEWKLETLCDLYETL--AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLA  339 (412)
Q Consensus       262 ~~~~~~~l~~~~~~~--~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~  339 (412)
                      .+.|...+..++...  .+.+++||++..+..+-+.+++..+++.+..+.|.....++.     -.++...+.+.|...+
T Consensus       107 ~SGKf~~L~~LL~~l~~~~~kVLIfsq~t~~LDilE~~l~~~~~~y~RlDG~~~~~~~k-----~~~~~~~i~Lltsag~  181 (328)
T 3hgt_A          107 NSGKFSVLRDLINLVQEYETETAIVCRPGRTMDLLEALLLGNKVHIKRYDGHSIKSAAA-----ANDFSCTVHLFSSEGI  181 (328)
T ss_dssp             TCHHHHHHHHHHHHHTTSCEEEEEEECSTHHHHHHHHHHTTSSCEEEESSSCCC------------CCSEEEEEEESSCC
T ss_pred             cCccHHHHHHHHHHHHhCCCEEEEEECChhHHHHHHHHHhcCCCceEeCCCCchhhhhh-----cccCCceEEEEECCCC
Confidence            355777777777665  347999999999999999999999999999999985543211     1244555666677777


Q ss_pred             CCCC-----CCCCCEEEEccCCCChhhH-HHhhhhcccCC----CCceEEEEeccCcHHH
Q 015158          340 RGID-----VQQVSLVINYDLPTQPENY-LHRIGRSGRFG----RKGVAINFVTRDDERM  389 (412)
Q Consensus       340 ~G~d-----~~~~~~vi~~~~~~s~~~~-~Q~~GR~~R~g----~~g~~~~~~~~~~~~~  389 (412)
                      -|+|     +..++.||.++..|++..= +|++-|+.|.|    ++-.++.+++....++
T Consensus       182 ~gin~~~~nl~~aD~VI~~DsdwNp~~d~iQa~~r~~R~~~gq~k~v~V~RLvt~~TiEh  241 (328)
T 3hgt_A          182 NFTKYPIKSKARFDMLICLDTTVDTSQKDIQYLLQYKRERKGLERYAPIVRLVAINSIDH  241 (328)
T ss_dssp             CTTTSCCCCCSCCSEEEECSTTCCTTSHHHHHHHCCC---------CCEEEEEETTSHHH
T ss_pred             CCcCcccccCCCCCEEEEECCCCCCCChHHHHHHHHhhhccCCCCcceEEEEeCCCCHHH
Confidence            7776     6789999999999999885 99999999973    3456888887776654

>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=97.70  E-value=0.00037  Score=63.09  Aligned_cols=71  Identities=8%  Similarity=0.013  Sum_probs=54.9

Q ss_pred             CChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhc
Q 015158           61 KPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGD  132 (412)
Q Consensus        61 ~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~  132 (412)
                      .|+|+|+..+..+...+..++..+-+.|||......++..+.. .++..++++.|+...+..+++.+..+..
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 QLRDYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCF-NKDKAVGILAHKGSMSAEVLDRTKQAIE  233 (385)
T ss_dssp             CCCHHHHHHHHHHHHSSEEEEEECSSSCHHHHHHHHHHHHHHS-SSSCEEEEEESSHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHhhccCcEEEEEEcCcCChhHHHHHHHHHHHHh-CCCCeEEEEeCCHHHHHHHHHHHHHHHH
Confidence            4899999999877655678999999999998766555543332 2456899999999988888877776553

>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=97.51  E-value=0.00067  Score=65.76  Aligned_cols=146  Identities=10%  Similarity=0.091  Sum_probs=86.1

Q ss_pred             CChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccC--cEE
Q 015158           61 KPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLG--VKV  138 (412)
Q Consensus        61 ~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~--~~~  138 (412)
                      .|+|+|+..+..+...+..++..+-|+|||.+....++..+... ++..++++.|+...+....+.++.+....+  +..
T Consensus       163 ~l~p~Q~~i~~~l~~~r~~~i~~~Rq~GKS~~~a~~~l~~~~~~-~~~~i~~va~t~~qA~~~~~~i~~~i~~~p~~~~~  241 (592)
T 3cpe_A          163 QLRDYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCFN-KDKAVGILAHKGSMSAEVLDRTKQAIELLPDFLQP  241 (592)
T ss_dssp             CCCHHHHHHHHHHHHCSEEEEEECSSSCHHHHHHHHHHHHHHTS-SSCEEEEEESSHHHHHHHHHHHHHHHTTSCTTTSC
T ss_pred             cCCHHHHHHHHhhccccEEEEEEcCccChHHHHHHHHHHHHHhC-CCCeEEEEECCHHHHHHHHHHHHHHHHhChHhhcc
Confidence            38999999998875567789999999999987655444444332 455899999999999988888877654432  111


Q ss_pred             EEE-EcCcchHHHHHHhcCCCcEEEeC--hHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCC--CCc
Q 015158          139 HAC-VGGTSVREDQRILSSGVHVVVGT--PGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLP--PKI  213 (412)
Q Consensus       139 ~~~-~~~~~~~~~~~~~~~~~~iii~T--~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~--~~~  213 (412)
                      ... .......     +.++..|.+.+  +..+.-         .+.+++|+||+|...+.  ...+..+...+.  .+.
T Consensus       242 ~~~~~~~~~i~-----~~nGs~i~~~s~~~~~lrG---------~~~~~~iiDE~~~~~~~--~~l~~~~~~~l~~~~~~  305 (592)
T 3cpe_A          242 GIVEWNKGSIE-----LDNGSSIGAYASSPDAVRG---------NSFAMIYIEDCAFIPNF--HDSWLAIQPVISSGRRS  305 (592)
T ss_dssp             CEEEECSSEEE-----ETTSCEEEEEECCHHHHHH---------SCCSEEEEETGGGCTTH--HHHHHHHHHHHSSSSCC
T ss_pred             ccccCCccEEE-----ecCCCEEEEEeCCCCCccC---------CCcceEEEehhccCCch--hHHHHHHHHHhccCCCc
Confidence            000 0111100     12233444333  232211         24679999999986442  233333333332  233


Q ss_pred             eEEEEeecCCh
Q 015158          214 QVGVFSATMPP  224 (412)
Q Consensus       214 ~~i~~SAT~~~  224 (412)
                       .+.+..|+..
T Consensus       306 -~ii~isTP~~  315 (592)
T 3cpe_A          306 -KIIITTTPNG  315 (592)
T ss_dssp             -EEEEEECCCT
T ss_pred             -eEEEEeCCCC
Confidence             4555556654

>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=97.41  E-value=0.00042  Score=56.80  Aligned_cols=40  Identities=15%  Similarity=0.126  Sum_probs=30.0

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHH
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRE  118 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  118 (412)
                      |+-.++.+++|+|||..++-.+.+....+   .+++++.|...
T Consensus        28 G~l~vitG~MgsGKTT~lL~~a~r~~~~g---~kVli~k~~~d   67 (214)
T 2j9r_A           28 GWIEVICGSMFSGKSEELIRRVRRTQFAK---QHAIVFKPCID   67 (214)
T ss_dssp             CEEEEEECSTTSCHHHHHHHHHHHHHHTT---CCEEEEECC--
T ss_pred             CEEEEEECCCCCcHHHHHHHHHHHHHHCC---CEEEEEEeccC
Confidence            44557899999999998877777666554   48999999764

>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=97.38  E-value=0.00039  Score=56.48  Aligned_cols=40  Identities=15%  Similarity=0.081  Sum_probs=29.6

Q ss_pred             cCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCH
Q 015158           75 KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTR  117 (412)
Q Consensus        75 ~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~  117 (412)
                      .|+-.++.+++|+|||..++-.+.+....+   .+++++.|..
T Consensus         7 ~g~i~v~~G~mgsGKTT~ll~~a~r~~~~g---~kV~v~k~~~   46 (191)
T 1xx6_A            7 HGWVEVIVGPMYSGKSEELIRRIRRAKIAK---QKIQVFKPEI   46 (191)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHHHTT---CCEEEEEEC-
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHHHHHCC---CEEEEEEecc
Confidence            355678899999999988776666555444   4899999874

>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=97.35  E-value=0.00026  Score=69.98  Aligned_cols=70  Identities=16%  Similarity=0.125  Sum_probs=56.3

Q ss_pred             CChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhcc-CCCceeEEEEcCCHHHHHHHHHHHHHhhc
Q 015158           61 KPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY-GLVECQALVLAPTRELAQQIEKVMRALGD  132 (412)
Q Consensus        61 ~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~-~~~~~~~lil~P~~~L~~q~~~~~~~~~~  132 (412)
                      .|++-|++++...  +..++|.|+.|||||.+..--+...+.. +....++++++.|+..+.++.+.+.....
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            3889999999864  5688999999999998877666655543 33446899999999999999999887643

>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=97.35  E-value=0.00044  Score=57.59  Aligned_cols=91  Identities=18%  Similarity=0.207  Sum_probs=53.5

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhc
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILS  155 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  155 (412)
                      |.-.++.+++|+|||+.++..+......+   .+++++.|...- +  .  ...+....++..                 
T Consensus        12 G~i~litG~mGsGKTT~ll~~~~r~~~~g---~kVli~~~~~d~-r--~--~~~i~srlG~~~-----------------   66 (223)
T 2b8t_A           12 GWIEFITGPMFAGKTAELIRRLHRLEYAD---VKYLVFKPKIDT-R--S--IRNIQSRTGTSL-----------------   66 (223)
T ss_dssp             CEEEEEECSTTSCHHHHHHHHHHHHHHTT---CCEEEEEECCCG-G--G--CSSCCCCCCCSS-----------------
T ss_pred             cEEEEEECCCCCcHHHHHHHHHHHHHhcC---CEEEEEEeccCc-h--H--HHHHHHhcCCCc-----------------
Confidence            55678899999999988877666655444   378888876531 0  0  001111111110                 


Q ss_pred             CCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhh
Q 015158          156 SGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEML  194 (412)
Q Consensus       156 ~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~  194 (412)
                        ..+-+.+.+.+...+.... ....+++||+||++.+.
T Consensus        67 --~~~~~~~~~~i~~~i~~~~-~~~~~dvViIDEaQ~l~  102 (223)
T 2b8t_A           67 --PSVEVESAPEILNYIMSNS-FNDETKVIGIDEVQFFD  102 (223)
T ss_dssp             --CCEEESSTHHHHHHHHSTT-SCTTCCEEEECSGGGSC
T ss_pred             --cccccCCHHHHHHHHHHHh-hCCCCCEEEEecCccCc
Confidence              1233455666666655432 23457999999999643

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=97.28  E-value=0.00081  Score=54.37  Aligned_cols=39  Identities=18%  Similarity=0.018  Sum_probs=28.2

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCH
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTR  117 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~  117 (412)
                      |+-.++.+|+|+|||..++..+......+   .+++++.|..
T Consensus         3 g~i~vi~G~~gsGKTT~ll~~~~~~~~~g---~~v~~~~~~~   41 (184)
T 2orw_A            3 GKLTVITGPMYSGKTTELLSFVEIYKLGK---KKVAVFKPKI   41 (184)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHHHHHTT---CEEEEEEEC-
T ss_pred             cEEEEEECCCCCCHHHHHHHHHHHHHHCC---CeEEEEeecc
Confidence            55678899999999988766555544433   4788888874

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=97.23  E-value=0.00098  Score=61.09  Aligned_cols=108  Identities=19%  Similarity=0.180  Sum_probs=65.0

Q ss_pred             ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcC
Q 015158           77 LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSS  156 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  156 (412)
                      +-.++.|+.|+|||....-.    +..    .+.++++|++++++++.+.+.+.    +.        .          .
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            45688999999999765321    111    25799999999998888776432    10        0          0


Q ss_pred             CCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEeec
Q 015158          157 GVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSAT  221 (412)
Q Consensus       157 ~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT  221 (412)
                      ....-+.|.++++..  ......-..+++|+||+-.+ +.   ..+..++...+. .+++++.-+
T Consensus       212 ~~~~~V~T~dsfL~~--~~~~~~~~~d~liiDE~sm~-~~---~~l~~l~~~~~~-~~vilvGD~  269 (446)
T 3vkw_A          212 ATKDNVRTVDSFLMN--YGKGARCQFKRLFIDEGLML-HT---GCVNFLVEMSLC-DIAYVYGDT  269 (446)
T ss_dssp             CCTTTEEEHHHHHHT--TTSSCCCCCSEEEEETGGGS-CH---HHHHHHHHHTTC-SEEEEEECT
T ss_pred             cccceEEEeHHhhcC--CCCCCCCcCCEEEEeCcccC-CH---HHHHHHHHhCCC-CEEEEecCc
Confidence            112447787776532  11111224789999999853 33   233344444443 556666555

>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=97.22  E-value=0.00085  Score=55.55  Aligned_cols=40  Identities=13%  Similarity=0.099  Sum_probs=31.2

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHH
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRE  118 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  118 (412)
                      |+-.++.+++|+|||..++..+.+....+   .+++++-|.+.
T Consensus        19 g~l~v~~G~MgsGKTT~lL~~~~r~~~~g---~kvli~kp~~D   58 (234)
T 2orv_A           19 GQIQVILGPMFSGKSTELMRRVRRFQIAQ---YKCLVIKYAKD   58 (234)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHHHHTTT---CCEEEEEETTC
T ss_pred             eEEEEEECCCCCcHHHHHHHHHHHHHHCC---CeEEEEeecCC
Confidence            55668899999999998887777665554   48999988764

>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=97.14  E-value=0.00079  Score=66.94  Aligned_cols=70  Identities=17%  Similarity=0.173  Sum_probs=56.4

Q ss_pred             CCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhcc-CCCceeEEEEcCCHHHHHHHHHHHHHhh
Q 015158           60 EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY-GLVECQALVLAPTRELAQQIEKVMRALG  131 (412)
Q Consensus        60 ~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~-~~~~~~~lil~P~~~L~~q~~~~~~~~~  131 (412)
                      ..|++.|++|+...  +..++|.|+.|||||.+...-+...+.. +....++|+++.|+..+.++.+.+....
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            35899999999873  5678999999999999887766666553 3344689999999999999998887753

>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=97.14  E-value=0.0016  Score=52.35  Aligned_cols=32  Identities=22%  Similarity=0.312  Sum_probs=22.6

Q ss_pred             hHHHHhhhhhhh---------cCccEEEECCCCCCchhHhH
Q 015158           63 SAIQQRGIVPFC---------KGLDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        63 ~~~Q~~a~~~~~---------~~~~~lv~~~tGsGKT~~~~   94 (412)
                      .+.|++++..+.         .++.+++.||+|+|||..+-
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            345555555443         36789999999999997653

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=97.10  E-value=0.00034  Score=54.43  Aligned_cols=19  Identities=21%  Similarity=0.354  Sum_probs=16.7

Q ss_pred             cCccEEEECCCCCCchhHh
Q 015158           75 KGLDVIQQAQSGTGKTATF   93 (412)
Q Consensus        75 ~~~~~lv~~~tGsGKT~~~   93 (412)
                      .++.+++.+|+|+|||..+
T Consensus        35 ~g~~~~l~G~~G~GKTtL~   53 (149)
T 2kjq_A           35 HGQFIYVWGEEGAGKSHLL   53 (149)
T ss_dssp             CCSEEEEESSSTTTTCHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            6788999999999999765

>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=97.09  E-value=0.0013  Score=58.77  Aligned_cols=36  Identities=17%  Similarity=0.108  Sum_probs=26.4

Q ss_pred             ChHHHHhhhhhhhc----C---ccEEEECCCCCCchhHhHHHH
Q 015158           62 PSAIQQRGIVPFCK----G---LDVIQQAQSGTGKTATFCSGI   97 (412)
Q Consensus        62 l~~~Q~~a~~~~~~----~---~~~lv~~~tGsGKT~~~~~~~   97 (412)
                      ++|||.+++..+..    |   ...++.||.|+|||..+...+
T Consensus         3 ~~pw~~~~~~~l~~~i~~~~~~~a~L~~G~~G~GKt~~a~~la   45 (334)
T 1a5t_A            3 WYPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALS   45 (334)
T ss_dssp             CCGGGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHHHHH
T ss_pred             CCCchHHHHHHHHHHHHcCCcceeEEEECCCCchHHHHHHHHH
Confidence            57888888776553    3   247999999999998765433

>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=97.06  E-value=0.0062  Score=50.52  Aligned_cols=41  Identities=15%  Similarity=0.221  Sum_probs=26.7

Q ss_pred             CCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEeec
Q 015158          180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSAT  221 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT  221 (412)
                      ....+||+||+|.+... ....+..++...+.+..+++.|..
T Consensus       101 ~~~~vliiDe~~~l~~~-~~~~l~~~l~~~~~~~~~i~~~~~  141 (226)
T 2chg_A          101 APFKIIFLDEADALTAD-AQAALRRTMEMYSKSCRFILSCNY  141 (226)
T ss_dssp             CSCEEEEEETGGGSCHH-HHHHHHHHHHHTTTTEEEEEEESC
T ss_pred             cCceEEEEeChhhcCHH-HHHHHHHHHHhcCCCCeEEEEeCC
Confidence            45679999999986543 245566666666666655555543

>3e2i_A Thymidine kinase; Zn-binding, ATP-binding, DNA synthesis, nucleotide-B transferase; HET: MSE; 2.01A {Staphylococcus aureus}

Probab=97.05  E-value=0.00056  Score=55.94  Aligned_cols=40  Identities=13%  Similarity=0.135  Sum_probs=28.5

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHH
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRE  118 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  118 (412)
                      |.-.++.+++|+|||..++..+......+   .+++++.|...
T Consensus        28 G~I~vitG~M~sGKTT~Llr~~~r~~~~g---~kvli~kp~~D   67 (219)
T 3e2i_A           28 GWIECITGSMFSGKSEELIRRLRRGIYAK---QKVVVFKPAID   67 (219)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHHHHHHHTT---CCEEEEEEC--
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHHHHcC---CceEEEEeccC
Confidence            55568899999999987766665554443   47899999764

>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=97.04  E-value=0.00096  Score=70.33  Aligned_cols=68  Identities=22%  Similarity=0.253  Sum_probs=57.5

Q ss_pred             CChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCC---CceeEEEEcCCHHHHHHHHHHHHHh
Q 015158           61 KPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGL---VECQALVLAPTRELAQQIEKVMRAL  130 (412)
Q Consensus        61 ~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~---~~~~~lil~P~~~L~~q~~~~~~~~  130 (412)
                      .+++-|.+++..-  +++++|.|+.|||||.+.+--++..+..+.   ...+++++++|++.+.++.+.+...
T Consensus        10 ~~t~eQ~~~i~~~--~~~~~v~a~AGSGKT~vl~~ri~~ll~~~~~~~~~~~il~~Tft~~aa~e~~~ri~~~   80 (1232)
T 3u4q_A           10 TWTDDQWNAIVST--GQDILVAAAAGSGKTAVLVERMIRKITAEENPIDVDRLLVVTFTNASAAEMKHRIAEA   80 (1232)
T ss_dssp             CCCHHHHHHHHCC--SSCEEEEECTTCCHHHHHHHHHHHHHSCSSSCCCGGGEEEECSSHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHhCC--CCCEEEEecCCCcHHHHHHHHHHHHHhcCCCCCCccceEEEeccHHHHHHHHHHHHHH
Confidence            3899999999875  779999999999999998877777766543   4568999999999999999888764

>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=97.00  E-value=0.0029  Score=56.27  Aligned_cols=36  Identities=14%  Similarity=0.061  Sum_probs=22.7

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEc
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLA  114 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~  114 (412)
                      +..+++.||+|+|||..+- .+...+...  +..++++.
T Consensus        37 ~~~lll~G~~GtGKT~la~-~i~~~~~~~--~~~~~~i~   72 (324)
T 1l8q_A           37 YNPIFIYGSVGTGKTHLLQ-AAGNEAKKR--GYRVIYSS   72 (324)
T ss_dssp             CSSEEEECSSSSSHHHHHH-HHHHHHHHT--TCCEEEEE
T ss_pred             CCeEEEECCCCCcHHHHHH-HHHHHHHHC--CCEEEEEE
Confidence            4689999999999997653 333333221  23455554

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=96.89  E-value=0.0026  Score=51.21  Aligned_cols=38  Identities=13%  Similarity=0.057  Sum_probs=29.8

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCC
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPT  116 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~  116 (412)
                      ++-.++.+|+|+|||.-.+..+.+....+   .+++++.|.
T Consensus        20 g~l~fiyG~MgsGKTt~Ll~~i~n~~~~~---~kvl~~kp~   57 (195)
T 1w4r_A           20 GQIQVILGPMFSGKSTELMRRVRRFQIAQ---YKCLVIKYA   57 (195)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHHHHHHHTT---CCEEEEEET
T ss_pred             eEEEEEECCCCCcHHHHHHHHHHHHHHcC---CeEEEEccc
Confidence            55678899999999977777776665544   489999886

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=96.79  E-value=0.0095  Score=52.38  Aligned_cols=40  Identities=8%  Similarity=0.135  Sum_probs=25.4

Q ss_pred             CceEEEEeCCchhhccCcHHHHHHHHHh---CCCCceEEEEeecCC
Q 015158          181 NIRIFVLDEADEMLSRGFKDQIYDIFQL---LPPKIQVGVFSATMP  223 (412)
Q Consensus       181 ~~~~iiiDE~h~~~~~~~~~~~~~i~~~---~~~~~~~i~~SAT~~  223 (412)
                      ..-+|++||+|.+..   ...+..++..   -....-+|+.++|+.
T Consensus       132 ~~~ii~lDE~d~l~~---q~~L~~l~~~~~~~~s~~~vI~i~n~~d  174 (318)
T 3te6_A          132 RKTLILIQNPENLLS---EKILQYFEKWISSKNSKLSIICVGGHNV  174 (318)
T ss_dssp             CEEEEEEECCSSSCC---THHHHHHHHHHHCSSCCEEEEEECCSSC
T ss_pred             CceEEEEecHHHhhc---chHHHHHHhcccccCCcEEEEEEecCcc
Confidence            456899999999872   2444444431   223456778888874

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=96.71  E-value=0.007  Score=46.51  Aligned_cols=20  Identities=10%  Similarity=0.061  Sum_probs=17.0

Q ss_pred             hcCccEEEECCCCCCchhHh
Q 015158           74 CKGLDVIQQAQSGTGKTATF   93 (412)
Q Consensus        74 ~~~~~~lv~~~tGsGKT~~~   93 (412)
                      ..+.++++.+|+|+|||..+
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            34678999999999999765

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=96.69  E-value=0.01  Score=53.94  Aligned_cols=19  Identities=32%  Similarity=0.314  Sum_probs=16.2

Q ss_pred             CccEEEECCCCCCchhHhH
Q 015158           76 GLDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~   94 (412)
                      +..+++.||+|+|||..+-
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            4689999999999997653

>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=96.50  E-value=0.0083  Score=55.73  Aligned_cols=38  Identities=13%  Similarity=0.046  Sum_probs=23.3

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEc
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLA  114 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~  114 (412)
                      .+.+++.||+|+|||..+- ++...+....++..++++.
T Consensus       130 ~~~lll~Gp~G~GKTtLa~-aia~~l~~~~~~~~v~~v~  167 (440)
T 2z4s_A          130 YNPLFIYGGVGLGKTHLLQ-SIGNYVVQNEPDLRVMYIT  167 (440)
T ss_dssp             SCCEEEECSSSSSHHHHHH-HHHHHHHHHCCSSCEEEEE
T ss_pred             CCeEEEECCCCCCHHHHHH-HHHHHHHHhCCCCeEEEee
Confidence            3579999999999997653 3333332222233455554

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=96.48  E-value=0.018  Score=44.25  Aligned_cols=39  Identities=8%  Similarity=0.052  Sum_probs=24.9

Q ss_pred             eEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEeecC
Q 015158          183 RIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATM  222 (412)
Q Consensus       183 ~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~  222 (412)
                      +.+++||+|.+... ....+..++...+.+.++|+.|...
T Consensus        78 g~l~ldei~~l~~~-~q~~Ll~~l~~~~~~~~~I~~t~~~  116 (145)
T 3n70_A           78 GTLVLSHPEHLTRE-QQYHLVQLQSQEHRPFRLIGIGDTS  116 (145)
T ss_dssp             SCEEEECGGGSCHH-HHHHHHHHHHSSSCSSCEEEEESSC
T ss_pred             cEEEEcChHHCCHH-HHHHHHHHHhhcCCCEEEEEECCcC
Confidence            57999999986543 3445555555555566666655544

>2zpa_A Uncharacterized protein YPFI; RNA modification enzyme, RNA helicase, acetyltransferase, GCN5 acetyltransferase; HET: ACO ADP; 2.35A {Escherichia coli K12}

Probab=96.46  E-value=0.0057  Score=59.06  Aligned_cols=113  Identities=19%  Similarity=0.257  Sum_probs=71.1

Q ss_pred             CChHHHHhhhhhhhc--CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEE
Q 015158           61 KPSAIQQRGIVPFCK--GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKV  138 (412)
Q Consensus        61 ~l~~~Q~~a~~~~~~--~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~  138 (412)
                      .++..|.+++..+..  ....++.|+-|.|||.+.=+++. .+. .    .++|.+|+..-+....+    +...     
T Consensus       175 ~~T~dQ~~al~~~~~~~~~~~vlta~RGRGKSa~lG~~~a-~~~-~----~~~vtAP~~~a~~~l~~----~~~~-----  239 (671)
T 2zpa_A          175 APQPEQQQLLKQLMTMPPGVAAVTAARGRGKSALAGQLIS-RIA-G----RAIVTAPAKASTDVLAQ----FAGE-----  239 (671)
T ss_dssp             SCCHHHHHHHHHHTTCCSEEEEEEECTTSSHHHHHHHHHH-HSS-S----CEEEECSSCCSCHHHHH----HHGG-----
T ss_pred             CCCHHHHHHHHHHHHhhhCeEEEecCCCCCHHHHHHHHHH-HHH-h----CcEEECCCHHHHHHHHH----HhhC-----
Confidence            578999999998876  34578999999999955433333 332 1    46999999875553332    2110     


Q ss_pred             EEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEE
Q 015158          139 HACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVF  218 (412)
Q Consensus       139 ~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~  218 (412)
                                          .+-+..|+.+..       .....+++|||||=.+.    ...+..++...+    .+++
T Consensus       240 --------------------~i~~~~Pd~~~~-------~~~~~dlliVDEAAaIp----~pll~~ll~~~~----~v~~  284 (671)
T 2zpa_A          240 --------------------KFRFIAPDALLA-------SDEQADWLVVDEAAAIP----APLLHQLVSRFP----RTLL  284 (671)
T ss_dssp             --------------------GCCBCCHHHHHH-------SCCCCSEEEEETGGGSC----HHHHHHHHTTSS----EEEE
T ss_pred             --------------------CeEEeCchhhhh-------CcccCCEEEEEchhcCC----HHHHHHHHhhCC----eEEE
Confidence                                133445555431       11357999999998652    345555555332    5777


Q ss_pred             eecCC
Q 015158          219 SATMP  223 (412)
Q Consensus       219 SAT~~  223 (412)
                      |.|..
T Consensus       285 ~tTv~  289 (671)
T 2zpa_A          285 TTTVQ  289 (671)
T ss_dssp             EEEBS
T ss_pred             EecCC
Confidence            77764

>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=96.34  E-value=0.017  Score=46.60  Aligned_cols=138  Identities=14%  Similarity=0.127  Sum_probs=71.8

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHH-HHHHHHHHHHHhhcccCcEEEEEEcCcchHH-HHHH
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRE-LAQQIEKVMRALGDYLGVKVHACVGGTSVRE-DQRI  153 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~-L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~  153 (412)
                      ...+++..++|.|||.+++..++..+..+.   +++++.=.+. ....-.+.+..+    ++.......+..... ....
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            357899999999999999888888887764   7888843221 000001111222    222221111100000 0000


Q ss_pred             hcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccC--cHHHHHHHHHhCCCCceEEEEeecCChHHHH
Q 015158          154 LSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRG--FKDQIYDIFQLLPPKIQVGVFSATMPPEALE  228 (412)
Q Consensus       154 ~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~--~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~  228 (412)
                           +.. .--..|.....  .+....+++||+||+-.....+  -...+..++...+....+|+.+--+++.+.+
T Consensus       101 -----~~~-~a~~~l~~a~~--~l~~~~yDlvILDEi~~al~~g~l~~~ev~~~l~~Rp~~~~vIlTGr~ap~~l~e  169 (196)
T 1g5t_A          101 -----DTA-ACMAVWQHGKR--MLADPLLDMVVLDELTYMVAYDYLPLEEVISALNARPGHQTVIITGRGCHRDILD  169 (196)
T ss_dssp             -----HHH-HHHHHHHHHHH--HTTCTTCSEEEEETHHHHHHTTSSCHHHHHHHHHTSCTTCEEEEECSSCCHHHHH
T ss_pred             -----HHH-HHHHHHHHHHH--HHhcCCCCEEEEeCCCccccCCCCCHHHHHHHHHhCcCCCEEEEECCCCcHHHHH
Confidence                 000 00112222211  2223578999999997654444  2456777777777777666666666654433

>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=96.27  E-value=0.0068  Score=51.06  Aligned_cols=20  Identities=10%  Similarity=0.018  Sum_probs=16.8

Q ss_pred             cCccEEEECCCCCCchhHhH
Q 015158           75 KGLDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        75 ~~~~~lv~~~tGsGKT~~~~   94 (412)
                      .++.+++.||+|+|||..+-
T Consensus        51 ~~~~~ll~G~~G~GKT~la~   70 (242)
T 3bos_A           51 GVQAIYLWGPVKSGRTHLIH   70 (242)
T ss_dssp             SCSEEEEECSTTSSHHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHHH
Confidence            35789999999999997653

>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=96.24  E-value=0.058  Score=46.38  Aligned_cols=18  Identities=28%  Similarity=0.390  Sum_probs=15.6

Q ss_pred             ccEEEECCCCCCchhHhH
Q 015158           77 LDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~   94 (412)
                      ..+++.||+|+|||..+-
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            578999999999997763

>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=96.19  E-value=0.017  Score=51.20  Aligned_cols=40  Identities=10%  Similarity=0.155  Sum_probs=25.9

Q ss_pred             CceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEee
Q 015158          181 NIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSA  220 (412)
Q Consensus       181 ~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SA  220 (412)
                      ..+++++||+|.+........+..++...+.+..+|+.|.
T Consensus       105 ~~~vliiDEi~~l~~~~~~~~L~~~le~~~~~~~iI~~~n  144 (324)
T 3u61_B          105 RQKVIVIDEFDRSGLAESQRHLRSFMEAYSSNCSIIITAN  144 (324)
T ss_dssp             CEEEEEEESCCCGGGHHHHHHHHHHHHHHGGGCEEEEEES
T ss_pred             CCeEEEEECCcccCcHHHHHHHHHHHHhCCCCcEEEEEeC
Confidence            5789999999987623334556666665555666665443

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=96.17  E-value=0.014  Score=47.78  Aligned_cols=18  Identities=22%  Similarity=0.270  Sum_probs=15.7

Q ss_pred             ccEEEECCCCCCchhHhH
Q 015158           77 LDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~   94 (412)
                      +.+++.||+|+|||..+.
T Consensus        55 ~~~~l~G~~GtGKT~la~   72 (202)
T 2w58_A           55 KGLYLHGSFGVGKTYLLA   72 (202)
T ss_dssp             CEEEEECSTTSSHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHH
Confidence            689999999999997653

>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=96.13  E-value=0.015  Score=52.98  Aligned_cols=38  Identities=29%  Similarity=0.428  Sum_probs=23.5

Q ss_pred             EEEEeCCchhhccCcHHH-HHHHHHhCCCCceEEEEeecC
Q 015158          184 IFVLDEADEMLSRGFKDQ-IYDIFQLLPPKIQVGVFSATM  222 (412)
Q Consensus       184 ~iiiDE~h~~~~~~~~~~-~~~i~~~~~~~~~~i~~SAT~  222 (412)
                      +||+||+|.+........ +..+.... .+..+|+.|..+
T Consensus       136 vlilDEi~~l~~~~~~~~~l~~l~~~~-~~~~iI~~t~~~  174 (384)
T 2qby_B          136 IIYLDEVDTLVKRRGGDIVLYQLLRSD-ANISVIMISNDI  174 (384)
T ss_dssp             EEEEETTHHHHHSTTSHHHHHHHHTSS-SCEEEEEECSST
T ss_pred             EEEEECHHHhccCCCCceeHHHHhcCC-cceEEEEEECCC
Confidence            999999999875432344 55555544 455555555443

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=96.12  E-value=0.005  Score=54.28  Aligned_cols=19  Identities=32%  Similarity=0.358  Sum_probs=16.0

Q ss_pred             CccEEEECCCCCCchhHhH
Q 015158           76 GLDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~   94 (412)
                      +.++++.||+|+|||..+-
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            3579999999999997763

>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=96.06  E-value=0.044  Score=50.37  Aligned_cols=129  Identities=17%  Similarity=0.219  Sum_probs=68.3

Q ss_pred             ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEc-C-CHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHh
Q 015158           77 LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLA-P-TRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL  154 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~-P-~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  154 (412)
                      ..+++.+++|+|||++....+......   +.+++++. + .+.-+   .+++..+....++.+.......         
T Consensus        98 ~vI~lvG~~GsGKTTt~~kLA~~l~~~---G~kVllv~~D~~r~~a---~eqL~~~~~~~gv~~~~~~~~~---------  162 (433)
T 3kl4_A           98 FIIMLVGVQGSGKTTTAGKLAYFYKKR---GYKVGLVAADVYRPAA---YDQLLQLGNQIGVQVYGEPNNQ---------  162 (433)
T ss_dssp             EEEEECCCTTSCHHHHHHHHHHHHHHT---TCCEEEEEECCSCHHH---HHHHHHHHHTTTCCEECCTTCS---------
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHc---CCeEEEEecCccchhH---HHHHHHHHHhcCCceeeccccC---------
Confidence            457889999999997764433322222   34666655 3 22222   2333333333344332111110         


Q ss_pred             cCCCcEEEeChHHHH-HHHHcCCCCCCCceEEEEeCCchhh---ccCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHH
Q 015158          155 SSGVHVVVGTPGRVF-DMLRRQSLRPDNIRIFVLDEADEML---SRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEIT  230 (412)
Q Consensus       155 ~~~~~iii~T~~~l~-~~~~~~~~~~~~~~~iiiDE~h~~~---~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~  230 (412)
                               .|..+. ..+...  ...+++++|+|++-+..   +..+...+..+.....+...++.++|+...+.....
T Consensus       163 ---------dp~~i~~~al~~a--~~~~~DvvIIDTaGr~~~~~d~~lm~el~~i~~~~~pd~vlLVlDa~~gq~a~~~a  231 (433)
T 3kl4_A          163 ---------NPIEIAKKGVDIF--VKNKMDIIIVDTAGRHGYGEETKLLEEMKEMYDVLKPDDVILVIDASIGQKAYDLA  231 (433)
T ss_dssp             ---------CHHHHHHHHHHHT--TTTTCSEEEEEECCCSSSCCTTHHHHHHHHHHHHHCCSEEEEEEEGGGGGGGHHHH
T ss_pred             ---------CHHHHHHHHHHHH--HhcCCCEEEEECCCCccccCCHHHHHHHHHHHHhhCCcceEEEEeCccchHHHHHH
Confidence                     121111 222221  12468999999997533   333456666777666667778889998765444443


Q ss_pred             H
Q 015158          231 R  231 (412)
Q Consensus       231 ~  231 (412)
                      .
T Consensus       232 ~  232 (433)
T 3kl4_A          232 S  232 (433)
T ss_dssp             H
T ss_pred             H
Confidence            3

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=95.99  E-value=0.019  Score=49.84  Aligned_cols=53  Identities=17%  Similarity=0.112  Sum_probs=29.6

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHHhhhhh--hhcCccEEEECCCCCCchhHh
Q 015158           39 DTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVP--FCKGLDVIQQAQSGTGKTATF   93 (412)
Q Consensus        39 ~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~--~~~~~~~lv~~~tGsGKT~~~   93 (412)
                      .+|+++.-.+...+.+...-.. +. ...+.+..  +..++.+++.||+|+|||..+
T Consensus        14 ~~~~~i~G~~~~~~~l~~~~~~-~~-~~~~~~~~~~~~~~~~~ll~G~~GtGKT~la   68 (285)
T 3h4m_A           14 VRYEDIGGLEKQMQEIREVVEL-PL-KHPELFEKVGIEPPKGILLYGPPGTGKTLLA   68 (285)
T ss_dssp             CCGGGSCSCHHHHHHHHHHTHH-HH-HCHHHHHHHCCCCCSEEEEESSSSSSHHHHH
T ss_pred             CCHHHhcCHHHHHHHHHHHHHH-Hh-hCHHHHHhcCCCCCCeEEEECCCCCcHHHHH
Confidence            4566776566666665431100 00 01111111  234578999999999999765

>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=95.98  E-value=0.02  Score=50.66  Aligned_cols=40  Identities=15%  Similarity=0.326  Sum_probs=26.1

Q ss_pred             CCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEee
Q 015158          180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSA  220 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SA  220 (412)
                      ....++|+||+|.+... ....+..++...+.+..+++.+.
T Consensus       109 ~~~~vliiDe~~~l~~~-~~~~L~~~le~~~~~~~~i~~~~  148 (327)
T 1iqp_A          109 ASFKIIFLDEADALTQD-AQQALRRTMEMFSSNVRFILSCN  148 (327)
T ss_dssp             CSCEEEEEETGGGSCHH-HHHHHHHHHHHTTTTEEEEEEES
T ss_pred             CCCeEEEEeCCCcCCHH-HHHHHHHHHHhcCCCCeEEEEeC
Confidence            35679999999987543 24556666666666666555443

>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=95.96  E-value=0.0083  Score=54.71  Aligned_cols=17  Identities=35%  Similarity=0.436  Sum_probs=15.0

Q ss_pred             cEEEECCCCCCchhHhH
Q 015158           78 DVIQQAQSGTGKTATFC   94 (412)
Q Consensus        78 ~~lv~~~tGsGKT~~~~   94 (412)
                      .+++.||+|+|||..+-
T Consensus        46 ~~li~G~~G~GKTtl~~   62 (389)
T 1fnn_A           46 RATLLGRPGTGKTVTLR   62 (389)
T ss_dssp             EEEEECCTTSSHHHHHH
T ss_pred             eEEEECCCCCCHHHHHH
Confidence            79999999999997763

>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=95.85  E-value=0.1  Score=47.96  Aligned_cols=129  Identities=16%  Similarity=0.156  Sum_probs=65.2

Q ss_pred             ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEc-C-CHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHh
Q 015158           77 LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLA-P-TRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL  154 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~-P-~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  154 (412)
                      ..+++.+++|+|||++..-.+.. +..  .+.+++++. . .+.-+   .+++..+....++.+.......         
T Consensus       101 ~vIlivG~~G~GKTTt~~kLA~~-l~~--~G~kVllv~~D~~R~aa---~eqL~~~~~~~gvpv~~~~~~~---------  165 (443)
T 3dm5_A          101 TILLMVGIQGSGKTTTVAKLARY-FQK--RGYKVGVVCSDTWRPGA---YHQLRQLLDRYHIEVFGNPQEK---------  165 (443)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH-HHT--TTCCEEEEECCCSSTHH---HHHHHHHHGGGTCEEECCTTCC---------
T ss_pred             eEEEEECcCCCCHHHHHHHHHHH-HHH--CCCeEEEEeCCCcchhH---HHHHHHHHHhcCCcEEecCCCC---------
Confidence            45788999999999876543333 222  234666655 2 23322   3444455544465543221111         


Q ss_pred             cCCCcEEEeChHHHH-HHHHcCCCCCCCceEEEEeCCchhh-ccCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHH
Q 015158          155 SSGVHVVVGTPGRVF-DMLRRQSLRPDNIRIFVLDEADEML-SRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITR  231 (412)
Q Consensus       155 ~~~~~iii~T~~~l~-~~~~~~~~~~~~~~~iiiDE~h~~~-~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~  231 (412)
                               .|..+. ..+...  ...++++||+|.+-... +......+..+.....+...++.+.|+...+......
T Consensus       166 ---------dp~~i~~~al~~a--~~~~~DvVIIDTaGrl~~d~~lm~el~~i~~~~~pd~vlLVvDA~~gq~a~~~a~  233 (443)
T 3dm5_A          166 ---------DAIKLAKEGVDYF--KSKGVDIIIVDTAGRHKEDKALIEEMKQISNVIHPHEVILVIDGTIGQQAYNQAL  233 (443)
T ss_dssp             ---------CHHHHHHHHHHHH--HHTTCSEEEEECCCCSSCCHHHHHHHHHHHHHHCCSEEEEEEEGGGGGGHHHHHH
T ss_pred             ---------CHHHHHHHHHHHH--HhCCCCEEEEECCCcccchHHHHHHHHHHHHhhcCceEEEEEeCCCchhHHHHHH
Confidence                     111111 111110  01247889999875432 1123344555555555666678888886554444333

>1sxj_E Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=95.75  E-value=0.067  Score=47.98  Aligned_cols=43  Identities=12%  Similarity=0.293  Sum_probs=29.5

Q ss_pred             CCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEeecCC
Q 015158          180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMP  223 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~  223 (412)
                      .+..++|+||+|. .+......+.+.+...+.+..+|+.|-.+.
T Consensus       133 ~~~~vlilDE~~~-L~~~~~~~L~~~le~~~~~~~~Il~t~~~~  175 (354)
T 1sxj_E          133 HRYKCVIINEANS-LTKDAQAALRRTMEKYSKNIRLIMVCDSMS  175 (354)
T ss_dssp             -CCEEEEEECTTS-SCHHHHHHHHHHHHHSTTTEEEEEEESCSC
T ss_pred             CCCeEEEEeCccc-cCHHHHHHHHHHHHhhcCCCEEEEEeCCHH
Confidence            3568999999998 444445667777777766766666665543

>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=95.63  E-value=0.022  Score=51.13  Aligned_cols=39  Identities=18%  Similarity=0.283  Sum_probs=26.1

Q ss_pred             CceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEee
Q 015158          181 NIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSA  220 (412)
Q Consensus       181 ~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SA  220 (412)
                      ...++++||+|.+... ....+..++...+....+++.+.
T Consensus       133 ~~~vliiDE~~~l~~~-~~~~Ll~~le~~~~~~~~il~~~  171 (353)
T 1sxj_D          133 PYKIIILDEADSMTAD-AQSALRRTMETYSGVTRFCLICN  171 (353)
T ss_dssp             SCEEEEETTGGGSCHH-HHHHHHHHHHHTTTTEEEEEEES
T ss_pred             CceEEEEECCCccCHH-HHHHHHHHHHhcCCCceEEEEeC
Confidence            4579999999987543 24556666666666666665543

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=95.56  E-value=0.038  Score=44.12  Aligned_cols=19  Identities=32%  Similarity=0.295  Sum_probs=16.0

Q ss_pred             CccEEEECCCCCCchhHhH
Q 015158           76 GLDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~   94 (412)
                      ..++++.||+|+|||..+.
T Consensus        43 ~~~vll~G~~G~GKT~la~   61 (187)
T 2p65_A           43 KNNPILLGDPGVGKTAIVE   61 (187)
T ss_dssp             SCEEEEESCGGGCHHHHHH
T ss_pred             CCceEEECCCCCCHHHHHH
Confidence            4678999999999997654

>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=95.50  E-value=0.034  Score=49.13  Aligned_cols=38  Identities=21%  Similarity=0.355  Sum_probs=24.8

Q ss_pred             CceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEe
Q 015158          181 NIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFS  219 (412)
Q Consensus       181 ~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~S  219 (412)
                      ...+||+||+|.+.... ...+..++...+.+..+++.|
T Consensus       107 ~~~viiiDe~~~l~~~~-~~~L~~~le~~~~~~~~il~~  144 (323)
T 1sxj_B          107 KHKIVILDEADSMTAGA-QQALRRTMELYSNSTRFAFAC  144 (323)
T ss_dssp             CCEEEEEESGGGSCHHH-HHTTHHHHHHTTTTEEEEEEE
T ss_pred             CceEEEEECcccCCHHH-HHHHHHHHhccCCCceEEEEe
Confidence            36799999999865432 344555566655566666655

>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=95.34  E-value=0.055  Score=47.38  Aligned_cols=39  Identities=5%  Similarity=0.154  Sum_probs=26.5

Q ss_pred             CCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEe
Q 015158          180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFS  219 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~S  219 (412)
                      ...+++|+||+|.+.... ...+.+.+..-+++..+|+.|
T Consensus        81 ~~~kvviIdead~lt~~a-~naLLk~LEep~~~t~fIl~t  119 (305)
T 2gno_A           81 YTRKYVIVHDCERMTQQA-ANAFLKALEEPPEYAVIVLNT  119 (305)
T ss_dssp             SSSEEEEETTGGGBCHHH-HHHTHHHHHSCCTTEEEEEEE
T ss_pred             CCceEEEeccHHHhCHHH-HHHHHHHHhCCCCCeEEEEEE
Confidence            457899999999875443 455666666666566555554

>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=95.27  E-value=0.043  Score=48.57  Aligned_cols=54  Identities=9%  Similarity=-0.027  Sum_probs=30.3

Q ss_pred             ccccccCCCCHHHHHHHHHCCCCCChHHHH-hhhhh-hhcCccEEEECCCCCCchhHhH
Q 015158           38 YDTFDAMGLQENLLRGIYAYGFEKPSAIQQ-RGIVP-FCKGLDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        38 ~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~-~a~~~-~~~~~~~lv~~~tGsGKT~~~~   94 (412)
                      -.+|+++.-.+...+.+...-.   +|... +.+.. ....+.+++.||+|+|||..+-
T Consensus        14 ~~~~~di~G~~~~~~~l~~~i~---~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~   69 (322)
T 3eie_A           14 NVKWEDVAGLEGAKEALKEAVI---LPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAK   69 (322)
T ss_dssp             CCCGGGSCSCHHHHHHHHHHTH---HHHHCGGGCCTTCCCCCEEEEECSSSSCHHHHHH
T ss_pred             CCCHHHhcChHHHHHHHHHHHH---HHHhCHHHHhcCCCCCCeEEEECCCCCcHHHHHH
Confidence            3467777666677666653210   11110 00011 1123579999999999997763

>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=95.26  E-value=0.14  Score=42.72  Aligned_cols=39  Identities=8%  Similarity=0.271  Sum_probs=22.9

Q ss_pred             CceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEee
Q 015158          181 NIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSA  220 (412)
Q Consensus       181 ~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SA  220 (412)
                      ...+||+||+|.+... ....+...+...+.+..+|+.|.
T Consensus       126 ~~~vlviDe~~~l~~~-~~~~l~~~l~~~~~~~~~i~~t~  164 (250)
T 1njg_A          126 RFKVYLIDEVHMLSRH-SFNALLKTLEEPPEHVKFLLATT  164 (250)
T ss_dssp             SSEEEEEETGGGSCHH-HHHHHHHHHHSCCTTEEEEEEES
T ss_pred             CceEEEEECcccccHH-HHHHHHHHHhcCCCceEEEEEeC
Confidence            4579999999986433 23444445554444555555543

>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=95.19  E-value=0.082  Score=47.85  Aligned_cols=19  Identities=32%  Similarity=0.345  Sum_probs=16.1

Q ss_pred             CccEEEECCCCCCchhHhH
Q 015158           76 GLDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~   94 (412)
                      +..+++.||+|+|||..+-
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_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=95.02  E-value=0.088  Score=46.94  Aligned_cols=39  Identities=18%  Similarity=0.390  Sum_probs=26.9

Q ss_pred             CCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEe
Q 015158          180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFS  219 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~S  219 (412)
                      ...+++|+||+|.+... ....+..++...+....+++.+
T Consensus       109 ~~~~viiiDe~~~l~~~-~~~~L~~~le~~~~~~~~il~~  147 (340)
T 1sxj_C          109 KGFKLIILDEADAMTNA-AQNALRRVIERYTKNTRFCVLA  147 (340)
T ss_dssp             CSCEEEEETTGGGSCHH-HHHHHHHHHHHTTTTEEEEEEE
T ss_pred             CCceEEEEeCCCCCCHH-HHHHHHHHHhcCCCCeEEEEEe
Confidence            34789999999987543 3456667777766666655544

>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=94.60  E-value=0.078  Score=52.77  Aligned_cols=79  Identities=19%  Similarity=0.179  Sum_probs=65.7

Q ss_pred             CCcEEEEEcchhHHHHHHHHHhc----CCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcC-CCcCCCCCCCCCEEEE
Q 015158          278 ITQSVIFVNTRRKVDWLTDKMRS----RDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTD-LLARGIDVQQVSLVIN  352 (412)
Q Consensus       278 ~~k~lif~~~~~~~~~~~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~-~~~~G~d~~~~~~vi~  352 (412)
                      +.+++|.++++.-+.+.++.+++    .+..+..++|+++..++..+++.+.+|+.+|+|+|. .+...+++.++..||+
T Consensus       417 g~qvlvlaPtr~La~Q~~~~l~~~~~~~gi~v~~l~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~~~~~~~l~lVVI  496 (780)
T 1gm5_A          417 GFQTAFMVPTSILAIQHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQEDVHFKNLGLVII  496 (780)
T ss_dssp             TSCEEEECSCHHHHHHHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHHCCCCSCCCEEEE
T ss_pred             CCeEEEEeCcHHHHHHHHHHHHHHhhhcCceEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhhhhhccCCceEEe
Confidence            46899999999888777766654    478999999999999999999999999999999998 4455678888888886


Q ss_pred             ccCC
Q 015158          353 YDLP  356 (412)
Q Consensus       353 ~~~~  356 (412)
                      .+..
T Consensus       497 DEaH  500 (780)
T 1gm5_A          497 DEQH  500 (780)
T ss_dssp             ESCC
T ss_pred             cccc
Confidence            5543

>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=94.55  E-value=0.024  Score=50.04  Aligned_cols=17  Identities=41%  Similarity=0.515  Sum_probs=14.7

Q ss_pred             cEEEECCCCCCchhHhH
Q 015158           78 DVIQQAQSGTGKTATFC   94 (412)
Q Consensus        78 ~~lv~~~tGsGKT~~~~   94 (412)
                      ++++.||+|+|||..+-
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            58999999999997653

>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=94.53  E-value=0.077  Score=50.38  Aligned_cols=42  Identities=12%  Similarity=0.106  Sum_probs=26.3

Q ss_pred             CCceEEEEeCCchhhccC--cHHHHHHHHHhCCCCceEEEEeecCC
Q 015158          180 DNIRIFVLDEADEMLSRG--FKDQIYDIFQLLPPKIQVGVFSATMP  223 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~~--~~~~~~~i~~~~~~~~~~i~~SAT~~  223 (412)
                      ....+|++||+|.+....  ....+..++..  ...++|+++++..
T Consensus       147 ~~~~vliIDEid~l~~~~~~~l~~L~~~l~~--~~~~iIli~~~~~  190 (516)
T 1sxj_A          147 GKHFVIIMDEVDGMSGGDRGGVGQLAQFCRK--TSTPLILICNERN  190 (516)
T ss_dssp             TTSEEEEECSGGGCCTTSTTHHHHHHHHHHH--CSSCEEEEESCTT
T ss_pred             CCCeEEEEECCCccchhhHHHHHHHHHHHHh--cCCCEEEEEcCCC
Confidence            345799999999876543  22444455444  2455777777653

>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=94.49  E-value=0.12  Score=46.62  Aligned_cols=39  Identities=8%  Similarity=0.294  Sum_probs=23.9

Q ss_pred             CCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEe
Q 015158          180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFS  219 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~S  219 (412)
                      ....++|+||+|.+.... ...+...+...+.+..+|+.|
T Consensus       118 ~~~~vliiDe~~~l~~~~-~~~Ll~~le~~~~~~~~Il~~  156 (373)
T 1jr3_A          118 GRFKVYLIDEVHMLSRHS-FNALLKTLEEPPEHVKFLLAT  156 (373)
T ss_dssp             SSSEEEEEECGGGSCHHH-HHHHHHHHHSCCSSEEEEEEE
T ss_pred             CCeEEEEEECcchhcHHH-HHHHHHHHhcCCCceEEEEEe
Confidence            346799999999875432 344555555555555444444

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=94.47  E-value=0.027  Score=52.26  Aligned_cols=18  Identities=33%  Similarity=0.298  Sum_probs=15.4

Q ss_pred             ccEEEECCCCCCchhHhH
Q 015158           77 LDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~   94 (412)
                      .+++++||+|+|||..+-
T Consensus        51 ~~vLL~GppGtGKTtlAr   68 (447)
T 3pvs_A           51 HSMILWGPPGTGKTTLAE   68 (447)
T ss_dssp             CEEEEECSTTSSHHHHHH
T ss_pred             cEEEEECCCCCcHHHHHH
Confidence            468999999999997763

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=94.25  E-value=0.041  Score=48.77  Aligned_cols=51  Identities=27%  Similarity=0.289  Sum_probs=32.4

Q ss_pred             hhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHH
Q 015158           73 FCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVM  127 (412)
Q Consensus        73 ~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~  127 (412)
                      +..|.-+++.|++|+|||..++..+......   +.+++|+..-.. ..|+..++
T Consensus        43 l~~G~LiiIaG~pG~GKTt~al~ia~~~a~~---g~~Vl~fSlEms-~~ql~~Rl   93 (338)
T 4a1f_A           43 FNKGSLVIIGARPSMGKTSLMMNMVLSALND---DRGVAVFSLEMS-AEQLALRA   93 (338)
T ss_dssp             BCTTCEEEEEECTTSCHHHHHHHHHHHHHHT---TCEEEEEESSSC-HHHHHHHH
T ss_pred             CCCCcEEEEEeCCCCCHHHHHHHHHHHHHHc---CCeEEEEeCCCC-HHHHHHHH
Confidence            3346678999999999997766555544432   347888775332 34444444

>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=94.18  E-value=0.45  Score=39.71  Aligned_cols=43  Identities=16%  Similarity=-0.103  Sum_probs=26.6

Q ss_pred             hcCccEEEECCCCCCchhHhHHHHHHhhccC---CCceeEEEEcCC
Q 015158           74 CKGLDVIQQAQSGTGKTATFCSGILQQLDYG---LVECQALVLAPT  116 (412)
Q Consensus        74 ~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~---~~~~~~lil~P~  116 (412)
                      ..|.-+.+.+|+|+|||..+...+...+...   .....++++...
T Consensus        22 ~~G~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~g~~~~~~~~i~~~   67 (243)
T 1n0w_A           22 ETGSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTE   67 (243)
T ss_dssp             ETTSEEEEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESS
T ss_pred             cCCeEEEEECCCCCcHHHHHHHHHHHHhCchhcCCCCCeEEEEECC
Confidence            3467789999999999987655444322210   012356776543

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=93.89  E-value=0.15  Score=47.49  Aligned_cols=42  Identities=17%  Similarity=0.079  Sum_probs=28.2

Q ss_pred             hhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCC
Q 015158           73 FCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPT  116 (412)
Q Consensus        73 ~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~  116 (412)
                      +..|.-++|.|++|+|||..++..+......  .+.+++|+..-
T Consensus       200 l~~G~liiI~G~pG~GKTtl~l~ia~~~~~~--~g~~Vl~~s~E  241 (454)
T 2r6a_A          200 FQRSDLIIVAARPSVGKTAFALNIAQNVATK--TNENVAIFSLE  241 (454)
T ss_dssp             BCTTCEEEEECCTTSCHHHHHHHHHHHHHHH--SSCCEEEEESS
T ss_pred             CCCCCEEEEECCCCCCHHHHHHHHHHHHHHh--CCCcEEEEECC
Confidence            4456778999999999997765555544332  12368887754

>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=93.79  E-value=0.15  Score=44.89  Aligned_cols=19  Identities=21%  Similarity=0.136  Sum_probs=16.0

Q ss_pred             CccEEEECCCCCCchhHhH
Q 015158           76 GLDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~   94 (412)
                      ...+++.||+|+|||..+-
T Consensus        38 ~~~vll~G~~GtGKT~la~   56 (324)
T 1hqc_A           38 LEHLLLFGPPGLGKTTLAH   56 (324)
T ss_dssp             CCCCEEECCTTCCCHHHHH
T ss_pred             CCcEEEECCCCCCHHHHHH
Confidence            3679999999999997653

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=93.67  E-value=0.1  Score=48.41  Aligned_cols=52  Identities=19%  Similarity=0.001  Sum_probs=31.8

Q ss_pred             hhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHH
Q 015158           73 FCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVM  127 (412)
Q Consensus        73 ~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~  127 (412)
                      +..|.-++|.|++|+|||..++..+......  .+.+++++..-.. ..|+...+
T Consensus       197 l~~G~l~ii~G~pg~GKT~lal~ia~~~a~~--~g~~vl~~slE~~-~~~l~~R~  248 (444)
T 2q6t_A          197 LGPGSLNIIAARPAMGKTAFALTIAQNAALK--EGVGVGIYSLEMP-AAQLTLRM  248 (444)
T ss_dssp             CCTTCEEEEEECTTSCHHHHHHHHHHHHHHT--TCCCEEEEESSSC-HHHHHHHH
T ss_pred             cCCCcEEEEEeCCCCCHHHHHHHHHHHHHHh--CCCeEEEEECCCC-HHHHHHHH
Confidence            3345678999999999997765555544432  1346888765322 33444443

>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=93.43  E-value=0.11  Score=47.68  Aligned_cols=19  Identities=26%  Similarity=0.345  Sum_probs=15.3

Q ss_pred             CccEEE--ECCCCCCchhHhH
Q 015158           76 GLDVIQ--QAQSGTGKTATFC   94 (412)
Q Consensus        76 ~~~~lv--~~~tGsGKT~~~~   94 (412)
                      +..++|  .||+|+|||..+-
T Consensus        50 ~~~~li~i~G~~G~GKT~L~~   70 (412)
T 1w5s_A           50 DVNMIYGSIGRVGIGKTTLAK   70 (412)
T ss_dssp             CEEEEEECTTCCSSSHHHHHH
T ss_pred             CCEEEEeCcCcCCCCHHHHHH
Confidence            356788  8999999997654

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=93.28  E-value=0.21  Score=45.83  Aligned_cols=79  Identities=10%  Similarity=0.214  Sum_probs=64.9

Q ss_pred             CCCcEEEEEcchhHHHHHHHHHhc---CCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcC-CCc---CCCCCCCCCE
Q 015158          277 AITQSVIFVNTRRKVDWLTDKMRS---RDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTD-LLA---RGIDVQQVSL  349 (412)
Q Consensus       277 ~~~k~lif~~~~~~~~~~~~~L~~---~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~-~~~---~G~d~~~~~~  349 (412)
                      ...++||.+|+++-+.++++.+++   .+..+..++|+.+..++....+.+..|+.+|+|+|+ .+.   .-++...++.
T Consensus        63 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~l~~~~~~Iiv~Tp~~l~~~l~~~~~~~~~~  142 (414)
T 3oiy_A           63 KGKKSALVFPTVTLVKQTLERLQKLADEKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREKLSQKRFDF  142 (414)
T ss_dssp             TTCCEEEEESSHHHHHHHHHHHHHHCCSSCCEEECCTTSCHHHHHHHHHHHHHTCCSEEEEEHHHHHHCHHHHTTCCCSE
T ss_pred             CCCEEEEEECCHHHHHHHHHHHHHHccCCceEEEEECCCChhhHHHHHHHhhcCCCCEEEECHHHHHHHHHHhccccccE
Confidence            457899999999999999999988   578999999999999998899999999999999998 221   1245567888


Q ss_pred             EEEccC
Q 015158          350 VINYDL  355 (412)
Q Consensus       350 vi~~~~  355 (412)
                      +|+-+.
T Consensus       143 iViDEa  148 (414)
T 3oiy_A          143 VFVDDV  148 (414)
T ss_dssp             EEESCH
T ss_pred             EEEeCh
Confidence            886554

>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=93.19  E-value=0.24  Score=46.51  Aligned_cols=43  Identities=26%  Similarity=0.364  Sum_probs=27.9

Q ss_pred             ceEEEEeCCchhhccC----------cHHHHHHHHHhCCCCceEEEEeecCCh
Q 015158          182 IRIFVLDEADEMLSRG----------FKDQIYDIFQLLPPKIQVGVFSATMPP  224 (412)
Q Consensus       182 ~~~iiiDE~h~~~~~~----------~~~~~~~i~~~~~~~~~~i~~SAT~~~  224 (412)
                      .++|++||+|.+....          ....+..++........++++.||-.+
T Consensus       298 p~iLfLDEId~l~~~~~~~~~~~~~~~~~~LL~~ld~~~~~~~v~vIaaTn~~  350 (489)
T 3hu3_A          298 PAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRP  350 (489)
T ss_dssp             SEEEEEESHHHHCBCTTSCCCHHHHHHHHHHHHHHHHSCTTSCEEEEEEESCG
T ss_pred             CcEEEecchhhhccccccccchHHHHHHHHHHHHhhccccCCceEEEEecCCc
Confidence            3689999999876421          223445555555556667777777654

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=93.08  E-value=0.15  Score=45.28  Aligned_cols=18  Identities=22%  Similarity=0.263  Sum_probs=15.6

Q ss_pred             ccEEEECCCCCCchhHhH
Q 015158           77 LDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~   94 (412)
                      .++++.||+|+|||..+-
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            579999999999997763

>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=92.88  E-value=0.95  Score=37.08  Aligned_cols=104  Identities=7%  Similarity=0.142  Sum_probs=66.8

Q ss_pred             CcEEEEEcchhHHHHHHHHHhcC-----CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCC-C-----cCCCCCCCC
Q 015158          279 TQSVIFVNTRRKVDWLTDKMRSR-----DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDL-L-----ARGIDVQQV  347 (412)
Q Consensus       279 ~k~lif~~~~~~~~~~~~~L~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~-~-----~~G~d~~~~  347 (412)
                      .++||.+++++-+.++++.+++.     +..+..++|+.+.....   +.+.++..+|+|+|+- +     ...+++..+
T Consensus        83 ~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~---~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~  159 (220)
T 1t6n_A           83 VSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDE---EVLKKNCPHIVVGTPGRILALARNKSLNLKHI  159 (220)
T ss_dssp             CCEEEECSCHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHH---HHHHHSCCSEEEECHHHHHHHHHTTSSCCTTC
T ss_pred             EEEEEEeCCHHHHHHHHHHHHHHHhhCCCceEEEEeCCCChHHHH---HHHhcCCCCEEEeCHHHHHHHHHhCCCCcccC
Confidence            48999999999998888777653     67889999998765543   3344567789999961 1     234667788


Q ss_pred             CEEEEccCCCC--hhhHHHhhhhcccCCCCceEEEEeccC
Q 015158          348 SLVINYDLPTQ--PENYLHRIGRSGRFGRKGVAINFVTRD  385 (412)
Q Consensus       348 ~~vi~~~~~~s--~~~~~Q~~GR~~R~g~~g~~~~~~~~~  385 (412)
                      +.+|+.+...-  ...+...+.+..+.-..+.-+++++..
T Consensus       160 ~~lViDEah~~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT  199 (220)
T 1t6n_A          160 KHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSAT  199 (220)
T ss_dssp             CEEEEESHHHHHSSHHHHHHHHHHHHTSCSSSEEEEEESC
T ss_pred             CEEEEcCHHHHhcccCcHHHHHHHHHhCCCcCeEEEEEee
Confidence            88886543211  123334444444433334455566554

>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=92.79  E-value=1.7  Score=37.78  Aligned_cols=19  Identities=26%  Similarity=0.394  Sum_probs=15.0

Q ss_pred             ccEEEECCCCCCchhHhHH
Q 015158           77 LDVIQQAQSGTGKTATFCS   95 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~~   95 (412)
                      +.+++.+++|+|||+....
T Consensus       105 ~vi~ivG~~GsGKTTl~~~  123 (306)
T 1vma_A          105 FVIMVVGVNGTGKTTSCGK  123 (306)
T ss_dssp             EEEEEECCTTSSHHHHHHH
T ss_pred             eEEEEEcCCCChHHHHHHH
Confidence            4577899999999976543

>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=92.64  E-value=2.7  Score=36.37  Aligned_cols=37  Identities=22%  Similarity=0.082  Sum_probs=22.1

Q ss_pred             cCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEc
Q 015158           75 KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLA  114 (412)
Q Consensus        75 ~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~  114 (412)
                      .++.+.+.++.|+|||..+...+......   +.+++++.
T Consensus        97 ~~~~i~i~g~~G~GKTT~~~~la~~~~~~---~~~v~l~~  133 (295)
T 1ls1_A           97 DRNLWFLVGLQGSGKTTTAAKLALYYKGK---GRRPLLVA  133 (295)
T ss_dssp             SSEEEEEECCTTTTHHHHHHHHHHHHHHT---TCCEEEEE
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHc---CCeEEEec
Confidence            45567788999999997654333222222   24566654

>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=92.55  E-value=0.93  Score=38.14  Aligned_cols=112  Identities=10%  Similarity=0.189  Sum_probs=68.2

Q ss_pred             CCCcEEEEEcchhHHHHHHHHHhcC----CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcC-CC------cCCCCCC
Q 015158          277 AITQSVIFVNTRRKVDWLTDKMRSR----DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTD-LL------ARGIDVQ  345 (412)
Q Consensus       277 ~~~k~lif~~~~~~~~~~~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~-~~------~~G~d~~  345 (412)
                      ...++||.+++++-+.++++.+++.    +..+..++|+.+.......+    .+..+|+|+|+ .+      ..++++.
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            3467999999999988888777653    77888999988765543322    24678999996 11      2456778


Q ss_pred             CCCEEEEccCC----CChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHH
Q 015158          346 QVSLVINYDLP----TQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQK  395 (412)
Q Consensus       346 ~~~~vi~~~~~----~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~  395 (412)
                      .++.+|+.+..    ++.......+-+..   ....-+++++..-...+..+.+
T Consensus       186 ~~~~lViDEah~l~~~~~~~~l~~i~~~~---~~~~~~l~~SAT~~~~v~~~~~  236 (249)
T 3ber_A          186 ALKYLVMDEADRILNMDFETEVDKILKVI---PRDRKTFLFSATMTKKVQKLQR  236 (249)
T ss_dssp             TCCEEEECSHHHHHHTTCHHHHHHHHHSS---CSSSEEEEEESSCCHHHHHHHH
T ss_pred             ccCEEEEcChhhhhccChHHHHHHHHHhC---CCCCeEEEEeccCCHHHHHHHH
Confidence            88888865432    11222222332222   2234456666654444444443

>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=91.89  E-value=0.79  Score=42.77  Aligned_cols=77  Identities=14%  Similarity=0.071  Sum_probs=55.3

Q ss_pred             HHHHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCC
Q 015158          266 LETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQ  345 (412)
Q Consensus       266 ~~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~  345 (412)
                      ...+...++. .+.++++.|.|...++.+.+.|.+.++........ .         .+  ....+.++...+..|+.+|
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---------EA--SDRGRYLMIGAAEHGFVDT  437 (483)
T ss_dssp             THHHHHHHHH-CCSCEEEEESCSSTTTTTHHHHGGGTCCCEECSCG-G---------GC--CTTCEEEEESCCCSCEEET
T ss_pred             HHHHHHHHHh-CCCeEEEEeCChHHHHHHHHHHHHcCCCceecCch-h---------hc--CCCcEEEEEcccccCcccC
Confidence            3455555543 24689999999999999999999988765544321 0         11  2345777888899999999


Q ss_pred             CCCEEEEccC
Q 015158          346 QVSLVINYDL  355 (412)
Q Consensus       346 ~~~~vi~~~~  355 (412)
                      ..+.+++.+.
T Consensus       438 ~~klaVITE~  447 (483)
T 3hjh_A          438 VRNLALICES  447 (483)
T ss_dssp             TTTEEEEEHH
T ss_pred             CCCEEEEEch
Confidence            9888887654

>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=91.33  E-value=1  Score=35.39  Aligned_cols=74  Identities=20%  Similarity=0.218  Sum_probs=53.5

Q ss_pred             CceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHH----hcCCCcEEEeChHHHHHHHHcCCCCCCC
Q 015158          106 VECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRI----LSSGVHVVVGTPGRVFDMLRRQSLRPDN  181 (412)
Q Consensus       106 ~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~iii~T~~~l~~~~~~~~~~~~~  181 (412)
                      ...++||.|+++..++.+.+.+...    +..+..++|+.+.......    ..+...|+|+|     .. ...+++...
T Consensus        33 ~~~~~lVF~~~~~~~~~l~~~L~~~----~~~~~~~~g~~~~~~R~~~~~~f~~g~~~vLvaT-----~~-~~~Gid~~~  102 (175)
T 2rb4_A           33 TIGQAIIFCQTRRNAKWLTVEMIQD----GHQVSLLSGELTVEQRASIIQRFRDGKEKVLITT-----NV-CARGIDVKQ  102 (175)
T ss_dssp             CCSEEEEECSCHHHHHHHHHHHHTT----TCCEEEECSSCCHHHHHHHHHHHHTTSCSEEEEC-----CS-CCTTTCCTT
T ss_pred             CCCCEEEEECCHHHHHHHHHHHHHc----CCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEe-----cc-hhcCCCccc
Confidence            3458999999999998888877764    7788889988765544322    24577899999     22 244667778


Q ss_pred             ceEEEEeC
Q 015158          182 IRIFVLDE  189 (412)
Q Consensus       182 ~~~iiiDE  189 (412)
                      +++||.-+
T Consensus       103 ~~~Vi~~d  110 (175)
T 2rb4_A          103 VTIVVNFD  110 (175)
T ss_dssp             EEEEEESS
T ss_pred             CCEEEEeC
Confidence            88888544

>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=90.86  E-value=7.9  Score=33.99  Aligned_cols=53  Identities=21%  Similarity=0.293  Sum_probs=29.8

Q ss_pred             hHHHHHHHHcCCCCCCCceEEEEeCCchhhc---cCcHHHHHHHHHhCCCCceEEEEeecC
Q 015158          165 PGRVFDMLRRQSLRPDNIRIFVLDEADEMLS---RGFKDQIYDIFQLLPPKIQVGVFSATM  222 (412)
Q Consensus       165 ~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~---~~~~~~~~~i~~~~~~~~~~i~~SAT~  222 (412)
                      .+.+...+.....   .--+||+||+|.+..   ..+...+..+....+ +.. +.++++.
T Consensus       124 ~~~l~~~l~~~~~---~~~vlvlDe~~~~~~~~~~~~~~~l~~~~~~~~-~~~-~i~~g~~  179 (357)
T 2fna_A          124 FANLLESFEQASK---DNVIIVLDEAQELVKLRGVNLLPALAYAYDNLK-RIK-FIMSGSE  179 (357)
T ss_dssp             HHHHHHHHHHTCS---SCEEEEEETGGGGGGCTTCCCHHHHHHHHHHCT-TEE-EEEEESS
T ss_pred             HHHHHHHHHhcCC---CCeEEEEECHHHhhccCchhHHHHHHHHHHcCC-CeE-EEEEcCc
Confidence            4445555543211   234899999999764   345556666665542 443 4455553

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}

Probab=90.76  E-value=1.1  Score=34.70  Aligned_cols=73  Identities=16%  Similarity=0.275  Sum_probs=53.3

Q ss_pred             eeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHH----hcCCCcEEEeChHHHHHHHHcCCCCCCCce
Q 015158          108 CQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRI----LSSGVHVVVGTPGRVFDMLRRQSLRPDNIR  183 (412)
Q Consensus       108 ~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~iii~T~~~l~~~~~~~~~~~~~~~  183 (412)
                      .++||.|+++..++.+.+.+...    +..+..++|+.+.......    ..+...|+|+|     .. ...+++...++
T Consensus        36 ~~~lVF~~~~~~~~~l~~~L~~~----~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vlv~T-----~~-~~~Gld~~~~~  105 (163)
T 2hjv_A           36 DSCIIFCRTKEHVNQLTDELDDL----GYPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVAT-----DV-AARGIDIENIS  105 (163)
T ss_dssp             SSEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEC-----GG-GTTTCCCSCCS
T ss_pred             CcEEEEECCHHHHHHHHHHHHHc----CCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEC-----Ch-hhcCCchhcCC
Confidence            47999999999999998888775    7788899988765443222    24567899999     22 23466777788


Q ss_pred             EEEEeCC
Q 015158          184 IFVLDEA  190 (412)
Q Consensus       184 ~iiiDE~  190 (412)
                      +||.-+.
T Consensus       106 ~Vi~~~~  112 (163)
T 2hjv_A          106 LVINYDL  112 (163)
T ss_dssp             EEEESSC
T ss_pred             EEEEeCC
Confidence            8876544

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=90.67  E-value=0.091  Score=48.24  Aligned_cols=55  Identities=16%  Similarity=0.256  Sum_probs=36.5

Q ss_pred             hhccccccCCCCHHHHHHHHHC---CCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHh
Q 015158           36 EVYDTFDAMGLQENLLRGIYAY---GFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATF   93 (412)
Q Consensus        36 ~~~~~f~~~~l~~~~~~~l~~~---~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~   93 (412)
                      .+-.+|++.+-.+...+.|...   ++..|..++...+   ...+.+++.||+|+|||+.+
T Consensus       175 ~p~~t~~digGl~~~k~~l~e~v~~pl~~pe~f~~~g~---~~prGvLLyGPPGTGKTllA  232 (434)
T 4b4t_M          175 KPTETYSDVGGLDKQIEELVEAIVLPMKRADKFKDMGI---RAPKGALMYGPPGTGKTLLA  232 (434)
T ss_dssp             SCSCCGGGSCSCHHHHHHHHHHTHHHHHCSHHHHHHCC---CCCCEEEEESCTTSSHHHHH
T ss_pred             CCCCChHhcCcHHHHHHHHHHHHHHHHhCHHHHHhCCC---CCCCeeEEECcCCCCHHHHH
Confidence            4556899988777777776532   2333444444332   22468999999999999775

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=90.25  E-value=0.32  Score=39.82  Aligned_cols=36  Identities=17%  Similarity=0.049  Sum_probs=28.6

Q ss_pred             CCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHh
Q 015158           58 GFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATF   93 (412)
Q Consensus        58 ~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~   93 (412)
                      .+..-+.-|+.++..+..|..+.+.+|.|+|||+.+
T Consensus         4 ~i~pk~~g~~~~l~~i~~Ge~~~liG~nGsGKSTLl   39 (208)
T 3b85_A            4 VIRPKTLGQKHYVDAIDTNTIVFGLGPAGSGKTYLA   39 (208)
T ss_dssp             CCCCCSHHHHHHHHHHHHCSEEEEECCTTSSTTHHH
T ss_pred             ccccCCHhHHHHHHhccCCCEEEEECCCCCCHHHHH
Confidence            344345567888888988999999999999999654

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19

Probab=90.23  E-value=1.6  Score=33.94  Aligned_cols=74  Identities=16%  Similarity=0.260  Sum_probs=53.4

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHH----hcCCCcEEEeChHHHHHHHHcCCCCCCCc
Q 015158          107 ECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRI----LSSGVHVVVGTPGRVFDMLRRQSLRPDNI  182 (412)
Q Consensus       107 ~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~iii~T~~~l~~~~~~~~~~~~~~  182 (412)
                      ..++||.|+++..++...+.+...    +..+..++|+.+.......    ..+...|+|+|     .. ...+++...+
T Consensus        30 ~~~~lVF~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T-----~~-~~~G~d~~~~   99 (165)
T 1fuk_A           30 VTQAVIFCNTRRKVEELTTKLRND----KFTVSAIYSDLPQQERDTIMKEFRSGSSRILIST-----DL-LARGIDVQQV   99 (165)
T ss_dssp             CSCEEEEESSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEE-----GG-GTTTCCCCSC
T ss_pred             CCCEEEEECCHHHHHHHHHHHHHc----CCCEEEEECCCCHHHHHHHHHHHHcCCCEEEEEc-----Ch-hhcCCCcccC
Confidence            357999999999999888888775    6778889988765444322    24667899999     22 2346677778


Q ss_pred             eEEEEeCC
Q 015158          183 RIFVLDEA  190 (412)
Q Consensus       183 ~~iiiDE~  190 (412)
                      ++||.-+.
T Consensus       100 ~~Vi~~~~  107 (165)
T 1fuk_A          100 SLVINYDL  107 (165)
T ss_dssp             SEEEESSC
T ss_pred             CEEEEeCC
Confidence            88877554

>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=89.92  E-value=1  Score=47.12  Aligned_cols=78  Identities=19%  Similarity=0.228  Sum_probs=64.4

Q ss_pred             CCCcEEEEEcchhHHHHHHHHHhc----CCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcC-CCcCCCCCCCCCEEE
Q 015158          277 AITQSVIFVNTRRKVDWLTDKMRS----RDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTD-LLARGIDVQQVSLVI  351 (412)
Q Consensus       277 ~~~k~lif~~~~~~~~~~~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~-~~~~G~d~~~~~~vi  351 (412)
                      .+.+++|.+++..-+.+.++.+++    .+..+..+++..+..++..+++.+.+|+.+|+|+|. .+...+.+.++..||
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            446899999999988888777764    367889999999999999999999999999999997 556667788888777


Q ss_pred             Ecc
Q 015158          352 NYD  354 (412)
Q Consensus       352 ~~~  354 (412)
                      +-+
T Consensus       731 iDE  733 (1151)
T 2eyq_A          731 VDE  733 (1151)
T ss_dssp             EES
T ss_pred             Eec
Confidence            544

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=89.86  E-value=0.29  Score=42.88  Aligned_cols=20  Identities=15%  Similarity=0.205  Sum_probs=16.8

Q ss_pred             CccEEEECCCCCCchhHhHH
Q 015158           76 GLDVIQQAQSGTGKTATFCS   95 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~   95 (412)
                      ++++++.||+|+|||..+..
T Consensus       152 ~~~lll~G~~GtGKT~La~a  171 (308)
T 2qgz_A          152 QKGLYLYGDMGIGKSYLLAA  171 (308)
T ss_dssp             CCEEEEECSTTSSHHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHHH
Confidence            57899999999999976543

>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=89.64  E-value=3.7  Score=32.05  Aligned_cols=75  Identities=9%  Similarity=0.066  Sum_probs=53.6

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHH----hcCCCcEEEeChHHHHHHHHcCCCCCCCc
Q 015158          107 ECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRI----LSSGVHVVVGTPGRVFDMLRRQSLRPDNI  182 (412)
Q Consensus       107 ~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~iii~T~~~l~~~~~~~~~~~~~~  182 (412)
                      ..++||.|+++..++.+.+.+...    +..+..++|+.........    ..+...|+|+|.     . ...+++...+
T Consensus        31 ~~~~lVF~~~~~~~~~l~~~L~~~----~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vLvaT~-----~-~~~Gldi~~~  100 (172)
T 1t5i_A           31 FNQVVIFVKSVQRCIALAQLLVEQ----NFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATN-----L-FGRGMDIERV  100 (172)
T ss_dssp             CSSEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEESS-----C-CSTTCCGGGC
T ss_pred             CCcEEEEECCHHHHHHHHHHHHhc----CCCEEEEECCCCHHHHHHHHHHHHCCCCcEEEECC-----c-hhcCcchhhC
Confidence            347999999999999888888775    6788889988765443222    346788999992     1 2345666777


Q ss_pred             eEEEEeCCc
Q 015158          183 RIFVLDEAD  191 (412)
Q Consensus       183 ~~iiiDE~h  191 (412)
                      ++||.-+..
T Consensus       101 ~~Vi~~d~p  109 (172)
T 1t5i_A          101 NIAFNYDMP  109 (172)
T ss_dssp             SEEEESSCC
T ss_pred             CEEEEECCC
Confidence            888765543

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=89.54  E-value=0.26  Score=41.31  Aligned_cols=51  Identities=20%  Similarity=0.126  Sum_probs=32.1

Q ss_pred             hcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHH
Q 015158           74 CKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMR  128 (412)
Q Consensus        74 ~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~  128 (412)
                      ..|..+++.+|+|+|||..++..+......   +.+++++..... ..+..+.+.
T Consensus        21 ~~G~~~~i~G~~GsGKTtl~~~~~~~~~~~---~~~v~~~~~e~~-~~~~~~~~~   71 (247)
T 2dr3_A           21 PERNVVLLSGGPGTGKTIFSQQFLWNGLKM---GEPGIYVALEEH-PVQVRQNMA   71 (247)
T ss_dssp             ETTCEEEEEECTTSSHHHHHHHHHHHHHHT---TCCEEEEESSSC-HHHHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHHHhc---CCeEEEEEccCC-HHHHHHHHH
Confidence            346778999999999998765544444332   246777765432 344444444

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=89.45  E-value=0.68  Score=48.17  Aligned_cols=79  Identities=10%  Similarity=0.223  Sum_probs=65.0

Q ss_pred             CCCcEEEEEcchhHHHHHHHHHhc---CCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcC-CCcC---CCCCCCCCE
Q 015158          277 AITQSVIFVNTRRKVDWLTDKMRS---RDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTD-LLAR---GIDVQQVSL  349 (412)
Q Consensus       277 ~~~k~lif~~~~~~~~~~~~~L~~---~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~-~~~~---G~d~~~~~~  349 (412)
                      .+.++||.+|+++-+.++++.+++   .++.+..++|+.+..++...++.+.+|+.+|+|+|+ .+..   -+++..+++
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   567899999999998888999999999999999997 2211   144567888


Q ss_pred             EEEccC
Q 015158          350 VINYDL  355 (412)
Q Consensus       350 vi~~~~  355 (412)
                      +|+-+.
T Consensus       200 lViDEa  205 (1104)
T 4ddu_A          200 VFVDDV  205 (1104)
T ss_dssp             EEESCH
T ss_pred             EEEeCC
Confidence            886554

>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=89.32  E-value=0.62  Score=38.62  Aligned_cols=73  Identities=11%  Similarity=0.074  Sum_probs=52.8

Q ss_pred             CCCcEEEEEcchhHHHHHHHHHhcC-----CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCC-C-----cCCCCCC
Q 015158          277 AITQSVIFVNTRRKVDWLTDKMRSR-----DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDL-L-----ARGIDVQ  345 (412)
Q Consensus       277 ~~~k~lif~~~~~~~~~~~~~L~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~-~-----~~G~d~~  345 (412)
                      ...++||.+++++-+.++++.+++.     +..+..++|+.+..++...+     ...+|+|+|+- +     ...+++.
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            3468999999999999888888653     67788899988766544332     25789999972 1     2345677


Q ss_pred             CCCEEEEcc
Q 015158          346 QVSLVINYD  354 (412)
Q Consensus       346 ~~~~vi~~~  354 (412)
                      .++.+|+-+
T Consensus       166 ~~~~lViDE  174 (230)
T 2oxc_A          166 SIRLFILDE  174 (230)
T ss_dssp             GCCEEEESS
T ss_pred             cCCEEEeCC
Confidence            788887544

>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=89.08  E-value=1.6  Score=35.17  Aligned_cols=117  Identities=13%  Similarity=0.098  Sum_probs=66.5

Q ss_pred             CCcEEEEEcchhHHHHHHHHHhcC-----CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcC-C----Cc-CCCCCCC
Q 015158          278 ITQSVIFVNTRRKVDWLTDKMRSR-----DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTD-L----LA-RGIDVQQ  346 (412)
Q Consensus       278 ~~k~lif~~~~~~~~~~~~~L~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~-~----~~-~G~d~~~  346 (412)
                      ..++||.+++++-+.++++.+++.     +..+..++|+.+..+...   .+ .+..+|+|+|+ .    +. ..+++..
T Consensus        71 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~---~~-~~~~~i~v~T~~~l~~~~~~~~~~~~~  146 (206)
T 1vec_A           71 NIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIM---RL-DDTVHVVIATPGRILDLIKKGVAKVDH  146 (206)
T ss_dssp             SCCEEEECSCHHHHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHH---HT-TSCCSEEEECHHHHHHHHHTTCSCCTT
T ss_pred             CeeEEEEeCcHHHHHHHHHHHHHHHhhcCCceEEEEeCCccHHHHHH---hc-CCCCCEEEeCHHHHHHHHHcCCcCccc
Confidence            357999999999988888777542     567888888877554322   12 34678999997 1    22 2345677


Q ss_pred             CCEEEEccCCC-ChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHH-HHHHhc
Q 015158          347 VSLVINYDLPT-QPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFD-IQKFYN  398 (412)
Q Consensus       347 ~~~vi~~~~~~-s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~-~~~~~~  398 (412)
                      ++.+|+.+... ....+...+.+..+.-+.+.-+++++..-...+.. +.+++.
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            88887644320 11122222333322212344556666654443333 344443

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=89.07  E-value=0.18  Score=45.65  Aligned_cols=54  Identities=26%  Similarity=0.324  Sum_probs=34.2

Q ss_pred             hccccccCCCCHHHHHHHHHC---CCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHh
Q 015158           37 VYDTFDAMGLQENLLRGIYAY---GFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATF   93 (412)
Q Consensus        37 ~~~~f~~~~l~~~~~~~l~~~---~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~   93 (412)
                      |-.+|++.+--+...+.|...   ++..|..++...+   ...+.+++.||+|+|||+.+
T Consensus       143 p~v~~~dIgGl~~~k~~l~e~v~~Pl~~pe~f~~~gi---~~prGvLL~GPPGTGKTllA  199 (405)
T 4b4t_J          143 PDSTYDMVGGLTKQIKEIKEVIELPVKHPELFESLGI---AQPKGVILYGPPGTGKTLLA  199 (405)
T ss_dssp             CSCCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHTC---CCCCCEEEESCSSSSHHHHH
T ss_pred             CCCCHHHhCCHHHHHHHHHHHHHHHHhCHHHHHhCCC---CCCCceEEeCCCCCCHHHHH
Confidence            446788887666666666532   2333333333322   23467999999999999775

>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=89.01  E-value=1.4  Score=35.91  Aligned_cols=71  Identities=25%  Similarity=0.333  Sum_probs=52.5

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHH----hcCCCcEEEeChHHHHHHHHcCCCCCCCc
Q 015158          107 ECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRI----LSSGVHVVVGTPGRVFDMLRRQSLRPDNI  182 (412)
Q Consensus       107 ~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~iii~T~~~l~~~~~~~~~~~~~~  182 (412)
                      +.++||.|+++.-++...+.+...    +..+..++|+.+.......    ..+..+|+|+|     +.+ ..+++..++
T Consensus        31 ~~~~lVF~~~~~~~~~l~~~L~~~----~~~~~~lhg~~~~~~r~~~~~~f~~g~~~vlvaT-----~~~-~~Gidi~~v  100 (212)
T 3eaq_A           31 PDRAMVFTRTKAETEEIAQGLLRL----GHPAQALHGDLSQGERERVLGAFRQGEVRVLVAT-----DVA-ARGLDIPQV  100 (212)
T ss_dssp             CSCEEEECSSHHHHHHHHHHHHHH----TCCEEEECSSSCHHHHHHHHHHHHSSSCCEEEEC-----TTT-TCSSSCCCB
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHHc----CCCEEEEECCCCHHHHHHHHHHHHCCCCeEEEec-----Chh-hcCCCCccC
Confidence            348999999999999888888775    7788899998775544322    34667899999     322 346677778


Q ss_pred             eEEEE
Q 015158          183 RIFVL  187 (412)
Q Consensus       183 ~~iii  187 (412)
                      ++||.
T Consensus       101 ~~Vi~  105 (212)
T 3eaq_A          101 DLVVH  105 (212)
T ss_dssp             SEEEE
T ss_pred             cEEEE
Confidence            88774

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=88.86  E-value=0.23  Score=49.62  Aligned_cols=17  Identities=29%  Similarity=0.302  Sum_probs=14.9

Q ss_pred             cEEEECCCCCCchhHhH
Q 015158           78 DVIQQAQSGTGKTATFC   94 (412)
Q Consensus        78 ~~lv~~~tGsGKT~~~~   94 (412)
                      ++++.||+|+|||..+-
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            59999999999998763

>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=88.58  E-value=2.3  Score=35.45  Aligned_cols=112  Identities=8%  Similarity=0.023  Sum_probs=68.5

Q ss_pred             CCcEEEEEcchhHHHHHHHHHhc----CCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcC-----CC-cCCCCCCCC
Q 015158          278 ITQSVIFVNTRRKVDWLTDKMRS----RDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTD-----LL-ARGIDVQQV  347 (412)
Q Consensus       278 ~~k~lif~~~~~~~~~~~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~-----~~-~~G~d~~~~  347 (412)
                      ..++||.+++++-+.++.+.+++    .+..+..++|+.+.......+..    ..+|+|+|+     .+ ...+++..+
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            46799999999998888777654    47889999999887665444432    478999997     11 234567788


Q ss_pred             CEEEEccCC----CChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHH
Q 015158          348 SLVINYDLP----TQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKF  396 (412)
Q Consensus       348 ~~vi~~~~~----~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~  396 (412)
                      +.+|+.+..    ++.......+   .+.-.+..-+++++..-...+..+.+.
T Consensus       178 ~~lViDEah~l~~~~~~~~~~~i---~~~~~~~~q~~~~SAT~~~~~~~~~~~  227 (242)
T 3fe2_A          178 TYLVLDEADRMLDMGFEPQIRKI---VDQIRPDRQTLMWSATWPKEVRQLAED  227 (242)
T ss_dssp             CEEEETTHHHHHHTTCHHHHHHH---HTTSCSSCEEEEEESCCCHHHHHHHHH
T ss_pred             cEEEEeCHHHHhhhCcHHHHHHH---HHhCCccceEEEEEeecCHHHHHHHHH
Confidence            888865432    1111222222   222223445666766654444444433

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}

Probab=88.42  E-value=2.9  Score=33.43  Aligned_cols=72  Identities=21%  Similarity=0.244  Sum_probs=52.7

Q ss_pred             eeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHH----hcCCCcEEEeChHHHHHHHHcCCCCCCCce
Q 015158          108 CQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRI----LSSGVHVVVGTPGRVFDMLRRQSLRPDNIR  183 (412)
Q Consensus       108 ~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~iii~T~~~l~~~~~~~~~~~~~~~  183 (412)
                      .++||.|+++.-++.+.+.+...    ++.+..++|+.+.......    ..+...|+|+|     ..+. .+++...++
T Consensus        55 ~~~lVF~~~~~~~~~l~~~L~~~----g~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT-----~~~~-~Gldi~~v~  124 (191)
T 2p6n_A           55 PPVLIFAEKKADVDAIHEYLLLK----GVEAVAIHGGKDQEERTKAIEAFREGKKDVLVAT-----DVAS-KGLDFPAIQ  124 (191)
T ss_dssp             SCEEEECSCHHHHHHHHHHHHHH----TCCEEEECTTSCHHHHHHHHHHHHHTSCSEEEEC-----HHHH-TTCCCCCCS
T ss_pred             CCEEEEECCHHHHHHHHHHHHHc----CCcEEEEeCCCCHHHHHHHHHHHhcCCCEEEEEc-----Cchh-cCCCcccCC
Confidence            47999999999999998888775    7788889988765443222    24678899999     3332 366777788


Q ss_pred             EEEEeC
Q 015158          184 IFVLDE  189 (412)
Q Consensus       184 ~iiiDE  189 (412)
                      +||.-+
T Consensus       125 ~VI~~d  130 (191)
T 2p6n_A          125 HVINYD  130 (191)
T ss_dssp             EEEESS
T ss_pred             EEEEeC
Confidence            877644

>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=88.37  E-value=1  Score=42.73  Aligned_cols=59  Identities=12%  Similarity=0.142  Sum_probs=55.0

Q ss_pred             CCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcC
Q 015158          278 ITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTD  336 (412)
Q Consensus       278 ~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~  336 (412)
                      .+++||.+|.+.-+....+.|++.+..+..+++..+..++..+...+..|..+++++|+
T Consensus        65 ~g~~lvi~P~~aL~~q~~~~l~~~gi~~~~l~~~~~~~~~~~~~~~~~~~~~~ilv~Tp  123 (523)
T 1oyw_A           65 NGLTVVVSPLISLMKDQVDQLQANGVAAACLNSTQTREQQLEVMTGCRTGQIRLLYIAP  123 (523)
T ss_dssp             SSEEEEECSCHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHHTCCSEEEECH
T ss_pred             CCCEEEECChHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECH
Confidence            47899999999999999999999999999999999999999999999999999999997

>3e70_C DPA, signal recognition particle receptor; FTSY, SRP-GTPase, protein-targeting, transport protein; HET: GDP; 1.97A {Pyrococcus furiosus} PDB: 3dmd_B 3dm9_B*

Probab=88.32  E-value=3.3  Score=36.39  Aligned_cols=53  Identities=23%  Similarity=0.334  Sum_probs=33.7

Q ss_pred             CceEEEEeCCchhh-ccCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHh
Q 015158          181 NIRIFVLDEADEML-SRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKF  233 (412)
Q Consensus       181 ~~~~iiiDE~h~~~-~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~  233 (412)
                      +.+++++|.+...- .......+..+...+.+...++.+.++...+.......+
T Consensus       211 ~~d~vliDtaG~~~~~~~l~~eL~~i~ral~~de~llvLDa~t~~~~~~~~~~~  264 (328)
T 3e70_C          211 GIDVVLIDTAGRSETNRNLMDEMKKIARVTKPNLVIFVGDALAGNAIVEQARQF  264 (328)
T ss_dssp             TCSEEEEEECCSCCTTTCHHHHHHHHHHHHCCSEEEEEEEGGGTTHHHHHHHHH
T ss_pred             cchhhHHhhccchhHHHHHHHHHHHHHHHhcCCCCEEEEecHHHHHHHHHHHHH
Confidence            45678899876532 233455666666666667778888888766555554443

>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=88.04  E-value=4.7  Score=32.29  Aligned_cols=115  Identities=8%  Similarity=0.045  Sum_probs=67.3

Q ss_pred             CCcEEEEEcchhHHHHHHHHHhcC--CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcC-C----C-cCCCCCCCCCE
Q 015158          278 ITQSVIFVNTRRKVDWLTDKMRSR--DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTD-L----L-ARGIDVQQVSL  349 (412)
Q Consensus       278 ~~k~lif~~~~~~~~~~~~~L~~~--~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~-~----~-~~G~d~~~~~~  349 (412)
                      ..+++|.+++++.+.++++.+++.  +..+..++|+.+.......+.    ...+|+|+|+ .    + ...+++..++.
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            467999999999999999888765  357778888776544333222    2578999996 1    1 23456778888


Q ss_pred             EEEccCCCC-hhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHH
Q 015158          350 VINYDLPTQ-PENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKF  396 (412)
Q Consensus       350 vi~~~~~~s-~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~  396 (412)
                      +|+.+...- ...+...+.+..+.-..+.-+++++..-...+..+.+.
T Consensus       148 iViDEah~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~  195 (207)
T 2gxq_A          148 AVLDEADEMLSMGFEEEVEALLSATPPSRQTLLFSATLPSWAKRLAER  195 (207)
T ss_dssp             EEEESHHHHHHTTCHHHHHHHHHTSCTTSEEEEECSSCCHHHHHHHHH
T ss_pred             EEEEChhHhhccchHHHHHHHHHhCCccCeEEEEEEecCHHHHHHHHH
Confidence            886543210 01122222222222233455666766644444444443

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=87.91  E-value=0.2  Score=46.10  Aligned_cols=55  Identities=16%  Similarity=0.190  Sum_probs=34.2

Q ss_pred             hhccccccCCCCHHHHHHHHHC---CCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHh
Q 015158           36 EVYDTFDAMGLQENLLRGIYAY---GFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATF   93 (412)
Q Consensus        36 ~~~~~f~~~~l~~~~~~~l~~~---~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~   93 (412)
                      .|-.+|++.+--+...+.|...   ++..|..++...   +...+.+++.||+|+|||+.+
T Consensus       203 ~P~vt~~DIgGl~~~k~~L~e~V~~pl~~pe~f~~~G---i~pprGILLyGPPGTGKTlLA  260 (467)
T 4b4t_H          203 KPDVTYSDVGGCKDQIEKLREVVELPLLSPERFATLG---IDPPKGILLYGPPGTGKTLCA  260 (467)
T ss_dssp             SCSCCCSSCTTCHHHHHHHHHHTHHHHHCHHHHHHHT---CCCCSEEEECSCTTSSHHHHH
T ss_pred             CCCCCHHHhccHHHHHHHHHHHHHHHhcCHHHHHHCC---CCCCCceEeeCCCCCcHHHHH
Confidence            3446788887667777776542   222222222221   223578999999999999765

>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=87.58  E-value=0.2  Score=43.76  Aligned_cols=53  Identities=21%  Similarity=0.241  Sum_probs=29.7

Q ss_pred             cccccCCCCHHHHHHHHHC---CCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhH
Q 015158           39 DTFDAMGLQENLLRGIYAY---GFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        39 ~~f~~~~l~~~~~~~l~~~---~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~   94 (412)
                      .+|+++.-.+...+.+...   ....+..++..   .+..++.+++.||+|+|||..+-
T Consensus        12 ~~~~di~G~~~~~~~l~~~v~~~~~~~~~~~~~---~~~~~~~vLL~Gp~GtGKT~la~   67 (301)
T 3cf0_A           12 VTWEDIGGLEDVKRELQELVQYPVEHPDKFLKF---GMTPSKGVLFYGPPGCGKTLLAK   67 (301)
T ss_dssp             CCGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHH---CCCCCSEEEEECSSSSSHHHHHH
T ss_pred             CCHHHhCCHHHHHHHHHHHHHHHhhCHHHHHHc---CCCCCceEEEECCCCcCHHHHHH
Confidence            4667776556665555431   11111111111   12346789999999999997763

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=87.38  E-value=0.18  Score=46.37  Aligned_cols=55  Identities=25%  Similarity=0.298  Sum_probs=33.5

Q ss_pred             hhccccccCCCCHHHHHHHHHC---CCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHh
Q 015158           36 EVYDTFDAMGLQENLLRGIYAY---GFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATF   93 (412)
Q Consensus        36 ~~~~~f~~~~l~~~~~~~l~~~---~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~   93 (412)
                      .+-.+|++.+--+...+.+...   ++..|..++...   +...+.+++.||+|+|||+.+
T Consensus       175 ~p~v~~~digGl~~~k~~l~e~v~~pl~~p~~f~~~g---~~~prGvLL~GPPGtGKTllA  232 (437)
T 4b4t_L          175 QGEITFDGIGGLTEQIRELREVIELPLKNPEIFQRVG---IKPPKGVLLYGPPGTGKTLLA  232 (437)
T ss_dssp             SCSSCSGGGCSCHHHHHHHHHHHHHHHHCHHHHHHHC---CCCCCEEEEESCTTSSHHHHH
T ss_pred             CCCCChhHhCChHHHHHHHHHHHHHHHhCHHHHHhCC---CCCCCeEEEECCCCCcHHHHH
Confidence            4456788886556666555431   222233333322   223468999999999999875

>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=87.34  E-value=2.1  Score=34.08  Aligned_cols=90  Identities=19%  Similarity=0.250  Sum_probs=50.8

Q ss_pred             CCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHH----HHHhcCCCcEE
Q 015158           86 GTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVRED----QRILSSGVHVV  161 (412)
Q Consensus        86 GsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~ii  161 (412)
                      .+.|-. .+.-++...   ..+.++||.|+++.-++.+.+.+...    ++.+..++|+.+....    .....+...|+
T Consensus        29 ~~~K~~-~L~~ll~~~---~~~~k~lVF~~~~~~~~~l~~~L~~~----g~~~~~lhg~~~~~~r~~~~~~f~~g~~~vL  100 (185)
T 2jgn_A           29 ESDKRS-FLLDLLNAT---GKDSLTLVFVETKKGADSLEDFLYHE----GYACTSIHGDRSQRDREEALHQFRSGKSPIL  100 (185)
T ss_dssp             GGGHHH-HHHHHHHHC----CCSCEEEEESCHHHHHHHHHHHHHT----TCCEEEEC--------CHHHHHHHHTSSSEE
T ss_pred             cHHHHH-HHHHHHHhc---CCCCeEEEEECCHHHHHHHHHHHHHc----CCceEEEeCCCCHHHHHHHHHHHHcCCCeEE
Confidence            345653 333444332   23458999999999999888888774    6778888887654332    22234677899


Q ss_pred             EeChHHHHHHHHcCCCCCCCceEEEEeC
Q 015158          162 VGTPGRVFDMLRRQSLRPDNIRIFVLDE  189 (412)
Q Consensus       162 i~T~~~l~~~~~~~~~~~~~~~~iiiDE  189 (412)
                      |+|     ..+ ..+++...+++||.-+
T Consensus       101 vaT-----~~~-~~Gldi~~~~~VI~~d  122 (185)
T 2jgn_A          101 VAT-----AVA-ARGLDISNVKHVINFD  122 (185)
T ss_dssp             EEE-----C-------CCCSBSEEEESS
T ss_pred             EEc-----Chh-hcCCCcccCCEEEEeC
Confidence            999     222 2355666777777633

>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=87.10  E-value=0.32  Score=51.13  Aligned_cols=48  Identities=21%  Similarity=0.261  Sum_probs=34.7

Q ss_pred             EEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHH
Q 015158           80 IQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMR  128 (412)
Q Consensus        80 lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~  128 (412)
                      +|.|+.|||||.+.+--+...+..+..+.++++++|... .-++.+.+.
T Consensus         5 lV~agAGSGKT~~l~~ri~~ll~~~~~~~~il~lVP~q~-TFt~~~rl~   52 (1166)
T 3u4q_B            5 FLVGRSGSGKTKLIINSIQDELRRAPFGKPIIFLVPDQM-TFLMEYELA   52 (1166)
T ss_dssp             EEEECTTSSHHHHHHHHHHHHHHHCTTSSCEEEECCGGG-HHHHHHHHT
T ss_pred             EEEeCCCCChHHHHHHHHHHHHHhCCCCCcEEEEecCcc-cHHHHHHHH
Confidence            789999999999988777776665544568999999764 333444443

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=87.04  E-value=0.59  Score=44.04  Aligned_cols=28  Identities=21%  Similarity=0.377  Sum_probs=20.7

Q ss_pred             hhcCccEEEECCCCCCchhHhHHHHHHhh
Q 015158           73 FCKGLDVIQQAQSGTGKTATFCSGILQQL  101 (412)
Q Consensus        73 ~~~~~~~lv~~~tGsGKT~~~~~~~~~~~  101 (412)
                      +..|..+++.||||||||+.. -+++..+
T Consensus       257 v~~g~~i~I~GptGSGKTTlL-~aL~~~i  284 (511)
T 2oap_1          257 IEHKFSAIVVGETASGKTTTL-NAIMMFI  284 (511)
T ss_dssp             HHTTCCEEEEESTTSSHHHHH-HHHGGGS
T ss_pred             HhCCCEEEEECCCCCCHHHHH-HHHHhhC
Confidence            456788999999999999764 3344443

>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=86.93  E-value=14  Score=33.75  Aligned_cols=36  Identities=22%  Similarity=0.083  Sum_probs=21.9

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEc
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLA  114 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~  114 (412)
                      +..+.+.++.|+|||++....+.....   .+.+++++.
T Consensus        98 ~~vi~i~G~~GsGKTT~~~~LA~~l~~---~g~~Vllvd  133 (425)
T 2ffh_A           98 RNLWFLVGLQGSGKTTTAAKLALYYKG---KGRRPLLVA  133 (425)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHHHHHT---TTCCEEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHH---cCCeEEEee
Confidence            345677899999999766443332222   234566654

>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=86.84  E-value=0.84  Score=41.76  Aligned_cols=47  Identities=19%  Similarity=0.240  Sum_probs=27.2

Q ss_pred             HHHhhhhhhh--cCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEc
Q 015158           65 IQQRGIVPFC--KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLA  114 (412)
Q Consensus        65 ~Q~~a~~~~~--~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~  114 (412)
                      -+..++..+.  .+..++|.+|||||||+.. .+++..+...  ...++++-
T Consensus       154 ~~~~~L~~l~~~~ggii~I~GpnGSGKTTlL-~allg~l~~~--~g~I~~~e  202 (418)
T 1p9r_A          154 HNHDNFRRLIKRPHGIILVTGPTGSGKSTTL-YAGLQELNSS--ERNILTVE  202 (418)
T ss_dssp             HHHHHHHHHHTSSSEEEEEECSTTSCHHHHH-HHHHHHHCCT--TSCEEEEE
T ss_pred             HHHHHHHHHHHhcCCeEEEECCCCCCHHHHH-HHHHhhcCCC--CCEEEEec
Confidence            3444555443  3456789999999999764 3344444321  23455543

>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=86.60  E-value=0.71  Score=43.32  Aligned_cols=26  Identities=19%  Similarity=0.308  Sum_probs=19.5

Q ss_pred             hhcCccEEEECCCCCCchhHhHHHHH
Q 015158           73 FCKGLDVIQQAQSGTGKTATFCSGIL   98 (412)
Q Consensus        73 ~~~~~~~lv~~~tGsGKT~~~~~~~~   98 (412)
                      +.++.+++|.++||||||.+.-..+.
T Consensus       164 L~~~pHlLIaG~TGSGKSt~L~~li~  189 (512)
T 2ius_A          164 LAKMPHLLVAGTTGSGASVGVNAMIL  189 (512)
T ss_dssp             GGGSCSEEEECCTTSSHHHHHHHHHH
T ss_pred             cccCceEEEECCCCCCHHHHHHHHHH
Confidence            33467899999999999977544443

>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=86.57  E-value=1.1  Score=43.12  Aligned_cols=59  Identities=3%  Similarity=0.025  Sum_probs=53.8

Q ss_pred             CCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHH--hcCCCcEEEEcC
Q 015158          278 ITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREF--RSGSSRVLITTD  336 (412)
Q Consensus       278 ~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f--~~g~~~vlv~t~  336 (412)
                      .+.+||.+|+++-++...+.|++.|+.+..++|+.+..++..+...+  ..+..+++++|+
T Consensus        84 ~g~~lVisP~~~L~~q~~~~l~~~gi~~~~l~~~~~~~~~~~~~~~l~~~~~~~~Ilv~Tp  144 (591)
T 2v1x_A           84 DGFTLVICPLISLMEDQLMVLKQLGISATMLNASSSKEHVKWVHAEMVNKNSELKLIYVTP  144 (591)
T ss_dssp             SSEEEEECSCHHHHHHHHHHHHHHTCCEEECCSSCCHHHHHHHHHHHHCTTCCCCEEEECH
T ss_pred             CCcEEEEeCHHHHHHHHHHHHHhcCCcEEEEeCCCCHHHHHHHHHHhhcccCCCCEEEECh
Confidence            47899999999999999999999999999999999999998888888  467899999998

>2l82_A Designed protein OR32; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, de novo protein; NMR {Artificial gene}

Probab=86.56  E-value=4.4  Score=28.23  Aligned_cols=115  Identities=16%  Similarity=0.157  Sum_probs=67.0

Q ss_pred             EEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCC--CcCCC-----CCCCCCEEEEc
Q 015158          281 SVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDL--LARGI-----DVQQVSLVINY  353 (412)
Q Consensus       281 ~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~--~~~G~-----d~~~~~~vi~~  353 (412)
                      .+||.+..+...++.+.++..|..+..++++.....|..-++.|.....++--.-+.  +.+.+     --|.+++|++.
T Consensus         5 fvvfssdpeilkeivreikrqgvrvvllysdqdekrrrerleefekqgvdvrtvedkedfrenireiwerypqldvvviv   84 (162)
T 2l82_A            5 FVVFSSDPEILKEIVREIKRQGVRVVLLYSDQDEKRRRERLEEFEKQGVDVRTVEDKEDFRENIREIWERYPQLDVVVIV   84 (162)
T ss_dssp             EEEEESCHHHHHHHHHHHHHTTCEEEEEECCSCHHHHHHHHHHHHTTTCEEEECCSHHHHHHHHHHHHHHCTTCCEEEEE
T ss_pred             EEEecCCHHHHHHHHHHHHhCCeEEEEEecCchHHHHHHHHHHHHHcCCceeeeccHHHHHHHHHHHHHhCCCCcEEEEE
Confidence            467778888888999999999999999999999998888888888754443222110  00000     03456666554


Q ss_pred             cCCCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHHhc
Q 015158          354 DLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYN  398 (412)
Q Consensus       354 ~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~  398 (412)
                      ... +..=..-.+--+.-.|  -.+++++.+.+...-+..++.+.
T Consensus        85 ttd-dkewikdfieeakerg--vevfvvynnkdddrrkeaqqefr  126 (162)
T 2l82_A           85 TTD-DKEWIKDFIEEAKERG--VEVFVVYNNKDDDRRKEAQQEFR  126 (162)
T ss_dssp             ECC-CHHHHHHHHHHHHHTT--CEEEEEEECSCHHHHHHHHHHHC
T ss_pred             ecC-cHHHHHHHHHHHHhcC--cEEEEEecCCCchhHHHHHHHhh
Confidence            432 1111111222222221  35666666666665555555444

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=86.54  E-value=0.23  Score=45.50  Aligned_cols=55  Identities=22%  Similarity=0.169  Sum_probs=33.0

Q ss_pred             hhccccccCCCCHHHHHHHHHC---CCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHh
Q 015158           36 EVYDTFDAMGLQENLLRGIYAY---GFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATF   93 (412)
Q Consensus        36 ~~~~~f~~~~l~~~~~~~l~~~---~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~   93 (412)
                      .+-.+|++.+--+...+.+...   ++..|..++...+   ...+.+++.||+|+|||+.+
T Consensus       166 ~p~v~~~digGl~~~k~~l~e~v~~pl~~p~~~~~~g~---~~prGiLL~GPPGtGKT~la  223 (428)
T 4b4t_K          166 KPDVTYADVGGLDMQKQEIREAVELPLVQADLYEQIGI---DPPRGVLLYGPPGTGKTMLV  223 (428)
T ss_dssp             SCSCCGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCC---CCCCEEEEESCTTTTHHHHH
T ss_pred             CCCCCHHHhccHHHHHHHHHHHHHHHHhCHHHHHhCCC---CCCceEEEECCCCCCHHHHH
Confidence            3445788886556666555431   2222333333222   23467999999999999775

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=86.38  E-value=0.57  Score=38.73  Aligned_cols=40  Identities=20%  Similarity=0.170  Sum_probs=25.3

Q ss_pred             hhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcC
Q 015158           73 FCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAP  115 (412)
Q Consensus        73 ~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P  115 (412)
                      +..|..+++.+|+|+|||..+...+......   +.+++++..
T Consensus        20 i~~G~~~~i~G~~GsGKTtl~~~l~~~~~~~---~~~v~~~~~   59 (235)
T 2w0m_A           20 IPQGFFIALTGEPGTGKTIFSLHFIAKGLRD---GDPCIYVTT   59 (235)
T ss_dssp             EETTCEEEEECSTTSSHHHHHHHHHHHHHHH---TCCEEEEES
T ss_pred             CcCCCEEEEEcCCCCCHHHHHHHHHHHHHHC---CCeEEEEEc
Confidence            3456778999999999997654433333222   235766653

>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=86.35  E-value=0.43  Score=38.48  Aligned_cols=19  Identities=42%  Similarity=0.618  Sum_probs=15.9

Q ss_pred             CccEEEECCCCCCchhHhH
Q 015158           76 GLDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~   94 (412)
                      ++-+++.+|||+|||..++
T Consensus        34 g~~ilI~GpsGsGKStLA~   52 (205)
T 2qmh_A           34 GLGVLITGDSGVGKSETAL   52 (205)
T ss_dssp             TEEEEEECCCTTTTHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHH
Confidence            5678999999999997654

>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=86.34  E-value=8.3  Score=35.60  Aligned_cols=32  Identities=25%  Similarity=0.268  Sum_probs=23.8

Q ss_pred             hhhhhhhcCccEEEECCCCCCchhHhHHHHHH
Q 015158           68 RGIVPFCKGLDVIQQAQSGTGKTATFCSGILQ   99 (412)
Q Consensus        68 ~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~   99 (412)
                      +.+..+.+|+..++.++.|+|||..+...+.+
T Consensus       143 D~L~pi~kGq~~~i~G~sGvGKTtL~~~l~~~  174 (473)
T 1sky_E          143 DLLAPYIKGGKIGLFGGAGVGKTVLIQELIHN  174 (473)
T ss_dssp             HHHSCEETTCEEEEECCSSSCHHHHHHHHHHH
T ss_pred             HHHhhhccCCEEEEECCCCCCccHHHHHHHhh
Confidence            44555667899999999999999776544433

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=86.30  E-value=0.39  Score=40.90  Aligned_cols=21  Identities=24%  Similarity=0.298  Sum_probs=17.6

Q ss_pred             hhcCccEEEECCCCCCchhHh
Q 015158           73 FCKGLDVIQQAQSGTGKTATF   93 (412)
Q Consensus        73 ~~~~~~~lv~~~tGsGKT~~~   93 (412)
                      +..|..+++.+|+|||||+..
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            456778899999999999764

>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=86.17  E-value=0.63  Score=42.96  Aligned_cols=44  Identities=14%  Similarity=0.224  Sum_probs=29.3

Q ss_pred             cCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHH
Q 015158           75 KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQ  121 (412)
Q Consensus        75 ~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~  121 (412)
                      ...+++|.|+||+|||......+.+.+..   +..++|+=|-.++..
T Consensus        52 ~~~h~~i~G~tGsGKs~~~~~li~~~~~~---g~~viv~Dpkge~~~   95 (437)
T 1e9r_A           52 EPRHLLVNGATGTGKSVLLRELAYTGLLR---GDRMVIVDPNGDMLS   95 (437)
T ss_dssp             GGGCEEEEECTTSSHHHHHHHHHHHHHHT---TCEEEEEEETTHHHH
T ss_pred             CcceEEEECCCCCCHHHHHHHHHHHHHHC---CCcEEEEeCCCchhH
Confidence            35789999999999998753333333333   246777777666543

>3hws_A ATP-dependent CLP protease ATP-binding subunit CL; CLPXP, AAA+ molecular machine, hexamer, asymmetric,, ATP-BIN chaperone, metal-binding; HET: ADP; 3.25A {Escherichia coli} PDB: 3hte_A

Probab=86.06  E-value=0.85  Score=40.89  Aligned_cols=20  Identities=20%  Similarity=0.247  Sum_probs=16.7

Q ss_pred             cCccEEEECCCCCCchhHhH
Q 015158           75 KGLDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        75 ~~~~~lv~~~tGsGKT~~~~   94 (412)
                      .+.++++.||+|+|||..+-
T Consensus        50 ~~~~vll~GppGtGKT~la~   69 (363)
T 3hws_A           50 GKSNILLIGPTGSGKTLLAE   69 (363)
T ss_dssp             CCCCEEEECCTTSSHHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHHH
Confidence            34689999999999998763

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=86.04  E-value=4.4  Score=36.72  Aligned_cols=72  Identities=19%  Similarity=0.263  Sum_probs=53.4

Q ss_pred             CceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHH----hcCCCcEEEeChHHHHHHHHcCCCCCCC
Q 015158          106 VECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRI----LSSGVHVVVGTPGRVFDMLRRQSLRPDN  181 (412)
Q Consensus       106 ~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~iii~T~~~l~~~~~~~~~~~~~  181 (412)
                      .+.++||.|+++..++.+.+.+.+.    +..+..++|+.........    ..+..+|+|+|     ..+ ..+++..+
T Consensus       275 ~~~~~lVf~~~~~~~~~l~~~L~~~----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlvaT-----~~~-~~Gidip~  344 (417)
T 2i4i_A          275 KDSLTLVFVETKKGADSLEDFLYHE----GYACTSIHGDRSQRDREEALHQFRSGKSPILVAT-----AVA-ARGLDISN  344 (417)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHHTSSCEEEEC-----HHH-HTTSCCCC
T ss_pred             CCCeEEEEECCHHHHHHHHHHHHHC----CCCeeEecCCCCHHHHHHHHHHHHcCCCCEEEEC-----Chh-hcCCCccc
Confidence            4568999999999999888888775    6788889988775544322    24677899999     333 34677778


Q ss_pred             ceEEEE
Q 015158          182 IRIFVL  187 (412)
Q Consensus       182 ~~~iii  187 (412)
                      +++||.
T Consensus       345 v~~Vi~  350 (417)
T 2i4i_A          345 VKHVIN  350 (417)
T ss_dssp             EEEEEE
T ss_pred             CCEEEE
Confidence            888775

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=85.96  E-value=0.78  Score=40.23  Aligned_cols=53  Identities=15%  Similarity=-0.034  Sum_probs=33.5

Q ss_pred             hhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHH
Q 015158           73 FCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRA  129 (412)
Q Consensus        73 ~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~  129 (412)
                      +..|.-++|.|++|+|||..++..+......+   .++++++-- .-..|+...+..
T Consensus        65 l~~G~l~li~G~pG~GKTtl~l~ia~~~a~~g---~~vl~~slE-~s~~~l~~R~~~  117 (315)
T 3bh0_A           65 YKRRNFVLIAARPSMGKTAFALKQAKNMSDND---DVVNLHSLE-MGKKENIKRLIV  117 (315)
T ss_dssp             BCTTCEEEEECCTTSSHHHHHHHHHHHHHTTT---CEEEEEESS-SCHHHHHHHHHH
T ss_pred             CCCCcEEEEEeCCCCCHHHHHHHHHHHHHHcC---CeEEEEECC-CCHHHHHHHHHH
Confidence            44567789999999999977665555444332   468887754 223444444443

>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=85.94  E-value=0.49  Score=38.78  Aligned_cols=36  Identities=14%  Similarity=-0.013  Sum_probs=24.6

Q ss_pred             hcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcC
Q 015158           74 CKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAP  115 (412)
Q Consensus        74 ~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P  115 (412)
                      ..|.-+++.+++|+|||..+...+.   .   .+.+++++.-
T Consensus        18 ~~G~~~~i~G~~GsGKTtl~~~l~~---~---~~~~v~~i~~   53 (220)
T 2cvh_A           18 APGVLTQVYGPYASGKTTLALQTGL---L---SGKKVAYVDT   53 (220)
T ss_dssp             CTTSEEEEECSTTSSHHHHHHHHHH---H---HCSEEEEEES
T ss_pred             cCCEEEEEECCCCCCHHHHHHHHHH---H---cCCcEEEEEC
Confidence            3467789999999999976654443   2   2236777664

>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=85.93  E-value=1.2  Score=46.79  Aligned_cols=53  Identities=26%  Similarity=0.231  Sum_probs=41.4

Q ss_pred             cEEEECCCCCCchhHhHHHHHHhhccC---------CCceeEEEEcCCHHHHHHHHHHHHHh
Q 015158           78 DVIQQAQSGTGKTATFCSGILQQLDYG---------LVECQALVLAPTRELAQQIEKVMRAL  130 (412)
Q Consensus        78 ~~lv~~~tGsGKT~~~~~~~~~~~~~~---------~~~~~~lil~P~~~L~~q~~~~~~~~  130 (412)
                      ..+|.|+.|||||.+...-++..+...         ....++|+|+=|++-+.++.+++.+.
T Consensus        18 ~~lV~AsAGSGKT~~L~~r~lrLll~~g~~~~~~~~~~~~~ILvvTFT~aAA~EMr~RI~~~   79 (1180)
T 1w36_B           18 ERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLVVTFTEAATAELRGRIRSN   79 (1180)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHHTTCSSSSSCSSCCCGGGEEEEESCHHHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCHHHHHHHHHHHHHhcCCcccccCCCCCHHHEEEEeccHHHHHHHHHHHHHH
Confidence            459999999999988877777766431         22457999999999888888877664

>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=85.91  E-value=1.3  Score=36.83  Aligned_cols=75  Identities=15%  Similarity=0.233  Sum_probs=45.8

Q ss_pred             CCCcEEEEEcchhHHHHHHHHHhcC----CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcC-----CCc-CCCCCCC
Q 015158          277 AITQSVIFVNTRRKVDWLTDKMRSR----DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTD-----LLA-RGIDVQQ  346 (412)
Q Consensus       277 ~~~k~lif~~~~~~~~~~~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~-----~~~-~G~d~~~  346 (412)
                      ...++||.+++++.+.++++.+++.    +..+...+|+.+..   ...+.+..+..+|+|+|+     .+. ..+++..
T Consensus        97 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~---~~~~~l~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~  173 (237)
T 3bor_A           97 KETQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVR---NEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKW  173 (237)
T ss_dssp             CSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECC----------------CCCSEEEECHHHHHHHHHTTSSCSTT
T ss_pred             CCceEEEEECcHHHHHHHHHHHHHHhhhcCceEEEEECCCchH---HHHHHHhcCCCCEEEECHHHHHHHHHhCCcCccc
Confidence            3468999999999999888888653    55677777765432   233444556789999995     222 3356777


Q ss_pred             CCEEEEcc
Q 015158          347 VSLVINYD  354 (412)
Q Consensus       347 ~~~vi~~~  354 (412)
                      ++.+|+-+
T Consensus       174 ~~~lViDE  181 (237)
T 3bor_A          174 IKMFVLDE  181 (237)
T ss_dssp             CCEEEEES
T ss_pred             CcEEEECC
Confidence            88887644

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=85.89  E-value=0.41  Score=40.14  Aligned_cols=51  Identities=20%  Similarity=0.220  Sum_probs=30.8

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHH
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRA  129 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~  129 (412)
                      |.-+++.|++|+|||..++..+.+.....  +..++|+.-.. -.++..+.+..
T Consensus        30 G~l~~i~G~pG~GKT~l~l~~~~~~~~~~--~~~v~~~s~E~-~~~~~~~~~~~   80 (251)
T 2zts_A           30 GTTVLLTGGTGTGKTTFAAQFIYKGAEEY--GEPGVFVTLEE-RARDLRREMAS   80 (251)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHHHHHHHH--CCCEEEEESSS-CHHHHHHHHHT
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHHhc--CCCceeecccC-CHHHHHHHHHH
Confidence            46789999999999977665554433221  23577766432 24445544443

>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=85.83  E-value=0.95  Score=39.80  Aligned_cols=55  Identities=11%  Similarity=0.053  Sum_probs=32.8

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhccC---------CCc----eeEEEEcCCHHH-HHHHHHHHHHh
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDYG---------LVE----CQALVLAPTREL-AQQIEKVMRAL  130 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~~---------~~~----~~~lil~P~~~L-~~q~~~~~~~~  130 (412)
                      |.-+++.+++|+|||..++..+.......         ..+    .+++|+.-...+ .+++.+.+..+
T Consensus        98 g~i~~i~G~~gsGKT~la~~la~~~~l~~~~~~~~~~~~~gg~~~~~v~yi~~e~~~~~~~l~~~~~~~  166 (322)
T 2i1q_A           98 QSVTEFAGVFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRPERIMQMAEHA  166 (322)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHHTTCGGGEECCTTTSCTTTTSSEEEEEEESSSCCCHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHhccccccccccccccCCCCCceEEEEECCCCCCHHHHHHHHHHc
Confidence            45689999999999977765555432110         112    578888765432 34444444443

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=85.71  E-value=1.8  Score=35.84  Aligned_cols=115  Identities=10%  Similarity=0.078  Sum_probs=65.8

Q ss_pred             CCcEEEEEcchhHHHHHHHHHhcC----CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcC-CC----c--CCCCCCC
Q 015158          278 ITQSVIFVNTRRKVDWLTDKMRSR----DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTD-LL----A--RGIDVQQ  346 (412)
Q Consensus       278 ~~k~lif~~~~~~~~~~~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~-~~----~--~G~d~~~  346 (412)
                      ..++||.+++++-+.++++.+++.    +..+..++|+.+.......+     +..+|+|+|+ .+    .  ..+++..
T Consensus        97 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~-----~~~~iiv~Tp~~l~~~l~~~~~~~~~~  171 (236)
T 2pl3_A           97 GLGVLIISPTRELAYQTFEVLRKVGKNHDFSAGLIIGGKDLKHEAERI-----NNINILVCTPGRLLQHMDETVSFHATD  171 (236)
T ss_dssp             CCCEEEECSSHHHHHHHHHHHHHHTTTSSCCEEEECCC--CHHHHHHH-----TTCSEEEECHHHHHHHHHHCSSCCCTT
T ss_pred             CceEEEEeCCHHHHHHHHHHHHHHhCCCCeeEEEEECCCCHHHHHHhC-----CCCCEEEECHHHHHHHHHhcCCccccc
Confidence            467999999999998888888654    46788888886544332222     3678999996 22    1  2366777


Q ss_pred             CCEEEEccCCCC-hhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHHh
Q 015158          347 VSLVINYDLPTQ-PENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFY  397 (412)
Q Consensus       347 ~~~vi~~~~~~s-~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~  397 (412)
                      ++.+|+.+...- ...+...+.+..+.-..+.-+++++..-...+..+.+.+
T Consensus       172 ~~~lViDEah~~~~~~~~~~~~~i~~~~~~~~~~l~~SAT~~~~~~~~~~~~  223 (236)
T 2pl3_A          172 LQMLVLDEADRILDMGFADTMNAVIENLPKKRQTLLFSATQTKSVKDLARLS  223 (236)
T ss_dssp             CCEEEETTHHHHHHTTTHHHHHHHHHTSCTTSEEEEEESSCCHHHHHHHHHS
T ss_pred             ccEEEEeChHHHhcCCcHHHHHHHHHhCCCCCeEEEEEeeCCHHHHHHHHHh
Confidence            888886543210 001122222222222234446666666554455554443

>2l8b_A Protein TRAI, DNA helicase I; RECD, hydrolase; NMR {Escherichia coli}

Probab=85.64  E-value=0.53  Score=37.18  Aligned_cols=59  Identities=10%  Similarity=0.059  Sum_probs=41.7

Q ss_pred             ChHHHHhhhhhhhcC--ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHH
Q 015158           62 PSAIQQRGIVPFCKG--LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQ  122 (412)
Q Consensus        62 l~~~Q~~a~~~~~~~--~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q  122 (412)
                      ..+-|..++..++..  +-.+|.+.-|++|+...+..++.....  .+.++.+++|+..-...
T Consensus        35 ~~~~~~~a~~~l~~s~~~~~iv~g~ggs~~~~~~~a~L~~~a~~--~Gr~V~vLAp~~~s~~~   95 (189)
T 2l8b_A           35 RTAGYSDAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMARE--QGREVQIIAADRRSQMN   95 (189)
T ss_dssp             CHHHHHHHHHHHHHHSCCEECCBCSSCSHHHHHHHHHHHHHHHH--TTCCEEEECSTTHHHHH
T ss_pred             cCccchhHHHHHhccCCceEEEecccchHHHHHHHHHHHHHHHh--cCeEEEEEcCchHHHHH
Confidence            456789999998754  467789999999998754444433322  34689999999765443

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=85.61  E-value=13  Score=34.76  Aligned_cols=35  Identities=14%  Similarity=0.118  Sum_probs=22.2

Q ss_pred             cEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcC
Q 015158           78 DVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAP  115 (412)
Q Consensus        78 ~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P  115 (412)
                      .+++++++|+|||+.+.-.+......   +.+++++..
T Consensus       103 vI~ivG~~GvGKTTl~~kLA~~l~~~---G~kVllVd~  137 (504)
T 2j37_W          103 VIMFVGLQGSGKTTTCSKLAYYYQRK---GWKTCLICA  137 (504)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHT---TCCEEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhC---CCeEEEEec
Confidence            57788999999997764443332222   345666654

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=85.48  E-value=0.23  Score=42.69  Aligned_cols=54  Identities=15%  Similarity=0.179  Sum_probs=26.3

Q ss_pred             hccccccCCCCHHHHHHHHHCCCCCChHH-HHhhhhhh--hcCccEEEECCCCCCchhHh
Q 015158           37 VYDTFDAMGLQENLLRGIYAYGFEKPSAI-QQRGIVPF--CKGLDVIQQAQSGTGKTATF   93 (412)
Q Consensus        37 ~~~~f~~~~l~~~~~~~l~~~~~~~l~~~-Q~~a~~~~--~~~~~~lv~~~tGsGKT~~~   93 (412)
                      +-.+|++.+-.+++.+.+...-.   .|+ ..+++..+  .-.+.+++.||+|+|||+.+
T Consensus         5 ~~~~~~di~g~~~~~~~l~~~i~---~~~~~~~~l~~~~l~~~~GvlL~Gp~GtGKTtLa   61 (274)
T 2x8a_A            5 PNVTWADIGALEDIREELTMAIL---APVRNPDQFKALGLVTPAGVLLAGPPGCGKTLLA   61 (274)
T ss_dssp             -------CCHHHHHHHHHHHHHT---HHHHSHHHHHHTTCCCCSEEEEESSTTSCHHHHH
T ss_pred             CCCCHHHhCCHHHHHHHHHHHHH---HHhhCHHHHHHcCCCCCCeEEEECCCCCcHHHHH
Confidence            34567777766666666653111   111 11222221  11244899999999999765

>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=85.45  E-value=8.1  Score=34.53  Aligned_cols=105  Identities=7%  Similarity=0.141  Sum_probs=66.3

Q ss_pred             CCcEEEEEcchhHHHHHHHHHhcC-----CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcC-CC-----cCCCCCCC
Q 015158          278 ITQSVIFVNTRRKVDWLTDKMRSR-----DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTD-LL-----ARGIDVQQ  346 (412)
Q Consensus       278 ~~k~lif~~~~~~~~~~~~~L~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~-~~-----~~G~d~~~  346 (412)
                      ..++||.|+++.-+.++++.+++.     +..+..++|+.+......   .+.++..+|+|+|. .+     ...+++..
T Consensus        76 ~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~---~~~~~~~~iiv~T~~~l~~~~~~~~~~~~~  152 (391)
T 1xti_A           76 QVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEE---VLKKNCPHIVVGTPGRILALARNKSLNLKH  152 (391)
T ss_dssp             CCCEEEECSCHHHHHHHHHHHHHHTTTCTTCCEEEECTTSCHHHHHH---HHHHSCCSEEEECHHHHHHHHHTTSSCCTT
T ss_pred             CeeEEEECCCHHHHHHHHHHHHHHHhhCCCeEEEEEeCCCCHHHHHH---HHhcCCCCEEEECHHHHHHHHHcCCccccc
Confidence            358999999999999888877653     678999999887655443   34456788999996 22     23456778


Q ss_pred             CCEEEEccCCC--ChhhHHHhhhhcccCCCCceEEEEeccC
Q 015158          347 VSLVINYDLPT--QPENYLHRIGRSGRFGRKGVAINFVTRD  385 (412)
Q Consensus       347 ~~~vi~~~~~~--s~~~~~Q~~GR~~R~g~~g~~~~~~~~~  385 (412)
                      ++.||+.+...  ....+...+-+..+.-....-+++++..
T Consensus       153 ~~~vViDEaH~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT  193 (391)
T 1xti_A          153 IKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSAT  193 (391)
T ss_dssp             CSEEEECSHHHHTSSHHHHHHHHHHHHTSCSSSEEEEEESS
T ss_pred             cCEEEEeCHHHHhhccchHHHHHHHHhhCCCCceEEEEEee
Confidence            88888654321  1123333333333333334445555544

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=85.39  E-value=0.5  Score=37.50  Aligned_cols=20  Identities=10%  Similarity=0.111  Sum_probs=16.4

Q ss_pred             cCccEEEECCCCCCchhHhH
Q 015158           75 KGLDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        75 ~~~~~lv~~~tGsGKT~~~~   94 (412)
                      .|+-+++.||+|+|||...-
T Consensus         4 ~g~~i~i~GpsGsGKSTL~~   23 (180)
T 1kgd_A            4 MRKTLVLLGAHGVGRRHIKN   23 (180)
T ss_dssp             CCCEEEEECCTTSSHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHH
Confidence            46678899999999997653

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=85.25  E-value=0.5  Score=37.52  Aligned_cols=19  Identities=26%  Similarity=0.288  Sum_probs=15.9

Q ss_pred             CccEEEECCCCCCchhHhH
Q 015158           76 GLDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~   94 (412)
                      ...+++.||+|+|||..+-
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            3679999999999997653

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=85.06  E-value=0.94  Score=42.51  Aligned_cols=31  Identities=16%  Similarity=0.115  Sum_probs=23.2

Q ss_pred             hHHHHhhhhhhhcCccEEEECCCCCCchhHh
Q 015158           63 SAIQQRGIVPFCKGLDVIQQAQSGTGKTATF   93 (412)
Q Consensus        63 ~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~   93 (412)
                      ...-+.+...+..+.++++.||+|+|||..+
T Consensus        28 ~~~i~~l~~al~~~~~VLL~GpPGtGKT~LA   58 (500)
T 3nbx_X           28 SHAIRLCLLAALSGESVFLLGPPGIAKSLIA   58 (500)
T ss_dssp             HHHHHHHHHHHHHTCEEEEECCSSSSHHHHH
T ss_pred             HHHHHHHHHHHhcCCeeEeecCchHHHHHHH
Confidence            3333445555667889999999999999765

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=85.01  E-value=0.4  Score=38.96  Aligned_cols=23  Identities=17%  Similarity=0.183  Sum_probs=18.4

Q ss_pred             hhhcCccEEEECCCCCCchhHhH
Q 015158           72 PFCKGLDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        72 ~~~~~~~~lv~~~tGsGKT~~~~   94 (412)
                      ++..++-+++.||+|+|||..+-
T Consensus         8 ~~~~~~~i~l~G~sGsGKsTl~~   30 (204)
T 2qor_A            8 HMARIPPLVVCGPSGVGKGTLIK   30 (204)
T ss_dssp             -CCCCCCEEEECCTTSCHHHHHH
T ss_pred             ccccCCEEEEECCCCCCHHHHHH
Confidence            35567889999999999997653

>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=85.00  E-value=0.63  Score=39.57  Aligned_cols=19  Identities=26%  Similarity=0.253  Sum_probs=16.5

Q ss_pred             cCccEEEECCCCCCchhHh
Q 015158           75 KGLDVIQQAQSGTGKTATF   93 (412)
Q Consensus        75 ~~~~~lv~~~tGsGKT~~~   93 (412)
                      .+.++++.||+|+|||..+
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            4578999999999999765

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=84.76  E-value=0.55  Score=37.95  Aligned_cols=20  Identities=20%  Similarity=0.140  Sum_probs=17.0

Q ss_pred             cCccEEEECCCCCCchhHhH
Q 015158           75 KGLDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        75 ~~~~~lv~~~tGsGKT~~~~   94 (412)
                      .++.+++.|++|+|||+.+-
T Consensus        24 ~~~~i~l~G~~GsGKsTl~~   43 (199)
T 3vaa_A           24 AMVRIFLTGYMGAGKTTLGK   43 (199)
T ss_dssp             CCCEEEEECCTTSCHHHHHH
T ss_pred             CCCEEEEEcCCCCCHHHHHH
Confidence            46789999999999998763

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=84.69  E-value=0.91  Score=37.41  Aligned_cols=27  Identities=33%  Similarity=0.389  Sum_probs=20.2

Q ss_pred             cEEEECCCCCCchhHhHHHHHHhhccC
Q 015158           78 DVIQQAQSGTGKTATFCSGILQQLDYG  104 (412)
Q Consensus        78 ~~lv~~~tGsGKT~~~~~~~~~~~~~~  104 (412)
                      ++++.++.|+|||..++-.+......+
T Consensus         8 ~I~~~~kgGvGKTt~a~~la~~l~~~G   34 (228)
T 2r8r_A            8 KVFLGAAPGVGKTYAMLQAAHAQLRQG   34 (228)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHHHHHTT
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHCC
Confidence            688999999999988766555544443

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=84.59  E-value=0.51  Score=41.59  Aligned_cols=19  Identities=21%  Similarity=0.209  Sum_probs=15.7

Q ss_pred             CccEEEECCCCCCchhHhH
Q 015158           76 GLDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~   94 (412)
                      ++.++|.||||+|||..+.
T Consensus        40 ~~lIvI~GPTgsGKTtLa~   58 (339)
T 3a8t_A           40 EKLLVLMGATGTGKSRLSI   58 (339)
T ss_dssp             CEEEEEECSTTSSHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHH
Confidence            3468899999999997764

>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=84.53  E-value=9.2  Score=36.36  Aligned_cols=89  Identities=11%  Similarity=0.128  Sum_probs=60.8

Q ss_pred             HHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHH----hcCCCcEEEeChHHHHHH
Q 015158           96 GILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRI----LSSGVHVVVGTPGRVFDM  171 (412)
Q Consensus        96 ~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~iii~T~~~l~~~  171 (412)
                      .+...+.....+.++||.|+++.-++.+++.+..... .+..+..++|+.........    ..+..+|+|+|.     .
T Consensus       328 ~l~~~~~~~~~~~~~iVF~~s~~~~~~l~~~L~~~~~-~~~~v~~~h~~~~~~~R~~~~~~f~~g~~~vLvaT~-----~  401 (563)
T 3i5x_A          328 HIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFK-KDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTD-----V  401 (563)
T ss_dssp             HHHHHHHHTTTCCEEEEECSCHHHHHHHHHHHHHHHT-TTSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEECG-----G
T ss_pred             HHHHHHhhcCCCCcEEEEcCcHHHHHHHHHHHHHhcc-CCceEEEecCCCCHHHHHHHHHHHhcCCCCEEEEcc-----h
Confidence            3333343334456899999999999999988887532 26778888888765544322    346789999993     2


Q ss_pred             HHcCCCCCCCceEEEEeCCc
Q 015158          172 LRRQSLRPDNIRIFVLDEAD  191 (412)
Q Consensus       172 ~~~~~~~~~~~~~iiiDE~h  191 (412)
                       ...+++..++++||.-..-
T Consensus       402 -~~~GiDip~v~~VI~~~~p  420 (563)
T 3i5x_A          402 -GARGMDFPNVHEVLQIGVP  420 (563)
T ss_dssp             -GTSSCCCTTCCEEEEESCC
T ss_pred             -hhcCCCcccCCEEEEECCC
Confidence             3457777888888765543

>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=84.46  E-value=1.2  Score=39.28  Aligned_cols=54  Identities=17%  Similarity=0.086  Sum_probs=32.2

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhcc---CCCceeEEEEcCCHHH-HHHHHHHHHH
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDY---GLVECQALVLAPTREL-AQQIEKVMRA  129 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~---~~~~~~~lil~P~~~L-~~q~~~~~~~  129 (412)
                      |.-+++.+++|+|||..++..+......   +..+.+++|+.-...+ ..++.+.+..
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            4678999999999997776555543322   1113578888765432 3334433444

>4ag6_A VIRB4 ATPase, type IV secretory pathway VIRB4 components-like P; hydrolase, type IV secretion, conjugation; 2.35A {Thermoanaerobacter pseudethanolicus} PDB: 4ag5_A

Probab=84.42  E-value=0.99  Score=40.96  Aligned_cols=41  Identities=22%  Similarity=0.299  Sum_probs=28.1

Q ss_pred             cCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHH
Q 015158           75 KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRE  118 (412)
Q Consensus        75 ~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  118 (412)
                      .+.+++|.++||+|||...-..+.....   .+.+++++=|..+
T Consensus        34 ~~~~~~i~G~~G~GKs~~~~~~~~~~~~---~~~~~~~~D~~~~   74 (392)
T 4ag6_A           34 TNSNWTILAKPGAGKSFTAKMLLLREYM---QGSRVIIIDPERE   74 (392)
T ss_dssp             CCCCEEEECCTTSSHHHHHHHHHHHHHT---TTCCEEEEESSCC
T ss_pred             ccCceEEEcCCCCCHHHHHHHHHHHHHH---CCCEEEEEeCCcC
Confidence            4678999999999999766444443332   2346777777544

>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=84.39  E-value=0.99  Score=39.20  Aligned_cols=19  Identities=21%  Similarity=0.302  Sum_probs=16.2

Q ss_pred             CccEEEECCCCCCchhHhH
Q 015158           76 GLDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~   94 (412)
                      ..++++.||+|+|||..+-
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            5689999999999997653

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=84.34  E-value=0.37  Score=43.90  Aligned_cols=55  Identities=24%  Similarity=0.310  Sum_probs=34.6

Q ss_pred             hhccccccCCCCHHHHHHHHH---CCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHh
Q 015158           36 EVYDTFDAMGLQENLLRGIYA---YGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATF   93 (412)
Q Consensus        36 ~~~~~f~~~~l~~~~~~~l~~---~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~   93 (412)
                      .+-.+|++.+=-+...+.|..   .++..|..++...+   .-.+.+++.||+|+|||+.+
T Consensus       176 ~p~v~~~DIgGld~~k~~L~e~v~~Pl~~pe~f~~~Gi---~~prGvLLyGPPGTGKTlLA  233 (437)
T 4b4t_I          176 SPTESYSDIGGLESQIQEIKESVELPLTHPELYEEMGI---KPPKGVILYGAPGTGKTLLA  233 (437)
T ss_dssp             SCCCCGGGTCSCHHHHHHHHHHHHHHHHCCHHHHHHTC---CCCSEEEEESSTTTTHHHHH
T ss_pred             CCCCcceecCcHHHHHHHHHHHHHHHHhCHHHHHhCCC---CCCCCCceECCCCchHHHHH
Confidence            455688888655666555543   23333444443332   22467999999999999765

>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=84.33  E-value=0.35  Score=38.73  Aligned_cols=21  Identities=19%  Similarity=0.241  Sum_probs=17.3

Q ss_pred             hhcCccEEEECCCCCCchhHh
Q 015158           73 FCKGLDVIQQAQSGTGKTATF   93 (412)
Q Consensus        73 ~~~~~~~lv~~~tGsGKT~~~   93 (412)
                      +..|..+++.||+|||||+.+
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            445777899999999999765

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=83.89  E-value=0.36  Score=42.68  Aligned_cols=24  Identities=21%  Similarity=0.512  Sum_probs=19.3

Q ss_pred             hhhhhcCccEEEECCCCCCchhHh
Q 015158           70 IVPFCKGLDVIQQAQSGTGKTATF   93 (412)
Q Consensus        70 ~~~~~~~~~~lv~~~tGsGKT~~~   93 (412)
                      ...+..++++++.||+|+|||..+
T Consensus        40 ~~~l~~~~~vll~G~pGtGKT~la   63 (331)
T 2r44_A           40 LIGICTGGHILLEGVPGLAKTLSV   63 (331)
T ss_dssp             HHHHHHTCCEEEESCCCHHHHHHH
T ss_pred             HHHHHcCCeEEEECCCCCcHHHHH
Confidence            334556789999999999999765

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=83.75  E-value=0.5  Score=38.30  Aligned_cols=21  Identities=33%  Similarity=0.382  Sum_probs=17.1

Q ss_pred             hcCccEEEECCCCCCchhHhH
Q 015158           74 CKGLDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        74 ~~~~~~lv~~~tGsGKT~~~~   94 (412)
                      ..|..+.+.||+|||||+.+-
T Consensus         4 ~~g~~i~l~G~~GsGKSTl~~   24 (207)
T 2j41_A            4 EKGLLIVLSGPSGVGKGTVRK   24 (207)
T ss_dssp             CCCCEEEEECSTTSCHHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHHH
Confidence            356778899999999997653

>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=83.65  E-value=1.2  Score=42.16  Aligned_cols=41  Identities=17%  Similarity=0.267  Sum_probs=25.4

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhccCCC-ceeEEEEcCC
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDYGLV-ECQALVLAPT  116 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~-~~~~lil~P~  116 (412)
                      ..+++|.+.||||||.+.-..++..+....+ ..+++++=|-
T Consensus       214 ~pHlLIaG~TGSGKS~~L~tlI~sLl~~~sP~ev~lilIDpK  255 (574)
T 2iut_A          214 MPHLLVAGTTGSGKSVGVNAMLLSILFKSTPSEARLIMIDPK  255 (574)
T ss_dssp             SCCEEEECCTTSSHHHHHHHHHHHHHTTCCTTTEEEEEECSS
T ss_pred             CCeeEEECCCCCCHHHHHHHHHHHHHHhCCCcceEEEEeCCC
Confidence            4589999999999998765555544433222 2344444443

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=83.63  E-value=0.49  Score=38.31  Aligned_cols=19  Identities=26%  Similarity=0.384  Sum_probs=15.0

Q ss_pred             cCccEEEECCCCCCchhHh
Q 015158           75 KGLDVIQQAQSGTGKTATF   93 (412)
Q Consensus        75 ~~~~~lv~~~tGsGKT~~~   93 (412)
                      .|+.+.+.||+|+|||...
T Consensus         3 ~g~~i~lvGpsGaGKSTLl   21 (198)
T 1lvg_A            3 GPRPVVLSGPSGAGKSTLL   21 (198)
T ss_dssp             --CCEEEECCTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4667899999999999765

>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=83.59  E-value=0.72  Score=41.14  Aligned_cols=41  Identities=22%  Similarity=0.144  Sum_probs=28.0

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHH
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTREL  119 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L  119 (412)
                      |.-++|.+|+|+|||..++..+......   +.+++|+..-..+
T Consensus        61 G~i~~I~GppGsGKSTLal~la~~~~~~---gg~VlyId~E~s~  101 (356)
T 3hr8_A           61 GRIVEIFGQESSGKTTLALHAIAEAQKM---GGVAAFIDAEHAL  101 (356)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHHHHHT---TCCEEEEESSCCC
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHhc---CCeEEEEeccccc
Confidence            5678899999999997765555443332   2468888765444

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=83.55  E-value=0.57  Score=42.03  Aligned_cols=21  Identities=19%  Similarity=0.306  Sum_probs=18.0

Q ss_pred             hhcCccEEEECCCCCCchhHh
Q 015158           73 FCKGLDVIQQAQSGTGKTATF   93 (412)
Q Consensus        73 ~~~~~~~lv~~~tGsGKT~~~   93 (412)
                      +..|..+++.+|||||||+..
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            456889999999999999754

>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=83.52  E-value=0.54  Score=37.22  Aligned_cols=20  Identities=20%  Similarity=0.149  Sum_probs=16.9

Q ss_pred             cCccEEEECCCCCCchhHhH
Q 015158           75 KGLDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        75 ~~~~~lv~~~tGsGKT~~~~   94 (412)
                      .++.+++.|++|+|||..+-
T Consensus        10 ~~~~i~i~G~~GsGKst~~~   29 (180)
T 3iij_A           10 LLPNILLTGTPGVGKTTLGK   29 (180)
T ss_dssp             CCCCEEEECSTTSSHHHHHH
T ss_pred             cCCeEEEEeCCCCCHHHHHH
Confidence            46679999999999998764

>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=83.48  E-value=0.67  Score=37.79  Aligned_cols=20  Identities=30%  Similarity=0.439  Sum_probs=16.3

Q ss_pred             cCccEEEECCCCCCchhHhH
Q 015158           75 KGLDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        75 ~~~~~lv~~~tGsGKT~~~~   94 (412)
                      .|.-+++.||+|+|||...-
T Consensus         7 ~g~~i~l~GpsGsGKsTl~~   26 (208)
T 3tau_A            7 RGLLIVLSGPSGVGKGTVRE   26 (208)
T ss_dssp             CCCEEEEECCTTSCHHHHHH
T ss_pred             CCcEEEEECcCCCCHHHHHH
Confidence            45678899999999997653

>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=83.46  E-value=0.52  Score=37.15  Aligned_cols=18  Identities=22%  Similarity=0.259  Sum_probs=15.3

Q ss_pred             CccEEEECCCCCCchhHh
Q 015158           76 GLDVIQQAQSGTGKTATF   93 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~   93 (412)
                      +..+++.|++|||||..+
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            456789999999999876

>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=83.36  E-value=0.99  Score=40.30  Aligned_cols=40  Identities=18%  Similarity=0.067  Sum_probs=28.5

Q ss_pred             cCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCH
Q 015158           75 KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTR  117 (412)
Q Consensus        75 ~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~  117 (412)
                      .|.-+++.+++|+|||..++..+......+   .+++|+....
T Consensus        62 ~G~ii~I~G~pGsGKTtLal~la~~~~~~g---~~vlyid~E~  101 (356)
T 1u94_A           62 MGRIVEIYGPESSGKTTLTLQVIAAAQREG---KTCAFIDAEH  101 (356)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHHHHHHTT---CCEEEEESSC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHCC---CeEEEEeCCC
Confidence            356789999999999988766555544332   3688877643

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=83.30  E-value=0.68  Score=36.75  Aligned_cols=19  Identities=21%  Similarity=0.149  Sum_probs=16.1

Q ss_pred             CccEEEECCCCCCchhHhH
Q 015158           76 GLDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~   94 (412)
                      .+.+++.|++|||||..+-
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            4578999999999998764

>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=83.19  E-value=0.9  Score=40.49  Aligned_cols=40  Identities=13%  Similarity=0.094  Sum_probs=28.3

Q ss_pred             cCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCH
Q 015158           75 KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTR  117 (412)
Q Consensus        75 ~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~  117 (412)
                      .|.-+++.+++|+|||..++..+......   +.+++|+....
T Consensus        60 ~G~iv~I~G~pGsGKTtLal~la~~~~~~---g~~vlyi~~E~   99 (349)
T 2zr9_A           60 RGRVIEIYGPESSGKTTVALHAVANAQAA---GGIAAFIDAEH   99 (349)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHT---TCCEEEEESSC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhC---CCeEEEEECCC
Confidence            46778999999999998776655554433   34688877543

>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=83.16  E-value=1.9  Score=36.60  Aligned_cols=44  Identities=14%  Similarity=0.172  Sum_probs=28.4

Q ss_pred             HHHHHHHHCCCCCChHHHHhhhhhhhcCc-----cEEEECCCCCCchhHhH
Q 015158           49 NLLRGIYAYGFEKPSAIQQRGIVPFCKGL-----DVIQQAQSGTGKTATFC   94 (412)
Q Consensus        49 ~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~-----~~lv~~~tGsGKT~~~~   94 (412)
                      .+.+.|.-.|+. |-.+ ..++..+++++     .+++.||+|+|||..+.
T Consensus        74 ~i~~~l~~qg~~-~~~~-~~~l~~~l~~~~~~~n~~~l~GppgtGKt~~a~  122 (267)
T 1u0j_A           74 RIYKILELNGYD-PQYA-ASVFLGWATKKFGKRNTIWLFGPATTGKTNIAE  122 (267)
T ss_dssp             HHHHHHHHTTCC-HHHH-HHHHHHHHTTCSTTCCEEEEECSTTSSHHHHHH
T ss_pred             HHHHHHHHcCCC-HHHH-HHHHHHHHhCCCCCCcEEEEECCCCCCHHHHHH
Confidence            566677666766 3322 22344455442     48899999999998764

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=83.05  E-value=1.6  Score=35.30  Aligned_cols=44  Identities=16%  Similarity=0.089  Sum_probs=26.0

Q ss_pred             HHHHHHHHHCCCCCChHHHHhhhhhhhcC----ccEEEECCCCCCchhHh
Q 015158           48 ENLLRGIYAYGFEKPSAIQQRGIVPFCKG----LDVIQQAQSGTGKTATF   93 (412)
Q Consensus        48 ~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~----~~~lv~~~tGsGKT~~~   93 (412)
                      ..+.+.|.--++. +-.+ ...+..++++    +.+++.+|+|+|||..+
T Consensus        28 ~~I~~~l~yq~~~-~~~f-~~~l~~~~~~iPkkn~ili~GPPGtGKTt~a   75 (212)
T 1tue_A           28 RPIVQFLRYQQIE-FITF-LGALKSFLKGTPKKNCLVFCGPANTGKSYFG   75 (212)
T ss_dssp             HHHHHHHHHTTCC-HHHH-HHHHHHHHHTCTTCSEEEEESCGGGCHHHHH
T ss_pred             HHHHHHHHHcCcC-HHHH-HHHHHHHHhcCCcccEEEEECCCCCCHHHHH
Confidence            3455555433333 4444 3344444443    35889999999999765

>2r2a_A Uncharacterized protein; zonular occludens toxin, structural genomics, APC84050.2, PS protein structure initiative; HET: MSE; 1.82A {Neisseria meningitidis MC58}

Probab=82.92  E-value=0.9  Score=36.77  Aligned_cols=22  Identities=23%  Similarity=0.299  Sum_probs=16.6

Q ss_pred             cEEEECCCCCCchhHhHHHHHH
Q 015158           78 DVIQQAQSGTGKTATFCSGILQ   99 (412)
Q Consensus        78 ~~lv~~~tGsGKT~~~~~~~~~   99 (412)
                      -.++.|++|||||..+...+..
T Consensus         7 i~l~tG~pGsGKT~~a~~~~~~   28 (199)
T 2r2a_A            7 ICLITGTPGSGKTLKMVSMMAN   28 (199)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEEeCCCCCHHHHHHHHHHH
Confidence            3589999999999876544443

>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=82.88  E-value=7.3  Score=32.47  Aligned_cols=113  Identities=10%  Similarity=0.046  Sum_probs=65.3

Q ss_pred             CcEEEEEcchhHHHHHHHHHhc----CCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcC-CC-----cCCCCCCCCC
Q 015158          279 TQSVIFVNTRRKVDWLTDKMRS----RDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTD-LL-----ARGIDVQQVS  348 (412)
Q Consensus       279 ~k~lif~~~~~~~~~~~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~-~~-----~~G~d~~~~~  348 (412)
                      .++||.+++++-+.++++.+++    .+..+..++|+.+.......   . ....+|+|+|+ .+     ...+++..++
T Consensus       101 ~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~---~-~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~  176 (253)
T 1wrb_A          101 PKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIRE---V-QMGCHLLVATPGRLVDFIEKNKISLEFCK  176 (253)
T ss_dssp             CSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCSHHHHHH---H-SSCCSEEEECHHHHHHHHHTTSBCCTTCC
T ss_pred             ceEEEEECCHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHH---h-CCCCCEEEECHHHHHHHHHcCCCChhhCC
Confidence            5899999999999888877764    35677788887765443222   2 34678999997 22     2235677788


Q ss_pred             EEEEccCC----CC-hhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHH
Q 015158          349 LVINYDLP----TQ-PENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQK  395 (412)
Q Consensus       349 ~vi~~~~~----~s-~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~  395 (412)
                      .+|+.+..    ++ ...+...+.+.......+.-+++++..-...+..+.+
T Consensus       177 ~lViDEah~~~~~~~~~~~~~i~~~~~~~~~~~~q~l~~SAT~~~~~~~~~~  228 (253)
T 1wrb_A          177 YIVLDEADRMLDMGFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAA  228 (253)
T ss_dssp             EEEEETHHHHHHTTCHHHHHHHHHSSCCCCGGGCEEEEEESSCCHHHHHHHH
T ss_pred             EEEEeCHHHHHhCchHHHHHHHHhhccCCCCCCcEEEEEEEeCCHHHHHHHH
Confidence            88754432    11 1222223332222211244566666654444444443

>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=82.84  E-value=0.51  Score=36.93  Aligned_cols=17  Identities=18%  Similarity=0.259  Sum_probs=14.3

Q ss_pred             cEEEECCCCCCchhHhH
Q 015158           78 DVIQQAQSGTGKTATFC   94 (412)
Q Consensus        78 ~~lv~~~tGsGKT~~~~   94 (412)
                      .+++.|++|||||+.+-
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            46889999999998764

>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=82.84  E-value=0.59  Score=37.24  Aligned_cols=20  Identities=35%  Similarity=0.605  Sum_probs=16.7

Q ss_pred             cCccEEEECCCCCCchhHhH
Q 015158           75 KGLDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        75 ~~~~~lv~~~tGsGKT~~~~   94 (412)
                      .+..+++.|++|||||.++-
T Consensus         9 ~~~~I~l~G~~GsGKSTv~~   28 (184)
T 1y63_A            9 KGINILITGTPGTGKTSMAE   28 (184)
T ss_dssp             SSCEEEEECSTTSSHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHH
Confidence            35678999999999998763

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=82.79  E-value=12  Score=35.82  Aligned_cols=80  Identities=10%  Similarity=0.117  Sum_probs=57.7

Q ss_pred             CCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHH----HhcCCCcEEEeChHHHHHHHHcCCCCCC
Q 015158          105 LVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQR----ILSSGVHVVVGTPGRVFDMLRRQSLRPD  180 (412)
Q Consensus       105 ~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~iii~T~~~l~~~~~~~~~~~~  180 (412)
                      ..+.++||.|+++.-++.+++.+..... .+..+..++|+........    ...+...|+|+|.     . ...+++..
T Consensus       286 ~~~~~~iVF~~t~~~~~~l~~~L~~~~~-~~~~v~~~hg~~~~~~R~~~~~~F~~g~~~vLVaT~-----~-~~~GiDip  358 (579)
T 3sqw_A          286 DSNYKAIIFAPTVKFTSFLCSILKNEFK-KDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTD-----V-GARGMDFP  358 (579)
T ss_dssp             TTCCEEEEECSSHHHHHHHHHHHHHHHT-TTSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEECG-----G-GTSSCCCT
T ss_pred             CCCCcEEEECCcHHHHHHHHHHHHHhhc-CCCcEEEecCCCCHHHHHHHHHHhhcCCCeEEEEcc-----h-hhcCCCcc
Confidence            3456899999999999999988887532 2677888888876544322    2346789999993     3 34577778


Q ss_pred             CceEEEEeCCc
Q 015158          181 NIRIFVLDEAD  191 (412)
Q Consensus       181 ~~~~iiiDE~h  191 (412)
                      ++++||.-..-
T Consensus       359 ~v~~VI~~~~p  369 (579)
T 3sqw_A          359 NVHEVLQIGVP  369 (579)
T ss_dssp             TCCEEEEESCC
T ss_pred             cCCEEEEcCCC
Confidence            88888876644

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=82.70  E-value=0.44  Score=42.02  Aligned_cols=54  Identities=11%  Similarity=-0.034  Sum_probs=29.9

Q ss_pred             ccccccCCCCHHHHHHHHHCCCCCChHHHH-hhhhh-hhcCccEEEECCCCCCchhHhH
Q 015158           38 YDTFDAMGLQENLLRGIYAYGFEKPSAIQQ-RGIVP-FCKGLDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        38 ~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~-~a~~~-~~~~~~~lv~~~tGsGKT~~~~   94 (412)
                      -.+|++++-.+...+.|...-.   +|.+. +.+.. ....+.+++.||+|+|||..+-
T Consensus         8 ~~~~~di~G~~~~k~~l~~~v~---~p~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~   63 (322)
T 1xwi_A            8 NVKWSDVAGLEGAKEALKEAVI---LPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAK   63 (322)
T ss_dssp             CCCGGGSCSCHHHHHHHHHHHH---HHHHCGGGSCTTCCCCSEEEEESSSSSCHHHHHH
T ss_pred             CCCHHHhcCHHHHHHHHHHHHH---HHHhCHHHHhCCCCCCceEEEECCCCccHHHHHH
Confidence            3467777666666666643100   11110 01111 1223679999999999997763

>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=82.61  E-value=7.9  Score=34.56  Aligned_cols=76  Identities=13%  Similarity=0.206  Sum_probs=56.2

Q ss_pred             CceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHH----hcCCCcEEEeChHHHHHHHHcCCCCCCC
Q 015158          106 VECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRI----LSSGVHVVVGTPGRVFDMLRRQSLRPDN  181 (412)
Q Consensus       106 ~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~iii~T~~~l~~~~~~~~~~~~~  181 (412)
                      ...++||.|+++.-++.+.+.+...    +..+..++|+.+.......    ..+..+|+|+|.      ....+++..+
T Consensus       242 ~~~~~lvf~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~------~~~~Gidip~  311 (395)
T 3pey_A          242 TIGSSIIFVATKKTANVLYGKLKSE----GHEVSILHGDLQTQERDRLIDDFREGRSKVLITTN------VLARGIDIPT  311 (395)
T ss_dssp             TSSEEEEECSCHHHHHHHHHHHHHT----TCCCEEECTTSCHHHHHHHHHHHHTTSCCEEEECG------GGSSSCCCTT
T ss_pred             cCCCEEEEeCCHHHHHHHHHHHHhc----CCcEEEeCCCCCHHHHHHHHHHHHCCCCCEEEECC------hhhcCCCccc
Confidence            3458999999999999888888775    6778888988765544322    245678999993      2345777888


Q ss_pred             ceEEEEeCCc
Q 015158          182 IRIFVLDEAD  191 (412)
Q Consensus       182 ~~~iiiDE~h  191 (412)
                      +++||.-+..
T Consensus       312 ~~~Vi~~~~p  321 (395)
T 3pey_A          312 VSMVVNYDLP  321 (395)
T ss_dssp             EEEEEESSCC
T ss_pred             CCEEEEcCCC
Confidence            9988876654

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=82.57  E-value=0.56  Score=40.64  Aligned_cols=19  Identities=21%  Similarity=0.212  Sum_probs=16.3

Q ss_pred             CccEEEECCCCCCchhHhH
Q 015158           76 GLDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~   94 (412)
                      ++.+++.||+|+|||..+-
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

>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=82.52  E-value=1.3  Score=39.41  Aligned_cols=42  Identities=12%  Similarity=-0.069  Sum_probs=27.3

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhccC---CCceeEEEEcCCH
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDYG---LVECQALVLAPTR  117 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~~---~~~~~~lil~P~~  117 (412)
                      |.-+++.+++|+|||..++..+.......   ..+.+++|+....
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            35678999999999977765555432211   1234788887654

>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=82.36  E-value=2.7  Score=34.57  Aligned_cols=74  Identities=8%  Similarity=0.125  Sum_probs=48.7

Q ss_pred             CCCcEEEEEcchhHHHHHHHHHhc---CCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcC-C-----CcCCCCCCCC
Q 015158          277 AITQSVIFVNTRRKVDWLTDKMRS---RDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTD-L-----LARGIDVQQV  347 (412)
Q Consensus       277 ~~~k~lif~~~~~~~~~~~~~L~~---~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~-~-----~~~G~d~~~~  347 (412)
                      ...++||.+++++-+.++++.+++   .+..+..++|+.+...+...   +. ...+|+|+|+ .     ....+++..+
T Consensus        93 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~-~~~~iiv~Tp~~l~~~~~~~~~~~~~~  168 (228)
T 3iuy_A           93 NGPGMLVLTPTRELALHVEAECSKYSYKGLKSICIYGGRNRNGQIED---IS-KGVDIIIATPGRLNDLQMNNSVNLRSI  168 (228)
T ss_dssp             CCCSEEEECSSHHHHHHHHHHHHHHCCTTCCEEEECC------CHHH---HH-SCCSEEEECHHHHHHHHHTTCCCCTTC
T ss_pred             CCCcEEEEeCCHHHHHHHHHHHHHhcccCceEEEEECCCChHHHHHH---hc-CCCCEEEECHHHHHHHHHcCCcCcccc
Confidence            346799999999999999888876   36778888887654433222   22 3578999996 1     1235667788


Q ss_pred             CEEEEcc
Q 015158          348 SLVINYD  354 (412)
Q Consensus       348 ~~vi~~~  354 (412)
                      +.+|+.+
T Consensus       169 ~~lViDE  175 (228)
T 3iuy_A          169 TYLVIDE  175 (228)
T ss_dssp             CEEEECC
T ss_pred             eEEEEEC
Confidence            8888654

>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=82.26  E-value=2.2  Score=48.36  Aligned_cols=47  Identities=23%  Similarity=0.148  Sum_probs=31.9

Q ss_pred             HHHHHHHHHCCCCCChHHHHhh----hhhhhcCccEEEECCCCCCchhHhHH
Q 015158           48 ENLLRGIYAYGFEKPSAIQQRG----IVPFCKGLDVIQQAQSGTGKTATFCS   95 (412)
Q Consensus        48 ~~~~~~l~~~~~~~l~~~Q~~a----~~~~~~~~~~lv~~~tGsGKT~~~~~   95 (412)
                      ..+.+.+...++. +.+.+..-    .+.+..+..++++||||+|||.++-.
T Consensus       892 ~~i~~~~~~~~l~-~~~~~~~K~~ql~e~~~~r~gvmlvGptgsGKTt~~~~  942 (2695)
T 4akg_A          892 QCLKDAGQRSGFS-MSEEFLKKCMQFYYMQKTQQALILVGKAGCGKTATWKT  942 (2695)
T ss_dssp             HHHHHHHHHHTCC-CCHHHHHHHHHHHHHHHHCSEEEEECSTTSSHHHHHHH
T ss_pred             HHHHHHHHHcCCc-ccHHHHHHHHHHHHHHHhcceEEEECCCCCCHHHHHHH
Confidence            4556666677777 56655332    23344567899999999999987643

>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=82.15  E-value=0.73  Score=40.12  Aligned_cols=18  Identities=28%  Similarity=0.132  Sum_probs=14.7

Q ss_pred             ccEEEECCCCCCchhHhH
Q 015158           77 LDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~   94 (412)
                      .-++|.||||+|||..+.
T Consensus         4 ~~i~i~GptgsGKt~la~   21 (322)
T 3exa_A            4 KLVAIVGPTAVGKTKTSV   21 (322)
T ss_dssp             EEEEEECCTTSCHHHHHH
T ss_pred             cEEEEECCCcCCHHHHHH
Confidence            456889999999997764

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=82.14  E-value=0.64  Score=36.41  Aligned_cols=18  Identities=17%  Similarity=0.226  Sum_probs=15.3

Q ss_pred             CccEEEECCCCCCchhHh
Q 015158           76 GLDVIQQAQSGTGKTATF   93 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~   93 (412)
                      +..+++.|+.|||||+.+
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            456899999999999765

>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=82.08  E-value=0.77  Score=38.82  Aligned_cols=19  Identities=21%  Similarity=0.136  Sum_probs=16.0

Q ss_pred             CccEEEECCCCCCchhHhH
Q 015158           76 GLDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~   94 (412)
                      .+.+++.||+|+|||..+-
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            4678999999999997653

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=82.06  E-value=0.54  Score=36.97  Aligned_cols=21  Identities=24%  Similarity=0.101  Sum_probs=16.9

Q ss_pred             hcCccEEEECCCCCCchhHhH
Q 015158           74 CKGLDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        74 ~~~~~~lv~~~tGsGKT~~~~   94 (412)
                      ..|.-+.+.||.|||||+.+-
T Consensus         7 ~~gei~~l~G~nGsGKSTl~~   27 (171)
T 4gp7_A            7 PELSLVVLIGSSGSGKSTFAK   27 (171)
T ss_dssp             ESSEEEEEECCTTSCHHHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHH
Confidence            356678899999999997653

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=82.05  E-value=0.64  Score=37.59  Aligned_cols=19  Identities=42%  Similarity=0.403  Sum_probs=16.1

Q ss_pred             cCccEEEECCCCCCchhHh
Q 015158           75 KGLDVIQQAQSGTGKTATF   93 (412)
Q Consensus        75 ~~~~~lv~~~tGsGKT~~~   93 (412)
                      .|.-+.+.||+|+|||+.+
T Consensus         6 ~g~ii~l~Gp~GsGKSTl~   24 (205)
T 3tr0_A            6 KANLFIISAPSGAGKTSLV   24 (205)
T ss_dssp             CCCEEEEECCTTSCHHHHH
T ss_pred             CCcEEEEECcCCCCHHHHH
Confidence            5667889999999999765

>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=82.04  E-value=0.71  Score=41.58  Aligned_cols=21  Identities=24%  Similarity=0.298  Sum_probs=17.3

Q ss_pred             hhcCccEEEECCCCCCchhHh
Q 015158           73 FCKGLDVIQQAQSGTGKTATF   93 (412)
Q Consensus        73 ~~~~~~~lv~~~tGsGKT~~~   93 (412)
                      +..|..+++.+|||||||+..
T Consensus       133 ~~~g~~i~ivG~~GsGKTTll  153 (372)
T 2ewv_A          133 HRKMGLILVTGPTGSGKSTTI  153 (372)
T ss_dssp             TSSSEEEEEECSSSSSHHHHH
T ss_pred             hcCCCEEEEECCCCCCHHHHH
Confidence            345778899999999999764

>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=82.01  E-value=0.72  Score=40.21  Aligned_cols=42  Identities=10%  Similarity=-0.066  Sum_probs=30.7

Q ss_pred             cEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHH
Q 015158           78 DVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELA  120 (412)
Q Consensus        78 ~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~  120 (412)
                      .+++.+|+|+|||..++..+......+ .+.+++|+..-.++.
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            578999999999988777666655431 245789988766553

>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=81.96  E-value=1.2  Score=38.64  Aligned_cols=22  Identities=23%  Similarity=0.300  Sum_probs=16.9

Q ss_pred             CccEEEECCCCCCchhHhHHHH
Q 015158           76 GLDVIQQAQSGTGKTATFCSGI   97 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~   97 (412)
                      ++.+++.+++|+|||+.+...+
T Consensus       105 g~vi~lvG~~GsGKTTl~~~LA  126 (296)
T 2px0_A          105 SKYIVLFGSTGAGKTTTLAKLA  126 (296)
T ss_dssp             SSEEEEEESTTSSHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHH
Confidence            4578889999999997664433

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=81.72  E-value=3.4  Score=47.58  Aligned_cols=46  Identities=15%  Similarity=0.104  Sum_probs=32.4

Q ss_pred             HHHHHHHHHCCCCCChHHHHhhhhh----hhcCccEEEECCCCCCchhHhH
Q 015158           48 ENLLRGIYAYGFEKPSAIQQRGIVP----FCKGLDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        48 ~~~~~~l~~~~~~~l~~~Q~~a~~~----~~~~~~~lv~~~tGsGKT~~~~   94 (412)
                      ..+.+.....++. +.+.+..=+-.    +..+..++++||||+|||.++-
T Consensus       875 ~ai~~~~~~~~L~-~~~~~v~KviQLye~~~vRhGvmlVGp~gsGKTt~~~  924 (3245)
T 3vkg_A          875 KKIQEIAKQRHLV-TKQEWVEKILQLHQILNINHGVMMVGPSGGGKTTSWE  924 (3245)
T ss_dssp             HHHHHHHHHTTCC-CCHHHHHHHHHHHHHHTTCSEEEEECSSSSSHHHHHH
T ss_pred             HHHHHHHHHcCCc-cCHHHHHHHHHHHHHHHheeeEEEECCCCCCHHHHHH
Confidence            5566667778887 66665543333    3346778999999999998874

>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=81.67  E-value=0.53  Score=41.64  Aligned_cols=21  Identities=33%  Similarity=0.488  Sum_probs=17.5

Q ss_pred             hhcCccEEEECCCCCCchhHh
Q 015158           73 FCKGLDVIQQAQSGTGKTATF   93 (412)
Q Consensus        73 ~~~~~~~lv~~~tGsGKT~~~   93 (412)
                      +..|..+.+.+|+|||||+..
T Consensus       168 i~~g~~v~i~G~~GsGKTTll  188 (330)
T 2pt7_A          168 IAIGKNVIVCGGTGSGKTTYI  188 (330)
T ss_dssp             HHHTCCEEEEESTTSCHHHHH
T ss_pred             ccCCCEEEEECCCCCCHHHHH
Confidence            446889999999999999743

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus}

Probab=81.61  E-value=3.4  Score=35.77  Aligned_cols=75  Identities=24%  Similarity=0.302  Sum_probs=53.7

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHH----hcCCCcEEEeChHHHHHHHHcCCCCCCCc
Q 015158          107 ECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRI----LSSGVHVVVGTPGRVFDMLRRQSLRPDNI  182 (412)
Q Consensus       107 ~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~iii~T~~~l~~~~~~~~~~~~~~  182 (412)
                      ..++||.|+++.-++.+.+.+...    ++.+..++|+.+.......    ..+..+|+|+|     +.+ ..+++..++
T Consensus        28 ~~~~LVF~~t~~~~~~l~~~L~~~----g~~~~~lhg~l~~~~r~~~~~~f~~g~~~vLVaT-----~va-~~Gidi~~v   97 (300)
T 3i32_A           28 PDRAMVFTRTKAETEEIAQGLLRL----GHPAQALHGDMSQGERERVMGAFRQGEVRVLVAT-----DVA-ARGLDIPQV   97 (300)
T ss_dssp             CSSEEEECSSHHHHHHHHHHHHTT----TCCEEEECSCCCTHHHHHHHHHHHHTSCCEEEEC-----STT-TCSTTCCCC
T ss_pred             CCCEEEEECCHHHHHHHHHHHHhC----CCCEEEEeCCCCHHHHHHHHHHhhcCCceEEEEe-----chh-hcCccccce
Confidence            358999999999888888777664    7888899998765544322    24678899999     332 346677788


Q ss_pred             eEEEEeCCc
Q 015158          183 RIFVLDEAD  191 (412)
Q Consensus       183 ~~iiiDE~h  191 (412)
                      ++||.=+.+
T Consensus        98 ~~VI~~d~p  106 (300)
T 3i32_A           98 DLVVHYRMP  106 (300)
T ss_dssp             SEEEESSCC
T ss_pred             eEEEEcCCC
Confidence            888754443

>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=81.46  E-value=0.77  Score=41.00  Aligned_cols=19  Identities=26%  Similarity=0.370  Sum_probs=15.7

Q ss_pred             cCccEEEECCCCCCchhHh
Q 015158           75 KGLDVIQQAQSGTGKTATF   93 (412)
Q Consensus        75 ~~~~~lv~~~tGsGKT~~~   93 (412)
                      .+..+++.||||||||+..
T Consensus       122 ~~g~i~I~GptGSGKTTlL  140 (356)
T 3jvv_A          122 PRGLVLVTGPTGSGKSTTL  140 (356)
T ss_dssp             SSEEEEEECSTTSCHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4557899999999999764

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=81.26  E-value=0.74  Score=37.87  Aligned_cols=21  Identities=19%  Similarity=0.226  Sum_probs=16.4

Q ss_pred             hhcCccEEEECCCCCCchhHh
Q 015158           73 FCKGLDVIQQAQSGTGKTATF   93 (412)
Q Consensus        73 ~~~~~~~lv~~~tGsGKT~~~   93 (412)
                      +..|.-+.+.||+|+|||...
T Consensus        20 i~~G~~~~lvGpsGsGKSTLl   40 (218)
T 1z6g_A           20 MNNIYPLVICGPSGVGKGTLI   40 (218)
T ss_dssp             --CCCCEEEECSTTSSHHHHH
T ss_pred             cCCCCEEEEECCCCCCHHHHH
Confidence            345778899999999999764

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=81.22  E-value=1.3  Score=40.93  Aligned_cols=41  Identities=17%  Similarity=0.037  Sum_probs=29.1

Q ss_pred             hhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCC
Q 015158           73 FCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPT  116 (412)
Q Consensus        73 ~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~  116 (412)
                      +..|.-++|.|++|+|||..++..+.+....   +.+++|++--
T Consensus       194 l~~G~liiIaG~pG~GKTtlal~ia~~~a~~---g~~vl~fSlE  234 (444)
T 3bgw_A          194 YKRRNFVLIAARPSMGKTAFALKQAKNMSDN---DDVVNLHSLE  234 (444)
T ss_dssp             BCSSCEEEEEECSSSSHHHHHHHHHHHHHHT---TCEEEEECSS
T ss_pred             CCCCcEEEEEeCCCCChHHHHHHHHHHHHHc---CCEEEEEECC
Confidence            3345678999999999998776666555443   3478887753

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=81.18  E-value=0.64  Score=39.30  Aligned_cols=18  Identities=33%  Similarity=0.324  Sum_probs=15.3

Q ss_pred             CccEEEECCCCCCchhHh
Q 015158           76 GLDVIQQAQSGTGKTATF   93 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~   93 (412)
                      .+.+++.||+|+|||..+
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            356899999999999765

>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=81.15  E-value=0.7  Score=36.81  Aligned_cols=19  Identities=21%  Similarity=0.221  Sum_probs=15.8

Q ss_pred             CccEEEECCCCCCchhHhH
Q 015158           76 GLDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~   94 (412)
                      +..+++.|++|||||+.+-
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            4568899999999998763

>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=81.10  E-value=1.7  Score=35.56  Aligned_cols=73  Identities=14%  Similarity=0.143  Sum_probs=45.8

Q ss_pred             CCCcEEEEEcchhHHHHHHHHHhc----CCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCC-C-----cCCCCCCC
Q 015158          277 AITQSVIFVNTRRKVDWLTDKMRS----RDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDL-L-----ARGIDVQQ  346 (412)
Q Consensus       277 ~~~k~lif~~~~~~~~~~~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~-~-----~~G~d~~~  346 (412)
                      ...++||.+++++-+.++++.+++    .+..+..++|+.+..+....   +  .+.+|+|+|+- +     ...+++..
T Consensus        81 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~---~--~~~~iiv~Tp~~l~~~~~~~~~~~~~  155 (224)
T 1qde_A           81 KAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEG---L--RDAQIVVGTPGRVFDNIQRRRFRTDK  155 (224)
T ss_dssp             CSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEECC-------------C--TTCSEEEECHHHHHHHHHTTSSCCTT
T ss_pred             CCceEEEEECCHHHHHHHHHHHHHHhcccCceEEEEeCCcchHHHHhc---C--CCCCEEEECHHHHHHHHHhCCcchhh
Confidence            346899999999998888887764    36778888887654433222   2  23789999962 1     23556777


Q ss_pred             CCEEEEcc
Q 015158          347 VSLVINYD  354 (412)
Q Consensus       347 ~~~vi~~~  354 (412)
                      ++.+|+.+
T Consensus       156 ~~~iViDE  163 (224)
T 1qde_A          156 IKMFILDE  163 (224)
T ss_dssp             CCEEEEET
T ss_pred             CcEEEEcC
Confidence            88888654

>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=80.78  E-value=2.6  Score=37.82  Aligned_cols=19  Identities=21%  Similarity=0.302  Sum_probs=16.1

Q ss_pred             CccEEEECCCCCCchhHhH
Q 015158           76 GLDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~   94 (412)
                      ..++++.||+|+|||..+-
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            4579999999999997763

>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=80.71  E-value=1  Score=36.34  Aligned_cols=20  Identities=15%  Similarity=0.179  Sum_probs=16.6

Q ss_pred             cCccEEEECCCCCCchhHhH
Q 015158           75 KGLDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        75 ~~~~~lv~~~tGsGKT~~~~   94 (412)
                      .|+-+++.||+|+|||...-
T Consensus        18 ~g~~ivl~GPSGaGKsTL~~   37 (197)
T 3ney_A           18 GRKTLVLIGASGVGRSHIKN   37 (197)
T ss_dssp             SCCEEEEECCTTSSHHHHHH
T ss_pred             CCCEEEEECcCCCCHHHHHH
Confidence            46778999999999997653

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=80.61  E-value=1.1  Score=39.10  Aligned_cols=19  Identities=32%  Similarity=0.412  Sum_probs=16.5

Q ss_pred             cCccEEEECCCCCCchhHh
Q 015158           75 KGLDVIQQAQSGTGKTATF   93 (412)
Q Consensus        75 ~~~~~lv~~~tGsGKT~~~   93 (412)
                      .+.++++.|++|+|||..+
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            4578999999999999765

>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=80.60  E-value=0.7  Score=36.05  Aligned_cols=17  Identities=12%  Similarity=-0.001  Sum_probs=14.3

Q ss_pred             cEEEECCCCCCchhHhH
Q 015158           78 DVIQQAQSGTGKTATFC   94 (412)
Q Consensus        78 ~~lv~~~tGsGKT~~~~   94 (412)
                      .+++.|+.|||||+.+-
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            46889999999998763

>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=80.58  E-value=0.69  Score=41.10  Aligned_cols=19  Identities=26%  Similarity=0.247  Sum_probs=15.8

Q ss_pred             CccEEEECCCCCCchhHhH
Q 015158           76 GLDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~   94 (412)
                      ..++++.||+|+|||..+-
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            3569999999999997653

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=80.53  E-value=0.6  Score=40.46  Aligned_cols=17  Identities=24%  Similarity=0.145  Sum_probs=14.7

Q ss_pred             ccEEEECCCCCCchhHh
Q 015158           77 LDVIQQAQSGTGKTATF   93 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~   93 (412)
                      ..+++.||+|+|||..+
T Consensus        37 ~~lLl~GppGtGKT~la   53 (293)
T 3t15_A           37 LILGIWGGKGQGKSFQC   53 (293)
T ss_dssp             SEEEEEECTTSCHHHHH
T ss_pred             eEEEEECCCCCCHHHHH
Confidence            56788999999999765

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=80.53  E-value=0.86  Score=38.50  Aligned_cols=17  Identities=18%  Similarity=0.051  Sum_probs=14.1

Q ss_pred             cEEEECCCCCCchhHhH
Q 015158           78 DVIQQAQSGTGKTATFC   94 (412)
Q Consensus        78 ~~lv~~~tGsGKT~~~~   94 (412)
                      .+++.||+|||||..+.
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            36889999999997763

>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=80.51  E-value=0.86  Score=39.58  Aligned_cols=17  Identities=24%  Similarity=0.296  Sum_probs=14.3

Q ss_pred             cEEEECCCCCCchhHhH
Q 015158           78 DVIQQAQSGTGKTATFC   94 (412)
Q Consensus        78 ~~lv~~~tGsGKT~~~~   94 (412)
                      -++|.+|||+|||..+.
T Consensus        12 ~i~i~GptgsGKt~la~   28 (316)
T 3foz_A           12 AIFLMGPTASGKTALAI   28 (316)
T ss_dssp             EEEEECCTTSCHHHHHH
T ss_pred             EEEEECCCccCHHHHHH
Confidence            46889999999997764

>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=80.47  E-value=0.73  Score=36.20  Aligned_cols=18  Identities=28%  Similarity=0.242  Sum_probs=15.4

Q ss_pred             CccEEEECCCCCCchhHh
Q 015158           76 GLDVIQQAQSGTGKTATF   93 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~   93 (412)
                      +..+++.|+.|||||+.+
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            567889999999999765

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=80.14  E-value=0.63  Score=36.98  Aligned_cols=19  Identities=32%  Similarity=0.403  Sum_probs=15.9

Q ss_pred             CccEEEECCCCCCchhHhH
Q 015158           76 GLDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~   94 (412)
                      |..+++.|++|||||+.+-
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            4568899999999998763

>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=80.13  E-value=1.3  Score=39.62  Aligned_cols=41  Identities=12%  Similarity=0.020  Sum_probs=28.3

Q ss_pred             cCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHH
Q 015158           75 KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRE  118 (412)
Q Consensus        75 ~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  118 (412)
                      .|.-++|.+++|+|||..++..+......   +.+++|+..-..
T Consensus        73 ~G~li~I~G~pGsGKTtlal~la~~~~~~---g~~vlyi~~E~s  113 (366)
T 1xp8_A           73 RGRITEIYGPESGGKTTLALAIVAQAQKA---GGTCAFIDAEHA  113 (366)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHT---TCCEEEEESSCC
T ss_pred             CCcEEEEEcCCCCChHHHHHHHHHHHHHC---CCeEEEEECCCC
Confidence            35678899999999998776655554433   246788775443

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=80.06  E-value=0.84  Score=36.88  Aligned_cols=19  Identities=32%  Similarity=0.349  Sum_probs=16.1

Q ss_pred             cCccEEEECCCCCCchhHh
Q 015158           75 KGLDVIQQAQSGTGKTATF   93 (412)
Q Consensus        75 ~~~~~lv~~~tGsGKT~~~   93 (412)
                      .+..+++.|+.|||||+.+
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            3667889999999999765

---

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	412
d2g9na1	218	c.37.1.19 (A:21-238) Initiation factor 4a {Human (	8e-55
d1hv8a1	208	c.37.1.19 (A:3-210) Putative DEAD box RNA helicase	7e-54
d2j0sa1	222	c.37.1.19 (A:22-243) Probable ATP-dependent RNA he	9e-54
d1qdea_	212	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	7e-52
d1t6na_	207	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	3e-45
d1fuka_	162	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	9e-45
d2j0sa2	168	c.37.1.19 (A:244-411) Probable ATP-dependent RNA h	1e-44
d1wrba1	238	c.37.1.19 (A:164-401) putative ATP-dependent RNA h	3e-44
d1veca_	206	c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Huma	5e-42
d1s2ma1	206	c.37.1.19 (A:46-251) Putative ATP-dependent RNA he	6e-42
d2rb4a1	168	c.37.1.19 (A:307-474) ATP-dependent RNA helicase D	1e-38
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	6e-35
d1s2ma2	171	c.37.1.19 (A:252-422) Putative ATP-dependent RNA h	9e-34
d1a1va2	299	c.37.1.14 (A:326-624) HCV helicase domain {Human h	9e-33
d1q0ua_	209	c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR	5e-32
d1hv8a2	155	c.37.1.19 (A:211-365) Putative DEAD box RNA helica	6e-32
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	1e-26
d1t5ia_	168	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	8e-25
d1gkub1	237	c.37.1.16 (B:1-250) Helicase-like "domain" of reve	1e-23
d1oywa2	206	c.37.1.19 (A:1-206) RecQ helicase domain {Escheric	5e-22
d1jr6a_	138	c.37.1.14 (A:) HCV helicase domain {Human hepatiti	4e-19
d2p6ra3	202	c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus	5e-19
d1oywa3	200	c.37.1.19 (A:207-406) RecQ helicase domain {Escher	6e-19
d2fwra1	200	c.37.1.19 (A:257-456) DNA repair protein RAD25 {Ar	1e-18
d1wp9a1	200	c.37.1.19 (A:1-200) putative ATP-dependent RNA hel	7e-16
d1t5la2	181	c.37.1.19 (A:415-595) Nucleotide excision repair e	2e-14
d1c4oa2	174	c.37.1.19 (A:410-583) Nucleotide excision repair e	1e-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	8e-06
d2eyqa5	211	c.37.1.19 (A:779-989) Transcription-repair couplin	7e-05
d1tf5a4	175	c.37.1.19 (A:396-570) Translocation ATPase SecA, n	8e-04
d1yksa2	299	c.37.1.14 (A:325-623) YFV helicase domain {Yellow	0.003

>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 =  178 bits (453), Expect = 8e-55
 Identities = 141/214 (65%), Positives = 169/214 (78%), Gaps = 1/214 (0%)

Query: 32  TSYDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTA 91
           ++++E+ D+FD M L E+LLRGIYAYGFEKPSAIQQR I+P  KG DVI QAQSGTGKTA
Sbjct: 5   SNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTA 64

Query: 92  TFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQ 151
           TF   ILQQ++  L   QALVLAPTRELAQQI+KV+ ALGDY+G   HAC+GGT+VR + 
Sbjct: 65  TFAISILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEV 124

Query: 152 RILSSGV-HVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLP 210
           + L     H++VGTPGRVFDML R+ L P  I++FVLDEADEMLSRGFKDQIYDIFQ L 
Sbjct: 125 QKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLN 184

Query: 211 PKIQVGVFSATMPPEALEITRKFMNKPVRILVKR 244
              QV + SATMP + LE+T+KFM  P+RILVK+
Sbjct: 185 SNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKK 218

>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 =  176 bits (446), Expect = 7e-54
 Identities = 72/207 (34%), Positives = 117/207 (56%), Gaps = 3/207 (1%)

Query: 38  YDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKG-LDVIQQAQSGTGKTATFCSG 96
           Y  F+ + L +N+L  I   GFEKP+ IQ + I  F     +++ QA++G+GKTA+F   
Sbjct: 3   YMNFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIP 62

Query: 97  ILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSS 156
           +++ ++      +A++L PTRELA Q+   + +L     +K+    GG ++    + L  
Sbjct: 63  LIELVNEN-NGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALK- 120

Query: 157 GVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVG 216
             ++VVGTPGR+ D + R +L   N++ F+LDEADEML+ GF   +  I        ++ 
Sbjct: 121 NANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEMLNMGFIKDVEKILNACNKDKRIL 180

Query: 217 VFSATMPPEALEITRKFMNKPVRILVK 243
           +FSATMP E L + +K+M     I  K
Sbjct: 181 LFSATMPREILNLAKKYMGDYSFIKAK 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 =  176 bits (446), Expect = 9e-54
 Identities = 141/219 (64%), Positives = 170/219 (77%), Gaps = 1/219 (0%)

Query: 27  GQDFFTSYD-EVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQS 85
             +F TS + +V  TFD MGL+E+LLRGIYAYGFEKPSAIQQR I    KG DVI Q+QS
Sbjct: 4   KVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQS 63

Query: 86  GTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGT 145
           GTGKTATF   +LQ LD  + E QAL+LAPTRELA QI+K + ALGDY+ V+ HAC+GGT
Sbjct: 64  GTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGT 123

Query: 146 SVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDI 205
           +V ED R L  G HVV GTPGRVFDM+RR+SLR   I++ VLDEADEML++GFK+QIYD+
Sbjct: 124 NVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDV 183

Query: 206 FQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKR 244
           ++ LPP  QV + SAT+P E LE+T KFM  P+RILVKR
Sbjct: 184 YRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKR 222

>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 =  171 bits (433), Expect = 7e-52
 Identities = 128/211 (60%), Positives = 157/211 (74%), Gaps = 1/211 (0%)

Query: 32  TSYDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTA 91
           T+YD+V   FD M L ENLLRG++ YGFE+PSAIQQR I+P  +G DV+ QAQSGTGKT 
Sbjct: 3   TNYDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTG 62

Query: 92  TFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQ 151
           TF    LQ++D  +   QAL+LAPTRELA QI+KV+ AL  ++ +KVHAC+GGTS  ED 
Sbjct: 63  TFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDA 122

Query: 152 RILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPP 211
             L     +VVGTPGRVFD ++R+  R D I++F+LDEADEMLS GFK+QIY IF LLPP
Sbjct: 123 EGLR-DAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLPP 181

Query: 212 KIQVGVFSATMPPEALEITRKFMNKPVRILV 242
             QV + SATMP + LE+T KFM  PVRILV
Sbjct: 182 TTQVVLLSATMPNDVLEVTTKFMRNPVRILV 212

>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 =  153 bits (387), Expect = 3e-45
 Identities = 81/206 (39%), Positives = 114/206 (55%), Gaps = 3/206 (1%)

Query: 40  TFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQ 99
            F    L+  LLR I   GFE PS +Q   I     G+DV+ QA+SG GKTA F    LQ
Sbjct: 2   GFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQ 61

Query: 100 QLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGG-TSVREDQRILSS-G 157
           QL+    +   LV+  TRELA QI K       Y+     A   G  S+++D+ +L    
Sbjct: 62  QLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNC 121

Query: 158 VHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSR-GFKDQIYDIFQLLPPKIQVG 216
            H+VVGTPGR+  + R +SL   +I+ F+LDE D+ML +   +  + +IF++ P + QV 
Sbjct: 122 PHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVM 181

Query: 217 VFSATMPPEALEITRKFMNKPVRILV 242
           +FSAT+  E   + RKFM  P+ I V
Sbjct: 182 MFSATLSKEIRPVCRKFMQDPMEIFV 207

>d1fuka_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 162

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  150 bits (380), Expect = 9e-45
 Identities = 107/161 (66%), Positives = 134/161 (83%)

Query: 252 IKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGD 311
           IKQF+VNVE+EE+K E L DLY+++++TQ+VIF NTRRKV+ LT K+R+   TVSA + D
Sbjct: 1   IKQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSD 60

Query: 312 MDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGR 371
           + Q  RD IM+EFRSGSSR+LI+TDLLARGIDVQQVSLVINYDLP   ENY+HRIGR GR
Sbjct: 61  LPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGR 120

Query: 372 FGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVADLL 412
           FGRKGVAINFVT +D   + +++KFY+  IEELP+++A LL
Sbjct: 121 FGRKGVAINFVTNEDVGAMRELEKFYSTQIEELPSDIATLL 161

>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 =  150 bits (380), Expect = 1e-44
 Identities = 117/168 (69%), Positives = 142/168 (84%)

Query: 245 DELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHT 304
           DELTLEGIKQF V VE+EEWK +TLCDLY+TL ITQ+VIF NT+RKVDWLT+KMR  + T
Sbjct: 1   DELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFT 60

Query: 305 VSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLH 364
           VS+ HGDM Q  R+ IM+EFRSG+SRVLI+TD+ ARG+DV QVSL+INYDLP   E Y+H
Sbjct: 61  VSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIH 120

Query: 365 RIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVADLL 412
           RIGRSGR+GRKGVAINFV  DD R+L DI+++Y+  I+E+P NVADL+
Sbjct: 121 RIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVADLI 168

>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 =  151 bits (383), Expect = 3e-44
 Identities = 64/220 (29%), Positives = 101/220 (45%), Gaps = 13/220 (5%)

Query: 36  EVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCS 95
            V + FD + L   +   I    +++P+ IQ+  I    +  D++  AQ+G+GKTA F  
Sbjct: 18  NVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLI 77

Query: 96  GILQQLDYGLVEC---------QALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTS 146
            I+  L    +           + L+LAPTRELA QI    +       ++     GG  
Sbjct: 78  PIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGAD 137

Query: 147 VREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIF 206
                R +  G H++V TPGR+ D + +  +  +  +  VLDEAD ML  GF+ QI  I 
Sbjct: 138 THSQIREVQMGCHLLVATPGRLVDFIEKNKISLEFCKYIVLDEADRMLDMGFEPQIRKII 197

Query: 207 QLL----PPKIQVGVFSATMPPEALEITRKFMNKPVRILV 242
           +          Q  +FSAT P E  ++   F+   + + V
Sbjct: 198 EESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTV 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 =  145 bits (365), Expect = 5e-42
 Identities = 75/202 (37%), Positives = 119/202 (58%), Gaps = 1/202 (0%)

Query: 40  TFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQ 99
            F+   L+  LL GI+  G+EKPS IQ+  I     G D++ +A++GTGK+  +   +L+
Sbjct: 4   EFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLE 63

Query: 100 QLDYGLVECQALVLAPTRELAQQI-EKVMRALGDYLGVKVHACVGGTSVREDQRILSSGV 158
           +LD      QA+V+ PTRELA Q+ +  ++      G KV A  GGT++R+D   L   V
Sbjct: 64  RLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTV 123

Query: 159 HVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVF 218
           HVV+ TPGR+ D++++   + D++++ VLDEAD++LS+ F   + DI   LP   Q+ ++
Sbjct: 124 HVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNRQILLY 183

Query: 219 SATMPPEALEITRKFMNKPVRI 240
           SAT P    +     + KP  I
Sbjct: 184 SATFPLSVQKFMNSHLEKPYEI 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 =  144 bits (364), Expect = 6e-42
 Identities = 87/202 (43%), Positives = 123/202 (60%)

Query: 39  DTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGIL 98
           +TF+   L+  LL GI+  GFEKPS IQ+  I     G D++ +A++GTGKTA F    L
Sbjct: 1   NTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTL 60

Query: 99  QQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGV 158
           +++   L + QAL++ PTRELA Q  +V+R LG + G+      GGT++R+D   L+  V
Sbjct: 61  EKVKPKLNKIQALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLNETV 120

Query: 159 HVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVF 218
           H++VGTPGRV D+  R+     +  +F++DEAD+MLSR FK  I  I   LPP  Q  +F
Sbjct: 121 HILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSRDFKTIIEQILSFLPPTHQSLLF 180

Query: 219 SATMPPEALEITRKFMNKPVRI 240
           SAT P    E   K ++KP  I
Sbjct: 181 SATFPLTVKEFMVKHLHKPYEI 202

>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 =  129 bits (324), Expect = 6e-35
 Identities = 52/332 (15%), Positives = 97/332 (29%), Gaps = 56/332 (16%)

Query: 75  KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYL 134
           K    I     G GKT  +   I+++        + L+LAPTR +A ++E+ +R      
Sbjct: 8   KKRLTIMDLHPGAGKTKRYLPAIVREAIKR--GLRTLILAPTRVVAAEMEEALR------ 59

Query: 135 GVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEML 194
                  +         R   +G  +V       F M     +R  N  + ++DEA    
Sbjct: 60  ------GLPIRYQTPAIRAEHTGREIVDLMCHATFTMRLLSPIRVPNYNLIIMDEAHFTD 113

Query: 195 SRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRDELTLEGIKQ 254
                 + Y   ++   +      +AT P         F      I+ +  E+       
Sbjct: 114 PASIAARGYISTRVEMGEAAGIFMTATPPG----SRDPFPQSNAPIMDEEREIPERSWNS 169

Query: 255 FHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQ 314
            H  V   +                ++V FV + +  + +   +R     V         
Sbjct: 170 GHEWVTDFKG---------------KTVWFVPSIKAGNDIAACLRKNGKKVIQLSRKTFD 214

Query: 315 NTRDIIMREFRSGSSRVLITTDLLARGIDV---------QQVSLVINYDLPTQ------- 358
           +                ++TTD+   G +          + +  VI  D   +       
Sbjct: 215 SEYIKTRTNDW----DFVVTTDISEMGANFKAERVIDPRRCMKPVILTDGEERVILAGPM 270

Query: 359 ---PENYLHRIGRSGRFGRKGVAINFVTRDDE 387
                +   R GR GR  +          +  
Sbjct: 271 PVTHSSAAQRRGRVGRNPKNENDQYIYMGEPL 302

>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 =  122 bits (305), Expect = 9e-34
 Identities = 69/163 (42%), Positives = 100/163 (61%), Gaps = 1/163 (0%)

Query: 246 ELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTV 305
           ELTL+GI Q++  VE+ + KL  L  L+  L I Q++IF N+  +V+ L  K+    ++ 
Sbjct: 1   ELTLKGITQYYAFVEERQ-KLHCLNTLFSKLQINQAIIFCNSTNRVELLAKKITDLGYSC 59

Query: 306 SATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHR 365
             +H  M Q  R+ +  EFR G  R L+ +DLL RGID+Q V++VIN+D P   E YLHR
Sbjct: 60  YYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHR 119

Query: 366 IGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANV 408
           IGRSGRFG  G+AIN +  +D   L+ I++     I  +PA +
Sbjct: 120 IGRSGRFGHLGLAINLINWNDRFNLYKIEQELGTEIAAIPATI 162

>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 = 9e-33
 Identities = 25/154 (16%), Positives = 53/154 (34%), Gaps = 15/154 (9%)

Query: 252 IKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGD 311
           I++  ++   E         L E +   + +IF ++++K D L  K+ +      A +  
Sbjct: 11  IEEVALSTTGEIPFYGKAIPL-EVIKGGRHLIFCHSKKKCDELAAKLVALGINAVAYYRG 69

Query: 312 MDQNTRDI----------IMREFRSGSSRVLITTDLLARG---IDVQQVSLVINYDLPTQ 358
           +D +               +    +G    +I  +          +     +    LP  
Sbjct: 70  LDVSVIPTSGDVVVVATDALMTGFTGDFDSVIDCNTCVTQTVDFSLDPTFTIETTTLPQD 129

Query: 359 PENYLHRIGRSGRFGRKGVAINFVTRDDERMLFD 392
             +   R GR+GR G+ G+       +    +FD
Sbjct: 130 AVSRTQRRGRTGR-GKPGIYRFVAPGERPSGMFD 162

>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 =  118 bits (296), Expect = 5e-32
 Identities = 62/207 (29%), Positives = 103/207 (49%), Gaps = 4/207 (1%)

Query: 40  TFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQ 99
            F     Q  ++  I    F KP+ IQ+R I    +G  ++ Q+Q+GTGKT  +   I++
Sbjct: 2   QFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIME 61

Query: 100 QLDYGLVECQALVLA----PTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILS 155
           ++     E QA++ A       ++  +  K+ +       +     +GGT  ++    L+
Sbjct: 62  KIKPERAEVQAVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLN 121

Query: 156 SGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQV 215
              H+V+GTPGR+ D +R Q+L      I V+DEAD ML  GF   +  I   +P  +Q+
Sbjct: 122 VQPHIVIGTPGRINDFIREQALDVHTAHILVVDEADLMLDMGFITDVDQIAARMPKDLQM 181

Query: 216 GVFSATMPPEALEITRKFMNKPVRILV 242
            VFSAT+P +     +K+M  P  + V
Sbjct: 182 LVFSATIPEKLKPFLKKYMENPTFVHV 208

>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 =  116 bits (291), Expect = 6e-32
 Identities = 58/153 (37%), Positives = 92/153 (60%), Gaps = 2/153 (1%)

Query: 252 IKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGD 311
           I+Q +V V + E + E LC L +       ++F  T+R    L   +R       A HGD
Sbjct: 4   IEQSYVEVNENE-RFEALCRLLKNKEF-YGLVFCKTKRDTKELASMLRDIGFKAGAIHGD 61

Query: 312 MDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGR 371
           + Q+ R+ ++R F+    R+LI TD+++RGIDV  ++ VINY LP  PE+Y+HRIGR+GR
Sbjct: 62  LSQSQREKVIRLFKQKKIRILIATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGR 121

Query: 372 FGRKGVAINFVTRDDERMLFDIQKFYNVVIEEL 404
            G+KG AI+ + R + + L  I++   + I++L
Sbjct: 122 AGKKGKAISIINRREYKKLRYIERAMKLKIKKL 154

>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 =  106 bits (264), Expect = 1e-26
 Identities = 38/214 (17%), Positives = 79/214 (36%), Gaps = 21/214 (9%)

Query: 186 VLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVKRD 245
            L  A E+L       +    + L  + + G   A+         ++  +      +K+ 
Sbjct: 81  KLHHAIELLETQGLSALRAYIKKLYEEAKAGSTKAS---------KEIFSDKR---MKKA 128

Query: 246 ELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTV 305
              L   K+  ++  K +   E + +  +    ++ ++F N R     + +++       
Sbjct: 129 ISLLVQAKEIGLDHPKMDKLKEIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKDGIKA 188

Query: 306 SATHGD--------MDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPT 357
               G         + Q  + +I+ EF  G   VL+ T +   G+DV +V LV+ Y+   
Sbjct: 189 KRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVATSVGEEGLDVPEVDLVVFYEPVP 248

Query: 358 QPENYLHRIGRSGRFGRKGVAINFVTRDDERMLF 391
                + 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 =  104 bits (261), Expect = 1e-26
 Identities = 23/161 (14%), Positives = 57/161 (35%), Gaps = 16/161 (9%)

Query: 257 VNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNT 316
            +V   +  + TL  + E L  T  +I+  T  + + + + ++++          +   T
Sbjct: 5   EDVAVNDESISTLSSILEKLG-TGGIIYARTGEEAEEIYESLKNKFR------IGIVTAT 57

Query: 317 RDIIMREFRSGSSRVLITT----DLLARGIDVQQ-VSLVINYDLPTQPENYLHRIGRSGR 371
           +     +F  G    LI T      L RG+D+ + +   +    P    ++   I     
Sbjct: 58  KKGDYEKFVEGEIDHLIGTAHYYGTLVRGLDLPERIRFAVFVGCP----SFRVTIEDIDS 113

Query: 372 FGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVADLL 412
              + 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 = 97.8 bits (242), Expect = 8e-25
 Identities = 57/159 (35%), Positives = 94/159 (59%), Gaps = 2/159 (1%)

Query: 251 GIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHG 310
           G++Q++V ++  E K   L DL + L   Q VIFV + ++   L   +  ++    A H 
Sbjct: 1   GLQQYYVKLKDNE-KNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHR 59

Query: 311 DMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSG 370
            M Q  R    ++F+    R+L+ T+L  RG+D+++V++  NYD+P   + YLHR+ R+G
Sbjct: 60  GMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAG 119

Query: 371 RFGRKGVAINFVT-RDDERMLFDIQKFYNVVIEELPANV 408
           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 = 96.5 bits (239), Expect = 1e-23
 Identities = 35/219 (15%), Positives = 67/219 (30%), Gaps = 26/219 (11%)

Query: 38  YDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGI 97
              F    L +      +     +P AIQ+       +       A +G GKT+   +  
Sbjct: 21  LCLFPEDFLLK-EFVEFFRKCVGEPRAIQKMWAKRILRKESFAATAPTGVGKTSFGLAMS 79

Query: 98  LQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKV------HACVGGTSVREDQ 151
           L          +  V+ PT  L  Q  + +R   +  GV        +        +E+ 
Sbjct: 80  LFLALK---GKRCYVIFPTSLLVIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENF 136

Query: 152 RILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSR-----------GFKD 200
                   +V+ T   +    R       +     +D+ D +L             GF  
Sbjct: 137 MQNLRNFKIVITTTQFLSKHYRELG----HFDFIFVDDVDAILKASKNVDKLLHLLGFHY 192

Query: 201 QIYDIFQLLPPKIQVGVFSATMPPE-ALEITRKFMNKPV 238
            +     +   +  + V +AT       E+ R+ +N  +
Sbjct: 193 DLKTKSWVGEARGCLMVSTATAKKGKKAELFRQLLNFDI 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 = 91.2 bits (225), Expect = 5e-22
 Identities = 32/208 (15%), Positives = 71/208 (34%), Gaps = 17/208 (8%)

Query: 40  TFDAMGLQEN---LLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSG 96
             + + L+     +L+  +  G+++    Q+  I     G D +    +G GK+  +   
Sbjct: 3   QAEVLNLESGAKQVLQETF--GYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIP 60

Query: 97  ILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSS 156
            L            +V++P   L +     ++A G               +       + 
Sbjct: 61  ALLLNG------LTVVVSPLISLMKDQVDQLQANGVAAACLNSTQTREQQLEVMTGCRTG 114

Query: 157 GVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRG--FKDQIYDIFQLL--PPK 212
            + ++   P R+      + L   N  +  +DEA  +   G  F+ +   + QL    P 
Sbjct: 115 QIRLLYIAPERLMLDNFLEHLAHWNPVLLAVDEAHCISQWGHDFRPEYAALGQLRQRFPT 174

Query: 213 IQVGVFSATMPPEALE--ITRKFMNKPV 238
           +     +AT      +  +    +N P+
Sbjct: 175 LPFMALTATADDTTRQDIVRLLGLNDPL 202

>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 = 81.3 bits (200), Expect = 4e-19
 Identities = 27/138 (19%), Positives = 52/138 (37%), Gaps = 13/138 (9%)

Query: 252 IKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGD 311
           I++  ++   E         L E +   + +IF ++++K D L  K+ +          +
Sbjct: 10  IEEVALSTTGEIPFYGKAIPL-EVIKGGRHLIFCHSKKKCDELAAKLVALGI-------N 61

Query: 312 MDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVS---LVINYDLPTQPENYLHRIGR 368
                R + +    +    V++ TD L  G      S      +   P    +   R GR
Sbjct: 62  AVAYYRGLDVSVIPTNGDVVVVATDALMTGFTGDFDSVIDCNTSDGKPQDAVSRTQRRGR 121

Query: 369 SGRFGRKGVAINFVTRDD 386
           +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 = 82.3 bits (202), Expect = 5e-19
 Identities = 25/183 (13%), Positives = 59/183 (32%), Gaps = 10/183 (5%)

Query: 45  GLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYG 104
            +    +  +   G E+    Q   +     G +++    +  GK        +  +   
Sbjct: 9   SISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGK---TLLAEMAMVREA 65

Query: 105 LVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGT 164
           +   ++L + P R LA +  +  +           +     S  E          ++V T
Sbjct: 66  IKGGKSLYVVPLRALAGEKYESFKKWEKIGLRIGISTGDYESRDEHLGD----CDIIVTT 121

Query: 165 PGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQ---IYDIFQLLPPKIQVGVFSAT 221
             +   ++R ++     +   V+DE   + S         +    + +   ++V   SAT
Sbjct: 122 SEKADSLIRNRASWIKAVSCLVVDEIHLLDSEKRGATLEILVTKMRRMNKALRVIGLSAT 181

Query: 222 MPP 224
            P 
Sbjct: 182 APN 184

>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 = 82.4 bits (202), Expect = 6e-19
 Identities = 33/139 (23%), Positives = 65/139 (46%), Gaps = 1/139 (0%)

Query: 259 VEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRD 318
           +EK +  L+ L    +       +I+ N+R KV+    +++S+  + +A H  ++ N R 
Sbjct: 12  MEKFK-PLDQLMRYVQEQRGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRA 70

Query: 319 IIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVA 378
            +  +F+    ++++ T     GI+   V  V+++D+P   E+Y    GR+GR G    A
Sbjct: 71  DVQEKFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEA 130

Query: 379 INFVTRDDERMLFDIQKFY 397
           + F    D   L    +  
Sbjct: 131 MLFYDPADMAWLRRCLEEK 149

>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 = 81.9 bits (201), Expect = 1e-18
 Identities = 25/130 (19%), Positives = 50/130 (38%), Gaps = 8/130 (6%)

Query: 259 VEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRD 318
               + K+  L ++ E     + +IF      V        S+   + A      +  R+
Sbjct: 74  AFNSKNKIRKLREILERHRKDKIIIFTRHNELVYR-----ISKVFLIPAITHRTSREERE 128

Query: 319 IIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVA 378
            I+  FR+G  R ++++ +L  GIDV   ++ +          Y+ R+GR  R  +    
Sbjct: 129 EILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQRLGRILRPSKGKKE 188

Query: 379 ---INFVTRD 385
                 ++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 = 73.7 bits (179), Expect = 7e-16
 Identities = 39/198 (19%), Positives = 74/198 (37%), Gaps = 5/198 (2%)

Query: 58  GFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTR 117
              +P   Q+  I   CK  + +    +G GKT         +L       + L+LAPT+
Sbjct: 6   DLIQPRIYQEV-IYAKCKETNCLIVLPTGLGKTLIAMMIAEYRLTKY--GGKVLMLAPTK 62

Query: 118 ELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSL 177
            L  Q  +  R L +    K+ A  G  S  E  +  +    +V  TP  + + L    +
Sbjct: 63  PLVLQHAESFRRLFNLPPEKIVALTGEKSPEERSKAWARAKVIVA-TPQTIENDLLAGRI 121

Query: 178 RPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKP 237
             +++ + V DEA   +       I   ++       V   +A+      +I     N  
Sbjct: 122 SLEDVSLIVFDEAHRAVGNYAYVFIAREYKRQAKNPLVIGLTASPGSTPEKIMEVINNLG 181

Query: 238 VRILVKRDELTLEGIKQF 255
           +  +  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 = 2e-14
 Identities = 34/142 (23%), Positives = 61/142 (42%), Gaps = 13/142 (9%)

Query: 280 QSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLA 339
           ++++   T++  + LTD ++     V+  H ++    R  I+R+ R G   VL+  +LL 
Sbjct: 33  RTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLR 92

Query: 340 RGIDVQQVSLVINYDLPT-----QPENYLHRIGRSGRFGRKGVAINFVTR--------DD 386
            G+D+ +VSLV   D           + +  IGR+ R     V +   T          +
Sbjct: 93  EGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNANGHVIMYADTITKSMEIAIQE 152

Query: 387 ERMLFDIQKFYNVVIEELPANV 408
            +    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 = 66.3 bits (161), Expect = 1e-13
 Identities = 31/121 (25%), Positives = 53/121 (43%), Gaps = 6/121 (4%)

Query: 280 QSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLA 339
           ++++ V T R  + LT  +          H ++D   R  ++R+ R G    L+  +LL 
Sbjct: 33  RTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLR 92

Query: 340 RGIDVQQVSLVINYDL-----PTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQ 394
            G+D+ +VSLV   D           + +  IGR+ R  R G    +  R  E M   I+
Sbjct: 93  EGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNAR-GEVWLYADRVSEAMQRAIE 151

Query: 395 K 395
           +
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 = 27/152 (17%), Positives = 52/152 (34%), Gaps = 39/152 (25%)

Query: 280 QSVIFVNTRRKVDWLTDKMRSRD------------------------------HTVSATH 309
             ++F +TRR  +    K+ +                                   +  H
Sbjct: 42  GVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHH 101

Query: 310 GDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVI-------NYDLPTQPENY 362
             +    R ++   FR G+ +V++ T  LA G+++    +++        Y    +   Y
Sbjct: 102 AGLLNGQRRVVEDAFRRGNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEY 161

Query: 363 LHRIGRSGRFGR--KGVAINFVTRDDERMLFD 392
               GR+GR G   +G AI  V + D  +   
Sbjct: 162 KQMAGRAGRPGMDERGEAIIIVGKRDREIAVK 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 = 8e-06
 Identities = 42/229 (18%), Positives = 81/229 (35%), Gaps = 30/229 (13%)

Query: 184 IFV-LDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILV 242
           +   L    + L + F  Q   +  L   KI V   S+          +K  N P   L+
Sbjct: 17  VCCNLTPLQKELYKLFLKQAKPVESLQTGKISVSSLSSIT------SLKKLCNHPA--LI 68

Query: 243 KRDELTLEGIKQFHVNVEKEEW-----------KLETLCDLYETLAITQS---VIFVNTR 288
               LT E      +++  + +           K+  L  +      T S   V+  N  
Sbjct: 69  YEKCLTGEEGFDGALDLFPQNYSTKAVEPQLSGKMLVLDYILAMTRTTTSDKVVLVSNYT 128

Query: 289 RKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSS---RVLITTDLLARGIDVQ 345
           + +D      R+R +      G M    R  I+  F + SS     ++++     G+++ 
Sbjct: 129 QTLDLFEKLCRNRRYLYVRLDGTMSIKKRAKIVERFNNPSSPEFIFMLSSKAGGCGLNLI 188

Query: 346 QVSLVINYDLPTQPENYLHRIGRSGRFGRKG--VAINFVTRD--DERML 390
             + ++ +D    P N    + R  R G+K        ++    +E++L
Sbjct: 189 GANRLVMFDPDWNPANDEQAMARVWRDGQKKTCYIYRLLSTGTIEEKIL 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 = 7e-05
 Identities = 19/99 (19%), Positives = 40/99 (40%), Gaps = 4/99 (4%)

Query: 282 VIFVNTRRKVDWLTDKMRSR---DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLL 338
           V ++    +      +  +    +  ++  HG M +   + +M +F      VL+ T ++
Sbjct: 34  VYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTII 93

Query: 339 ARGIDVQQVSLVINYDLPTQPENYLHRI-GRSGRFGRKG 376
             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 = 8e-04
 Identities = 20/119 (16%), Positives = 42/119 (35%), Gaps = 10/119 (8%)

Query: 279 TQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLL 338
              ++        + ++  ++++       +    +    II    + G+  V I T++ 
Sbjct: 35  QPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREAQIIEEAGQKGA--VTIATNMA 92

Query: 339 ARGIDVQQVSLVINYD--------LPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERM 389
            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 = 0.003
 Identities = 16/115 (13%), Positives = 35/115 (30%), Gaps = 24/115 (20%)

Query: 280 QSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLA 339
            +  F+ + R  + +   +R    +V   +      T +      +      ++ TD+  
Sbjct: 38  PTAWFLPSIRAANVMAASLRKAGKSVVVLNRK----TFEREYPTIKQKKPDFILATDIAE 93

Query: 340 RGIDVQQVSLVINYDLPTQPENY-------------------LHRIGRSGRFGRK 375
            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	412
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	100.0
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	100.0
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	100.0
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	100.0
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	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
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	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
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	99.98
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	99.98
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
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	99.95
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.95
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	99.93
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.93
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	99.92
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	99.92
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	99.9
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	99.86
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	99.85
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	99.85
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	99.85
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.84
d1wp9a2	286	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.81
d2p6ra4	201	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.81
d2fwra1	200	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.8
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	99.79
d1gm5a4	206	RecG helicase domain {Thermotoga maritima [TaxId:	99.76
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	99.74
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	99.74
d1a1va2	299	HCV helicase domain {Human hepatitis C virus (HCV)	99.7
d1gkub2	248	Helicase-like "domain" of reverse gyrase {Archaeon	99.69
d1z3ix2	298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	99.62
d1z3ix1	346	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	99.59
d1z63a1	230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	99.56
d1z5za1	244	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	99.53
d1yksa2	299	YFV helicase domain {Yellow fever virus [TaxId: 11	99.46
d1tf5a4	175	Translocation ATPase SecA, nucleotide-binding doma	99.41
d1tf5a3	273	Translocation ATPase SecA, nucleotide-binding doma	99.08
d1nkta3	288	Translocation ATPase SecA, nucleotide-binding doma	99.01
d1nkta4	219	Translocation ATPase SecA, nucleotide-binding doma	98.91
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	98.48
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	98.1
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	97.86
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	97.71
d1ls1a2	207	GTPase domain of the signal sequence recognition p	97.44
d2qy9a2	211	GTPase domain of the signal recognition particle r	97.41
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	97.33
d1j8yf2	211	GTPase domain of the signal sequence recognition p	97.22
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	97.1
d1okkd2	207	GTPase domain of the signal recognition particle r	97.04
d1vmaa2	213	GTPase domain of the signal recognition particle r	97.02
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	96.87
d2b8ta1	139	Thymidine kinase, TK1, N-terminal domain {Ureaplas	96.76
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	96.67
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	96.64
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	96.54
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	96.53
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	96.43
d1t5la1	413	Nucleotide excision repair enzyme UvrB {Bacillus c	96.43
d1xbta1	133	Thymidine kinase, TK1, N-terminal domain {Human (H	96.33
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	96.3
d1xx6a1	141	Thymidine kinase, TK1, N-terminal domain {Clostrid	96.29
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	96.05
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	96.03
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	95.64
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	95.6
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	94.96
d1g5ta_	157	ATP:corrinoid adenosyltransferase CobA {Salmonella	94.81
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	94.64
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	93.76
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	93.62
d1c4oa1	408	Nucleotide excision repair enzyme UvrB {Thermus th	93.5
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	93.36
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	93.34
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	93.32
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	93.07
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	92.78
d1w36b1	485	Exodeoxyribonuclease V beta chain (RecB), N-termin	92.46
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	92.19
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	91.83
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	91.61
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	91.17
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	91.11
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	90.96
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	90.71
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	90.59
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	90.3
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	90.3
d2eyqa2	117	Transcription-repair coupling factor, TRCF {Escher	90.22
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	90.11
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	90.06
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	90.0
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	89.85
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	89.82
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	89.77
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	89.33
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	89.31
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	89.22
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	89.13
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	88.97
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	88.64
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	88.29
d1yksa2	299	YFV helicase domain {Yellow fever virus [TaxId: 11	88.28
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	88.23
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	87.99
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	87.93
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	87.86
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	87.71
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	87.54
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	87.48
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	87.38
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	87.27
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	87.07
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	86.78
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	86.54
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	86.37
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	85.95
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	85.9
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	85.76
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	85.68
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	85.6
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	85.46
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	84.59
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	84.56
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	84.53
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	84.43
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	84.42
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	84.4
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	84.23
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	84.01
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	83.88
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	83.59
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	83.59
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	83.57
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	83.34
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	83.24
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	82.87
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	82.82
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	82.72
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	82.66
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	82.52
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	81.84
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	81.72
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	81.54
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	81.22
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	81.12
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	80.76
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	80.69
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	80.65
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	80.53
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	80.23

>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-37  Score=260.14  Aligned_cols=205  Identities=66%  Similarity=1.017  Sum_probs=192.1

Q ss_pred             ccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCH
Q 015158           38 YDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTR  117 (412)
Q Consensus        38 ~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~  117 (412)
                      ..+|+++++++.+.++|...||..|+|.|.++++.+++|+++++.++||||||++|+++++..+.......++++++|++
T Consensus        16 ~~sF~~l~L~~~l~~~L~~~g~~~pt~IQ~~aIp~il~g~dvi~~a~TGSGKTlayllPil~~l~~~~~~~~~lil~Ptr   95 (222)
T d2j0sa1          16 TPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTR   95 (222)
T ss_dssp             CCSGGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTTSCSCCEEEECSSH
T ss_pred             CCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCeEEEcCcchhhhhhhcccccccccccccCceeEEecchH
Confidence            45799999999999999999999999999999999999999999999999999999999999998877788999999999


Q ss_pred             HHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccC
Q 015158          118 ELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRG  197 (412)
Q Consensus       118 ~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~  197 (412)
                      +|+.|..+.+..++...++.+..+.|+............+++|+|+||+++.+++.......++++++|+||||.+.+.+
T Consensus        96 eLa~Qi~~~~~~l~~~~~i~~~~~~g~~~~~~~~~~l~~~~~Ilv~TPgrl~~~~~~~~~~~~~l~~lVlDEaD~ll~~~  175 (222)
T d2j0sa1          96 ELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKG  175 (222)
T ss_dssp             HHHHHHHHHHHHHTTTTTCCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHTSTT
T ss_pred             HHHHHHHHHHHHHhCccceeEEEEeecccchhhHHHhccCCeEEeCCCCcHHhcccccccccccceeeeecchhHhhhcC
Confidence            99999999999999888999999999998877777777788999999999999999988889999999999999999999


Q ss_pred             cHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEe
Q 015158          198 FKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILV  242 (412)
Q Consensus       198 ~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~  242 (412)
                      |...+..++..++++.|.+++|||++++..+....++.+|+.+.+
T Consensus       176 f~~~i~~I~~~l~~~~Q~ilfSAT~~~~v~~l~~~~l~~Pv~I~V  220 (222)
T d2j0sa1         176 FKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILV  220 (222)
T ss_dssp             THHHHHHHHTTSCTTCEEEEEESCCCHHHHTTGGGTCSSCEEECC
T ss_pred             cHHHHHHHHHhCCCCCEEEEEEEeCCHHHHHHHHHHCCCCEEEEE
Confidence            999999999999999999999999999888888889988876654

>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=3.1e-36  Score=250.55  Aligned_cols=202  Identities=37%  Similarity=0.635  Sum_probs=186.4

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHH
Q 015158           39 DTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRE  118 (412)
Q Consensus        39 ~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  118 (412)
                      .+|+++++++++.++|...||..|+|.|+++++.+++|+++++.+|||||||++|+++++..+.....+.++++++|+++
T Consensus         3 ~~F~~l~L~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllP~l~~~~~~~~~~~~lil~pt~e   82 (206)
T d1veca_           3 NEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRE   82 (206)
T ss_dssp             SSGGGSCCCHHHHHHHHTTTCCSCCHHHHHHHHHHHTTCCEEEECCSSSTTHHHHHHHHHHHCCTTSCSCCEEEECSCHH
T ss_pred             CChhccCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEeeccCccccccccccchhhcccccccCcceEEEeecch
Confidence            58999999999999999999999999999999999999999999999999999999999999888778889999999999


Q ss_pred             HHHHHHHHHHHhhccc-CcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccC
Q 015158          119 LAQQIEKVMRALGDYL-GVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRG  197 (412)
Q Consensus       119 L~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~  197 (412)
                      |+.|..+.+..+.... +.......|+............+++|+|+||+++..++.......++++++|+||||.+.+.+
T Consensus        83 l~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~ivv~TPgrl~~~~~~~~~~~~~l~~lVlDEaD~ll~~~  162 (206)
T d1veca_          83 LALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQD  162 (206)
T ss_dssp             HHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEEETHHHHTSTT
T ss_pred             hhHHHHHHHHHHhhcccCcccccccCCccHHHHHHHHHhccCeEEeCCccccccccchhccccccceEEEeccccccccc
Confidence            9999999998876544 466777777777777777777889999999999999999988889999999999999999999


Q ss_pred             cHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEE
Q 015158          198 FKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRI  240 (412)
Q Consensus       198 ~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~  240 (412)
                      |...+..++..++++.|++++|||++++..+....++.+|..+
T Consensus       163 f~~~i~~I~~~~~~~~Q~~l~SAT~~~~v~~l~~~~l~~P~~I  205 (206)
T d1veca_         163 FVQIMEDIILTLPKNRQILLYSATFPLSVQKFMNSHLEKPYEI  205 (206)
T ss_dssp             THHHHHHHHHHSCTTCEEEEEESCCCHHHHHHHHHHCSSCEEE
T ss_pred             hHHHHHHHHHhCCCCCEEEEEEecCCHHHHHHHHHHCCCCEEE
Confidence            9999999999999999999999999999999999999988754

>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=2.1e-36  Score=253.15  Aligned_cols=212  Identities=66%  Similarity=1.041  Sum_probs=190.1

Q ss_pred             CChhhhccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEE
Q 015158           32 TSYDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQAL  111 (412)
Q Consensus        32 ~~~~~~~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~l  111 (412)
                      +++.++..+|+++++++.+.++|...||..|++.|..+++.++.|+++++.+|||||||++|+++++..+.....+.+++
T Consensus         5 ~~~~e~i~sF~~l~L~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllp~l~~i~~~~~~~~al   84 (218)
T d2g9na1           5 SNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDLKATQAL   84 (218)
T ss_dssp             CCCCCCCCCGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEE
T ss_pred             CCCCCccCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEEcccchhhhhhhhhhhhheecccccCccEE
Confidence            44567788999999999999999999999999999999999999999999999999999999999999988777788999


Q ss_pred             EEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHH-HHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCC
Q 015158          112 VLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQ-RILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEA  190 (412)
Q Consensus       112 il~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~  190 (412)
                      |++|+++|+.|..+.+..+....+.......++....... ......++|+|+||+++..++.+.....++++++|+|||
T Consensus        85 il~Pt~eL~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IvV~TP~rl~~~l~~~~~~~~~l~~lVlDEa  164 (218)
T d2g9na1          85 VLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEA  164 (218)
T ss_dssp             EECSSHHHHHHHHHHHHHHHTTTTCCEEEECC--CCCSTTTSSSSCCCSEEEECHHHHHHHHHTTSSCSTTCCEEEEESH
T ss_pred             EEcccchhhhhHHHHHhhhccccceeEEeeecccchhHHHHHHhcCCCEEEEeCChhHHHHHhcCCcccccceEEEeeec
Confidence            9999999999999999999988888887777766544332 223356799999999999999988888999999999999


Q ss_pred             chhhccCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEec
Q 015158          191 DEMLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILVK  243 (412)
Q Consensus       191 h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~  243 (412)
                      |.+.+.+|...+..++..++.+.|.+++|||++++.......++.+|..+.+.
T Consensus       165 D~ll~~~f~~~~~~Il~~~~~~~Q~il~SAT~~~~v~~~~~~~l~~pv~i~v~  217 (218)
T d2g9na1         165 DEMLSRGFKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVK  217 (218)
T ss_dssp             HHHHHTTCHHHHHHHHHHSCTTCEEEEEESCCCHHHHHHHHHHCSSCEEEECC
T ss_pred             chhhcCchHHHHHHHHHhCCCCCeEEEEEecCCHHHHHHHHHHCCCCEEEEEe
Confidence            99999999999999999999999999999999999999999999999877653

>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=6.7e-36  Score=249.19  Aligned_cols=208  Identities=61%  Similarity=0.950  Sum_probs=183.9

Q ss_pred             ChhhhccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEE
Q 015158           33 SYDEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALV  112 (412)
Q Consensus        33 ~~~~~~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~li  112 (412)
                      ..+++..+|+++++++++.++|...||.+|++.|.++++.++.|+++++.+|||||||++|+++++..+.....++++++
T Consensus         4 ~~~~~~~sF~~l~l~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKT~a~~lp~i~~l~~~~~~~~~li   83 (212)
T d1qdea_           4 NYDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALM   83 (212)
T ss_dssp             SCCCCCCCGGGGTCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEE
T ss_pred             CCcccccChhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEeecccccchhhhhHhhhHhhhhccCCCcceEE
Confidence            45566789999999999999999999999999999999999999999999999999999999999999988878889999


Q ss_pred             EcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCch
Q 015158          113 LAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADE  192 (412)
Q Consensus       113 l~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~  192 (412)
                      ++|+++++.|....+..+............++.....+.... .+++|+|+||+++.+++....+.+.+++++|+||||.
T Consensus        84 l~pt~el~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~IvI~TP~~l~~~~~~~~~~l~~l~~lVlDEad~  162 (212)
T d1qdea_          84 LAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGL-RDAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADE  162 (212)
T ss_dssp             ECSSHHHHHHHHHHHHHHTTTSCCCEEEECC----------C-TTCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHH
T ss_pred             EcccHHHhhhhhhhhcccccccccceeeEeeccchhHHHHHh-cCCcEEEECCCccccccccCceecCcceEEeehhhhh
Confidence            999999999999999998877777777777766655444433 4679999999999999999999999999999999999


Q ss_pred             hhccCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEE
Q 015158          193 MLSRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRIL  241 (412)
Q Consensus       193 ~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~  241 (412)
                      +.+.+|...+..+++.++++.|.+++|||+++........++.+|+.+.
T Consensus       163 lld~~f~~~v~~I~~~~~~~~Q~vl~SAT~~~~v~~l~~~~l~~Pv~i~  211 (212)
T d1qdea_         163 MLSSGFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRIL  211 (212)
T ss_dssp             HHHTTCHHHHHHHHHHSCTTCEEEEEESSCCHHHHHHHHHHCSSCEEEC
T ss_pred             hcccchHHHHHHHHHhCCCCCeEEEEEeeCCHHHHHHHHHHCCCCEEEe
Confidence            9999999999999999999999999999999999999999999987653

>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=2.5e-35  Score=245.21  Aligned_cols=202  Identities=41%  Similarity=0.640  Sum_probs=181.9

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHH
Q 015158           40 TFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTREL  119 (412)
Q Consensus        40 ~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L  119 (412)
                      .|+++++++++.++|...||..|+|.|.++++.+++|+++++.+|||||||++|+++++..+.......++++++|+++|
T Consensus         2 ~F~dl~L~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvl~~A~TGsGKTla~~lp~l~~~~~~~~~~~~lil~PtreL   81 (207)
T d1t6na_           2 GFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTREL   81 (207)
T ss_dssp             CSTTSCCCHHHHHHHHHTTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCTTCCCEEEECSCHHH
T ss_pred             CccccCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCeEEEeccccccccccccceeeeecccCCCceEEEEeccchh
Confidence            68999999999999999999999999999999999999999999999999999999999998887778899999999999


Q ss_pred             HHHHHHHHHHhhccc-CcEEEEEEcCcchHHHHHH-hcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhcc-
Q 015158          120 AQQIEKVMRALGDYL-GVKVHACVGGTSVREDQRI-LSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSR-  196 (412)
Q Consensus       120 ~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~-~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~-  196 (412)
                      +.|..+.+..+.... ........|+......... ....++|+|+||+++.+++.+..+.++++.++|+||||.+.+. 
T Consensus        82 ~~qi~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~ilI~TP~rl~~~~~~~~~~l~~l~~lVlDEaD~ll~~~  161 (207)
T d1t6na_          82 AFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQL  161 (207)
T ss_dssp             HHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEESHHHHHSSH
T ss_pred             hHHHHHHHHHHHhhCCCceeEEEeccccHHHHHHHHHhcCCCEEEeCcchhhhhccCCceeccccceeehhhhhhhhhcC
Confidence            999999999988765 3566677777776555433 3567899999999999999988888999999999999999874 


Q ss_pred             CcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEE
Q 015158          197 GFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRIL  241 (412)
Q Consensus       197 ~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~  241 (412)
                      ++...+..+...++++.|++++|||++++..+....++.+|..+.
T Consensus       162 ~~~~~i~~I~~~~~~~~Q~il~SAT~~~~v~~l~~~~l~~P~~I~  206 (207)
T d1t6na_         162 DMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIF  206 (207)
T ss_dssp             HHHHHHHHHHHTSCSSSEEEEEESCCCTTTHHHHHTTCSSCEEEE
T ss_pred             CcHHHHHHHHHhCCCCCEEEEEeeeCCHHHHHHHHHHCCCCEEEe
Confidence            788899999999999999999999999998899999999887664

>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=7.5e-35  Score=242.90  Aligned_cols=203  Identities=35%  Similarity=0.599  Sum_probs=183.3

Q ss_pred             ccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCc-cEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCC
Q 015158           38 YDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGL-DVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPT  116 (412)
Q Consensus        38 ~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~-~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~  116 (412)
                      +-+|+++++++.+.++|..+||..|+|.|.++++.++.|+ ++++.+|||+|||++|+++++...... .+++++|++|+
T Consensus         3 ~msf~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~g~~d~iv~a~TGsGKT~~~~l~~~~~~~~~-~~~~~lil~pt   81 (208)
T d1hv8a1           3 YMNFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNEN-NGIEAIILTPT   81 (208)
T ss_dssp             CCCGGGSSCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCSS-SSCCEEEECSC
T ss_pred             ccCHHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeeeechhcccccceeecccccccccc-cCcceEEEeec
Confidence            4589999999999999999999999999999999998874 999999999999999999998876543 56789999999


Q ss_pred             HHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhcc
Q 015158          117 RELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSR  196 (412)
Q Consensus       117 ~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~  196 (412)
                      ++|+.|..+.+..+....+..+....|+.....+.... .+++|+|+||++|.+++.+..+.+++++++|+||||.+.+.
T Consensus        82 ~~l~~q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l-~~~~IlV~TP~~l~~~l~~~~~~~~~l~~lViDEad~l~~~  160 (208)
T d1hv8a1          82 RELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKAL-KNANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEMLNM  160 (208)
T ss_dssp             HHHHHHHHHHHHHHHCSSCCCEEEECTTSCHHHHHHHH-HTCSEEEECHHHHHHHHHTTCSCTTSCCEEEEETHHHHHTT
T ss_pred             cccchhhhhhhhhhcccCCeEEEEeeCCCChHHHHHhc-CCCCEEEEChHHHHHHHHcCCCCcccCcEEEEEChHHhhcC
Confidence            99999999999999988888999999988766655444 35799999999999999988888999999999999999999


Q ss_pred             CcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEe
Q 015158          197 GFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILV  242 (412)
Q Consensus       197 ~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~  242 (412)
                      ++...+..++..++++.|++++|||++++..+....+++++..+..
T Consensus       161 ~~~~~i~~I~~~~~~~~Q~i~~SAT~~~~v~~~~~~~l~~~~~I~~  206 (208)
T d1hv8a1         161 GFIKDVEKILNACNKDKRILLFSATMPREILNLAKKYMGDYSFIKA  206 (208)
T ss_dssp             TTHHHHHHHHHTSCSSCEEEEECSSCCHHHHHHHHHHCCSEEEEEC
T ss_pred             CChHHHHHHHHhCCCCCeEEEEEccCCHHHHHHHHHHCCCCeEEEE
Confidence            9999999999999999999999999999989999999988776653

>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=2.2e-34  Score=240.05  Aligned_cols=204  Identities=43%  Similarity=0.670  Sum_probs=192.2

Q ss_pred             cccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHH
Q 015158           39 DTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRE  118 (412)
Q Consensus        39 ~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  118 (412)
                      ++|+++++++.+.++|++.||..|+|.|+++++.+++|+++++.+|||||||++|+++++..+.....+.+.++++|+..
T Consensus         1 ~sF~~l~L~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvi~~a~tGsGKTlay~lp~i~~~~~~~~~~~~~~~~~~~~   80 (206)
T d1s2ma1           1 NTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVPTRE   80 (206)
T ss_dssp             CCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEECSSHH
T ss_pred             CChHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEecCCcchhhhhhccccccccccccccccceeeccchh
Confidence            47999999999999999999999999999999999999999999999999999999999999887778889999999999


Q ss_pred             HHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCc
Q 015158          119 LAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGF  198 (412)
Q Consensus       119 L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~  198 (412)
                      ++.+....+..+....++.+...+|+............+++|+|+||+.+..++....+.+.+++++|+||||.+.+.+|
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~lV~DEaD~l~~~~f  160 (206)
T d1s2ma1          81 LALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLNETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSRDF  160 (206)
T ss_dssp             HHHHHHHHHHHHTTTTTCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEEESHHHHSSHHH
T ss_pred             hhhhhhhhhhhcccccCeeEEeecCccchhhHHHHhcccceEEEECCcccccccccceeecccceEEEeechhhhhhhhh
Confidence            99999999999988889999999999988888888888899999999999999999888899999999999999999999


Q ss_pred             HHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEe
Q 015158          199 KDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILV  242 (412)
Q Consensus       199 ~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~  242 (412)
                      ...+..+++.+++..|++++|||++++.......++.+|..+..
T Consensus       161 ~~~v~~I~~~l~~~~Q~il~SATl~~~v~~~~~~~l~~P~~I~~  204 (206)
T d1s2ma1         161 KTIIEQILSFLPPTHQSLLFSATFPLTVKEFMVKHLHKPYEINL  204 (206)
T ss_dssp             HHHHHHHHTTSCSSCEEEEEESCCCHHHHHHHHHHCSSCEEESC
T ss_pred             HHHHHHHHHhCCCCCEEEEEEEeCCHHHHHHHHHHCCCCEEEEe
Confidence            99999999999999999999999999999999999998876643

>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=9.3e-35  Score=259.28  Aligned_cols=272  Identities=18%  Similarity=0.139  Sum_probs=184.1

Q ss_pred             hhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHH
Q 015158           73 FCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQR  152 (412)
Q Consensus        73 ~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  152 (412)
                      +.+++++++.+|||||||++++.+++.....  .+.++||++|+++|++|+.+.++.+.....    ...       ...
T Consensus         6 ~~~~~~~lv~~~TGsGKT~~~l~~~~~~~~~--~~~~~lvi~Ptr~La~q~~~~l~~~~~~~~----~~~-------~~~   72 (305)
T d2bmfa2           6 FRKKRLTIMDLHPGAGKTKRYLPAIVREAIK--RGLRTLILAPTRVVAAEMEEALRGLPIRYQ----TPA-------IRA   72 (305)
T ss_dssp             SSTTCEEEECCCTTSSTTTTHHHHHHHHHHH--HTCCEEEEESSHHHHHHHHHHTTTSCCBCC----C------------
T ss_pred             hhcCCcEEEEECCCCCHHHHHHHHHHHHHHh--cCCEEEEEccHHHHHHHHHHHHhcCCccee----eeE-------Eee
Confidence            5578999999999999999887777655432  235899999999999999988876532211    110       011


Q ss_pred             HhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHh--CCCCceEEEEeecCChHHHHHH
Q 015158          153 ILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQL--LPPKIQVGVFSATMPPEALEIT  230 (412)
Q Consensus       153 ~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~--~~~~~~~i~~SAT~~~~~~~~~  230 (412)
                      .......++++|++.|...... .....+++++|+||+|++..+++  ....++..  .....+.+++|||++.....  
T Consensus        73 ~~~~~~~i~~~t~~~l~~~~~~-~~~~~~~~~vViDE~H~~~~~~~--~~~~~l~~~~~~~~~~~v~~SAT~~~~~~~--  147 (305)
T d2bmfa2          73 EHTGREIVDLMCHATFTMRLLS-PIRVPNYNLIIMDEAHFTDPASI--AARGYISTRVEMGEAAGIFMTATPPGSRDP--  147 (305)
T ss_dssp             ---CCCSEEEEEHHHHHHHHTS-SSCCCCCSEEEEESTTCCSHHHH--HHHHHHHHHHHHTSCEEEEECSSCTTCCCS--
T ss_pred             cccCccccccCCcHHHHHHHhc-CccccceeEEEeeeeeecchhhH--HHHHHHHHhhccccceEEEeecCCCcceee--
Confidence            1234568999999998776654 34467899999999998865542  12222221  23577899999998642110  


Q ss_pred             HHhcCCCeEEEecCCccccCCceEEEEEeccchhhHHHHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecC
Q 015158          231 RKFMNKPVRILVKRDELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHG  310 (412)
Q Consensus       231 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~  310 (412)
                        .....            ..+......... ..+... ...+. ...++++|||++++.++.+++.|++.++.+..+||
T Consensus       148 --~~~~~------------~~~~~~~~~~~~-~~~~~~-~~~~~-~~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~l~~  210 (305)
T d2bmfa2         148 --FPQSN------------APIMDEEREIPE-RSWNSG-HEWVT-DFKGKTVWFVPSIKAGNDIAACLRKNGKKVIQLSR  210 (305)
T ss_dssp             --SCCCS------------SCEEEEECCCCC-SCCSSC-CHHHH-SSCSCEEEECSCHHHHHHHHHHHHHHTCCCEECCT
T ss_pred             --ecccC------------CcceEEEEeccH-HHHHHH-HHHHH-hhCCCEEEEeccHHHHHHHHHHHHhCCCCEEEeCC
Confidence              00000            001111111111 001111 11122 23478999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEcc--------------------CCCChhhHHHhhhhcc
Q 015158          311 DMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYD--------------------LPTQPENYLHRIGRSG  370 (412)
Q Consensus       311 ~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~--------------------~~~s~~~~~Q~~GR~~  370 (412)
                      ++....    ...|++|..+++|+|+++++|+|++ +++|+..+                    .|.|..+|.||+||+|
T Consensus       211 ~~~~~~----~~~~~~~~~~~lvaT~~~~~G~~~~-~~~Vi~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~Qr~GR~G  285 (305)
T d2bmfa2         211 KTFDSE----YIKTRTNDWDFVVTTDISEMGANFK-AERVIDPRRCMKPVILTDGEERVILAGPMPVTHSSAAQRRGRVG  285 (305)
T ss_dssp             TCHHHH----GGGGGTSCCSEEEECGGGGTTCCCC-CSEEEECCEEEEEEEECSSSCEEEEEEEEECCHHHHHHHHTTSS
T ss_pred             cChHHH----HhhhhccchhhhhhhHHHHhcCCCC-ccEEEEcCCceeeeEecCCCCceEEeccccCCHHHHhhhhcCcC
Confidence            985544    4567889999999999999999994 66665322                    3568899999999999


Q ss_pred             cCCCCceEEEEecc
Q 015158          371 RFGRKGVAINFVTR  384 (412)
Q Consensus       371 R~g~~g~~~~~~~~  384 (412)
                      |.|+.+...+++..
T Consensus       286 R~~~~~~~~~~~~~  299 (305)
T d2bmfa2         286 RNPKNENDQYIYMG  299 (305)
T ss_dssp             CSSSCCCEEEEECS
T ss_pred             cCCCCceEEEEECC
Confidence            99988877666544

>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=4.7e-34  Score=242.40  Aligned_cols=208  Identities=31%  Similarity=0.469  Sum_probs=187.9

Q ss_pred             hhhccccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccC---------C
Q 015158           35 DEVYDTFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYG---------L  105 (412)
Q Consensus        35 ~~~~~~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~---------~  105 (412)
                      ..+..+|+++++++++.++|...||..|++.|.++++.+++|+|+++.+|||||||++|+++++..+...         .
T Consensus        17 ~~~~~~F~~l~l~~~l~~~L~~~g~~~pt~iQ~~~ip~il~g~dvvi~a~TGsGKTlayllp~l~~l~~~~~~~~~~~~~   96 (238)
T d1wrba1          17 TNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKT   96 (238)
T ss_dssp             CSCCCSSGGGSCCCSTTTTTTTTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHTTCC------CC
T ss_pred             CCccCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHhhhhhCCCCEEEECCCCCCcceeeHHHHHHHHHhcccccccccCC
Confidence            4467899999999999999999999999999999999999999999999999999999999999987432         2


Q ss_pred             CceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEE
Q 015158          106 VECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIF  185 (412)
Q Consensus       106 ~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~i  185 (412)
                      ..+++++++|+++|+.|..+.+..+....++.+..+.|+............+++|+|+||++|.+++......+.++.++
T Consensus        97 ~~~~alil~pt~el~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~ivV~TP~~l~~~~~~~~~~l~~v~~l  176 (238)
T d1wrba1          97 AYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEKNKISLEFCKYI  176 (238)
T ss_dssp             BCCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCSHHHHHHHSSCCSEEEECHHHHHHHHHTTSBCCTTCCEE
T ss_pred             CCceEEEeccchhhhcchheeeeecccCCCcEEEEEeccchhhHHHhhcccCCceeecCHHHHHhHHccCceecccccee
Confidence            35679999999999999999999998888899999999888877777777889999999999999999888888999999


Q ss_pred             EEeCCchhhccCcHHHHHHHHHhCCC----CceEEEEeecCChHHHHHHHHhcCCCeEEEe
Q 015158          186 VLDEADEMLSRGFKDQIYDIFQLLPP----KIQVGVFSATMPPEALEITRKFMNKPVRILV  242 (412)
Q Consensus       186 iiDE~h~~~~~~~~~~~~~i~~~~~~----~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~  242 (412)
                      |+||+|.+++.+|...+..++..+..    +.|.+++|||++.++..+...++++|+.+.+
T Consensus       177 ViDEaD~ll~~~f~~~i~~Il~~~~~~~~~~~Q~il~SAT~~~~v~~l~~~~~~~p~~i~v  237 (238)
T d1wrba1         177 VLDEADRMLDMGFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTV  237 (238)
T ss_dssp             EEETHHHHHHTTCHHHHHHHHHSSCCCCGGGCEEEEEESSCCHHHHHHHHHHCSSCEEEEE
T ss_pred             eeehhhhhhhhccHHHHHHHHHHhcCCCCCCCEEEEEeeeCCHHHHHHHHHHCCCCEEEEe
Confidence            99999999999999999999886542    5699999999999999999999998877653

>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=1.1e-32  Score=230.93  Aligned_cols=203  Identities=34%  Similarity=0.520  Sum_probs=178.4

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHH
Q 015158           40 TFDAMGLQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTREL  119 (412)
Q Consensus        40 ~f~~~~l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L  119 (412)
                      .|+++++++.+.++|+..||.+|+|.|+++++.+++|+++++.+|||||||++|+++++............++++|+..+
T Consensus         2 ~F~~l~L~~~l~~~l~~~g~~~pt~iQ~~aip~~l~G~dvii~a~TGSGKTlayllp~l~~~~~~~~~~~~~~~~~~~~~   81 (209)
T d1q0ua_           2 QFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPERAEVQAVITAPTREL   81 (209)
T ss_dssp             CGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCTTSCSCCEEEECSSHHH
T ss_pred             ccccCCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCeEeecccccccceeeeeeeccccccccccccccccccccch
Confidence            69999999999999999999999999999999999999999999999999999999999998877777889999999999


Q ss_pred             HHHHHHHHHHhhccc----CcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhc
Q 015158          120 AQQIEKVMRALGDYL----GVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLS  195 (412)
Q Consensus       120 ~~q~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~  195 (412)
                      +.+..+.+.......    ...+....+.............+++|+|+||+++..+..+......+++++|+||||.+.+
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~TP~~l~~~~~~~~~~~~~l~~lViDEad~ll~  161 (209)
T d1q0ua_          82 ATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLNVQPHIVIGTPGRINDFIREQALDVHTAHILVVDEADLMLD  161 (209)
T ss_dssp             HHHHHHHHHHHHTTSCGGGCCCEEEECCCSHHHHTTCCCSSCCSEEEECHHHHHHHHHTTCCCGGGCCEEEECSHHHHHH
T ss_pred             hHHHHHHHHhhhccccccccccccccccchhhHHHHHHhccCceEEEecCchhhhhhhhhccccccceEEEEeecccccc
Confidence            998888776654332    3455555555554444344556789999999999999998888889999999999999999


Q ss_pred             cCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCCCeEEEe
Q 015158          196 RGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNKPVRILV  242 (412)
Q Consensus       196 ~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~  242 (412)
                      ++|...+..++..++++.|.+++|||++++....+..++.+|..+.+
T Consensus       162 ~~f~~~v~~I~~~~~~~~Q~il~SATl~~~v~~l~~~~l~~p~~i~V  208 (209)
T d1q0ua_         162 MGFITDVDQIAARMPKDLQMLVFSATIPEKLKPFLKKYMENPTFVHV  208 (209)
T ss_dssp             TTCHHHHHHHHHTSCTTCEEEEEESCCCGGGHHHHHHHCSSCEEEEC
T ss_pred             cccHHHHHHHHHHCCCCCEEEEEEccCCHHHHHHHHHHCCCCEEEEe
Confidence            99999999999999999999999999999988999999998887653

>d1fuka_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.98  E-value=1.1e-31  Score=213.25  Aligned_cols=161  Identities=66%  Similarity=1.019  Sum_probs=149.9

Q ss_pred             ceEEEEEeccchhhHHHHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcE
Q 015158          252 IKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRV  331 (412)
Q Consensus       252 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~v  331 (412)
                      ++++++.+...+.+.+.|.++++....+++||||+++..++.+++.|...++.+..+||+++..+|..+++.|++|+.++
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            46778888777889999999999998899999999999999999999999999999999999999999999999999999


Q ss_pred             EEEcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHHhccccccCChhhhhc
Q 015158          332 LITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPANVADL  411 (412)
Q Consensus       332 lv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  411 (412)
                      ||||+++++|+|+|++++||++++|+++..|+||+||+||.|+.|.|++++++.+...++.+++.++..++++|.++.+|
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 015158          412 L  412 (412)
Q Consensus       412 ~  412 (412)
                      |
T Consensus       161 ~  161 (162)
T d1fuka_         161 L  161 (162)
T ss_dssp             T
T ss_pred             h
Confidence            6

>d2j0sa2 c.37.1.19 (A:244-411) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.98  E-value=1.2e-31  Score=214.17  Aligned_cols=167  Identities=69%  Similarity=1.138  Sum_probs=160.0

Q ss_pred             ccccCCceEEEEEeccchhhHHHHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHh
Q 015158          246 ELTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFR  325 (412)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~  325 (412)
                      +....+++++++.++....+...|.++++.....++||||++++.++.+++.|+..+..+..+||+++..+|..+++.|+
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            45568899999999988889999999999998899999999999999999999999999999999999999999999999


Q ss_pred             cCCCcEEEEcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHHhccccccCC
Q 015158          326 SGSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELP  405 (412)
Q Consensus       326 ~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  405 (412)
                      +|+.++||||+++++|+|+|++++||+++.|+++..|+||+||+||.|+.|.+++|+.+.+...++.+++.++.+++++|
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             hhhhhcC
Q 015158          406 ANVADLL  412 (412)
Q Consensus       406 ~~~~~l~  412 (412)
                      .++.+++
T Consensus       162 ~~~~dii  168 (168)
T d2j0sa2         162 MNVADLI  168 (168)
T ss_dssp             SCCTTTC
T ss_pred             cChHHhC
Confidence            9888775

>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=1.9e-30  Score=208.68  Aligned_cols=164  Identities=41%  Similarity=0.714  Sum_probs=155.4

Q ss_pred             cccCCceEEEEEeccchhhHHHHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhc
Q 015158          247 LTLEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRS  326 (412)
Q Consensus       247 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~  326 (412)
                      .+..++.+++..++. ..+...|.++++....+++||||++++.++.++..|...|+.+..+||+++..+|..+++.|++
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            345778888888876 6799999999999988999999999999999999999999999999999999999999999999


Q ss_pred             CCCcEEEEcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHHhccccccCCh
Q 015158          327 GSSRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEELPA  406 (412)
Q Consensus       327 g~~~vlv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  406 (412)
                      |+.++||||+++++|+|+|++++||+++.|+++..|+||+||+||.|+.|.++.|+.+.+...++.+++.++..++++|.
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             hhhhc
Q 015158          407 NVADL  411 (412)
Q Consensus       407 ~~~~l  411 (412)
                      .+.+.
T Consensus       161 ~~d~~  165 (171)
T d1s2ma2         161 TIDKS  165 (171)
T ss_dssp             SCCGG
T ss_pred             ccchh
Confidence            87653

>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=1e-28  Score=197.32  Aligned_cols=156  Identities=35%  Similarity=0.653  Sum_probs=143.6

Q ss_pred             ceEEEEEeccchhhHHHHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcE
Q 015158          252 IKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRV  331 (412)
Q Consensus       252 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~v  331 (412)
                      +.+++..+.. +.+.+.|.++++....+++||||++++.++.+++.|.+.++.+..+||+++..+|..+++.|++|+.++
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            5667777765 789999999999998899999999999999999999999999999999999999999999999999999


Q ss_pred             EEEcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccC-cHHHHHHHHHHhccccccCChhh
Q 015158          332 LITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRD-DERMLFDIQKFYNVVIEELPANV  408 (412)
Q Consensus       332 lv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~  408 (412)
                      ||+|+++++|+|+|.+++||++++|+++..|+||+||+||.|+.|.|++++++. +...+..+++.++..++++|+++
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            999999999999999999999999999999999999999999999999999775 56777889999999999998765

>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=1.1e-28  Score=195.19  Aligned_cols=153  Identities=37%  Similarity=0.660  Sum_probs=143.7

Q ss_pred             CCceEEEEEeccchhhHHHHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCC
Q 015158          250 EGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSS  329 (412)
Q Consensus       250 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~  329 (412)
                      .++.+.+..++. ..+.+.|.++++.. ..++||||++++.++.+++.|++.++.+..+|++++..+|..+++.|++|+.
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            467888888866 67999999998765 4689999999999999999999999999999999999999999999999999


Q ss_pred             cEEEEcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHHhccccccC
Q 015158          330 RVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFYNVVIEEL  404 (412)
Q Consensus       330 ~vlv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~  404 (412)
                      ++||||+++++|+|+|.+++||++++|+|+..|+||+||+||.|+.|.+++++++.+...++.+++.++.+++++
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            999999999999999999999999999999999999999999999999999999999999999999999887765

>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=1.2e-26  Score=189.86  Aligned_cols=142  Identities=23%  Similarity=0.381  Sum_probs=128.8

Q ss_pred             cCCceEEEEEeccchhhHHHHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCC
Q 015158          249 LEGIKQFHVNVEKEEWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGS  328 (412)
Q Consensus       249 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~  328 (412)
                      ++++...+.   ....+.+.+..+++.....++||||++++.++.++..|...++.+..+||+++..+|..+++.|.+|+
T Consensus         4 RpNi~y~v~---~~~~k~~~L~~~l~~~~~~~~IIF~~t~~~~~~l~~~l~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~   80 (200)
T d1oywa3           4 RPNIRYMLM---EKFKPLDQLMRYVQEQRGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDD   80 (200)
T ss_dssp             CTTEEEEEE---ECSSHHHHHHHHHHHTTTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTS
T ss_pred             CCCcEEEEE---cCCcHHHHHHHHHHhcCCCCEEEEEeeehhhHHhhhhhccCCceeEEecCCCcHHHHHHHHHHHhccc
Confidence            455543332   23457888999999888889999999999999999999999999999999999999999999999999


Q ss_pred             CcEEEEcCCCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHH
Q 015158          329 SRVLITTDLLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDI  393 (412)
Q Consensus       329 ~~vlv~t~~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~  393 (412)
                      .++||+|+++++|+|+|++++||+++.|.|+..|+|++||+||.|++|.+++|+.+.+...++.+
T Consensus        81 ~~ilvaTd~~~~GiD~p~v~~VI~~~~P~~~~~y~qr~GR~gR~g~~g~ai~~~~~~d~~~l~~~  145 (200)
T d1oywa3          81 LQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLRRC  145 (200)
T ss_dssp             CSEEEECTTSCTTTCCTTCCEEEESSCCSSHHHHHHHHTTSCTTSSCEEEEEEECHHHHHHHHHH
T ss_pred             ceEEEecchhhhccCCCCCCEEEECCCccchHHHHHHhhhhhcCCCCceEEEecCHHHHHHHHhh
Confidence            99999999999999999999999999999999999999999999999999999999887766544

>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=99.95  E-value=1.3e-27  Score=198.70  Aligned_cols=185  Identities=16%  Similarity=0.206  Sum_probs=141.1

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHH
Q 015158           46 LQENLLRGIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEK  125 (412)
Q Consensus        46 l~~~~~~~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~  125 (412)
                      +++.+...|++.|+.+|+|+|+++++.+.+|+++++.+|||+|||.+++++++..+...   +++++++|+++|+.|+.+
T Consensus        10 ~~~~~~~~l~~~g~~~l~~~Q~~ai~~l~~~~~~il~apTGsGKT~~a~l~i~~~~~~~---~~vl~l~P~~~L~~q~~~   86 (202)
T d2p6ra3          10 ISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKG---GKSLYVVPLRALAGEKYE   86 (202)
T ss_dssp             HHHHHHHHHHCC---CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHHTT---CCEEEEESSHHHHHHHHH
T ss_pred             hhHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCchhHHHHHHHHHHhhcc---CcceeecccHHHHHHHHH
Confidence            56778889999999999999999999999999999999999999999988888776544   489999999999999999


Q ss_pred             HHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHH
Q 015158          126 VMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDI  205 (412)
Q Consensus       126 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i  205 (412)
                      .++++... ...+....++.....   .....+.++++|+..+...+.+....+.++++||+||+|.+.+..+...+..+
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            99887653 344555555544222   22346789999999999998887777788999999999998876644433333


Q ss_pred             ---HHhCCCCceEEEEeecCChHHHHHHHHhcCCCeE
Q 015158          206 ---FQLLPPKIQVGVFSATMPPEALEITRKFMNKPVR  239 (412)
Q Consensus       206 ---~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~  239 (412)
                         +...+++.++++||||+++ ..+ +..+++....
T Consensus       163 l~~i~~~~~~~~~l~lSATl~n-~~~-~~~~l~~~~~  197 (202)
T d2p6ra3         163 VTKMRRMNKALRVIGLSATAPN-VTE-IAEWLDADYY  197 (202)
T ss_dssp             HHHHHHHCTTCEEEEEECCCTT-HHH-HHHHTTCEEE
T ss_pred             HHHHHhcCCCCcEEEEcCCCCc-HHH-HHHHcCCCee
Confidence               3345678899999999864 333 4455554443

>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=99.93  E-value=3.7e-27  Score=196.71  Aligned_cols=188  Identities=15%  Similarity=0.160  Sum_probs=138.5

Q ss_pred             ccccCCCCHHHHHHHHHC-CCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHH
Q 015158           40 TFDAMGLQENLLRGIYAY-GFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRE  118 (412)
Q Consensus        40 ~f~~~~l~~~~~~~l~~~-~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  118 (412)
                      ..+.++|.+.....|++. ||.++||+|.++++.+++|+++++.+|||+|||.+|.++++..      ..++++++|+++
T Consensus         3 ~~e~~~l~~~~~~~l~~~fg~~~~rp~Q~~ai~~~l~g~~vlv~apTGsGKT~~~~~~~~~~------~~~~~~v~P~~~   76 (206)
T d1oywa2           3 QAEVLNLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLL------NGLTVVVSPLIS   76 (206)
T ss_dssp             CCCCSSHHHHHHHHHHHTTCCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHS------SSEEEEECSCHH
T ss_pred             chhhCCCCHHHHHHHHHhcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCCCcchhhhhhhhc------cCceEEeccchh
Confidence            345677888888888875 9999999999999999999999999999999999998887753      247999999999


Q ss_pred             HHHHHHHHHHHhhcccCcEEEEEEcCcch----HHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhh
Q 015158          119 LAQQIEKVMRALGDYLGVKVHACVGGTSV----REDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEML  194 (412)
Q Consensus       119 L~~q~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~  194 (412)
                      |+.|+.+.++.+..    ...........    ............++++|++.+............+++++|+||+|++.
T Consensus        77 L~~q~~~~l~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~t~~~~~~~~~~~~~~~~~v~~lviDEaH~~~  152 (206)
T d1oywa2          77 LMKDQVDQLQANGV----AAACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDNFLEHLAHWNPVLLAVDEAHCIS  152 (206)
T ss_dssp             HHHHHHHHHHHTTC----CEEEECTTSCHHHHHHHHHHHHHTCCSEEEECHHHHTSTTHHHHHTTSCEEEEEESSGGGGC
T ss_pred             hhhhHHHHHHhhcc----cccccccccccccchhHHHHHhcCCceEEEEechhhhchhhcccchhheeeeeeeeeeeeee
Confidence            99999999988743    23333222221    12233345678999999988754433333345679999999999988


Q ss_pred             ccCcH--H---HHHHHHHhCCCCceEEEEeecCChHHHHHHHHh--cCCCe
Q 015158          195 SRGFK--D---QIYDIFQLLPPKIQVGVFSATMPPEALEITRKF--MNKPV  238 (412)
Q Consensus       195 ~~~~~--~---~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~--~~~~~  238 (412)
                      +++..  .   .+..+...+ ++.+++++|||+++...+.+.+.  +.+|+
T Consensus       153 ~~~~~~~~~~~~~~~l~~~~-~~~~ii~lSATl~~~v~~di~~~L~l~~p~  202 (206)
T d1oywa2         153 QWGHDFRPEYAALGQLRQRF-PTLPFMALTATADDTTRQDIVRLLGLNDPL  202 (206)
T ss_dssp             TTSSCCCHHHHGGGGHHHHC-TTSCEEEEESCCCHHHHHHHHHHHTCCSCE
T ss_pred             ccccchHHHHHHHHHHHHhC-CCCceEEEEeCCCHHHHHHHHHHcCCCCCc
Confidence            76532  1   223444444 47889999999998876555444  45654

>d1wp9a1 c.37.1.19 (A:1-200) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

Probab=99.93  E-value=2.7e-25  Score=184.61  Aligned_cols=163  Identities=20%  Similarity=0.160  Sum_probs=128.7

Q ss_pred             CChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEE
Q 015158           61 KPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHA  140 (412)
Q Consensus        61 ~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~  140 (412)
                      +|++||.++++.+. ++++++++|||+|||+++++++...+..  .+.++++++|+++|++|+.+.+.++....+..+..
T Consensus         9 ~pr~~Q~~~~~~~~-~~n~lv~~pTGsGKT~i~~~~~~~~~~~--~~~~il~i~P~~~L~~q~~~~~~~~~~~~~~~v~~   85 (200)
T d1wp9a1           9 QPRIYQEVIYAKCK-ETNCLIVLPTGLGKTLIAMMIAEYRLTK--YGGKVLMLAPTKPLVLQHAESFRRLFNLPPEKIVA   85 (200)
T ss_dssp             CCCHHHHHHHHHGG-GSCEEEECCTTSCHHHHHHHHHHHHHHH--SCSCEEEECSSHHHHHHHHHHHHHHBCSCGGGEEE
T ss_pred             CCCHHHHHHHHHHh-cCCeEEEeCCCCcHHHHHHHHHHHHHHh--cCCcEEEEcCchHHHHHHHHHHHHhhcccccceee
Confidence            59999999999886 4578999999999999888777655543  23579999999999999999999998777777877


Q ss_pred             EEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEee
Q 015158          141 CVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSA  220 (412)
Q Consensus       141 ~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SA  220 (412)
                      ..++........... ...++++|++.+.+.+.......+++++||+||||.+........+.........+.+++++||
T Consensus        86 ~~~~~~~~~~~~~~~-~~~i~i~t~~~~~~~~~~~~~~~~~~~~vIiDE~H~~~~~~~~~~~~~~~~~~~~~~~~l~~SA  164 (200)
T d1wp9a1          86 LTGEKSPEERSKAWA-RAKVIVATPQTIENDLLAGRISLEDVSLIVFDEAHRAVGNYAYVFIAREYKRQAKNPLVIGLTA  164 (200)
T ss_dssp             ECSCSCHHHHHHHHH-HCSEEEECHHHHHHHHHTTSCCTTSCSEEEEETGGGCSTTCHHHHHHHHHHHHCSSCCEEEEES
T ss_pred             eecccchhHHHHhhh-cccccccccchhHHHHhhhhhhccccceEEEEehhhhhcchhHHHHHHHHHhcCCCCcEEEEEe
Confidence            777766554444333 3589999999999998888888889999999999997765544444444444455778999999


Q ss_pred             cCChHHH
Q 015158          221 TMPPEAL  227 (412)
Q Consensus       221 T~~~~~~  227 (412)
                      ||.....
T Consensus       165 Tp~~~~~  171 (200)
T d1wp9a1         165 SPGSTPE  171 (200)
T ss_dssp             CSCSSHH
T ss_pred             cCCCcHH
Confidence            9965433

>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=5.2e-24  Score=167.26  Aligned_cols=122  Identities=25%  Similarity=0.358  Sum_probs=106.0

Q ss_pred             HHHHHHHh-cCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCC
Q 015158          268 TLCDLYET-LAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQ  346 (412)
Q Consensus       268 ~l~~~~~~-~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~  346 (412)
                      .+.++.+. ..++++||||++++.++.+++.|++.|+.+..+||+++..+|.+++++|++|+++|||+|+++++|+|+|+
T Consensus        20 ll~~i~~~~~~g~r~lvfc~t~~~~~~l~~~L~~~Gi~a~~~Hg~~~~~eR~~~l~~F~~G~~~vLVaT~v~~~GiDip~   99 (174)
T d1c4oa2          20 LMEGIRERAARGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLREGLDIPE   99 (174)
T ss_dssp             HHHHHHHHHHTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESCCCCTTCCCTT
T ss_pred             HHHHHHHHHhcCCcEEEEEcchhHHHHHHHHHHhcCCceEEEecccchHHHHHHHHHHHCCCeEEEEeeeeeeeeccCCC
Confidence            44444333 25679999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCEEEEccCCC-----ChhhHHHhhhhcccCCCCceEEEEeccCcHHHH
Q 015158          347 VSLVINYDLPT-----QPENYLHRIGRSGRFGRKGVAINFVTRDDERML  390 (412)
Q Consensus       347 ~~~vi~~~~~~-----s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~  390 (412)
                      +++||+++.|.     |...|.|++||+||.|+ |.++++.......+.
T Consensus       100 V~~Vi~~~~~~~~~~~~~~~~iq~~GR~gR~~~-g~~~~~~~~~~~~~~  147 (174)
T d1c4oa2         100 VSLVAILDADKEGFLRSERSLIQTIGRAARNAR-GEVWLYADRVSEAMQ  147 (174)
T ss_dssp             EEEEEETTTTSCSGGGSHHHHHHHHGGGTTSTT-CEEEEECSSCCHHHH
T ss_pred             CcEEEEeccccccccchhHHHHHHhhhhhhcCC-CeeEEeecCCCHHHH
Confidence            99999999765     45779999999999875 777777766554433

>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=99.92  E-value=1.5e-24  Score=184.78  Aligned_cols=174  Identities=20%  Similarity=0.203  Sum_probs=126.1

Q ss_pred             HHHHCCCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhc
Q 015158           53 GIYAYGFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGD  132 (412)
Q Consensus        53 ~l~~~~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~  132 (412)
                      .+...++.+|+++|+++++.+++|+++++.+|||+|||++++++++.....+   .+++|++|+++|+.|+.++++++..
T Consensus        35 ~~~~~~~~~p~~~Q~~~i~~~l~g~~~~i~apTGsGKT~~~~~~~~~~~~~~---~rvliv~Pt~~La~Q~~~~l~~~~~  111 (237)
T d1gkub1          35 EFFRKCVGEPRAIQKMWAKRILRKESFAATAPTGVGKTSFGLAMSLFLALKG---KRCYVIFPTSLLVIQAAETIRKYAE  111 (237)
T ss_dssp             HHHHTTTCSCCHHHHHHHHHHHTTCCEECCCCBTSCSHHHHHHHHHHHHTTS---CCEEEEESCHHHHHHHHHHHHHHHT
T ss_pred             HHHHhccCCCCHHHHHHHHHHHCCCCEEEEecCCChHHHHHHHHHHHHHHhc---CeEEEEeccHHHHHHHHHHHHHHHH
Confidence            3445577889999999999999999999999999999999988887665543   5899999999999999999999876


Q ss_pred             ccCcE----EEEEEcCcchHHHHHH--hcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHH
Q 015158          133 YLGVK----VHACVGGTSVREDQRI--LSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIF  206 (412)
Q Consensus       133 ~~~~~----~~~~~~~~~~~~~~~~--~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~  206 (412)
                      ..++.    +....++.........  ....++|+|+||+.+.+..    ....++++||+||+|.+.+.+  ..+....
T Consensus       112 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~Ilv~Tp~~l~~~~----~~~~~~~~vVvDE~d~~l~~~--~~~~~~~  185 (237)
T d1gkub1         112 KAGVGTENLIGYYHGRIPKREKENFMQNLRNFKIVITTTQFLSKHY----RELGHFDFIFVDDVDAILKAS--KNVDKLL  185 (237)
T ss_dssp             TTCCSGGGSEEECCSSCCSHHHHHHHHSGGGCSEEEEEHHHHHHCS----TTSCCCSEEEESCHHHHHTST--HHHHHHH
T ss_pred             HcCCceEEEEeeeecccchhhhhhhhccccccceeccChHHHHHhh----hhcCCCCEEEEEChhhhhhcc--cchhHHH
Confidence            65443    3334444433333222  2345789999999876533    235689999999999987665  2333333


Q ss_pred             Hh-------------CCCCceEEEEeecCChHHH-HHHHHhcC
Q 015158          207 QL-------------LPPKIQVGVFSATMPPEAL-EITRKFMN  235 (412)
Q Consensus       207 ~~-------------~~~~~~~i~~SAT~~~~~~-~~~~~~~~  235 (412)
                      ..             .+...+++++|||+++... ...+.+++
T Consensus       186 ~~~g~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~l~r~ll~  228 (237)
T d1gkub1         186 HLLGFHYDLKTKSWVGEARGCLMVSTATAKKGKKAELFRQLLN  228 (237)
T ss_dssp             HHTTEEEETTTTEEEECCSSEEEECCCCSCCCTTHHHHHHHHC
T ss_pred             HhcCChHHHHHHHhhCCCCCeEEEEeCCCCcccHHHHHHHHhC
Confidence            22             2346679999999875432 23344443

>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=5.2e-23  Score=164.57  Aligned_cols=118  Identities=25%  Similarity=0.395  Sum_probs=102.1

Q ss_pred             HHHHHHHHhc-CCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCC
Q 015158          267 ETLCDLYETL-AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQ  345 (412)
Q Consensus       267 ~~l~~~~~~~-~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~  345 (412)
                      +.+.++.+.. .+.++||||++++.++.++..|++.|+.+..+||++++.+|.+++++|++|+++|||||+++++|+|+|
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            3444444332 457899999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCEEEEccCCC-----ChhhHHHhhhhcccCCCCceEEEEeccC
Q 015158          346 QVSLVINYDLPT-----QPENYLHRIGRSGRFGRKGVAINFVTRD  385 (412)
Q Consensus       346 ~~~~vi~~~~~~-----s~~~~~Q~~GR~~R~g~~g~~~~~~~~~  385 (412)
                      ++++||+++.|.     |...|.||+||+||.|. |.++++....
T Consensus        99 ~v~~VI~~d~p~~~~~~s~~~yi~R~GRagR~g~-~~~~~~~~~~  142 (181)
T d1t5la2          99 EVSLVAILDADKEGFLRSERSLIQTIGRAARNAN-GHVIMYADTI  142 (181)
T ss_dssp             TEEEEEETTTTSCSGGGSHHHHHHHHGGGTTSTT-CEEEEECSSC
T ss_pred             CCCEEEEecCCcccccccHHHHHHHHHhhccccC-ceeEeecchh
Confidence            999999999985     67899999999999975 4444444443

>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=99.86  E-value=1.1e-20  Score=156.23  Aligned_cols=171  Identities=19%  Similarity=0.245  Sum_probs=132.0

Q ss_pred             CHHHHHHH-HHCCCCCChHHHHhhhhhhhc----C--ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHH
Q 015158           47 QENLLRGI-YAYGFEKPSAIQQRGIVPFCK----G--LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTREL  119 (412)
Q Consensus        47 ~~~~~~~l-~~~~~~~l~~~Q~~a~~~~~~----~--~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L  119 (412)
                      +....+.+ ..++|. +++-|.+++..+.+    +  .+.+++|.||||||.+|+.+++..+..+   .++++++|+..|
T Consensus        41 ~~~~~~~~~~~lP~~-lt~~Q~~~~~~i~~~~~~~~~~~~LL~GdvGsGKT~V~~~a~~~~~~~g---~qv~~l~Pt~~L  116 (233)
T d2eyqa3          41 DREQYQLFCDSFPFE-TTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDNH---KQVAVLVPTTLL  116 (233)
T ss_dssp             CHHHHHHHHHTCCSC-CCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHTTT---CEEEEECSSHHH
T ss_pred             CHHHHHhhhhccccc-cchhHHHHHHHHHHHHhccCccCeEEEcCCCCCcHHHHHHHHHHHHHcC---CceEEEccHHHh
Confidence            34444444 446777 99999999998764    2  4689999999999999999999888766   499999999999


Q ss_pred             HHHHHHHHHHhhcccCcEEEEEEcCcchHHH----HHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhc
Q 015158          120 AQQIEKVMRALGDYLGVKVHACVGGTSVRED----QRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLS  195 (412)
Q Consensus       120 ~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~  195 (412)
                      +.|+++.++++....+.++..+++.......    .....+..+|+|+|...+.     ....++++++||+||-|++.-
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            9999999999988889999999988876543    3445678899999955443     455668999999999998432


Q ss_pred             cCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHH
Q 015158          196 RGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITR  231 (412)
Q Consensus       196 ~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~  231 (412)
                      .    +-..+ .....++.++.+||||.+.......
T Consensus       192 k----Q~~~l-~~~~~~~~~l~~SATPiprtl~~~~  222 (233)
T d2eyqa3         192 R----HKERI-KAMRANVDILTLTATPIPRTLNMAM  222 (233)
T ss_dssp             H----HHHHH-HHHHTTSEEEEEESSCCCHHHHHHH
T ss_pred             H----HHHHH-HhhCCCCCEEEEecchhHHHHHHHH
Confidence            2    22222 2233578899999999987655444

>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=99.85  E-value=7.4e-22  Score=170.83  Aligned_cols=153  Identities=17%  Similarity=0.130  Sum_probs=113.3

Q ss_pred             CChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEE
Q 015158           61 KPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHA  140 (412)
Q Consensus        61 ~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~  140 (412)
                      +||++|.+|+..++++++.++.+|||+|||+++...+......  ...++||++|+++|+.||.+++.++.......+..
T Consensus       113 ~~rdyQ~~av~~~l~~~~~il~~pTGsGKT~i~~~i~~~~~~~--~~~k~Liivp~~~Lv~Q~~~~f~~~~~~~~~~~~~  190 (282)
T d1rifa_         113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLEN--YEGKILIIVPTTALTTQMADDFVDYRLFSHAMIKK  190 (282)
T ss_dssp             CCCHHHHHHHHHHHHHSEEEECCCTTSCHHHHHHHHHHHHHHH--CSSEEEEECSSHHHHHHHHHHHHHHTSCCGGGEEE
T ss_pred             ccchHHHHHHHHHHhcCCceeEEEcccCccHHHHHHHHHhhhc--ccceEEEEEcCchhHHHHHHHHHHhhcccccccee
Confidence            4999999999999999999999999999998876555433332  23589999999999999999999986554444555


Q ss_pred             EEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEee
Q 015158          141 CVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSA  220 (412)
Q Consensus       141 ~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SA  220 (412)
                      +.++......   ......++++|++++.+...   ..++++++||+||||++.+    ..+..++..+.+...++++||
T Consensus       191 ~~~g~~~~~~---~~~~~~i~i~t~qs~~~~~~---~~~~~f~~VIvDEaH~~~a----~~~~~il~~~~~~~~rlGlTa  260 (282)
T d1rifa_         191 IGGGASKDDK---YKNDAPVVVGTWQTVVKQPK---EWFSQFGMMMNDECHLATG----KSISSIISGLNNCMFKFGLSG  260 (282)
T ss_dssp             CSTTCSSTTC---CCTTCSEEEECHHHHTTSCG---GGGGGEEEEEEETGGGCCH----HHHHHHTTTCTTCCEEEEECS
T ss_pred             ecceeccccc---ccccceEEEEeeehhhhhcc---cccCCCCEEEEECCCCCCc----hhHHHHHHhccCCCeEEEEEe
Confidence            5554432211   22346899999988754322   2245799999999998643    456677777765566799999


Q ss_pred             cCChH
Q 015158          221 TMPPE  225 (412)
Q Consensus       221 T~~~~  225 (412)
                      ||+..
T Consensus       261 T~~~~  265 (282)
T d1rifa_         261 SLRDG  265 (282)
T ss_dssp             SCCTT
T ss_pred             ecCCC
Confidence            98653

>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=99.85  E-value=6.2e-21  Score=160.75  Aligned_cols=170  Identities=20%  Similarity=0.242  Sum_probs=131.2

Q ss_pred             HHHHHHHHHCCCCCChHHHHhhhhhhhc----C--ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHH
Q 015158           48 ENLLRGIYAYGFEKPSAIQQRGIVPFCK----G--LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQ  121 (412)
Q Consensus        48 ~~~~~~l~~~~~~~l~~~Q~~a~~~~~~----~--~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~  121 (412)
                      +.....++..+|. |+..|++|+..+..    +  .+.+++|.||||||.+|+.+++..+..+.   ++++++||..|+.
T Consensus        71 ~l~~~f~~~LPFe-LT~~Q~~ai~ei~~d~~~~~~m~rLL~GdvGSGKT~Va~~a~~~~~~~g~---q~~~m~Pt~~La~  146 (264)
T d1gm5a3          71 KLAEEFIKSLPFK-LTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEAGF---QTAFMVPTSILAI  146 (264)
T ss_dssp             HHHHHHHHHSSSC-CCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHHTS---CEEEECSCHHHHH
T ss_pred             HHHHHHHhhcccc-CCchHHHHHHHHHHHhhccCcceeeeeccccccccHHHHHHHHHHHhccc---ceeEEeehHhhhH
Confidence            3444555677888 99999999999874    2  46799999999999999999998887764   8999999999999


Q ss_pred             HHHHHHHHhhcccCcEEEEEEcCcchHHH----HHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccC
Q 015158          122 QIEKVMRALGDYLGVKVHACVGGTSVRED----QRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRG  197 (412)
Q Consensus       122 q~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~  197 (412)
                      |+++.+.++....+..+..++|+.+....    .....++.+|+|+|..-+..     ...+.++++||+||-|++.-..
T Consensus       147 Qh~~~~~~~f~~~~~~v~~l~~~~~~~~r~~~~~~~~~g~~~iiIGThsl~~~-----~~~f~~LglviiDEqH~fgv~Q  221 (264)
T d1gm5a3         147 QHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQE-----DVHFKNLGLVIIDEQHRFGVKQ  221 (264)
T ss_dssp             HHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHH-----CCCCSCCCEEEEESCCCC----
T ss_pred             HHHHHHHHhhhhccccceeeccccchHHHHHHHHHHHCCCCCEEEeehHHhcC-----CCCccccceeeeccccccchhh
Confidence            99999999998889999999998876554    33446789999999766543     3445789999999999864322


Q ss_pred             cHHHHHHHHHhCCCCceEEEEeecCChHHHHHHH
Q 015158          198 FKDQIYDIFQLLPPKIQVGVFSATMPPEALEITR  231 (412)
Q Consensus       198 ~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~  231 (412)
                           +..+.....++.++.+||||.+.......
T Consensus       222 -----r~~l~~~~~~~~~l~~SATPiprtl~~~~  250 (264)
T d1gm5a3         222 -----REALMNKGKMVDTLVMSATPIPRSMALAF  250 (264)
T ss_dssp             ------CCCCSSSSCCCEEEEESSCCCHHHHHHH
T ss_pred             -----HHHHHHhCcCCCEEEEECCCCHHHHHHHH
Confidence                 11111223467899999999887655443

>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=99.85  E-value=1.1e-21  Score=149.51  Aligned_cols=103  Identities=25%  Similarity=0.417  Sum_probs=91.7

Q ss_pred             HhcCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEc
Q 015158          274 ETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINY  353 (412)
Q Consensus       274 ~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~  353 (412)
                      +....+++||||++++.|+.+++.|++.|+.+..+|++++..       .|++|+.++||||+++++|+| |+++.||++
T Consensus        31 ~~~~~~k~IVFc~t~~~ae~la~~L~~~G~~~~~~H~~~~~~-------~~~~~~~~vlvaTd~~~~GiD-~~v~~Vi~~  102 (138)
T d1jr6a_          31 EVIKGGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVS-------VIPTNGDVVVVATDALMTGFT-GDFDSVIDC  102 (138)
T ss_dssp             HHHTTSCEEEECSCHHHHHHHHHHHHHHTCEEEEECTTCCSC-------CCTTSSCEEEEESSSSCSSSC-CCBSEEEEC
T ss_pred             hhcCCCCEEEEeCcHHHHHHHHHHHhccccchhhhhccchhh-------hhhhhhcceeehhHHHHhccc-cccceEEEE
Confidence            444568999999999999999999999999999999999854       467899999999999999999 999999985


Q ss_pred             ----cCCCChhhHHHhhhhcccCCCCceEEEEeccCc
Q 015158          354 ----DLPTQPENYLHRIGRSGRFGRKGVAINFVTRDD  386 (412)
Q Consensus       354 ----~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~  386 (412)
                          ++|.+...|.||+||+|| |++|. ++|+.+.+
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                468999999999999999 89994 77877654

>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=99.84  E-value=6.8e-21  Score=157.63  Aligned_cols=136  Identities=18%  Similarity=0.185  Sum_probs=102.1

Q ss_pred             CChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEE
Q 015158           61 KPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHA  140 (412)
Q Consensus        61 ~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~  140 (412)
                      +|++||++++..+.++++.++.+|||+|||.+++..+.. +     +.++||+||+++|+.||.+++..+...   .+..
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            499999999999999999999999999999987655433 2     237999999999999999999887532   2333


Q ss_pred             EEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEee
Q 015158          141 CVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSA  220 (412)
Q Consensus       141 ~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SA  220 (412)
                      ..|+..         ....++++|++++.......   .+.+++||+||||++.+..    +..+...++ ...+++|||
T Consensus       141 ~~~~~~---------~~~~i~i~t~~~~~~~~~~~---~~~~~lvIiDEaH~~~a~~----~~~i~~~~~-~~~~lgLTA  203 (206)
T d2fz4a1         141 FSGRIK---------ELKPLTVSTYDSAYVNAEKL---GNRFMLLIFDEVHHLPAES----YVQIAQMSI-APFRLGLTA  203 (206)
T ss_dssp             ESSSCB---------CCCSEEEEEHHHHHHTHHHH---TTTCSEEEEECSSCCCTTT----HHHHHHTCC-CSEEEEEEE
T ss_pred             cccccc---------cccccccceehhhhhhhHhh---CCcCCEEEEECCeeCCcHH----HHHHHhccC-CCcEEEEec
Confidence            333322         23579999999987655432   2468999999999976443    344555443 456799999


Q ss_pred             cC
Q 015158          221 TM  222 (412)
Q Consensus       221 T~  222 (412)
                      |+
T Consensus       204 Tl  205 (206)
T d2fz4a1         204 TF  205 (206)
T ss_dssp             SC
T ss_pred             CC
Confidence            98

>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=99.81  E-value=7.5e-20  Score=159.79  Aligned_cols=119  Identities=22%  Similarity=0.394  Sum_probs=104.5

Q ss_pred             HHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCC--------CCHHHHHHHHHHHhcCCCcEEEEcCCCcC
Q 015158          269 LCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGD--------MDQNTRDIIMREFRSGSSRVLITTDLLAR  340 (412)
Q Consensus       269 l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~--------~~~~~r~~~~~~f~~g~~~vlv~t~~~~~  340 (412)
                      +.+++......++||||+++..++.+++.|.+.++.+..++|.        ++..+|..+++.|++|+++|||+|+++++
T Consensus       152 l~~~~~~~~~~k~iiF~~~~~~~~~~~~~L~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~F~~g~~~vLv~T~~~~~  231 (286)
T d1wp9a2         152 IREQLQRKQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVATSVGEE  231 (286)
T ss_dssp             HHHHHHHCTTCCEEEECSCHHHHHHHHHHHHHTTCCEEEECCSSCC-------CCHHHHHHHHHHHTSCSEEEECGGGGG
T ss_pred             HHHHHHhCCCCcEEEEeCcHHhHHHHHHHHHHcCCceEEeeccccccccchhchHHHHHHHHHHHcCCCcEEEEccceec
Confidence            3344455677899999999999999999999999998888764        55567899999999999999999999999


Q ss_pred             CCCCCCCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHH
Q 015158          341 GIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDER  388 (412)
Q Consensus       341 G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~  388 (412)
                      |+|+|++++||++++|+|+..|+||+||+||.+ +|.+++++++...+
T Consensus       232 Gld~~~~~~Vi~~d~~~~~~~~~Qr~GR~gR~~-~~~~~~l~~~~~~e  278 (286)
T d1wp9a2         232 GLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRHM-PGRVIILMAKGTRD  278 (286)
T ss_dssp             GGGSTTCCEEEESSCCHHHHHHHHHHTTSCSCC-CSEEEEEEETTSHH
T ss_pred             cccCCCCCEEEEeCCCCCHHHHHHHHHhCCCCC-CCEEEEEEeCCCHH
Confidence            999999999999999999999999999999975 78889999887554

>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=99.81  E-value=7.8e-20  Score=149.62  Aligned_cols=121  Identities=23%  Similarity=0.382  Sum_probs=101.1

Q ss_pred             HHHHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcC------------------------------CCeeEEecCCCCHH
Q 015158          266 LETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSR------------------------------DHTVSATHGDMDQN  315 (412)
Q Consensus       266 ~~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~------------------------------~~~~~~~~~~~~~~  315 (412)
                      .+.+.+.+++  ++++||||+|++.|+.++..|.+.                              ...+.++|++|++.
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            3455555554  468999999999999888877642                              12378999999999


Q ss_pred             HHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEE-------ccCCCChhhHHHhhhhcccCCC--CceEEEEeccCc
Q 015158          316 TRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVIN-------YDLPTQPENYLHRIGRSGRFGR--KGVAINFVTRDD  386 (412)
Q Consensus       316 ~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~-------~~~~~s~~~~~Q~~GR~~R~g~--~g~~~~~~~~~~  386 (412)
                      +|..+++.|++|.++|||||++++.|+|+|..++||.       .+.|.+..+|.||+||+||.|.  .|.++++..+.+
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       5667899999999999999985  678888777765


Q ss_pred             HH
Q 015158          387 ER  388 (412)
Q Consensus       387 ~~  388 (412)
                      .+
T Consensus       188 ~~  189 (201)
T d2p6ra4         188 RE  189 (201)
T ss_dssp             HH
T ss_pred             hH
Confidence            54

>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=99.80  E-value=2.9e-20  Score=153.32  Aligned_cols=109  Identities=21%  Similarity=0.370  Sum_probs=100.8

Q ss_pred             hhhHHHHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCC
Q 015158          263 EWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGI  342 (412)
Q Consensus       263 ~~~~~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~  342 (412)
                      ..+.+.+.+++..+..+++||||++...++.+.+.|.     +..+||+++..+|..+++.|++|+.+|||+|+++++|+
T Consensus        78 ~~K~~~l~~ll~~~~~~k~lvf~~~~~~~~~l~~~l~-----~~~i~g~~~~~~R~~~l~~F~~~~~~vLv~~~~~~~Gi  152 (200)
T d2fwra1          78 KNKIRKLREILERHRKDKIIIFTRHNELVYRISKVFL-----IPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGI  152 (200)
T ss_dssp             SHHHHHHHHHHHHTSSSCBCCBCSCHHHHHHHHHHTT-----CCBCCSSSCSHHHHTHHHHHHHSSCSBCBCSSCCCSSS
T ss_pred             HHHHHHHHHHHHhCCCCcEEEEeCcHHHHHHHHhhcC-----cceeeCCCCHHHHHHHHHHhhcCCeeeeeecchhhccc
Confidence            3477889999999888999999999999999998884     44579999999999999999999999999999999999


Q ss_pred             CCCCCCEEEEccCCCChhhHHHhhhhcccCCCCc
Q 015158          343 DVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKG  376 (412)
Q Consensus       343 d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g  376 (412)
                      |+|.+++||++++|+|+..+.|++||++|.|+.+
T Consensus       153 dl~~~~~vi~~~~~~s~~~~~Q~iGR~~R~~~~k  186 (200)
T d2fwra1         153 DVPDANVGVIMSGSGSAREYIQRLGRILRPSKGK  186 (200)
T ss_dssp             CSCCBSEEEEECCSSCCHHHHHHHHHSBCCCTTT
T ss_pred             CCCCCCEEEEeCCCCCHHHHHHHHHhcCCCCCCC
Confidence            9999999999999999999999999999998754

>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=99.79  E-value=1.2e-19  Score=141.04  Aligned_cols=136  Identities=21%  Similarity=0.222  Sum_probs=91.6

Q ss_pred             hhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHH
Q 015158           73 FCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQR  152 (412)
Q Consensus        73 ~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  152 (412)
                      +.+|+++++.+|||+|||.+++..++.....  .+.++++++|++.+++|+.+.+...    +..+........      
T Consensus         4 l~~~~~~il~~~tGsGKT~~~~~~~~~~~~~--~~~~vli~~p~~~l~~q~~~~~~~~----~~~~~~~~~~~~------   71 (140)
T d1yksa1           4 LKKGMTTVLDFHPGAGKTRRFLPQILAECAR--RRLRTLVLAPTRVVLSEMKEAFHGL----DVKFHTQAFSAH------   71 (140)
T ss_dssp             TSTTCEEEECCCTTSSTTTTHHHHHHHHHHH--TTCCEEEEESSHHHHHHHHHHTTTS----CEEEESSCCCCC------
T ss_pred             HHcCCcEEEEcCCCCChhHHHHHHHHHHhhh--cCceeeeeecchhHHHHHHHHhhhh----hhhhcccccccc------
Confidence            4568999999999999998887776655543  2468999999999999998766443    222222211111      


Q ss_pred             HhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcH-HHHHHHHHhCCCCceEEEEeecCC
Q 015158          153 ILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFK-DQIYDIFQLLPPKIQVGVFSATMP  223 (412)
Q Consensus       153 ~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~-~~~~~i~~~~~~~~~~i~~SAT~~  223 (412)
                       ......+.++|...+.+... ......++++||+||||++....+. ..+...... .++.++++||||||
T Consensus        72 -~~~~~~~~~~~~~~l~~~~~-~~~~~~~~~lvIiDEaH~~~~~~~~~~~~~~~~~~-~~~~~~l~lTATPp  140 (140)
T d1yksa1          72 -GSGREVIDAMCHATLTYRML-EPTRVVNWEVIIMDEAHFLDPASIAARGWAAHRAR-ANESATILMTATPP  140 (140)
T ss_dssp             -CCSSCCEEEEEHHHHHHHHT-SSSCCCCCSEEEETTTTCCSHHHHHHHHHHHHHHH-TTSCEEEEECSSCT
T ss_pred             -cccccchhhhhHHHHHHHHh-ccccccceeEEEEccccccChhhHHHHHHHHHHhh-CCCCCEEEEEcCCC
Confidence             11235677888887766543 3455678999999999987544322 122222333 35789999999996

>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=99.76  E-value=3e-19  Score=144.72  Aligned_cols=132  Identities=19%  Similarity=0.303  Sum_probs=103.3

Q ss_pred             hHHHHHHHHHhc--CCCcEEEEEcchhHHH--------HHHHHHhcC---CCeeEEecCCCCHHHHHHHHHHHhcCCCcE
Q 015158          265 KLETLCDLYETL--AITQSVIFVNTRRKVD--------WLTDKMRSR---DHTVSATHGDMDQNTRDIIMREFRSGSSRV  331 (412)
Q Consensus       265 ~~~~l~~~~~~~--~~~k~lif~~~~~~~~--------~~~~~L~~~---~~~~~~~~~~~~~~~r~~~~~~f~~g~~~v  331 (412)
                      +.+.+.+.++..  .++++.++||.++..+        ...+.|.+.   +..+..+||.|++++|++++.+|.+|+++|
T Consensus        14 ~~~~v~~~I~~el~~g~QvyvVcP~Ieese~~~~~~~~e~~~~l~~~~~p~~~v~~lHG~m~~~eke~~m~~F~~g~~~i   93 (206)
T d1gm5a4          14 RVNEVYEFVRQEVMRGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDI   93 (206)
T ss_dssp             THHHHHHHHHHHTTTSCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHHHHHTTTSSSB
T ss_pred             cHHHHHHHHHHHHHcCCCEEEEEeeecccccccchhhHHHHHHHHHhcCCCCeEEEEeecccHHHHHHHHHHHHCCCEEE
Confidence            344455554443  4467888898765443        344555432   567889999999999999999999999999


Q ss_pred             EEEcCCCcCCCCCCCCCEEEEccCCC-ChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHH
Q 015158          332 LITTDLLARGIDVQQVSLVINYDLPT-QPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKF  396 (412)
Q Consensus       332 lv~t~~~~~G~d~~~~~~vi~~~~~~-s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~  396 (412)
                      ||||.++++|+|+|++++||+.+.+. ..+++.|..||+||.|..|.|++++++.+....+.+..+
T Consensus        94 LVaTtViE~GIDip~a~~iii~~a~~fglsqlhQlrGRvGR~~~~~~~~l~~~~~~~~~~~rl~~~  159 (206)
T d1gm5a4          94 LVSTTVIEVGIDVPRANVMVIENPERFGLAQLHQLRGRVGRGGQEAYCFLVVGDVGEEAMERLRFF  159 (206)
T ss_dssp             CCCSSCCCSCSCCTTCCEEEBCSCSSSCTTHHHHHHHTSCCSSTTCEEECCCCSCCHHHHHHHHHH
T ss_pred             EEEehhhhccccccCCcEEEEEccCCccHHHHHhhhhheeeccccceeEeeeccccccchhhhhhc
Confidence            99999999999999999999888775 899999999999999999999999988777666665443

>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=1.6e-17  Score=132.81  Aligned_cols=109  Identities=17%  Similarity=0.253  Sum_probs=100.4

Q ss_pred             CCCcEEEEEcchhHHHHHHHHHhcC--CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEcc
Q 015158          277 AITQSVIFVNTRRKVDWLTDKMRSR--DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYD  354 (412)
Q Consensus       277 ~~~k~lif~~~~~~~~~~~~~L~~~--~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~  354 (412)
                      .++++.++||..+..+.+.+.+++.  +..+..+||.|++.++++++.+|.+|+++|||||.++++|+|+|+++++|+.+
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            5689999999999999999988874  66899999999999999999999999999999999999999999999999877


Q ss_pred             CC-CChhhHHHhhhhcccCCCCceEEEEeccC
Q 015158          355 LP-TQPENYLHRIGRSGRFGRKGVAINFVTRD  385 (412)
Q Consensus       355 ~~-~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~  385 (412)
                      .. +..+++.|..||+||.+..+.|++++++.
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            65 58899999999999999999999998653

>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=99.74  E-value=6.4e-18  Score=130.08  Aligned_cols=128  Identities=16%  Similarity=0.103  Sum_probs=87.2

Q ss_pred             cCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHh
Q 015158           75 KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRIL  154 (412)
Q Consensus        75 ~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  154 (412)
                      +.+..++.+|||+|||..+...+..      .+.+++|++|++.|++|+.+.+.+....   ......++...       
T Consensus         7 ~~~~~ll~apTGsGKT~~~~~~~~~------~~~~vli~~P~~~l~~q~~~~~~~~~~~---~~~~~~~~~~~-------   70 (136)
T d1a1va1           7 SFQVAHLHAPTGSGKSTKVPAAYAA------QGYKVLVLNPSVAATLGFGAYMSKAHGV---DPNIRTGVRTI-------   70 (136)
T ss_dssp             SCEEEEEECCTTSCTTTHHHHHHHT------TTCCEEEEESCHHHHHHHHHHHHHHHSC---CCEEECSSCEE-------
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHHH------cCCcEEEEcChHHHHHHHHHHHHHHhhc---ccccccccccc-------
Confidence            3467899999999999876443321      2358999999999999999999886532   22233333221       


Q ss_pred             cCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCC--CCceEEEEeecC
Q 015158          155 SSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLP--PKIQVGVFSATM  222 (412)
Q Consensus       155 ~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~--~~~~~i~~SAT~  222 (412)
                      .....++++|++.......   ..+.++++||+||+|++.... ...+..++..+.  +..+++++||||
T Consensus        71 ~~~~~~~~~~~~~~~~~~~---~~~~~~~~vIiDE~H~~~~~~-~~~~~~~l~~~~~~~~~~~l~~TATP  136 (136)
T d1a1va1          71 TTGSPITYSTYGKFLADGG---CSGGAYDIIICDECHSTDATS-ILGIGTVLDQAETAGARLVVLATATP  136 (136)
T ss_dssp             CCCCSEEEEEHHHHHHTTG---GGGCCCSEEEEETTTCCSHHH-HHHHHHHHHHTTTTTCSEEEEEESSC
T ss_pred             ccccceEEEeeeeeccccc---hhhhcCCEEEEecccccCHHH-HHHHHHHHHHHHHCCCCcEEEEeCCC
Confidence            1234688899887654432   235689999999999864332 334455555443  466799999997

>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=99.70  E-value=2.4e-18  Score=144.07  Aligned_cols=107  Identities=18%  Similarity=0.216  Sum_probs=93.5

Q ss_pred             CCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHH----------HHHHHHHhcCCCcEEEEcCCCcC---CCC
Q 015158          277 AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTR----------DIIMREFRSGSSRVLITTDLLAR---GID  343 (412)
Q Consensus       277 ~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r----------~~~~~~f~~g~~~vlv~t~~~~~---G~d  343 (412)
                      +.+++||||++++.++++++.|++.|+++..+|++++.+.|          ..+++.|.+|+.+++|+|+...+   |+|
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            35799999999999999999999999999999999998776          45788899999999999998877   778


Q ss_pred             CCCCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEecc
Q 015158          344 VQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTR  384 (412)
Q Consensus       344 ~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~  384 (412)
                      ++.+.+|++++.|.|..+|+||+||+|| |++|....++..
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            8888999999999999999999999999 888877665544

>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=99.69  E-value=1.4e-19  Score=154.23  Aligned_cols=120  Identities=17%  Similarity=0.255  Sum_probs=101.8

Q ss_pred             hhhHHHHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEc----CCC
Q 015158          263 EWKLETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITT----DLL  338 (412)
Q Consensus       263 ~~~~~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t----~~~  338 (412)
                      +.+...+.++++... +++||||++++.++.+++.|++.      +||+++..+|.+++++|++|+++|||||    +.+
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            446677888887654 68999999999999999999863      7999999999999999999999999999    568


Q ss_pred             cCCCCCCC-CCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHH
Q 015158          339 ARGIDVQQ-VSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDI  393 (412)
Q Consensus       339 ~~G~d~~~-~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~  393 (412)
                      ++|+|+|. +++||+++.|+    |.|++||+||.|..|.+++++...+......+
T Consensus        84 ~rGlDip~~v~~VI~~d~P~----~~~r~gR~~R~g~~~~~~~~~~~~~~~~~~~l  135 (248)
T d1gkub2          84 VRGLDLPERIRFAVFVGCPS----FRVTIEDIDSLSPQMVKLLAYLYRNVDEIERL  135 (248)
T ss_dssp             -CCSCCTTTCCEEEEESCCE----EEEECSCGGGSCHHHHHHHHTTTSCHHHHHTT
T ss_pred             hhccCccccccEEEEeCCCc----chhhhhhhhccCcceEeeeeccHhhHHHHHHH
Confidence            99999996 99999999994    88999999999999999888887776654433

>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=99.62  E-value=3.9e-15  Score=130.15  Aligned_cols=158  Identities=15%  Similarity=0.133  Sum_probs=105.0

Q ss_pred             CChHHHHhhhhhhh---------cCccEEEECCCCCCchhHhHHHHHHhhccCC----CceeEEEEcCCHHHHHHHHHHH
Q 015158           61 KPSAIQQRGIVPFC---------KGLDVIQQAQSGTGKTATFCSGILQQLDYGL----VECQALVLAPTRELAQQIEKVM  127 (412)
Q Consensus        61 ~l~~~Q~~a~~~~~---------~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~----~~~~~lil~P~~~L~~q~~~~~  127 (412)
                      .|+|||.+++..+.         .+..+++..++|.|||.+++..+........    ...++|||||. +|..||.+++
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            48999999998653         3457899999999999876554443333221    23469999996 5889999999


Q ss_pred             HHhhcccCcEEEEEEcCcchHHHHHH---h-----cCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcH
Q 015158          128 RALGDYLGVKVHACVGGTSVREDQRI---L-----SSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFK  199 (412)
Q Consensus       128 ~~~~~~~~~~~~~~~~~~~~~~~~~~---~-----~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~  199 (412)
                      .++.... ..+..++++.........   .     ....+++++|++.+.....  .+...++++||+||+|.+.+..  
T Consensus       134 ~k~~~~~-~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~i~sy~~~~~~~~--~l~~~~~~~vI~DEaH~ikn~~--  208 (298)
T d1z3ix2         134 GKWLGGR-VQPVAIDGGSKDEIDSKLVNFISQQGMRIPTPILIISYETFRLHAE--VLHKGKVGLVICDEGHRLKNSD--  208 (298)
T ss_dssp             HHHHGGG-CCEEEECSSCHHHHHHHHHHHHCCCSSCCSCCEEEEEHHHHHHHTT--TTTTSCCCEEEETTGGGCCTTC--
T ss_pred             HhhcCCc-eeEEEEeCchHHHHHHHHHHhhhccCccccceEEEEeecccccchh--cccccceeeeeccccccccccc--
Confidence            9987643 334445554433222111   1     1235799999999876543  3334568999999999987665  


Q ss_pred             HHHHHHHHhCCCCceEEEEeecCChH
Q 015158          200 DQIYDIFQLLPPKIQVGVFSATMPPE  225 (412)
Q Consensus       200 ~~~~~i~~~~~~~~~~i~~SAT~~~~  225 (412)
                      .........+. ....+++||||-.+
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            22222333333 45679999999653

>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=99.59  E-value=8.4e-15  Score=129.32  Aligned_cols=119  Identities=18%  Similarity=0.234  Sum_probs=104.2

Q ss_pred             hhhHHHHHHHHHh---cCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCc---EEEEcC
Q 015158          263 EWKLETLCDLYET---LAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSR---VLITTD  336 (412)
Q Consensus       263 ~~~~~~l~~~~~~---~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~---vlv~t~  336 (412)
                      ..|...+..++..   ..++|+|||++.....+.+.+.|.+.|+.+..++|.++..+|..+++.|+++..+   +|++|.
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            4466666666653   4568999999999999999999999999999999999999999999999987543   667788


Q ss_pred             CCcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEE
Q 015158          337 LLARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINF  381 (412)
Q Consensus       337 ~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~  381 (412)
                      +++.|+|+..+++||+++++|++....|++||+.|.|+...+.++
T Consensus       180 agg~GlnL~~a~~vi~~d~~wnp~~~~Qa~~R~~R~GQ~~~V~v~  224 (346)
T d1z3ix1         180 AGGCGLNLIGANRLVMFDPDWNPANDEQAMARVWRDGQKKTCYIY  224 (346)
T ss_dssp             GSCTTCCCTTEEEEEECSCCSSHHHHHHHHTTSSSTTCCSCEEEE
T ss_pred             hhhhccccccceEEEEecCCCccchHhHhhhcccccCCCCceEEE
Confidence            999999999999999999999999999999999999987655443

>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=99.56  E-value=4.7e-15  Score=124.56  Aligned_cols=150  Identities=15%  Similarity=0.138  Sum_probs=100.6

Q ss_pred             CChHHHHhhhhhhh----cCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCc
Q 015158           61 KPSAIQQRGIVPFC----KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGV  136 (412)
Q Consensus        61 ~l~~~Q~~a~~~~~----~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~  136 (412)
                      +|+|||.+++..+.    .+..+++..++|.|||..++..+.... ......++||+|| ..+..||.+++.++....  
T Consensus        12 ~L~~yQ~~~v~~~~~~~~~~~g~iLaDe~GlGKT~~~i~~~~~~~-~~~~~~~~LIv~p-~~l~~~W~~e~~~~~~~~--   87 (230)
T d1z63a1          12 NLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAVFSDAK-KENELTPSLVICP-LSVLKNWEEELSKFAPHL--   87 (230)
T ss_dssp             CCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHHHHHHHHH-HTTCCSSEEEEEC-STTHHHHHHHHHHHCTTS--
T ss_pred             chhHHHHHHHHHHHHhhhcCCCEEEEeCCCCChHHHHHHhhhhhh-hcccccccceecc-hhhhhHHHHHHHhhcccc--
Confidence            48999999997654    345689999999999998765544333 3334457999999 577888999999886532  


Q ss_pred             EEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEE
Q 015158          137 KVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVG  216 (412)
Q Consensus       137 ~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i  216 (412)
                      .+..........     ...+++++++|++.+.+...   +....+++||+||+|.+.+..  .........+. ....+
T Consensus        88 ~~~~~~~~~~~~-----~~~~~~vvi~~~~~~~~~~~---l~~~~~~~vI~DEah~~k~~~--s~~~~~~~~l~-a~~r~  156 (230)
T d1z63a1          88 RFAVFHEDRSKI-----KLEDYDIILTTYAVLLRDTR---LKEVEWKYIVIDEAQNIKNPQ--TKIFKAVKELK-SKYRI  156 (230)
T ss_dssp             CEEECSSSTTSC-----CGGGSSEEEEEHHHHTTCHH---HHTCCEEEEEEETGGGGSCTT--SHHHHHHHTSC-EEEEE
T ss_pred             cceeeccccchh-----hccCcCEEEeeHHHHHhHHH---HhcccceEEEEEhhhcccccc--hhhhhhhhhhc-cceEE
Confidence            333222211111     12346899999998754322   112368899999999987655  22233334443 45579


Q ss_pred             EEeecCChH
Q 015158          217 VFSATMPPE  225 (412)
Q Consensus       217 ~~SAT~~~~  225 (412)
                      ++||||-.+
T Consensus       157 ~LTgTPi~n  165 (230)
T d1z63a1         157 ALTGTPIEN  165 (230)
T ss_dssp             EECSSCSTT
T ss_pred             EEecchHHh
Confidence            999999754

>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=99.53  E-value=2.9e-14  Score=120.63  Aligned_cols=123  Identities=16%  Similarity=0.218  Sum_probs=90.9

Q ss_pred             hhhHHHHHHHHHhc--CCCcEEEEEcchhHHHHHHHHHhcC-CCeeEEecCCCCHHHHHHHHHHHhcC-CCcEEEE-cCC
Q 015158          263 EWKLETLCDLYETL--AITQSVIFVNTRRKVDWLTDKMRSR-DHTVSATHGDMDQNTRDIIMREFRSG-SSRVLIT-TDL  337 (412)
Q Consensus       263 ~~~~~~l~~~~~~~--~~~k~lif~~~~~~~~~~~~~L~~~-~~~~~~~~~~~~~~~r~~~~~~f~~g-~~~vlv~-t~~  337 (412)
                      ..|...+.+++...  .++|+||||+.....+.+...+... +..+..++|+++..+|..++++|.++ ...++++ +.+
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            45777777777653  5679999999999999998888754 78889999999999999999999886 4566655 579


Q ss_pred             CcCCCCCCCCCEEEEccCCCChhhHHHhhhhcccCCCCce--EEEEeccC
Q 015158          338 LARGIDVQQVSLVINYDLPTQPENYLHRIGRSGRFGRKGV--AINFVTRD  385 (412)
Q Consensus       338 ~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~--~~~~~~~~  385 (412)
                      .++|+|+..+++||+++++||+..+.|++||+.|.|+...  ++.++..+
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=99.46  E-value=1.3e-13  Score=118.07  Aligned_cols=101  Identities=14%  Similarity=0.221  Sum_probs=81.0

Q ss_pred             CCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCCCCCEEEEccC--
Q 015158          278 ITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDL--  355 (412)
Q Consensus       278 ~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~~~~~vi~~~~--  355 (412)
                      .++++|||++...++.+++.|++.|..+..+||.+...++.    .|.+++.++||+|+++++|+|+ ++.+||+.+.  
T Consensus        36 ~g~~~~F~~s~~~~~~~a~~L~~~g~~V~~l~~~~~~~e~~----~~~~~~~~~~~~t~~~~~~~~~-~~~~vid~g~~~  110 (299)
T d1yksa2          36 KRPTAWFLPSIRAANVMAASLRKAGKSVVVLNRKTFEREYP----TIKQKKPDFILATDIAEMGANL-CVERVLDCRTAF  110 (299)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHTTCCEEECCSSSCC------------CCCSEEEESSSTTCCTTC-CCSEEEECCEEE
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHhcCCeEEEEcCcCcHhHHh----hhhcCCcCEEEEechhhhceec-CceEEEecCcee
Confidence            57999999999999999999999999999999999877754    4678999999999999999999 5999986653  


Q ss_pred             -----------------CCChhhHHHhhhhcccCCCCceEEEEec
Q 015158          356 -----------------PTQPENYLHRIGRSGRFGRKGVAINFVT  383 (412)
Q Consensus       356 -----------------~~s~~~~~Q~~GR~~R~g~~g~~~~~~~  383 (412)
                                       |.|.++..||.||+||.+....++.++.
T Consensus       111 ~~~~~~~~~~~~~~~~~~~~~~~~~qr~gr~gr~~~~~~~~~~y~  155 (299)
T d1yksa2         111 KPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNRDGDSYYYS  155 (299)
T ss_dssp             EEEEETTTTEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEEC
T ss_pred             ceeeecCCCCeeEEeeeecCHHHHHHhcccccccCCCceEEEEeC
Confidence                             2577888999999999865544555554

>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=99.41  E-value=1.6e-12  Score=100.13  Aligned_cols=123  Identities=15%  Similarity=0.230  Sum_probs=97.7

Q ss_pred             cchhhHHHHHHHHHh-c-CCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcC-CCcEEEEcCC
Q 015158          261 KEEWKLETLCDLYET-L-AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSG-SSRVLITTDL  337 (412)
Q Consensus       261 ~~~~~~~~l~~~~~~-~-~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g-~~~vlv~t~~  337 (412)
                      ....|...+.+.+.. + .+.++||++.|++..+.+++.|++.++...+++......+ ..++.  ..| ...|.|+|++
T Consensus        15 T~~eK~~AIi~eV~~~~~~grPVLIgT~SIe~SE~ls~~L~~~gi~h~vLnAk~~~~E-a~II~--~Ag~~g~VtIATNm   91 (175)
T d1tf5a4          15 TMEGKFKAVAEDVAQRYMTGQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHERE-AQIIE--EAGQKGAVTIATNM   91 (175)
T ss_dssp             SHHHHHHHHHHHHHHHHHHTCCEEEEESCHHHHHHHHHHHHTTTCCCEEECSSCHHHH-HHHHT--TTTSTTCEEEEETT
T ss_pred             CHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHcCCCceeehhhhHHHH-HHHHH--hccCCCceeehhhH
Confidence            334565555554433 2 4579999999999999999999999999999998754333 23333  344 4569999999


Q ss_pred             CcCCCCCC--------CCCEEEEccCCCChhhHHHhhhhcccCCCCceEEEEeccCc
Q 015158          338 LARGIDVQ--------QVSLVINYDLPTQPENYLHRIGRSGRFGRKGVAINFVTRDD  386 (412)
Q Consensus       338 ~~~G~d~~--------~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~  386 (412)
                      +++|.|++        +--|||....+.|.....|..||+||.|.+|.+..|++-.|
T Consensus        92 AGRGtDikl~~~v~~~GGLhVI~t~~~~s~Rid~Ql~GR~gRQGdpGs~~~~~sleD  148 (175)
T d1tf5a4          92 AGRGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGDPGITQFYLSMED  148 (175)
T ss_dssp             SSTTCCCCCCTTSGGGTSEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEETTS
T ss_pred             HHcCCCccchHHHHhCCCcEEEEeccCcchhHHHHHhcchhhhCCCcccEEEEEcCH
Confidence            99999986        34478999999999999999999999999999999987655

>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=99.08  E-value=1.2e-09  Score=89.50  Aligned_cols=167  Identities=21%  Similarity=0.246  Sum_probs=120.2

Q ss_pred             CCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcE
Q 015158           58 GFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVK  137 (412)
Q Consensus        58 ~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~  137 (412)
                      |.. +++.|.-.--.+.+|+  +..+.||-|||+++.++++-....+   +.+-+|+.+.-|+..-++++..+...+|+.
T Consensus        78 G~R-hyDVQLiGgi~L~~G~--iaem~TGEGKTL~a~l~a~l~al~g---~~vhvvTvNdyLA~RDae~m~~iy~~lGls  151 (273)
T d1tf5a3          78 GMF-PFKVQLMGGVALHDGN--IAEMKTGEGKTLTSTLPVYLNALTG---KGVHVVTVNEYLASRDAEQMGKIFEFLGLT  151 (273)
T ss_dssp             SCC-CCHHHHHHHHHHHTTS--EEECCTTSCHHHHHHHHHHHHHTTS---SCEEEEESSHHHHHHHHHHHHHHHHHTTCC
T ss_pred             ceE-EehhHHHHHHHHHhhh--heeecCCCcchhHHHHHHHHHHhcC---CCceEEecCccccchhhhHHhHHHHHcCCC
Confidence            555 8888888888888886  8999999999998877776655444   378899999999999999999999999999


Q ss_pred             EEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCC-------CCCCCceEEEEeCCchhh-ccCc-----------
Q 015158          138 VHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQS-------LRPDNIRIFVLDEADEML-SRGF-----------  198 (412)
Q Consensus       138 ~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~-------~~~~~~~~iiiDE~h~~~-~~~~-----------  198 (412)
                      +.....+..........  .++|+++|...|.--+.+..       ...+.+.+.|+||++.++ +...           
T Consensus       152 vg~~~~~~~~~~r~~~Y--~~di~Ygt~~e~~fDyLrd~~~~~~~~~~~r~~~~aIvDEvDsiliDeartpliisg~~~~  229 (273)
T d1tf5a3         152 VGLNLNSMSKDEKREAY--AADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSILIDEARTPLIISGQSMT  229 (273)
T ss_dssp             EEECCTTSCHHHHHHHH--HSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEEETHHHHHTTTTTCEEEEEEEEEE
T ss_pred             ccccccccCHHHHHHHh--hCCceecchhhhhhhhcchhhhcChhhhccCCCCEEEEEcchhhhhhccCCceEeccCccc
Confidence            99988776655444333  46899999988744333222       224678899999999865 2220           


Q ss_pred             --HHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhcCC
Q 015158          199 --KDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFMNK  236 (412)
Q Consensus       199 --~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~  236 (412)
                        .-.+..++...   .++-+||+|...+..++ ...++-
T Consensus       230 ~a~it~q~~f~~y---~~l~gmtgta~~~~~e~-~~iy~l  265 (273)
T d1tf5a3         230 LATITFQNYFRMY---EKLAGMTGTAKTEEEEF-RNIYNM  265 (273)
T ss_dssp             EEEEEHHHHHTTS---SEEEEEESCCGGGHHHH-HHHHCC
T ss_pred             hhhhhHHHHHHHH---HHHhCCccccHHHHHHH-HhccCC
Confidence              11234444443   47899999987655444 444443

>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=98.91  E-value=1.8e-08  Score=78.68  Aligned_cols=125  Identities=19%  Similarity=0.236  Sum_probs=98.8

Q ss_pred             cchhhHHHHHHHHHh-c-CCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcC-CCcEEEEcCC
Q 015158          261 KEEWKLETLCDLYET-L-AITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSG-SSRVLITTDL  337 (412)
Q Consensus       261 ~~~~~~~~l~~~~~~-~-~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g-~~~vlv~t~~  337 (412)
                      ....+...+.+-++. + .+.|+||-+.|++..+.+.+.|.+.++...++++.....+ ..|+.  +.| ...|.|+|++
T Consensus        15 T~~~K~~Avv~ei~~~h~~GqPVLVGT~SVe~SE~lS~lL~~~gi~h~vLNAK~herE-AeIIA--qAG~~GaVTIATNM   91 (219)
T d1nkta4          15 TEEAKYIAVVDDVAERYAKGQPVLIGTTSVERSEYLSRQFTKRRIPHNVLNAKYHEQE-ATIIA--VAGRRGGVTVATNM   91 (219)
T ss_dssp             CHHHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHTTCCCEEECSSCHHHH-HHHHH--TTTSTTCEEEEETT
T ss_pred             CHHHHHHHHHHHHHHHHhcCCCEEEeeCcHHHHHHHHHHHHHhccchhccchhhHHHH-HHHHH--hcccCCcEEeeccc
Confidence            334566555554444 3 5579999999999999999999999999999999743222 33333  456 4459999999


Q ss_pred             CcCCCCCC----------------------------------------------------CCCEEEEccCCCChhhHHHh
Q 015158          338 LARGIDVQ----------------------------------------------------QVSLVINYDLPTQPENYLHR  365 (412)
Q Consensus       338 ~~~G~d~~----------------------------------------------------~~~~vi~~~~~~s~~~~~Q~  365 (412)
                      .++|.|+.                                                    +--+||-.....|...=.|.
T Consensus        92 AGRGTDI~LGgn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGL~VIGTErHeSrRIDnQL  171 (219)
T d1nkta4          92 AGRGTDIVLGGNVDFLTDQRLRERGLDPVETPEEYEAAWHSELPIVKEEASKEAKEVIEAGGLYVLGTERHESRRIDNQL  171 (219)
T ss_dssp             CSTTCCCCTTCCHHHHHHHHHHHTTCCTTTSHHHHHHHHHHHHHHHHHHTTHHHHHHHHTTSEEEEECSCCSSHHHHHHH
T ss_pred             cCCCCceeecCchhhhhHHHhhhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcEEEeccccccccccccc
Confidence            99999984                                                    22378888999999999999


Q ss_pred             hhhcccCCCCceEEEEeccCcHH
Q 015158          366 IGRSGRFGRKGVAINFVTRDDER  388 (412)
Q Consensus       366 ~GR~~R~g~~g~~~~~~~~~~~~  388 (412)
                      .||+||-|.+|.+..|++-.|.-
T Consensus       172 RGRsGRQGDPGsSrFflSLeDdL  194 (219)
T d1nkta4         172 RGRSGRQGDPGESRFYLSLGDEL  194 (219)
T ss_dssp             HHTSSGGGCCEEEEEEEETTSHH
T ss_pred             cccccccCCCccceeEEeccHHH
Confidence            99999999999999999887763

>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=98.48  E-value=3.9e-07  Score=79.97  Aligned_cols=143  Identities=19%  Similarity=0.188  Sum_probs=85.2

Q ss_pred             CCChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHH--HHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcE
Q 015158           60 EKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGI--LQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVK  137 (412)
Q Consensus        60 ~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~--~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~  137 (412)
                      ....++|+.|+..++.++-.+|.||+|||||.+....+  +.... ...+.++++++||..-+..+.+.........+..
T Consensus       147 ~~~~~~Q~~A~~~al~~~~~vI~G~pGTGKTt~i~~~l~~l~~~~-~~~~~~I~l~ApTgkAA~~L~e~~~~~~~~~~~~  225 (359)
T d1w36d1         147 SDEINWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQMA-DGERCRIRLAAPTGKAAARLTESLGKALRQLPLT  225 (359)
T ss_dssp             TTSCCHHHHHHHHHHTBSEEEEECCTTSTHHHHHHHHHHHHHHTC-SSCCCCEEEEBSSHHHHHHHHHHHTHHHHHSSCC
T ss_pred             cccccHHHHHHHHHHcCCeEEEEcCCCCCceehHHHHHHHHHHHH-hccCCeEEEecCcHHHHHHHHHHHHHHHhhcCch
Confidence            34678999999999999999999999999997753322  22222 2245689999999987777766654432211110


Q ss_pred             EEEEEcCcchHHHHHHhcCCCcEEEeChHHHH------HHHHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCCC
Q 015158          138 VHACVGGTSVREDQRILSSGVHVVVGTPGRVF------DMLRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPP  211 (412)
Q Consensus       138 ~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~------~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~  211 (412)
                      .....              ....-..|.+++.      ..+.........++++|+||+-.+.    ...+..++..++.
T Consensus       226 ~~~~~--------------~~~~~~~t~~~ll~~~~~~~~~~~~~~~~l~~d~lIIDEaSmv~----~~l~~~ll~~~~~  287 (359)
T d1w36d1         226 DEQKK--------------RIPEDASTLHRLLGAQPGSQRLRHHAGNPLHLDVLVVDEASMID----LPMMSRLIDALPD  287 (359)
T ss_dssp             SCCCC--------------SCSCCCBTTTSCC-----------CTTSCCSCSEEEECSGGGCB----HHHHHHHHHTCCT
T ss_pred             hhhhh--------------hhhhhhhHHHHHHhhhhcchHHHHhhhcccccceeeehhhhccC----HHHHHHHHHHhcC
Confidence            00000              0000011111111      1112223334568999999999753    3456677888888


Q ss_pred             CceEEEEeec
Q 015158          212 KIQVGVFSAT  221 (412)
Q Consensus       212 ~~~~i~~SAT  221 (412)
                      +.++|++.-.
T Consensus       288 ~~~lILvGD~  297 (359)
T d1w36d1         288 HARVIFLGDR  297 (359)
T ss_dssp             TCEEEEEECT
T ss_pred             CCEEEEECCh
Confidence            8888877655

>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=98.10  E-value=2.5e-06  Score=73.56  Aligned_cols=69  Identities=16%  Similarity=0.118  Sum_probs=53.2

Q ss_pred             CChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhcc-CCCceeEEEEcCCHHHHHHHHHHHHHhh
Q 015158           61 KPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY-GLVECQALVLAPTRELAQQIEKVMRALG  131 (412)
Q Consensus        61 ~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~-~~~~~~~lil~P~~~L~~q~~~~~~~~~  131 (412)
                      +|+|-|++|+..  ....++|.|++|||||.+++.-+...+.. +....+++++++|+++++.+.+.+.+..
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            488999999976  34568999999999998876655544432 2234579999999999998888777754

>d1pjra1 c.37.1.19 (A:1-318) DEXX box DNA helicase {Bacillus stearothermophilus, PcrA [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Bacillus stearothermophilus, PcrA [TaxId: 1422]

Probab=97.86  E-value=1.5e-05  Score=68.89  Aligned_cols=68  Identities=18%  Similarity=0.201  Sum_probs=53.8

Q ss_pred             CChHHHHhhhhhhhcCccEEEECCCCCCchhHhHHHHHHhhccC-CCceeEEEEcCCHHHHHHHHHHHHHh
Q 015158           61 KPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDYG-LVECQALVLAPTRELAQQIEKVMRAL  130 (412)
Q Consensus        61 ~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~-~~~~~~lil~P~~~L~~q~~~~~~~~  130 (412)
                      .|++-|++++...  +..++|.|+.|||||.+++-.+...+... ....+++++++++..+..+...+...
T Consensus        11 ~L~~eQ~~~v~~~--~g~~lV~g~aGSGKTt~l~~ri~~ll~~~~~~p~~il~lt~t~~aa~~~~~~~~~~   79 (318)
T d1pjra1          11 HLNKEQQEAVRTT--EGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTNKAAREMRERVQSL   79 (318)
T ss_dssp             TSCHHHHHHHHCC--SSCEEEEECTTSCHHHHHHHHHHHHHHTTCCCGGGEEEEESSHHHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHhCC--CCCEEEEecCCccHHHHHHHHHHHHHHcCCCCHHHeEeEeccHHHHHHHHHHHHhh
Confidence            3889999999864  45699999999999998876665555433 23357999999999999988887664

>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=97.71  E-value=2.8e-05  Score=62.48  Aligned_cols=42  Identities=5%  Similarity=0.083  Sum_probs=29.4

Q ss_pred             CCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEeecC
Q 015158          180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATM  222 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~  222 (412)
                      ....++|+||+|.+.... ...+.+++...+.+..+++.|-.+
T Consensus       107 ~~~kviIide~d~l~~~a-~n~Llk~lEep~~~~~fIl~t~~~  148 (207)
T d1a5ta2         107 GGAKVVWVTDAALLTDAA-ANALLKTLEEPPAETWFFLATREP  148 (207)
T ss_dssp             SSCEEEEESCGGGBCHHH-HHHHHHHHTSCCTTEEEEEEESCG
T ss_pred             CccceEEechhhhhhhhh-hHHHHHHHHhhcccceeeeeecCh
Confidence            457899999999876543 566777777766677656655443

>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=97.44  E-value=0.00012  Score=58.21  Aligned_cols=135  Identities=23%  Similarity=0.270  Sum_probs=72.2

Q ss_pred             ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcC
Q 015158           77 LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSS  156 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  156 (412)
                      +-+++++|||+|||.+..-.+......+   .++.+++.-.-- ....++++.++...++.+...............   
T Consensus        11 ~vi~lvGp~GvGKTTTiaKLA~~~~~~g---~kV~lit~Dt~R-~gA~eQL~~~a~~l~v~~~~~~~~~~~~~~~~~---   83 (207)
T d1ls1a2          11 NLWFLVGLQGSGKTTTAAKLALYYKGKG---RRPLLVAADTQR-PAAREQLRLLGEKVGVPVLEVMDGESPESIRRR---   83 (207)
T ss_dssp             EEEEEECCTTTTHHHHHHHHHHHHHHTT---CCEEEEECCSSC-HHHHHHHHHHHHHHTCCEEECCTTCCHHHHHHH---
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHHHCC---CcEEEEeccccc-chHHHHHHHHHHhcCCccccccccchhhHHHHH---
Confidence            3356799999999987655444333332   355555542111 112344445544446655443322221110000   


Q ss_pred             CCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhh-ccCcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHhc
Q 015158          157 GVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEML-SRGFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKFM  234 (412)
Q Consensus       157 ~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~-~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~  234 (412)
                                 .....     ...+.++|++|=+-+.. +......+..+.....+...++.++|+...+.......++
T Consensus        84 -----------~~~~~-----~~~~~d~vlIDTaGr~~~d~~~~~el~~~~~~~~~~~~llv~~a~~~~~~~~~~~~f~  146 (207)
T d1ls1a2          84 -----------VEEKA-----RLEARDLILVDTAGRLQIDEPLMGELARLKEVLGPDEVLLVLDAMTGQEALSVARAFD  146 (207)
T ss_dssp             -----------HHHHH-----HHHTCCEEEEECCCCSSCCHHHHHHHHHHHHHHCCSEEEEEEEGGGTHHHHHHHHHHH
T ss_pred             -----------HHHHH-----hhccCcceeecccccchhhhhhHHHHHHHHhhcCCceEEEEeccccchhHHHHHHHHH
Confidence                       00000     11356889999776533 2224466667777777777789999998876666665543

>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=97.41  E-value=0.00016  Score=57.33  Aligned_cols=133  Identities=17%  Similarity=0.228  Sum_probs=68.7

Q ss_pred             EEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCC
Q 015158           79 VIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGV  158 (412)
Q Consensus        79 ~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  158 (412)
                      +++++|||+|||.+..=.+......   +.++.+++.-.--.. -.++++.++...++.+............        
T Consensus        12 i~lvGptGvGKTTTiAKLA~~~~~~---g~kV~lit~Dt~R~g-A~eQL~~~a~~l~v~~~~~~~~~d~~~~--------   79 (211)
T d2qy9a2          12 ILMVGVNGVGKTTTIGKLARQFEQQ---GKSVMLAAGDTFRAA-AVEQLQVWGQRNNIPVIAQHTGADSASV--------   79 (211)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHHTT---TCCEEEECCCTTCHH-HHHHHHHHHHHTTCCEECCSTTCCHHHH--------
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHC---CCcEEEEeccccccc-chhhhhhhhhhcCCcccccccCCCHHHH--------
Confidence            5679999999998875544333222   235555554221111 2445555555556665433222211110        


Q ss_pred             cEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhh-ccCcHHHHHHHHHhCC------CCceEEEEeecCChHHHHHHH
Q 015158          159 HVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEML-SRGFKDQIYDIFQLLP------PKIQVGVFSATMPPEALEITR  231 (412)
Q Consensus       159 ~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~-~~~~~~~~~~i~~~~~------~~~~~i~~SAT~~~~~~~~~~  231 (412)
                               +.+.....  ..+++++|++|=+-+.- +.....++..+.....      +...++.++|+...+......
T Consensus        80 ---------l~~~~~~a--~~~~~d~ilIDTaGr~~~d~~~~~el~~l~~~~~~~~~~~p~~~~LVl~a~~~~~~~~~~~  148 (211)
T d2qy9a2          80 ---------IFDAIQAA--KARNIDVLIADTAGRLQNKSHLMEELKKIVRVMKKLDVEAPHEVMLTIDASTGQNAVSQAK  148 (211)
T ss_dssp             ---------HHHHHHHH--HHTTCSEEEECCCCCGGGHHHHHHHHHHHHHHHTTTCTTCCSEEEEEEEGGGTHHHHHHHH
T ss_pred             ---------HHHHHHHH--HHcCCCEEEeccCCCccccHHHHHHHHHHHHHHhhhcccCcceeeeehhcccCcchHHHHh
Confidence                     11111110  11357899999876532 2223345555544432      356689999998876555554


Q ss_pred             Hhc
Q 015158          232 KFM  234 (412)
Q Consensus       232 ~~~  234 (412)
                      .++
T Consensus       149 ~~~  151 (211)
T d2qy9a2         149 LFH  151 (211)
T ss_dssp             HHH
T ss_pred             hhh
Confidence            443

>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=97.22  E-value=0.00029  Score=55.91  Aligned_cols=133  Identities=20%  Similarity=0.226  Sum_probs=64.0

Q ss_pred             cEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCC
Q 015158           78 DVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSG  157 (412)
Q Consensus        78 ~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  157 (412)
                      -+++++|||+|||.+..=.+......+  ..-.++.+.+--...  .++++.++...++.+............       
T Consensus        14 vi~lvGptGvGKTTTiAKLA~~~~~~g--~kV~lit~Dt~R~ga--~eQL~~~a~~l~v~~~~~~~~~~~~~~-------   82 (211)
T d1j8yf2          14 VIMLVGVQGTGKATTAGKLAYFYKKKG--FKVGLVGADVYRPAA--LEQLQQLGQQIGVPVYGEPGEKDVVGI-------   82 (211)
T ss_dssp             EEEEECSCCC----HHHHHHHHHHHTT--CCEEEEECCCSSHHH--HHHHHHHHHHHTCCEECCTTCCCHHHH-------
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCC--CceEEEEeeccccch--hHHHHHhccccCcceeecccchhhhHH-------
Confidence            356799999999988654443332222  233444444332221  344445554446555322211111000       


Q ss_pred             CcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhh-cc--CcHHHHHHHHHhCCCCceEEEEeecCChHHHHHHHHh
Q 015158          158 VHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEML-SR--GFKDQIYDIFQLLPPKIQVGVFSATMPPEALEITRKF  233 (412)
Q Consensus       158 ~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~-~~--~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~  233 (412)
                                +.+.+...  ...+.++|++|=+=+.. +.  .....+..+.....+...++.++|+...+.......+
T Consensus        83 ----------~~~a~~~~--~~~~~d~IlIDTaGr~~~~~~~~~~~el~~~~~~~~~~~~~LVl~a~~~~~~~~~~~~~  149 (211)
T d1j8yf2          83 ----------AKRGVEKF--LSEKMEIIIVDTAGRHGYGEEAALLEEMKNIYEAIKPDEVTLVIDASIGQKAYDLASKF  149 (211)
T ss_dssp             ----------HHHHHHHH--HHTTCSEEEEECCCSCCTTCHHHHHHHHHHHHHHHCCSEEEEEEEGGGGGGHHHHHHHH
T ss_pred             ----------HHHHHHHh--hccCCceEEEecCCcCccchhhHHHHHHHHHHhhcCCceEEEEEecccCcchHHHHhhh
Confidence                      00101100  11357899999775421 11  1234566677777777778999999876555544433

>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=97.10  E-value=0.0011  Score=52.84  Aligned_cols=44  Identities=14%  Similarity=0.284  Sum_probs=27.8

Q ss_pred             CceEEEEeCCchhhccC-cHHHHHHHHHhCCCCceEEEEeecCCh
Q 015158          181 NIRIFVLDEADEMLSRG-FKDQIYDIFQLLPPKIQVGVFSATMPP  224 (412)
Q Consensus       181 ~~~~iiiDE~h~~~~~~-~~~~~~~i~~~~~~~~~~i~~SAT~~~  224 (412)
                      ..+++++|++|.+.... +...+..++..+......+++|+..++
T Consensus        97 ~~dll~iDDi~~i~~~~~~~~~lf~lin~~~~~~~~iiits~~~p  141 (213)
T d1l8qa2          97 SVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHP  141 (213)
T ss_dssp             TCSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESSCG
T ss_pred             hccchhhhhhhhhcCchHHHHHHHHHHHHHhhccceEEEecCCcc
Confidence            57899999999886433 445566666665444334555555443

>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=97.04  E-value=0.0015  Score=51.58  Aligned_cols=133  Identities=20%  Similarity=0.258  Sum_probs=64.5

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEc-CC-HHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHH
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLA-PT-RELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRI  153 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~-P~-~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  153 (412)
                      ++-+++++|||+|||.+..=.+......   +.++.+++ .+ +.=+.   ++++.++...++.+............   
T Consensus         6 ~~vi~lvGptGvGKTTTiaKLA~~~~~~---g~kV~lit~Dt~R~gA~---eQL~~~a~~l~i~~~~~~~~~d~~~~---   76 (207)
T d1okkd2           6 GRVVLVVGVNGVGKTTTIAKLGRYYQNL---GKKVMFCAGDTFRAAGG---TQLSEWGKRLSIPVIQGPEGTDPAAL---   76 (207)
T ss_dssp             SSEEEEECSTTSSHHHHHHHHHHHHHTT---TCCEEEECCCCSSTTHH---HHHHHHHHHHTCCEECCCTTCCHHHH---
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHC---CCcEEEEEeccccccch---hhHhhcccccCceEEeccCCccHHHH---
Confidence            3556889999999998875544333322   23555554 33 23222   23334443345554332222111110   


Q ss_pred             hcCCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhc-cCcHHHHHHHHHhC------CCCceEEEEeecCChHH
Q 015158          154 LSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLS-RGFKDQIYDIFQLL------PPKIQVGVFSATMPPEA  226 (412)
Q Consensus       154 ~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~-~~~~~~~~~i~~~~------~~~~~~i~~SAT~~~~~  226 (412)
                                    +......  ...++.++|++|=+=+... ......+..+....      .+...++.++||...+.
T Consensus        77 --------------~~~~~~~--~~~~~~d~ilIDTaGr~~~d~~l~~el~~~~~~~~~~~~~~p~~~~LVl~a~~~~~~  140 (207)
T d1okkd2          77 --------------AYDAVQA--MKARGYDLLFVDTAGRLHTKHNLMEELKKVKRAIAKADPEEPKEVWLVLDAVTGQNG  140 (207)
T ss_dssp             --------------HHHHHHH--HHHHTCSEEEECCCCCCTTCHHHHHHHHHHHHHHHHHCTTCCSEEEEEEETTBCTHH
T ss_pred             --------------HHHHHHH--HHHCCCCEEEcCccccchhhHHHHHHHHHHHHHhhhcccCCCceEEEEeecccCchH
Confidence                          0000000  0012468899997765332 21223333333322      34556889999988765


Q ss_pred             HHHHHHh
Q 015158          227 LEITRKF  233 (412)
Q Consensus       227 ~~~~~~~  233 (412)
                      ...+..+
T Consensus       141 ~~~~~~~  147 (207)
T d1okkd2         141 LEQAKKF  147 (207)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHh
Confidence            5544444

>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=97.02  E-value=0.00066  Score=53.91  Aligned_cols=133  Identities=18%  Similarity=0.228  Sum_probs=65.4

Q ss_pred             cEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCC
Q 015158           78 DVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSG  157 (412)
Q Consensus        78 ~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  157 (412)
                      -+++++|||+|||.+..-.+......+  .+-.++-+.+--.+  -.++++.++...++.+.............      
T Consensus        13 vi~lvGptGvGKTTTiAKLAa~~~~~~--~kV~lit~Dt~R~g--A~eQL~~~a~~l~i~~~~~~~~~d~~~~~------   82 (213)
T d1vmaa2          13 VIMVVGVNGTGKTTSCGKLAKMFVDEG--KSVVLAAADTFRAA--AIEQLKIWGERVGATVISHSEGADPAAVA------   82 (213)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHHTT--CCEEEEEECTTCHH--HHHHHHHHHHHHTCEEECCSTTCCHHHHH------
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCC--CceEEEeecccccc--hhHHHHHHhhhcCccccccCCCCcHHHHH------
Confidence            467799999999988654444333332  23344555543222  13444555544566654322211111100      


Q ss_pred             CcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhc-cCcHHHHHHHHHhCC------CCceEEEEeecCChHHHHHH
Q 015158          158 VHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLS-RGFKDQIYDIFQLLP------PKIQVGVFSATMPPEALEIT  230 (412)
Q Consensus       158 ~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~-~~~~~~~~~i~~~~~------~~~~~i~~SAT~~~~~~~~~  230 (412)
                              .......     ..+++++|++|=+-+... .....++..+.....      +...++.++||...+.....
T Consensus        83 --------~~~~~~~-----~~~~~d~ilIDTaGr~~~d~~~~~el~~~~~~~~~~~~~~p~~~~LVl~a~~~~~~~~~~  149 (213)
T d1vmaa2          83 --------FDAVAHA-----LARNKDVVIIDTAGRLHTKKNLMEELRKVHRVVKKKIPDAPHETLLVIDATTGQNGLVQA  149 (213)
T ss_dssp             --------HHHHHHH-----HHTTCSEEEEEECCCCSCHHHHHHHHHHHHHHGGGTCTTCCSEEEEEEEGGGHHHHHHHH
T ss_pred             --------HHHHHHH-----HHcCCCEEEEeccccccchHHHHHHHHHHHhhhhhccccccceeEEeeccccCcchhhhh
Confidence                    0000000     113568899997764321 112344444444432      34468899999876544444


Q ss_pred             HHh
Q 015158          231 RKF  233 (412)
Q Consensus       231 ~~~  233 (412)
                      ..+
T Consensus       150 ~~~  152 (213)
T d1vmaa2         150 KIF  152 (213)
T ss_dssp             HHH
T ss_pred             hhh
Confidence            333

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=96.87  E-value=0.0072  Score=49.02  Aligned_cols=39  Identities=8%  Similarity=0.267  Sum_probs=25.5

Q ss_pred             CCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEe
Q 015158          180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFS  219 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~S  219 (412)
                      ....++|+||+|.+... ....+.+.+...+.+..+++.|
T Consensus       114 ~~~kviiIde~d~l~~~-~q~~Llk~lE~~~~~~~~il~t  152 (239)
T d1njfa_         114 GRFKVYLIDEVHMLSRH-SFNALLKTLEEPPEHVKFLLAT  152 (239)
T ss_dssp             SSSEEEEEETGGGSCHH-HHHHHHHHHHSCCTTEEEEEEE
T ss_pred             CCCEEEEEECcccCCHH-HHHHHHHHHhcCCCCeEEEEEc
Confidence            34679999999987543 3455666666655566555544

>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=96.76  E-value=0.0012  Score=48.42  Aligned_cols=88  Identities=16%  Similarity=0.155  Sum_probs=52.9

Q ss_pred             EEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCC
Q 015158           79 VIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGV  158 (412)
Q Consensus        79 ~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  158 (412)
                      -++.||+.||||.-.+..+......+   .+++++-|...-         +..    -.+....|..           -.
T Consensus         5 ~~i~GpMfsGKTteLi~~~~~~~~~~---~kv~~ikp~~D~---------R~~----~~i~s~~g~~-----------~~   57 (139)
T d2b8ta1           5 EFITGPMFAGKTAELIRRLHRLEYAD---VKYLVFKPKIDT---------RSI----RNIQSRTGTS-----------LP   57 (139)
T ss_dssp             EEEECSTTSCHHHHHHHHHHHHHHTT---CCEEEEEECCCG---------GGC----SSCCCCCCCS-----------SC
T ss_pred             EEEEccccCHHHHHHHHHHHHHHHCC---CcEEEEEEcccc---------ccc----ceEEcccCce-----------ee
Confidence            47899999999987666554443333   479999997552         111    1111111111           12


Q ss_pred             cEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhh
Q 015158          159 HVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEML  194 (412)
Q Consensus       159 ~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~  194 (412)
                      .+.+.+...+.+.+..... ....++|.+||+|.+.
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            4566666666666554433 3578999999999753

>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=96.67  E-value=0.0066  Score=49.58  Aligned_cols=42  Identities=10%  Similarity=0.241  Sum_probs=28.5

Q ss_pred             CCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEeecC
Q 015158          180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATM  222 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~  222 (412)
                      ..+.++|+||+|.+... ....+..++...+.++.+++.+-.+
T Consensus       130 ~~~~iiiide~d~l~~~-~~~~l~~~~e~~~~~~~~Il~tn~~  171 (252)
T d1sxje2         130 HRYKCVIINEANSLTKD-AQAALRRTMEKYSKNIRLIMVCDSM  171 (252)
T ss_dssp             -CCEEEEEECTTSSCHH-HHHHHHHHHHHSTTTEEEEEEESCS
T ss_pred             CCceEEEeccccccccc-cchhhhcccccccccccceeeeccc
Confidence            35679999999987544 3556677777777777666655443

>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: gamma subunit of DNA polymerase III, N-domain
species: Thermotoga maritima [TaxId: 2336]

Probab=96.64  E-value=0.0023  Score=50.26  Aligned_cols=42  Identities=5%  Similarity=0.107  Sum_probs=31.4

Q ss_pred             CCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEeecC
Q 015158          180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATM  222 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~  222 (412)
                      ...+++|+||||.+... ....+.+.+..-+.+..++++|..+
T Consensus        78 ~~~KviIId~ad~l~~~-aqNaLLK~LEEPp~~t~fiLit~~~  119 (198)
T d2gnoa2          78 YTRKYVIVHDCERMTQQ-AANAFLKALEEPPEYAVIVLNTRRW  119 (198)
T ss_dssp             SSSEEEEETTGGGBCHH-HHHHTHHHHHSCCTTEEEEEEESCG
T ss_pred             CCCEEEEEeCccccchh-hhhHHHHHHhCCCCCceeeeccCCh
Confidence            45789999999987554 3667778888777777777766554

>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=96.54  E-value=0.0057  Score=50.04  Aligned_cols=89  Identities=18%  Similarity=0.153  Sum_probs=67.0

Q ss_pred             CCCcEEEEEcchhHHHHHH----HHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCC-CcCCCCCCCCCEEE
Q 015158          277 AITQSVIFVNTRRKVDWLT----DKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDL-LARGIDVQQVSLVI  351 (412)
Q Consensus       277 ~~~k~lif~~~~~~~~~~~----~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~-~~~G~d~~~~~~vi  351 (412)
                      .+.++++.+++.--+.+.+    +.+...+..+..+||+++..+|.+++....+|+.+|+|+|-+ +...+.+.++..||
T Consensus       131 ~g~q~~~m~Pt~~La~Qh~~~~~~~f~~~~~~v~~l~~~~~~~~r~~~~~~~~~g~~~iiIGThsl~~~~~~f~~Lglvi  210 (264)
T d1gm5a3         131 AGFQTAFMVPTSILAIQHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQEDVHFKNLGLVI  210 (264)
T ss_dssp             HTSCEEEECSCHHHHHHHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHHCCCCSCCCEEE
T ss_pred             cccceeEEeehHhhhHHHHHHHHHhhhhccccceeeccccchHHHHHHHHHHHCCCCCEEEeehHHhcCCCCccccceee
Confidence            3468999999986666554    555556889999999999999999999999999999999974 46678888888888


Q ss_pred             EccCCCChhhHHHhhh
Q 015158          352 NYDLPTQPENYLHRIG  367 (412)
Q Consensus       352 ~~~~~~s~~~~~Q~~G  367 (412)
                      +.+...  -.+.||-+
T Consensus       211 iDEqH~--fgv~Qr~~  224 (264)
T d1gm5a3         211 IDEQHR--FGVKQREA  224 (264)
T ss_dssp             EESCCC--C-----CC
T ss_pred             eccccc--cchhhHHH
Confidence            766532  24566543

>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=96.53  E-value=0.0019  Score=52.10  Aligned_cols=42  Identities=19%  Similarity=0.309  Sum_probs=28.3

Q ss_pred             CCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEeecC
Q 015158          180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSATM  222 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~  222 (412)
                      ....++|+||+|.+.... ...+...+...+....+++.+...
T Consensus       100 ~~~kviiiDe~d~~~~~~-~~~ll~~~e~~~~~~~~i~~~~~~  141 (224)
T d1sxjb2         100 GKHKIVILDEADSMTAGA-QQALRRTMELYSNSTRFAFACNQS  141 (224)
T ss_dssp             TCCEEEEEESGGGSCHHH-HHTTHHHHHHTTTTEEEEEEESCG
T ss_pred             cceEEEEEecccccchhH-HHHHhhhccccccceeeeeccCch
Confidence            456799999999876553 445555666666666666666554

>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=96.43  E-value=0.0047  Score=49.67  Aligned_cols=42  Identities=17%  Similarity=0.385  Sum_probs=27.3

Q ss_pred             CCCCCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEe
Q 015158          177 LRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFS  219 (412)
Q Consensus       177 ~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~S  219 (412)
                      .......++|+||+|.+.... ...+..++...+....+++.+
T Consensus        95 ~~~~~~kiiiiDe~d~~~~~~-~~~Ll~~le~~~~~~~~~~~~  136 (227)
T d1sxjc2          95 IFSKGFKLIILDEADAMTNAA-QNALRRVIERYTKNTRFCVLA  136 (227)
T ss_dssp             SSSCSCEEEEETTGGGSCHHH-HHHHHHHHHHTTTTEEEEEEE
T ss_pred             ccCCCeEEEEEeccccchhhH-HHHHHHHhhhcccceeecccc
Confidence            334456799999999876553 556666666666566544444

>d1t5la1 c.37.1.19 (A:2-414) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Bacillus caldotenax [TaxId: 1395]

Probab=96.43  E-value=0.0021  Score=56.51  Aligned_cols=65  Identities=26%  Similarity=0.364  Sum_probs=49.4

Q ss_pred             ChHHHHhhhhhhhc----C-ccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhc
Q 015158           62 PSAIQQRGIVPFCK----G-LDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGD  132 (412)
Q Consensus        62 l~~~Q~~a~~~~~~----~-~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~  132 (412)
                      |.--|=+|+..+.+    | +..++.|-||||||+++. .++...     +..+|||+|+..++.|++++++.+..
T Consensus        12 p~gDQP~aI~~l~~~l~~g~~~q~l~GltGS~ka~~iA-~l~~~~-----~rp~LVVt~n~~~A~qL~~dL~~~l~   81 (413)
T d1t5la1          12 PQGDQPQAIAKLVDGLRRGVKHQTLLGATGTGKTFTIS-NVIAQV-----NKPTLVIAHNKTLAGQLYSELKEFFP   81 (413)
T ss_dssp             CCTTHHHHHHHHHHHHHHTCSEEEEEECTTSCHHHHHH-HHHHHH-----TCCEEEECSSHHHHHHHHHHHHHHCT
T ss_pred             CCCCCHHHHHHHHHHHhcCCCcEEEeCCCCcHHHHHHH-HHHHHh-----CCCEEEEeCCHHHHHHHHHHHHHHcC
Confidence            66677777776665    3 567899999999997653 233332     23699999999999999999999864

>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=96.33  E-value=0.0043  Score=45.05  Aligned_cols=38  Identities=11%  Similarity=0.084  Sum_probs=26.9

Q ss_pred             cEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHH
Q 015158           78 DVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRE  118 (412)
Q Consensus        78 ~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  118 (412)
                      =-++.||+.||||.-.+..+......   +.+++++-|...
T Consensus         4 L~li~GpMfsGKTt~Li~~~~~~~~~---g~~v~~ikp~~D   41 (133)
T d1xbta1           4 IQVILGPMFSGKSTELMRRVRRFQIA---QYKCLVIKYAKD   41 (133)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHTT---TCCEEEEEETTC
T ss_pred             EEEEEecccCHHHHHHHHHHHHHHHc---CCcEEEEecccc
Confidence            35789999999998765555444333   347999988654

>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=96.30  E-value=0.03  Score=44.62  Aligned_cols=109  Identities=17%  Similarity=0.086  Sum_probs=79.7

Q ss_pred             EEEeccchhhHHHHHHHHHh--cCCCcEEEEEcchhHHHHHHHHHhc----CCCeeEEecCCCCHHHHHHHHHHHhcCCC
Q 015158          256 HVNVEKEEWKLETLCDLYET--LAITQSVIFVNTRRKVDWLTDKMRS----RDHTVSATHGDMDQNTRDIIMREFRSGSS  329 (412)
Q Consensus       256 ~~~~~~~~~~~~~l~~~~~~--~~~~k~lif~~~~~~~~~~~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~  329 (412)
                      ...-+....|.......+..  ..+.++++.+|+.--+.+.++.+++    .+..+..+||..+..+|..++..+.+|+.
T Consensus        80 LL~GdvGsGKT~V~~~a~~~~~~~g~qv~~l~Pt~~La~Q~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~g~~  159 (233)
T d2eyqa3          80 LVCGDVGFGKTEVAMRAAFLAVDNHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKI  159 (233)
T ss_dssp             EEECCCCTTTHHHHHHHHHHHHTTTCEEEEECSSHHHHHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTTCC
T ss_pred             EEEcCCCCCcHHHHHHHHHHHHHcCCceEEEccHHHhHHHHHHHHHHHHhhCCCEEEeccCcccchhHHHHHHHHhCCCC
Confidence            33344444455444443322  2457899999999888888777765    57789999999999999999999999999


Q ss_pred             cEEEEcC-CCcCCCCCCCCCEEEEccCCCChhhHHHhh
Q 015158          330 RVLITTD-LLARGIDVQQVSLVINYDLPTQPENYLHRI  366 (412)
Q Consensus       330 ~vlv~t~-~~~~G~d~~~~~~vi~~~~~~s~~~~~Q~~  366 (412)
                      +|+|+|- .+...+.++++-.||+.+...  ..+.|+.
T Consensus       160 ~iviGths~l~~~~~f~~LgLiIiDEeH~--fg~kQ~~  195 (233)
T d2eyqa3         160 DILIGTHKLLQSDVKFKDLGLLIVDEEHR--FGVRHKE  195 (233)
T ss_dssp             SEEEECTHHHHSCCCCSSEEEEEEESGGG--SCHHHHH
T ss_pred             CEEEeehhhhccCCccccccceeeechhh--hhhHHHH
Confidence            9999998 556678888888888665542  2344544

>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=96.29  E-value=0.0031  Score=46.30  Aligned_cols=40  Identities=15%  Similarity=0.098  Sum_probs=27.4

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHH
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRE  118 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  118 (412)
                      |.=-++.||+.||||.-.+..+......+   .+++++-|...
T Consensus         7 G~l~lI~GpMfSGKTteLi~~~~~~~~~g---~~vl~i~~~~D   46 (141)
T d1xx6a1           7 GWVEVIVGPMYSGKSEELIRRIRRAKIAK---QKIQVFKPEID   46 (141)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHHTT---CCEEEEEEC--
T ss_pred             eeEEEEEeccccHHHHHHHHHHHHhhhcC---CcEEEEEeccc
Confidence            34457899999999987766554443333   47999999755

>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=96.05  E-value=0.011  Score=47.66  Aligned_cols=41  Identities=15%  Similarity=0.325  Sum_probs=25.0

Q ss_pred             CCceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEeec
Q 015158          180 DNIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSAT  221 (412)
Q Consensus       180 ~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT  221 (412)
                      ....++++||+|.+.... ...+..++.....+..+++.+..
T Consensus       108 ~~~~iilide~d~~~~~~-~~~ll~~l~~~~~~~~~i~~~n~  148 (231)
T d1iqpa2         108 ASFKIIFLDEADALTQDA-QQALRRTMEMFSSNVRFILSCNY  148 (231)
T ss_dssp             CSCEEEEEETGGGSCHHH-HHHHHHHHHHTTTTEEEEEEESC
T ss_pred             CCceEEeehhhhhcchhH-HHHHhhhcccCCcceEEEeccCC
Confidence            456789999999865543 34555555555555544444433

>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=96.03  E-value=0.0096  Score=48.42  Aligned_cols=54  Identities=20%  Similarity=0.163  Sum_probs=30.8

Q ss_pred             hccccccCCCCHHHHHHHHHC--CCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHh
Q 015158           37 VYDTFDAMGLQENLLRGIYAY--GFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATF   93 (412)
Q Consensus        37 ~~~~f~~~~l~~~~~~~l~~~--~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~   93 (412)
                      |-.+|+++.-.++..+.+...  .+..+..+++.-   ....+.+++.||+|+|||..+
T Consensus         4 p~~~~~di~G~~~~k~~l~~~i~~l~~~~~~~~~g---~~~~~giLl~GppGtGKT~la   59 (247)
T d1ixza_           4 PKVTFKDVAGAEEAKEELKEIVEFLKNPSRFHEMG---ARIPKGVLLVGPPGVGKTHLA   59 (247)
T ss_dssp             CSCCGGGCCSCHHHHHHHHHHHHHHHCHHHHHHTT---CCCCSEEEEECCTTSSHHHHH
T ss_pred             CCCcHHHHccHHHHHHHHHHHHHHHHCHHHHHHcC---CCCCceEEEecCCCCChhHHH
Confidence            345788876666666655421  011122222211   112356899999999999776

>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=95.64  E-value=0.0031  Score=51.09  Aligned_cols=40  Identities=18%  Similarity=0.283  Sum_probs=24.9

Q ss_pred             CceEEEEeCCchhhccCcHHHHHHHHHhCCCCceEEEEeec
Q 015158          181 NIRIFVLDEADEMLSRGFKDQIYDIFQLLPPKIQVGVFSAT  221 (412)
Q Consensus       181 ~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT  221 (412)
                      ...++|+||+|.+.... ...+..+....+....++..+..
T Consensus       108 ~~~viiiDe~d~l~~~~-~~~l~~~~~~~~~~~~~i~~~~~  147 (237)
T d1sxjd2         108 PYKIIILDEADSMTADA-QSALRRTMETYSGVTRFCLICNY  147 (237)
T ss_dssp             SCEEEEETTGGGSCHHH-HHHHHHHHHHTTTTEEEEEEESC
T ss_pred             CceEEEEecccccCHHH-HHHHhhccccccccccccccccc
Confidence            45689999999876543 34455555555555555544443

>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=95.60  E-value=0.015  Score=45.38  Aligned_cols=123  Identities=15%  Similarity=0.160  Sum_probs=80.7

Q ss_pred             HHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHH----hcCCCcEEEeChHHHHHH
Q 015158           96 GILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRI----LSSGVHVVVGTPGRVFDM  171 (412)
Q Consensus        96 ~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~iii~T~~~l~~~  171 (412)
                      ++...+..   +.++.||||...-.+...+.+.+...  +.++..+||.-+.......    ..++.+|+|+|     ..
T Consensus        23 ~I~~El~r---GgQvy~V~p~I~~~e~~~~~l~~~~p--~~~i~~lHGkm~~~eke~im~~F~~g~~~ILv~T-----tv   92 (211)
T d2eyqa5          23 AILREILR---GGQVYYLYNDVENIQKAAERLAELVP--EARIAIGHGQMRERELERVMNDFHHQRFNVLVCT-----TI   92 (211)
T ss_dssp             HHHHHHTT---TCEEEEECCCSSCHHHHHHHHHHHCT--TSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEES-----ST
T ss_pred             HHHHHHHc---CCeEEEEEcCccchhhHHHHHHHhCC--ceEEEEEEeccCHHHHHHHHHHHHcCCcceEEEe-----hh
Confidence            34444443   45999999999888888888888754  6788999998887665433    45778999999     33


Q ss_pred             HHcCCCCCCCceEEEEeCCchhhccCcHHHHHHHHHhCC---CCceEEEEeec---CChHHHHHHHHh
Q 015158          172 LRRQSLRPDNIRIFVLDEADEMLSRGFKDQIYDIFQLLP---PKIQVGVFSAT---MPPEALEITRKF  233 (412)
Q Consensus       172 ~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~i~~~~~---~~~~~i~~SAT---~~~~~~~~~~~~  233 (412)
                      ++ -..+..+..++|+..|+++.    ..++-.+.....   .....++++-.   ++....+.+..+
T Consensus        93 IE-vGiDvpnA~~iiI~~a~rfG----LaQLhQLRGRVGR~~~~s~c~l~~~~~~~~~~~a~~RL~~l  155 (211)
T d2eyqa5          93 IE-TGIDIPTANTIIIERADHFG----LAQLHQLRGRVGRSHHQAYAWLLTPHPKAMTTDAQKRLEAI  155 (211)
T ss_dssp             TG-GGSCCTTEEEEEETTTTSSC----HHHHHHHHTTCCBTTBCEEEEEEECCGGGSCHHHHHHHHHH
T ss_pred             hh-hccCCCCCcEEEEecchhcc----ccccccccceeeecCccceEEEEecCCcCCCchHHHHHHHH
Confidence            33 35677788999999999842    234444444432   23345555532   444444444433

>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=94.96  E-value=0.016  Score=49.06  Aligned_cols=53  Identities=23%  Similarity=0.314  Sum_probs=36.1

Q ss_pred             hHHHHhhhhh-hhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHH
Q 015158           63 SAIQQRGIVP-FCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTREL  119 (412)
Q Consensus        63 ~~~Q~~a~~~-~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L  119 (412)
                      .+.+...+.. +..+++++|.|+||||||... -+++..+..   ..+++.+-.+.++
T Consensus       152 ~~~~~~~l~~~v~~~~nili~G~tgSGKTT~l-~al~~~i~~---~~rivtiEd~~El  205 (323)
T d1g6oa_         152 KEQAISAIKDGIAIGKNVIVCGGTGSGKTTYI-KSIMEFIPK---EERIISIEDTEEI  205 (323)
T ss_dssp             HHHHHHHHHHHHHHTCCEEEEESTTSSHHHHH-HHHGGGSCT---TCCEEEEESSCCC
T ss_pred             HHHHHHHHHHHHHhCCCEEEEeeccccchHHH-HHHhhhccc---ccceeeccchhhh
Confidence            3455555555 345689999999999999764 455555543   3478888776665

>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=94.81  E-value=0.057  Score=39.87  Aligned_cols=136  Identities=15%  Similarity=0.168  Sum_probs=70.8

Q ss_pred             EEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHH-HHHHhcCC
Q 015158           79 VIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVRE-DQRILSSG  157 (412)
Q Consensus        79 ~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~  157 (412)
                      +.|-...|-|||.+++-.++..+.++.   +++++-=.+.-..  ..+...+ ...+........+..... ....... 
T Consensus         5 i~vytG~GKGKTTAAlG~alRA~G~G~---rV~ivQFlKg~~~--~ge~~~~-~~~~~~~~~~~~~~~~~~~~~e~~~~-   77 (157)
T d1g5ta_           5 IIVFTGNGKGKTTAAFGTAARAVGHGK---NVGVVQFIKGTWP--NGERNLL-EPHGVEFQVMATGFTWETQNREADTA-   77 (157)
T ss_dssp             EEEEESSSSCHHHHHHHHHHHHHHTTC---CEEEEESSCCSSC--CHHHHHH-GGGTCEEEECCTTCCCCGGGHHHHHH-
T ss_pred             EEEEeCCCCCcHHHHHHHHHHHhcCCC---EEEEEEEecCCcc--cchhhhh-cccCcEEEEecCCCcccCCChHHHHH-
Confidence            567778999999999999988887764   7877763321100  0001111 112333322111111000 0000000 


Q ss_pred             CcEEEeChHHHHHHHHcCCCCCCCceEEEEeCCchhhccCc--HHHHHHHHHhCCCCceEEEEeecCChHHHH
Q 015158          158 VHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADEMLSRGF--KDQIYDIFQLLPPKIQVGVFSATMPPEALE  228 (412)
Q Consensus       158 ~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~--~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~  228 (412)
                            ..+...+... .......+++||+||+-...+.++  ...+..++...|+..-+|+..-.+++++.+
T Consensus        78 ------~a~~~~~~a~-~~~~~~~~dllILDEi~~Ai~~gli~~~~v~~ll~~rp~~~evVlTGr~~p~~L~e  143 (157)
T d1g5ta_          78 ------ACMAVWQHGK-RMLADPLLDMVVLDELTYMVAYDYLPLEEVISALNARPGHQTVIITGRGCHRDILD  143 (157)
T ss_dssp             ------HHHHHHHHHH-HHTTCTTCSEEEEETHHHHHHTTSSCHHHHHHHHHTSCTTCEEEEECSSCCHHHHH
T ss_pred             ------HHHHHHHHHH-HHhhcCccCEEeHHHHHHHHHcCCCCHHHHHHHHHhCCCCCEEEEECCCCCHHHHH
Confidence                  0011111111 123345689999999998877663  456777777777777655555556654433

>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=94.64  E-value=0.54  Score=35.11  Aligned_cols=76  Identities=17%  Similarity=0.237  Sum_probs=60.4

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHH----hcCCCcEEEeChHHHHHHHHcCCCCCCCc
Q 015158          107 ECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRI----LSSGVHVVVGTPGRVFDMLRRQSLRPDNI  182 (412)
Q Consensus       107 ~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~iii~T~~~l~~~~~~~~~~~~~~  182 (412)
                      +.++||.|+++.-++.+.+.+.+.    |+.+..++|+.+.......    ..++.+|+|+|     . +...+++..++
T Consensus        31 g~r~lvfc~t~~~~~~l~~~L~~~----Gi~a~~~Hg~~~~~eR~~~l~~F~~G~~~vLVaT-----~-v~~~GiDip~V  100 (174)
T d1c4oa2          31 GERTLVTVLTVRMAEELTSFLVEH----GIRARYLHHELDAFKRQALIRDLRLGHYDCLVGI-----N-LLREGLDIPEV  100 (174)
T ss_dssp             TCEEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEES-----C-CCCTTCCCTTE
T ss_pred             CCcEEEEEcchhHHHHHHHHHHhc----CCceEEEecccchHHHHHHHHHHHCCCeEEEEee-----e-eeeeeccCCCC
Confidence            458999999999999888888875    8999999999886555333    45788999999     3 23567788899


Q ss_pred             eEEEEeCCch
Q 015158          183 RIFVLDEADE  192 (412)
Q Consensus       183 ~~iiiDE~h~  192 (412)
                      ++||+=.++.
T Consensus       101 ~~Vi~~~~~~  110 (174)
T d1c4oa2         101 SLVAILDADK  110 (174)
T ss_dssp             EEEEETTTTS
T ss_pred             cEEEEecccc
Confidence            9999877665

>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=93.76  E-value=0.025  Score=48.73  Aligned_cols=17  Identities=24%  Similarity=0.405  Sum_probs=15.3

Q ss_pred             ccEEEECCCCCCchhHh
Q 015158           77 LDVIQQAQSGTGKTATF   93 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~   93 (412)
                      .++++.||||.|||..+
T Consensus        69 ~niLfiGPTGvGKTElA   85 (364)
T d1um8a_          69 SNILLIGPTGSGKTLMA   85 (364)
T ss_dssp             CCEEEECCTTSSHHHHH
T ss_pred             cceeeeCCCCccHHHHH
Confidence            57999999999999876

>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=93.62  E-value=0.11  Score=39.91  Aligned_cols=114  Identities=13%  Similarity=0.125  Sum_probs=61.2

Q ss_pred             ccEEEECCCCCCchhHhHHHHHHhhccCC----CceeEEEEcCCHHHH------HHHHHHHHHhhccc----CcEEEEEE
Q 015158           77 LDVIQQAQSGTGKTATFCSGILQQLDYGL----VECQALVLAPTRELA------QQIEKVMRALGDYL----GVKVHACV  142 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~~~~~~~~~~~~----~~~~~lil~P~~~L~------~q~~~~~~~~~~~~----~~~~~~~~  142 (412)
                      .|.++++++|.|||...-..+. .+..+.    -..+-+|-.....|.      .++.+.++.+....    +--+..+.
T Consensus        44 ~n~lLvG~pGVGKTalv~~LA~-ri~~~~vp~~L~~~~i~~ld~~~LiAg~~~rG~~E~rl~~il~e~~~~~~~iILfID  122 (195)
T d1jbka_          44 NNPVLIGEPGVGKTAIVEGLAQ-RIINGEVPEGLKGRRVLALDMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFID  122 (195)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHH-HHHHTCSCGGGTTCEEEEECHHHHHTTTCSHHHHHHHHHHHHHHHHHSTTTEEEEEE
T ss_pred             CCeEEEecCCcccHHHHHHHHH-HHHhCCCCHHHcCceEEEeeHHHHhccCCccHHHHHHHHHHHHHHhcCCCcEEEEcc
Confidence            5899999999999976543333 332221    112345655555554      35666555433211    11222222


Q ss_pred             c------------CcchHHH-HHHh-cCCCc-EEEeChHHHHHHHHcCCCCCCCceEEEEeCCc
Q 015158          143 G------------GTSVRED-QRIL-SSGVH-VVVGTPGRVFDMLRRQSLRPDNIRIFVLDEAD  191 (412)
Q Consensus       143 ~------------~~~~~~~-~~~~-~~~~~-iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h  191 (412)
                      .            +...... ...+ .+... |.-+||+.+...++......+.|..|-++|..
T Consensus       123 eih~l~~~g~~~g~~d~~~~Lkp~L~rg~l~~IgatT~eey~~~~e~d~aL~rrF~~I~V~Ep~  186 (195)
T d1jbka_         123 ELHTMVGAGKADGAMDAGNMLKPALARGELHCVGATTLDEYRQYIEKDAALERRFQKVFVAEPS  186 (195)
T ss_dssp             TGGGGTT------CCCCHHHHHHHHHTTSCCEEEEECHHHHHHHTTTCHHHHTTEEEEECCCCC
T ss_pred             hHHHHhcCCCCCCcccHHHHHHHHHhCCCceEEecCCHHHHHHHHHcCHHHHhcCCEeecCCCC
Confidence            1            1111111 1112 23334 44577888887777666556788999999975

>d1c4oa1 c.37.1.19 (A:2-409) Nucleotide excision repair enzyme UvrB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Thermus thermophilus [TaxId: 274]

Probab=93.50  E-value=0.052  Score=47.38  Aligned_cols=66  Identities=35%  Similarity=0.446  Sum_probs=47.5

Q ss_pred             CChHHHHhhhhhhh----cCc-cEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhc
Q 015158           61 KPSAIQQRGIVPFC----KGL-DVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGD  132 (412)
Q Consensus        61 ~l~~~Q~~a~~~~~----~~~-~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~  132 (412)
                      .|+--|-+|+..+.    .|+ ...+.+.+|||||++.. .++....     ..+|||||+...+.++++.+..+..
T Consensus         8 ~p~~dqp~aI~~l~~~L~~g~~~~~L~GlsgS~ka~~~A-~l~~~~~-----rp~LvVt~~~~~A~~l~~dL~~~l~   78 (408)
T d1c4oa1           8 SPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVTMA-KVIEALG-----RPALVLAPNKILAAQLAAEFRELFP   78 (408)
T ss_dssp             CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHH-HHHHHHT-----CCEEEEESSHHHHHHHHHHHHHHCT
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCcEEEecCCCCHHHHHHH-HHHHHhC-----CCEEEEeCCHHHHHHHHHHHHHhcC
Confidence            35666766666654    344 46889999999996543 2333221     2699999999999999999998864

>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=93.36  E-value=0.25  Score=36.64  Aligned_cols=74  Identities=15%  Similarity=0.236  Sum_probs=56.1

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHH----hcCCCcEEEeChHHHHHHHHcCCCCCCCc
Q 015158          107 ECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRI----LSSGVHVVVGTPGRVFDMLRRQSLRPDNI  182 (412)
Q Consensus       107 ~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~iii~T~~~l~~~~~~~~~~~~~~  182 (412)
                      ..++||.|.++.-++++++.+...    +..+..++|+.........    ..+...|+|+|.     . ...+++..++
T Consensus        27 ~~k~iIF~~s~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~l~~f~~~~~~iLv~Td-----v-~~rGiDi~~v   96 (162)
T d1fuka_          27 VTQAVIFCNTRRKVEELTTKLRND----KFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTD-----L-LARGIDVQQV   96 (162)
T ss_dssp             CSCEEEEESSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEG-----G-GTTTCCCCSC
T ss_pred             CCcEEEEEEEEchHHHHHHHHhhc----CceEEEeccCCchhhHHHHHHHHhhcccceeeccc-----c-ccccccCCCc
Confidence            357999999999999998887765    7788999988876655333    346778999993     2 3557788889


Q ss_pred             eEEEEeCC
Q 015158          183 RIFVLDEA  190 (412)
Q Consensus       183 ~~iiiDE~  190 (412)
                      ++||.=+.
T Consensus        97 ~~VI~~d~  104 (162)
T d1fuka_          97 SLVINYDL  104 (162)
T ss_dssp             SEEEESSC
T ss_pred             eEEEEecc
Confidence            88887554

>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=93.34  E-value=0.026  Score=47.48  Aligned_cols=18  Identities=22%  Similarity=0.359  Sum_probs=16.0

Q ss_pred             CccEEEECCCCCCchhHh
Q 015158           76 GLDVIQQAQSGTGKTATF   93 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~   93 (412)
                      .+++++.||||+|||..+
T Consensus        49 ~~~iLl~GPpG~GKT~lA   66 (309)
T d1ofha_          49 PKNILMIGPTGVGKTEIA   66 (309)
T ss_dssp             CCCEEEECCTTSSHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            478999999999999876

>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=93.32  E-value=0.059  Score=43.99  Aligned_cols=26  Identities=23%  Similarity=0.267  Sum_probs=19.4

Q ss_pred             ccEEEECCCCCCchhHhHHHHHHhhcc
Q 015158           77 LDVIQQAQSGTGKTATFCSGILQQLDY  103 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~~~~~~~~~~  103 (412)
                      .++++.||+|+|||.++ -.++..+..
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            57999999999999765 345555543

>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=93.07  E-value=0.16  Score=38.49  Aligned_cols=94  Identities=20%  Similarity=0.232  Sum_probs=66.5

Q ss_pred             eeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHH----hcCCCcEEEeChHHHHHHHHcCCCCCCCce
Q 015158          108 CQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRI----LSSGVHVVVGTPGRVFDMLRRQSLRPDNIR  183 (412)
Q Consensus       108 ~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~iii~T~~~l~~~~~~~~~~~~~~~  183 (412)
                      .+++|.|+++.-++.....+...    |+.+..++|+.+.......    ..+..+|+|+|     .. ...+++..+++
T Consensus        32 ~~~iif~~~~~~~~~~~~~l~~~----g~~~~~~hg~~~~~eR~~~l~~Fr~g~~~vLVaT-----dv-~~rGiDip~v~  101 (181)
T d1t5la2          32 ERTLVTTLTKKMAEDLTDYLKEA----GIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGI-----NL-LREGLDIPEVS  101 (181)
T ss_dssp             CEEEEECSSHHHHHHHHHHHHTT----TCCEEEECSSCCHHHHHHHHHHHHHTSCSEEEES-----CC-CSSSCCCTTEE
T ss_pred             CeEEEEeehhhhhHHHHHHHHhC----CcceeEecCCccHHHHHHHHHHHHCCCCCEEEeh-----hH-HHccCCCCCCC
Confidence            48999999999888888777765    8999999999887655333    35789999999     33 34577888999


Q ss_pred             EEEEeCCchhh-ccCcHHHHHHHHHhCCC
Q 015158          184 IFVLDEADEML-SRGFKDQIYDIFQLLPP  211 (412)
Q Consensus       184 ~iiiDE~h~~~-~~~~~~~~~~i~~~~~~  211 (412)
                      +||.-++.... ..++...+.++-+....
T Consensus       102 ~VI~~d~p~~~~~~s~~~yi~R~GRagR~  130 (181)
T d1t5la2         102 LVAILDADKEGFLRSERSLIQTIGRAARN  130 (181)
T ss_dssp             EEEETTTTSCSGGGSHHHHHHHHGGGTTS
T ss_pred             EEEEecCCcccccccHHHHHHHHHhhccc
Confidence            99998887522 12233334444444433

>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=92.78  E-value=0.034  Score=42.38  Aligned_cols=25  Identities=24%  Similarity=0.272  Sum_probs=18.5

Q ss_pred             ccEEEECCCCCCchhHhHHHHHHhhc
Q 015158           77 LDVIQQAQSGTGKTATFCSGILQQLD  102 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~~~~~~~~~  102 (412)
                      ++++|.||+|+|||..+. .++..+.
T Consensus         2 k~v~ItG~~GtGKTtl~~-~i~~~l~   26 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTLIH-KASEVLK   26 (189)
T ss_dssp             CCEEEESCCSSCHHHHHH-HHHHHHH
T ss_pred             cEEEEECCCCCcHHHHHH-HHHHHHH
Confidence            578999999999998553 4444443

>d1w36b1 c.37.1.19 (B:1-485) Exodeoxyribonuclease V beta chain (RecB), N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Exodeoxyribonuclease V beta chain (RecB), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=92.46  E-value=0.11  Score=46.49  Aligned_cols=53  Identities=25%  Similarity=0.169  Sum_probs=38.7

Q ss_pred             ccEEEECCCCCCchhHhHHHHHHhhccCC---------CceeEEEEcCCHHHHHHHHHHHHH
Q 015158           77 LDVIQQAQSGTGKTATFCSGILQQLDYGL---------VECQALVLAPTRELAQQIEKVMRA  129 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~~~~~~~~~~~~---------~~~~~lil~P~~~L~~q~~~~~~~  129 (412)
                      +..+|.|+.|||||.+...-++..+..+.         ....+|+|+=|+.-+.++.+++..
T Consensus        17 g~~lv~A~AGsGKT~~l~~r~~~ll~~~~~~~~~~~~~~~~~IL~lTFT~kAA~Emk~RI~~   78 (485)
T d1w36b1          17 GERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLVVTFTEAATAELRGRIRS   78 (485)
T ss_dssp             SCEEEECCTTSCHHHHHHHHHHHHHTTCSSSSSCSSCCCGGGEEEEESCHHHHHHHHHHHHH
T ss_pred             CCeEEEEcCchHHHHHHHHHHHHHHhhCcccccccCCCCcccEeEeccHHHHHHHHHHHHHH
Confidence            46899999999999888776666553221         123599999888877777776644

>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=92.19  E-value=0.082  Score=46.10  Aligned_cols=40  Identities=23%  Similarity=0.294  Sum_probs=27.3

Q ss_pred             ChHHHHhhhhhhhcC--ccEEEECCCCCCchhHhHHHHHHhhc
Q 015158           62 PSAIQQRGIVPFCKG--LDVIQQAQSGTGKTATFCSGILQQLD  102 (412)
Q Consensus        62 l~~~Q~~a~~~~~~~--~~~lv~~~tGsGKT~~~~~~~~~~~~  102 (412)
                      +.+.|.+.+..+...  .-+++.||||||||++.. .++..+.
T Consensus       142 ~~~~~~~~l~~l~~~~~GliLvtGpTGSGKSTTl~-~~l~~~~  183 (401)
T d1p9ra_         142 MTAHNHDNFRRLIKRPHGIILVTGPTGSGKSTTLY-AGLQELN  183 (401)
T ss_dssp             CCHHHHHHHHHHHTSSSEEEEEECSTTSCHHHHHH-HHHHHHC
T ss_pred             ccHHHHHHHHHHHhhhhceEEEEcCCCCCccHHHH-HHhhhhc
Confidence            446666667666654  346789999999998753 4555554

>d1g41a_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=91.83  E-value=0.032  Score=49.35  Aligned_cols=18  Identities=22%  Similarity=0.359  Sum_probs=16.2

Q ss_pred             CccEEEECCCCCCchhHh
Q 015158           76 GLDVIQQAQSGTGKTATF   93 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~   93 (412)
                      .+|+++.||||+|||+.+
T Consensus        49 ksNILliGPTGvGKTlLA   66 (443)
T d1g41a_          49 PKNILMIGPTGVGKTEIA   66 (443)
T ss_dssp             CCCEEEECCTTSSHHHHH
T ss_pred             cccEEEECCCCCCHHHHH
Confidence            468999999999999876

>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=91.61  E-value=0.05  Score=40.47  Aligned_cols=19  Identities=16%  Similarity=0.176  Sum_probs=16.2

Q ss_pred             CccEEEECCCCCCchhHhH
Q 015158           76 GLDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~   94 (412)
                      .+++++.||+|+|||+++-
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            4678999999999998764

>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=91.17  E-value=0.077  Score=42.54  Aligned_cols=38  Identities=18%  Similarity=0.165  Sum_probs=28.6

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCC
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPT  116 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~  116 (412)
                      |.-+++.+++|+|||..++..+.+....+   ..+++++-.
T Consensus        26 gsl~li~G~pGsGKT~l~~qia~~~~~~~---~~~~~is~e   63 (242)
T d1tf7a2          26 DSIILATGATGTGKTLLVSRFVENACANK---ERAILFAYE   63 (242)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHHHHTTT---CCEEEEESS
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHHhc---cccceeecc
Confidence            46789999999999988877777665443   467777643

>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=91.11  E-value=0.71  Score=34.37  Aligned_cols=76  Identities=11%  Similarity=0.116  Sum_probs=56.6

Q ss_pred             CceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHH----HhcCCCcEEEeChHHHHHHHHcCCCCCCC
Q 015158          106 VECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQR----ILSSGVHVVVGTPGRVFDMLRRQSLRPDN  181 (412)
Q Consensus       106 ~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~iii~T~~~l~~~~~~~~~~~~~  181 (412)
                      ...++||.|+++.-++.++..+...    +..+..++|+........    ...+...++|+|.-      ...++++.+
T Consensus        31 ~~~k~iVF~~~~~~~~~l~~~L~~~----g~~~~~~h~~~~~~~r~~~~~~f~~~~~~ilv~Td~------~~~Gid~~~  100 (171)
T d1s2ma2          31 QINQAIIFCNSTNRVELLAKKITDL----GYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDL------LTRGIDIQA  100 (171)
T ss_dssp             CCSEEEEECSSHHHHHHHHHHHHHH----TCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESSC------SSSSCCCTT
T ss_pred             CCCceEEEEeeeehhhHhHHhhhcc----cccccccccccchhhhhhhhhhcccCccccccchhH------hhhccccce
Confidence            3458999999999888888888776    788888998887655433    23467889999932      345777888


Q ss_pred             ceEEEEeCCc
Q 015158          182 IRIFVLDEAD  191 (412)
Q Consensus       182 ~~~iiiDE~h  191 (412)
                      +++||.-++.
T Consensus       101 v~~VI~~d~p  110 (171)
T d1s2ma2         101 VNVVINFDFP  110 (171)
T ss_dssp             EEEEEESSCC
T ss_pred             eEEEEecCCc
Confidence            8888866555

>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=90.96  E-value=0.056  Score=40.79  Aligned_cols=19  Identities=21%  Similarity=0.372  Sum_probs=16.1

Q ss_pred             cCccEEEECCCCCCchhHh
Q 015158           75 KGLDVIQQAQSGTGKTATF   93 (412)
Q Consensus        75 ~~~~~lv~~~tGsGKT~~~   93 (412)
                      .|+-+++.||+|||||+++
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            4666789999999999875

>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=90.71  E-value=0.62  Score=36.02  Aligned_cols=74  Identities=12%  Similarity=0.208  Sum_probs=54.3

Q ss_pred             CCCcEEEEEcchhHHHHHHHHHhc----CCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcC-----CC-cCCCCCCC
Q 015158          277 AITQSVIFVNTRRKVDWLTDKMRS----RDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTD-----LL-ARGIDVQQ  346 (412)
Q Consensus       277 ~~~k~lif~~~~~~~~~~~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~-----~~-~~G~d~~~  346 (412)
                      .+.+++|.|++++.+.++.+.+++    .+..+...+|+.+..+..+.++     ..+|+|+|+     .+ ...+++.+
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            345899999999999988777765    3667888888887666544432     367999996     22 44678889


Q ss_pred             CCEEEEccC
Q 015158          347 VSLVINYDL  355 (412)
Q Consensus       347 ~~~vi~~~~  355 (412)
                      ++++|+.+.
T Consensus       146 l~~lViDEa  154 (208)
T d1hv8a1         146 VKYFILDEA  154 (208)
T ss_dssp             CCEEEEETH
T ss_pred             CcEEEEECh
Confidence            999986543

>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=90.59  E-value=0.53  Score=36.22  Aligned_cols=71  Identities=14%  Similarity=0.221  Sum_probs=52.7

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHH----hcCCCcEEEeChHHHHHHHHcCCCCCCCc
Q 015158          107 ECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRI----LSSGVHVVVGTPGRVFDMLRRQSLRPDNI  182 (412)
Q Consensus       107 ~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~iii~T~~~l~~~~~~~~~~~~~~  182 (412)
                      +.++||.|+++..++.+++.+...    ++.+..++|+.........    ..+..+|+|+|.     . ...+++..++
T Consensus        30 ~~~~IIF~~t~~~~~~l~~~l~~~----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~ilvaTd-----~-~~~GiD~p~v   99 (200)
T d1oywa3          30 GKSGIIYCNSRAKVEDTAARLQSK----GISAAAYHAGLENNVRADVQEKFQRDDLQIVVATV-----A-FGMGINKPNV   99 (200)
T ss_dssp             TCCEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECT-----T-SCTTTCCTTC
T ss_pred             CCCEEEEEeeehhhHHhhhhhccC----CceeEEecCCCcHHHHHHHHHHHhcccceEEEecc-----h-hhhccCCCCC
Confidence            457999999999999888877775    7888999998876554322    346788999993     2 2446677788


Q ss_pred             eEEEE
Q 015158          183 RIFVL  187 (412)
Q Consensus       183 ~~iii  187 (412)
                      ++||.
T Consensus       100 ~~VI~  104 (200)
T d1oywa3         100 RFVVH  104 (200)
T ss_dssp             CEEEE
T ss_pred             CEEEE
Confidence            87764

>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=90.30  E-value=0.06  Score=40.54  Aligned_cols=19  Identities=32%  Similarity=0.581  Sum_probs=16.1

Q ss_pred             CccEEEECCCCCCchhHhH
Q 015158           76 GLDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~   94 (412)
                      +.++++.||+|+|||+.+-
T Consensus         5 ~~~I~i~G~~GsGKTT~~~   23 (174)
T d1y63a_           5 GINILITGTPGTGKTSMAE   23 (174)
T ss_dssp             SCEEEEECSTTSSHHHHHH
T ss_pred             CCEEEEEeCCCCCHHHHHH
Confidence            4578999999999998763

>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=90.22  E-value=0.32  Score=33.77  Aligned_cols=77  Identities=14%  Similarity=0.083  Sum_probs=58.0

Q ss_pred             HHHHHHHHHhcCCCcEEEEEcchhHHHHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCCCcCCCCCC
Q 015158          266 LETLCDLYETLAITQSVIFVNTRRKVDWLTDKMRSRDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDLLARGIDVQ  345 (412)
Q Consensus       266 ~~~l~~~~~~~~~~k~lif~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~~~~G~d~~  345 (412)
                      ...|..+++.. ..++|+.|.+...++.+.+.|++.++.+..+.+. .         .+..+  .+.|+...+..|+-++
T Consensus        23 ~~~L~~~i~~~-~~~Vli~a~s~g~~erl~e~L~~~~i~~~~~~~~-~---------~~~~~--~~~i~~~~l~~GF~~~   89 (117)
T d2eyqa2          23 LDALRKFLETF-DGPVVFSVESEGRREALGELLARIKIAPQRIMRL-D---------EASDR--GRYLMIGAAEHGFVDT   89 (117)
T ss_dssp             THHHHHHHTTC-CSCCCEEESSHHHHHHHHHHHGGGTCCCEECSSG-G---------GCCTT--CCEEEECCCCSCEEET
T ss_pred             HHHHHHHHHhC-CCeEEEEECCccHHHHHHHHHHHcCCCceEecCh-h---------hhcCc--eEEEEEecCccccccC
Confidence            45677777654 3689999999999999999999999888766542 1         12333  3566678899999999


Q ss_pred             CCCEEEEccC
Q 015158          346 QVSLVINYDL  355 (412)
Q Consensus       346 ~~~~vi~~~~  355 (412)
                      ..+.+|+.+.
T Consensus        90 ~~~l~vItE~   99 (117)
T d2eyqa2          90 VRNLALICES   99 (117)
T ss_dssp             TTTEEEEEHH
T ss_pred             CCCEEEEEch
Confidence            9999886654

>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=90.11  E-value=0.13  Score=45.32  Aligned_cols=42  Identities=17%  Similarity=0.301  Sum_probs=29.0

Q ss_pred             cCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHH
Q 015158           75 KGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTREL  119 (412)
Q Consensus        75 ~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L  119 (412)
                      ..++++|.|+||+|||..+...+.+.+..+   ..++|+=|-.++
T Consensus        49 ~~~H~~I~G~tGsGKT~~l~~li~~~~~~g---~~~iiiD~kge~   90 (433)
T d1e9ra_          49 EPRHLLVNGATGTGKSVLLRELAYTGLLRG---DRMVIVDPNGDM   90 (433)
T ss_dssp             GGGCEEEEECTTSSHHHHHHHHHHHHHHTT---CEEEEEEETTHH
T ss_pred             ccceEEEEeCCCCcHHHHHHHHHHHHHhCC---CCEEEEeCChhH
Confidence            357899999999999977544444444433   367777776554

>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=90.06  E-value=0.65  Score=34.51  Aligned_cols=96  Identities=17%  Similarity=0.224  Sum_probs=64.8

Q ss_pred             EEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHH----hc
Q 015158           80 IQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRI----LS  155 (412)
Q Consensus        80 lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~  155 (412)
                      ++..+....|... +..++...    ...++|+.|.++.-++...+.+...    +..+..++|+.+.......    ..
T Consensus        12 ~v~v~~~~~K~~~-L~~ll~~~----~~~k~iiF~~~~~~~~~~~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~fk~   82 (168)
T d2j0sa2          12 FVAVEREEWKFDT-LCDLYDTL----TITQAVIFCNTKRKVDWLTEKMREA----NFTVSSMHGDMPQKERESIMKEFRS   82 (168)
T ss_dssp             EEEESSTTHHHHH-HHHHHHHH----TSSEEEEECSSHHHHHHHHHHHHHT----TCCCEEECTTSCHHHHHHHHHHHHH
T ss_pred             EEEecChHHHHHH-HHHHHHhC----CCCceEEEeeeHHHHHHHHHHhhhc----ccchhhhhhhhhHHHHHHHHHHHhc
Confidence            4444444556433 33344332    2348999999999999888877775    6788888988876655333    34


Q ss_pred             CCCcEEEeChHHHHHHHHcCCCCCCCceEEEEeCC
Q 015158          156 SGVHVVVGTPGRVFDMLRRQSLRPDNIRIFVLDEA  190 (412)
Q Consensus       156 ~~~~iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~  190 (412)
                      +...|+|+|.     . ...++++.++++||.=++
T Consensus        83 g~~~iLv~Td-----~-~~rGiDi~~v~~VIn~d~  111 (168)
T d2j0sa2          83 GASRVLISTD-----V-WARGLDVPQVSLIINYDL  111 (168)
T ss_dssp             TSSCEEEECG-----G-GSSSCCCTTEEEEEESSC
T ss_pred             CCccEEeccc-----h-hcccccccCcceEEEecC
Confidence            6789999993     2 355778888988875443

>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=90.00  E-value=0.077  Score=43.33  Aligned_cols=17  Identities=29%  Similarity=0.380  Sum_probs=14.8

Q ss_pred             ccEEEECCCCCCchhHh
Q 015158           77 LDVIQQAQSGTGKTATF   93 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~   93 (412)
                      +.+++.||+|+|||..+
T Consensus        33 ~~ilL~GpPGtGKT~la   49 (273)
T d1gvnb_          33 TAFLLGGQPGSGKTSLR   49 (273)
T ss_dssp             EEEEEECCTTSCTHHHH
T ss_pred             EEEEEECCCCCCHHHHH
Confidence            45889999999999875

>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=89.85  E-value=0.079  Score=39.70  Aligned_cols=18  Identities=22%  Similarity=0.285  Sum_probs=15.2

Q ss_pred             ccEEEECCCCCCchhHhH
Q 015158           77 LDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~   94 (412)
                      .++++.|++|||||+.+-
T Consensus         5 ~~I~i~G~pGsGKTTia~   22 (173)
T d1rkba_           5 PNILLTGTPGVGKTTLGK   22 (173)
T ss_dssp             CCEEEECSTTSSHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHH
Confidence            368899999999998764

>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=89.82  E-value=0.09  Score=42.03  Aligned_cols=17  Identities=29%  Similarity=0.317  Sum_probs=15.2

Q ss_pred             ccEEEECCCCCCchhHh
Q 015158           77 LDVIQQAQSGTGKTATF   93 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~   93 (412)
                      .++++.||+|+|||..+
T Consensus        36 ~~~L~~GPpGtGKT~lA   52 (238)
T d1in4a2          36 DHVLLAGPPGLGKTTLA   52 (238)
T ss_dssp             CCEEEESSTTSSHHHHH
T ss_pred             CeEEEECCCCCcHHHHH
Confidence            47899999999999876

>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=89.77  E-value=0.063  Score=39.43  Aligned_cols=16  Identities=19%  Similarity=0.271  Sum_probs=13.5

Q ss_pred             cEEEECCCCCCchhHh
Q 015158           78 DVIQQAQSGTGKTATF   93 (412)
Q Consensus        78 ~~lv~~~tGsGKT~~~   93 (412)
                      -+++.|++|||||+.+
T Consensus         4 lIii~G~pGsGKTTla   19 (152)
T d1ly1a_           4 IILTIGCPGSGKSTWA   19 (152)
T ss_dssp             EEEEECCTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            3678999999999865

>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=89.33  E-value=0.11  Score=41.54  Aligned_cols=41  Identities=17%  Similarity=-0.018  Sum_probs=26.8

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhcc---CCCceeEEEEcCC
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDY---GLVECQALVLAPT  116 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~---~~~~~~~lil~P~  116 (412)
                      |+-+++.+++|+|||..++..+.+....   ...+..++++.-.
T Consensus        34 G~~~li~G~pGsGKT~l~lq~~~~~~~~~~~~~~~~~~~~i~~~   77 (251)
T d1szpa2          34 GSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTE   77 (251)
T ss_dssp             SSEEEEEESTTSSHHHHHHHHTTTTTSCTTTTCCSCEEEEEESS
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHhhhhhhhccCCceEEEEeec
Confidence            5788999999999998776555543321   2234456666543

>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=89.31  E-value=0.43  Score=37.46  Aligned_cols=106  Identities=11%  Similarity=0.129  Sum_probs=67.4

Q ss_pred             CCcEEEEEcchhHHHHHHHHHhc----CCCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcC------CCcCCCCCCCC
Q 015158          278 ITQSVIFVNTRRKVDWLTDKMRS----RDHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTD------LLARGIDVQQV  347 (412)
Q Consensus       278 ~~k~lif~~~~~~~~~~~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~------~~~~G~d~~~~  347 (412)
                      ..+.+|++++++-+.++++.+++    .++.+..+.|+.+..+....++   . ..+|+|+|+      .-...+++.++
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            35689999999999999887765    3567888888887665544433   2 367999997      22567788889


Q ss_pred             CEEEEccCC--CChhhHHHhhhhcccCCCCceEEEEeccCcHH
Q 015158          348 SLVINYDLP--TQPENYLHRIGRSGRFGRKGVAINFVTRDDER  388 (412)
Q Consensus       348 ~~vi~~~~~--~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~  388 (412)
                      +++|+-+..  .+ ..|...+.+..+.=+...-.++++..-.+
T Consensus       161 ~~lVlDEaD~ll~-~~f~~~i~~I~~~l~~~~Q~ilfSAT~~~  202 (222)
T d2j0sa1         161 KMLVLDEADEMLN-KGFKEQIYDVYRYLPPATQVVLISATLPH  202 (222)
T ss_dssp             CEEEEETHHHHTS-TTTHHHHHHHHTTSCTTCEEEEEESCCCH
T ss_pred             eeeeecchhHhhh-cCcHHHHHHHHHhCCCCCEEEEEEEeCCH
Confidence            999864421  11 12333333444432334456677765443

>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=89.22  E-value=0.072  Score=39.95  Aligned_cols=17  Identities=29%  Similarity=0.311  Sum_probs=14.3

Q ss_pred             cEEEECCCCCCchhHhH
Q 015158           78 DVIQQAQSGTGKTATFC   94 (412)
Q Consensus        78 ~~lv~~~tGsGKT~~~~   94 (412)
                      -+++.||+|||||+.+-
T Consensus         4 lI~i~G~~GsGKTTva~   20 (176)
T d2bdta1           4 LYIITGPAGVGKSTTCK   20 (176)
T ss_dssp             EEEEECSTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            46889999999998763

>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=89.13  E-value=0.094  Score=41.96  Aligned_cols=17  Identities=24%  Similarity=0.263  Sum_probs=15.2

Q ss_pred             ccEEEECCCCCCchhHh
Q 015158           77 LDVIQQAQSGTGKTATF   93 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~   93 (412)
                      .++++.||+|+|||..+
T Consensus        36 ~~~Ll~GPpG~GKTtla   52 (239)
T d1ixsb2          36 EHLLLFGPPGLGKTTLA   52 (239)
T ss_dssp             CCEEEECCTTSCHHHHH
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            57899999999999776

>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=88.97  E-value=0.06  Score=41.00  Aligned_cols=19  Identities=16%  Similarity=0.134  Sum_probs=16.0

Q ss_pred             CccEEEECCCCCCchhHhH
Q 015158           76 GLDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~   94 (412)
                      -+.+++.||+|+|||+.+-
T Consensus         7 ~K~I~i~G~~GsGKTTla~   25 (192)
T d1lw7a2           7 AKTVAILGGESSGKSVLVN   25 (192)
T ss_dssp             CEEEEEECCTTSHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHH
Confidence            3679999999999997653

>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Escherichia coli [TaxId: 562]

Probab=88.64  E-value=0.068  Score=43.37  Aligned_cols=55  Identities=22%  Similarity=0.204  Sum_probs=31.0

Q ss_pred             hhccccccCCCCHHHHHHHHHC--CCCCChHHHHhhhhhhhcCccEEEECCCCCCchhHh
Q 015158           36 EVYDTFDAMGLQENLLRGIYAY--GFEKPSAIQQRGIVPFCKGLDVIQQAQSGTGKTATF   93 (412)
Q Consensus        36 ~~~~~f~~~~l~~~~~~~l~~~--~~~~l~~~Q~~a~~~~~~~~~~lv~~~tGsGKT~~~   93 (412)
                      .+..+|++..-.++..+.+.+.  .+..+..+|+..   +...+.+++.||+|+|||..+
T Consensus         6 ~~~~t~~Di~Gl~~~k~~l~e~v~~~~~~~~~~~~g---~~~~~~iLL~GppGtGKT~la   62 (256)
T d1lv7a_           6 QIKTTFADVAGCDEAKEEVAELVEYLREPSRFQKLG---GKIPKGVLMVGPPGTGKTLLA   62 (256)
T ss_dssp             SSCCCGGGSCSCHHHHHHTHHHHHHHHCGGGC--------CCCCEEEEECCTTSCHHHHH
T ss_pred             CCCCCHHHHhchHHHHHHHHHHHHHHHCHHHHHHcC---CCCCCeEEeeCCCCCCccHHH
Confidence            3445788887776666665421  011122222211   112467899999999999775

>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=88.29  E-value=0.07  Score=43.44  Aligned_cols=18  Identities=28%  Similarity=0.314  Sum_probs=15.3

Q ss_pred             CccEEEECCCCCCchhHh
Q 015158           76 GLDVIQQAQSGTGKTATF   93 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~   93 (412)
                      .+.+++.||+|+|||..+
T Consensus        38 ~~giLL~GppGtGKT~l~   55 (258)
T d1e32a2          38 PRGILLYGPPGTGKTLIA   55 (258)
T ss_dssp             CCEEEEECCTTSSHHHHH
T ss_pred             CceeEEecCCCCCchHHH
Confidence            357899999999999764

>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=88.28  E-value=0.28  Score=40.43  Aligned_cols=53  Identities=19%  Similarity=0.134  Sum_probs=39.4

Q ss_pred             eeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeC
Q 015158          108 CQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGT  164 (412)
Q Consensus       108 ~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T  164 (412)
                      ++++|.||+..-++++++.+++.    +.++..++|............+..+|+++|
T Consensus        37 g~~~~F~~s~~~~~~~a~~L~~~----g~~V~~l~~~~~~~e~~~~~~~~~~~~~~t   89 (299)
T d1yksa2          37 RPTAWFLPSIRAANVMAASLRKA----GKSVVVLNRKTFEREYPTIKQKKPDFILAT   89 (299)
T ss_dssp             SCEEEECSCHHHHHHHHHHHHHT----TCCEEECCSSSCC--------CCCSEEEES
T ss_pred             CCEEEEeCCHHHHHHHHHHHHhc----CCeEEEEcCcCcHhHHhhhhcCCcCEEEEe
Confidence            47999999999999999988875    677889999887777666677788999999

>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=88.23  E-value=0.37  Score=39.21  Aligned_cols=43  Identities=16%  Similarity=0.035  Sum_probs=28.9

Q ss_pred             hhcCccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCH
Q 015158           73 FCKGLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTR  117 (412)
Q Consensus        73 ~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~  117 (412)
                      +..|.-+++.|+||+|||..++..+.+....  .+.+++++..-.
T Consensus        32 ~~~G~l~vi~G~~G~GKT~~~~~la~~~a~~--~g~~v~~~s~E~   74 (277)
T d1cr2a_          32 ARGGEVIMVTSGSGMGKSTFVRQQALQWGTA--MGKKVGLAMLEE   74 (277)
T ss_dssp             BCTTCEEEEECSTTSSHHHHHHHHHHHHHHT--SCCCEEEEESSS
T ss_pred             CCCCeEEEEEeCCCCCHHHHHHHHHHhhhhh--cccceeEeeecc
Confidence            4456778999999999997665555443221  234788887643

>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=87.99  E-value=0.1  Score=39.32  Aligned_cols=20  Identities=20%  Similarity=0.346  Sum_probs=16.6

Q ss_pred             hcCccEEEECCCCCCchhHh
Q 015158           74 CKGLDVIQQAQSGTGKTATF   93 (412)
Q Consensus        74 ~~~~~~lv~~~tGsGKT~~~   93 (412)
                      .+|..+++.|++|||||+++
T Consensus         4 ~~g~~I~l~G~~GsGKTTia   23 (183)
T d1m8pa3           4 TQGFTIFLTGYMNSGKDAIA   23 (183)
T ss_dssp             TCCEEEEEECSTTSSHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHH
Confidence            34666789999999999876

>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=87.93  E-value=0.43  Score=34.18  Aligned_cols=65  Identities=22%  Similarity=0.315  Sum_probs=48.3

Q ss_pred             eeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCCCceEEE
Q 015158          108 CQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRILSSGVHVVVGTPGRVFDMLRRQSLRPDNIRIFV  186 (412)
Q Consensus       108 ~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iii~T~~~l~~~~~~~~~~~~~~~~ii  186 (412)
                      .++||.|+++.-++++++.|...    ++.+..++++......   ..+..+++|+|     ..+. ..++ .+++.||
T Consensus        36 ~k~IVFc~t~~~ae~la~~L~~~----G~~~~~~H~~~~~~~~---~~~~~~vlvaT-----d~~~-~GiD-~~v~~Vi  100 (138)
T d1jr6a_          36 GRHLIFCHSKKKCDELAAKLVAL----GINAVAYYRGLDVSVI---PTNGDVVVVAT-----DALM-TGFT-GDFDSVI  100 (138)
T ss_dssp             SCEEEECSCHHHHHHHHHHHHHH----TCEEEEECTTCCSCCC---TTSSCEEEEES-----SSSC-SSSC-CCBSEEE
T ss_pred             CCEEEEeCcHHHHHHHHHHHhcc----ccchhhhhccchhhhh---hhhhcceeehh-----HHHH-hccc-cccceEE
Confidence            47999999999999999988876    7889899988765433   34678999999     3333 3454 4566664

>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=87.86  E-value=0.11  Score=38.74  Aligned_cols=18  Identities=17%  Similarity=0.233  Sum_probs=15.3

Q ss_pred             ccEEEECCCCCCchhHhH
Q 015158           77 LDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~   94 (412)
                      +++++.|++|+|||.++-
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            468899999999998763

>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=87.71  E-value=0.097  Score=42.17  Aligned_cols=17  Identities=29%  Similarity=0.403  Sum_probs=14.9

Q ss_pred             ccEEEECCCCCCchhHh
Q 015158           77 LDVIQQAQSGTGKTATF   93 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~   93 (412)
                      +.+++.||+|+|||..+
T Consensus        41 ~~vLL~GppGtGKT~la   57 (246)
T d1d2na_          41 VSVLLEGPPHSGKTALA   57 (246)
T ss_dssp             EEEEEECSTTSSHHHHH
T ss_pred             eEEEEECcCCCCHHHHH
Confidence            46899999999999775

>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=87.54  E-value=0.12  Score=38.75  Aligned_cols=19  Identities=21%  Similarity=0.247  Sum_probs=15.6

Q ss_pred             cCccEEEECCCCCCchhHh
Q 015158           75 KGLDVIQQAQSGTGKTATF   93 (412)
Q Consensus        75 ~~~~~lv~~~tGsGKT~~~   93 (412)
                      +.+-+++.|++|||||..+
T Consensus         2 ~~kiI~l~G~~GsGKsTva   20 (178)
T d1qhxa_           2 TTRMIILNGGSSAGKSGIV   20 (178)
T ss_dssp             CCCEEEEECCTTSSHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHH
Confidence            3456788999999999776

>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=87.48  E-value=0.16  Score=39.75  Aligned_cols=26  Identities=19%  Similarity=-0.013  Sum_probs=20.7

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhh
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQL  101 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~  101 (412)
                      |+-+++.+|+|+|||..++..+.+..
T Consensus        23 G~v~~i~G~~GsGKT~l~l~la~~~~   48 (242)
T d1n0wa_          23 GSITEMFGEFRTGKTQICHTLAVTCQ   48 (242)
T ss_dssp             TSEEEEECCTTSSHHHHHHHHHHHTT
T ss_pred             CEEEEEEeCCCCCHHHHHHHHHHHHH
Confidence            56789999999999987766666554

>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=87.38  E-value=2.3  Score=34.06  Aligned_cols=33  Identities=6%  Similarity=0.045  Sum_probs=25.5

Q ss_pred             EEEeChHHHHHHHHcCCCCCCCceEEEEeCCch
Q 015158          160 VVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADE  192 (412)
Q Consensus       160 iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~  192 (412)
                      |.-|||+.+...++......+.|..|-++|-..
T Consensus       151 IgatT~eey~~~~e~d~al~rrF~~I~V~Eps~  183 (268)
T d1r6bx2         151 IGSTTYQEFSNIFEKDRALARRFQKIDITEPSI  183 (268)
T ss_dssp             EEEECHHHHHCCCCCTTSSGGGEEEEECCCCCH
T ss_pred             EEeCCHHHHHHHHhhcHHHHhhhcccccCCCCH
Confidence            445778888777766666678899999999984

>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=87.27  E-value=0.16  Score=38.77  Aligned_cols=20  Identities=20%  Similarity=0.335  Sum_probs=16.5

Q ss_pred             CccEEEECCCCCCchhHhHH
Q 015158           76 GLDVIQQAQSGTGKTATFCS   95 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~   95 (412)
                      |-++++.||+|||||+.+-.
T Consensus         3 ~~riil~G~pGSGKsT~a~~   22 (190)
T d1ak2a1           3 GVRAVLLGPPGAGKGTQAPK   22 (190)
T ss_dssp             CCEEEEECCTTSSHHHHHHH
T ss_pred             ccEEEEECCCCCCHHHHHHH
Confidence            45688899999999988743

>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=87.07  E-value=0.88  Score=33.75  Aligned_cols=74  Identities=9%  Similarity=0.122  Sum_probs=52.9

Q ss_pred             eeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHH----hcCCCcEEEeChHHHHHHHHcCCCCCCCce
Q 015158          108 CQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRI----LSSGVHVVVGTPGRVFDMLRRQSLRPDNIR  183 (412)
Q Consensus       108 ~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~iii~T~~~l~~~~~~~~~~~~~~~  183 (412)
                      .++||.|+++.-++.+.+.+.+.    +..+..++|+.+.......    ..+...++|+|     ..+ ..++++..++
T Consensus        28 ~k~iIF~~~~~~~~~l~~~L~~~----~~~~~~ihg~~~~~~r~~~l~~F~~g~~~iLv~T-----~~~-~~Gid~~~~~   97 (168)
T d1t5ia_          28 NQVVIFVKSVQRCIALAQLLVEQ----NFPAIAIHRGMPQEERLSRYQQFKDFQRRILVAT-----NLF-GRGMDIERVN   97 (168)
T ss_dssp             SSEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEES-----SCC-STTCCGGGCS
T ss_pred             CeEEEEEeeeecchhhhhhhccc----cccccccccccchhhhhhhhhhhccccceeeecc-----ccc-cchhhcccch
Confidence            47999999999888888777765    7788899998876554332    34678899999     222 3456666777


Q ss_pred             EEEEeCCc
Q 015158          184 IFVLDEAD  191 (412)
Q Consensus       184 ~iiiDE~h  191 (412)
                      +||.=+.-
T Consensus        98 ~vi~~~~p  105 (168)
T d1t5ia_          98 IAFNYDMP  105 (168)
T ss_dssp             EEEESSCC
T ss_pred             hhhhhhcc
Confidence            77665543

>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=86.78  E-value=0.16  Score=40.86  Aligned_cols=53  Identities=8%  Similarity=-0.026  Sum_probs=29.3

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCChHH-HHhhhhh-----hhcCccEEEECCCCCCchhHhH
Q 015158           40 TFDAMGLQENLLRGIYAYGFEKPSAI-QQRGIVP-----FCKGLDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        40 ~f~~~~l~~~~~~~l~~~~~~~l~~~-Q~~a~~~-----~~~~~~~lv~~~tGsGKT~~~~   94 (412)
                      +|+++...+...+.|..+  -.-+.. ....+..     ....+.+++.||+|+|||.++-
T Consensus        12 ~~~dlig~~~~~~~L~~~--l~~~~~~~~~~~~~~~~~~~~~~~~lll~GPpG~GKTt~a~   70 (253)
T d1sxja2          12 NLQQVCGNKGSVMKLKNW--LANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAH   70 (253)
T ss_dssp             SGGGCCSCHHHHHHHHHH--HHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHH
T ss_pred             CHHHhcCCHHHHHHHHHH--HHhhhhcchhhhhhhcccCCCCCceEEEECCCCCCHHHHHH
Confidence            577777777777666531  000111 1111111     1112578999999999997763

>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=86.54  E-value=0.17  Score=38.28  Aligned_cols=17  Identities=18%  Similarity=0.296  Sum_probs=14.8

Q ss_pred             cEEEECCCCCCchhHhH
Q 015158           78 DVIQQAQSGTGKTATFC   94 (412)
Q Consensus        78 ~~lv~~~tGsGKT~~~~   94 (412)
                      ++++.||+|||||+.+-
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            47899999999998774

>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=86.37  E-value=1.2  Score=32.36  Aligned_cols=72  Identities=15%  Similarity=0.327  Sum_probs=51.4

Q ss_pred             ceeEEEEcCCHHHHHHHHHHHHHhhcccCcEEEEEEcCcchHHHHHH----hcCCCcEEEeChHHHHHHHHcCCCCCCCc
Q 015158          107 ECQALVLAPTRELAQQIEKVMRALGDYLGVKVHACVGGTSVREDQRI----LSSGVHVVVGTPGRVFDMLRRQSLRPDNI  182 (412)
Q Consensus       107 ~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~iii~T~~~l~~~~~~~~~~~~~~  182 (412)
                      ..++||.|+++.-++++.+.+...    +..+..++++.+.......    ..++..++|+|.-     + ..++++..+
T Consensus        28 ~~k~IIF~~s~~~~~~l~~~L~~~----g~~~~~~~~~~~~~~r~~~~~~f~~~~~~ilv~T~~-----~-~~Gid~~~v   97 (155)
T d1hv8a2          28 EFYGLVFCKTKRDTKELASMLRDI----GFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDV-----M-SRGIDVNDL   97 (155)
T ss_dssp             TCCEEEECSSHHHHHHHHHHHHHT----TCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECTT-----H-HHHCCCSCC
T ss_pred             CCCEEEEECchHHHHHHHhhhccc----ccccccccccchhhhhhhhhhhhhcccceeeeehhH-----H-hhhhhhccC
Confidence            347999999999998888888775    7788889988765544322    3467789999932     2 124566778


Q ss_pred             eEEEEe
Q 015158          183 RIFVLD  188 (412)
Q Consensus       183 ~~iiiD  188 (412)
                      ++||.=
T Consensus        98 ~~Vi~~  103 (155)
T d1hv8a2          98 NCVINY  103 (155)
T ss_dssp             SEEEES
T ss_pred             cEEEEe
Confidence            888743

>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=85.95  E-value=0.21  Score=39.44  Aligned_cols=39  Identities=18%  Similarity=0.106  Sum_probs=25.6

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCC
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPT  116 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~  116 (412)
                      |.-+++.+++|+|||..++-.+......+  ...++++..-
T Consensus        26 G~~~~I~G~~G~GKT~la~~~~~~~~~~~--~~~~~~~s~e   64 (242)
T d1tf7a1          26 GRSTLVSGTSGTGKTLFSIQFLYNGIIEF--DEPGVFVTFE   64 (242)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHHHHHH--CCCEEEEESS
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHHhc--CCCccccccc
Confidence            56789999999999977655444333221  1357777653

>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=85.90  E-value=0.15  Score=38.69  Aligned_cols=18  Identities=22%  Similarity=0.329  Sum_probs=15.3

Q ss_pred             cEEEECCCCCCchhHhHH
Q 015158           78 DVIQQAQSGTGKTATFCS   95 (412)
Q Consensus        78 ~~lv~~~tGsGKT~~~~~   95 (412)
                      ++++.||+|||||+.+-.
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            578999999999987744

>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=85.76  E-value=0.16  Score=37.93  Aligned_cols=18  Identities=28%  Similarity=0.270  Sum_probs=14.8

Q ss_pred             ccEEEECCCCCCchhHhH
Q 015158           77 LDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~   94 (412)
                      +-+++.|++|||||..+-
T Consensus         7 ~iivl~G~~GsGKsT~a~   24 (171)
T d1knqa_           7 HIYVLMGVSGSGKSAVAS   24 (171)
T ss_dssp             EEEEEECSTTSCHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHH
Confidence            446789999999998764

>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=85.68  E-value=0.21  Score=37.32  Aligned_cols=19  Identities=16%  Similarity=0.097  Sum_probs=15.7

Q ss_pred             ccEEEECCCCCCchhHhHH
Q 015158           77 LDVIQQAQSGTGKTATFCS   95 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~~   95 (412)
                      +.+++.|++|+|||+++-.
T Consensus         3 ~~Iil~G~~GsGKSTia~~   21 (170)
T d1e6ca_           3 EPIFMVGARGCGMTTVGRE   21 (170)
T ss_dssp             CCEEEESCTTSSHHHHHHH
T ss_pred             CCEEEECCCCCCHHHHHHH
Confidence            4678899999999987743

>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=85.60  E-value=0.2  Score=37.94  Aligned_cols=18  Identities=17%  Similarity=0.296  Sum_probs=15.0

Q ss_pred             cEEEECCCCCCchhHhHH
Q 015158           78 DVIQQAQSGTGKTATFCS   95 (412)
Q Consensus        78 ~~lv~~~tGsGKT~~~~~   95 (412)
                      .+++.||+|||||+.+-.
T Consensus         2 ~I~i~G~pGSGKsT~a~~   19 (182)
T d1s3ga1           2 NIVLMGLPGAGKGTQADR   19 (182)
T ss_dssp             EEEEECSTTSSHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            478899999999987743

>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=85.46  E-value=0.24  Score=39.63  Aligned_cols=51  Identities=10%  Similarity=-0.079  Sum_probs=32.0

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhccC---CCceeEEEEcCCHHHHHHHHHH
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDYG---LVECQALVLAPTRELAQQIEKV  126 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~~---~~~~~~lil~P~~~L~~q~~~~  126 (412)
                      |+-++|.+++|+|||..++..+.+....+   .....++++.........+...
T Consensus        37 G~~~~i~G~~GsGKT~lalq~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   90 (258)
T d1v5wa_          37 MAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPDRLRD   90 (258)
T ss_dssp             SEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHhhhhcccccceEEEechHHHHHHHHHHH
Confidence            56789999999999988776666554332   2233566666554444334333

>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=84.59  E-value=0.25  Score=37.89  Aligned_cols=22  Identities=18%  Similarity=0.176  Sum_probs=17.7

Q ss_pred             hhcCccEEEECCCCCCchhHhH
Q 015158           73 FCKGLDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        73 ~~~~~~~lv~~~tGsGKT~~~~   94 (412)
                      +.+.+-+++.||+|||||+.+-
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            3456678899999999998764

>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=84.56  E-value=0.2  Score=37.83  Aligned_cols=18  Identities=22%  Similarity=0.226  Sum_probs=14.8

Q ss_pred             ccEEEECCCCCCchhHhH
Q 015158           77 LDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~   94 (412)
                      +-+++.|++|||||+..-
T Consensus         2 kiI~i~G~~GsGKsT~~~   19 (190)
T d1khta_           2 KVVVVTGVPGVGSTTSSQ   19 (190)
T ss_dssp             CEEEEECCTTSCHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHH
Confidence            457889999999997653

>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=84.53  E-value=0.22  Score=39.91  Aligned_cols=26  Identities=15%  Similarity=-0.050  Sum_probs=21.0

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhh
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQL  101 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~  101 (412)
                      |+-++|.+|+|+|||..++..+.+..
T Consensus        36 G~~~li~G~pGsGKT~~~lq~~~~~~   61 (254)
T d1pzna2          36 QAITEVFGEFGSGKTQLAHTLAVMVQ   61 (254)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHHHTT
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHHHhh
Confidence            56789999999999988776666554

>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=84.43  E-value=0.32  Score=39.33  Aligned_cols=45  Identities=18%  Similarity=0.077  Sum_probs=32.4

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHH
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQI  123 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~  123 (412)
                      |+-+.+.+|+|+|||..++..+......+   ..++|+---.+...++
T Consensus        54 g~itei~G~~gsGKTtl~l~~~~~~q~~g---~~~vyidtE~~~~~~~   98 (263)
T d1u94a1          54 GRIVEIYGPESSGKTTLTLQVIAAAQREG---KTCAFIDAEHALDPIY   98 (263)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHHHHHHTT---CCEEEEESSCCCCHHH
T ss_pred             ceEEEEecCCCcHHHHHHHHHHHHHHcCC---CEEEEEccccccCHHH
Confidence            46788999999999988877777766543   4677776655544433

>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=84.42  E-value=0.21  Score=37.65  Aligned_cols=17  Identities=18%  Similarity=0.124  Sum_probs=14.6

Q ss_pred             cEEEECCCCCCchhHhH
Q 015158           78 DVIQQAQSGTGKTATFC   94 (412)
Q Consensus        78 ~~lv~~~tGsGKT~~~~   94 (412)
                      ++++.||+|||||+.+-
T Consensus         2 ~I~i~G~pGSGKsT~~~   18 (179)
T d1e4va1           2 RIILLGAPVAGKGTQAQ   18 (179)
T ss_dssp             EEEEEESTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            47889999999998873

>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=84.40  E-value=0.22  Score=38.02  Aligned_cols=18  Identities=22%  Similarity=0.314  Sum_probs=15.2

Q ss_pred             ccEEEECCCCCCchhHhH
Q 015158           77 LDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~   94 (412)
                      -.+++.||+|||||+.+-
T Consensus         4 m~I~i~GppGsGKsT~a~   21 (189)
T d1zaka1           4 LKVMISGAPASGKGTQCE   21 (189)
T ss_dssp             CCEEEEESTTSSHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHH
Confidence            358899999999998774

>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=84.23  E-value=1.2  Score=34.21  Aligned_cols=113  Identities=6%  Similarity=0.119  Sum_probs=68.7

Q ss_pred             CcEEEEEcchhHHHHHHHHHhcC-----CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCC-----C-cCCCCCCCC
Q 015158          279 TQSVIFVNTRRKVDWLTDKMRSR-----DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTDL-----L-ARGIDVQQV  347 (412)
Q Consensus       279 ~k~lif~~~~~~~~~~~~~L~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~~-----~-~~G~d~~~~  347 (412)
                      ..++|.+++++.+..+.+.++..     ........|+.+.......   +.....+++|+|+-     + ...+++.++
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            56899999999999888888653     2356777777765543332   33456789999981     1 246788899


Q ss_pred             CEEEEccCC--CChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHH
Q 015158          348 SLVINYDLP--TQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQ  394 (412)
Q Consensus       348 ~~vi~~~~~--~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~  394 (412)
                      ++++..+..  .+...|.+.+-+..+.-....-+++++..-.+.+..+.
T Consensus       147 ~~lVlDEaD~ll~~~~~~~~i~~I~~~~~~~~Q~il~SAT~~~~v~~l~  195 (207)
T d1t6na_         147 KHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVC  195 (207)
T ss_dssp             CEEEEESHHHHHSSHHHHHHHHHHHHTSCSSSEEEEEESCCCTTTHHHH
T ss_pred             ceeehhhhhhhhhcCCcHHHHHHHHHhCCCCCEEEEEeeeCCHHHHHHH
Confidence            998865432  12223444444444443334456666665333333333

>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=84.01  E-value=0.24  Score=39.50  Aligned_cols=28  Identities=14%  Similarity=0.070  Sum_probs=22.5

Q ss_pred             cCccEEEECCCCCCchhHhHHHHHHhhc
Q 015158           75 KGLDVIQQAQSGTGKTATFCSGILQQLD  102 (412)
Q Consensus        75 ~~~~~lv~~~tGsGKT~~~~~~~~~~~~  102 (412)
                      .|.-++|.+++|+|||..++..+++...
T Consensus        33 ~G~l~~i~G~~G~GKT~~~l~~a~~~~~   60 (258)
T d2i1qa2          33 SQSVTEFAGVFGSGKTQIMHQSCVNLQN   60 (258)
T ss_dssp             TTEEEEEEESTTSSHHHHHHHHHHHTTC
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHh
Confidence            3567899999999999888777776653

>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=83.88  E-value=2.2  Score=32.63  Aligned_cols=116  Identities=13%  Similarity=0.069  Sum_probs=67.5

Q ss_pred             CCCcEEEEEcchhHHHHHHHHHhcC-----CCeeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcC------CCcCCCCCC
Q 015158          277 AITQSVIFVNTRRKVDWLTDKMRSR-----DHTVSATHGDMDQNTRDIIMREFRSGSSRVLITTD------LLARGIDVQ  345 (412)
Q Consensus       277 ~~~k~lif~~~~~~~~~~~~~L~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~t~------~~~~G~d~~  345 (412)
                      ....++|.+++++.+..+.+.+...     +..+....|+.........+    ....+++|+|+      .-...+++.
T Consensus        70 ~~~~~lil~pt~el~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l----~~~~~ivv~TPgrl~~~~~~~~~~~~  145 (206)
T d1veca_          70 DNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRL----DDTVHVVIATPGRILDLIKKGVAKVD  145 (206)
T ss_dssp             CSCCEEEECSCHHHHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHHT----TSCCSEEEECHHHHHHHHHTTCSCCT
T ss_pred             cCcceEEEeecchhhHHHHHHHHHHhhcccCcccccccCCccHHHHHHHH----HhccCeEEeCCccccccccchhcccc
Confidence            4457999999999999888877542     45666777776655543333    34678999997      223456777


Q ss_pred             CCCEEEEccCC--CChhhHHHhhhhcccCCCCceEEEEeccCcHHHHHHHHHHh
Q 015158          346 QVSLVINYDLP--TQPENYLHRIGRSGRFGRKGVAINFVTRDDERMLFDIQKFY  397 (412)
Q Consensus       346 ~~~~vi~~~~~--~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~  397 (412)
                      +++++|+.+..  .+ ..|.+.+-+..+.=+...-+++++..-.+.+..+.+.+
T Consensus       146 ~l~~lVlDEaD~ll~-~~f~~~i~~I~~~~~~~~Q~~l~SAT~~~~v~~l~~~~  198 (206)
T d1veca_         146 HVQMIVLDEADKLLS-QDFVQIMEDIILTLPKNRQILLYSATFPLSVQKFMNSH  198 (206)
T ss_dssp             TCCEEEEETHHHHTS-TTTHHHHHHHHHHSCTTCEEEEEESCCCHHHHHHHHHH
T ss_pred             ccceEEEeccccccc-cchHHHHHHHHHhCCCCCEEEEEEecCCHHHHHHHHHH
Confidence            89988864421  11 11222222222221223455666766545445554443

>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=83.59  E-value=0.28  Score=36.77  Aligned_cols=23  Identities=30%  Similarity=0.560  Sum_probs=16.7

Q ss_pred             cEEEECCCCCCchhHhHHHHHHhh
Q 015158           78 DVIQQAQSGTGKTATFCSGILQQL  101 (412)
Q Consensus        78 ~~lv~~~tGsGKT~~~~~~~~~~~  101 (412)
                      ++++.||+|+|||+.+ ..++..+
T Consensus         2 ki~I~G~~G~GKSTLl-~~i~~~l   24 (178)
T d1ye8a1           2 KIIITGEPGVGKTTLV-KKIVERL   24 (178)
T ss_dssp             EEEEECCTTSSHHHHH-HHHHHHH
T ss_pred             EEEEECCCCcHHHHHH-HHHHhcC
Confidence            4789999999999753 3444444

>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=83.59  E-value=0.17  Score=42.70  Aligned_cols=19  Identities=26%  Similarity=0.267  Sum_probs=16.2

Q ss_pred             cCccEEEECCCCCCchhHh
Q 015158           75 KGLDVIQQAQSGTGKTATF   93 (412)
Q Consensus        75 ~~~~~lv~~~tGsGKT~~~   93 (412)
                      .+.++++.|++|+|||+.+
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            4568999999999999765

>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=83.57  E-value=0.28  Score=37.47  Aligned_cols=19  Identities=21%  Similarity=0.270  Sum_probs=15.8

Q ss_pred             ccEEEECCCCCCchhHhHH
Q 015158           77 LDVIQQAQSGTGKTATFCS   95 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~~   95 (412)
                      -++++.||+|||||+.+-.
T Consensus         7 mrIiliG~PGSGKtT~a~~   25 (189)
T d2ak3a1           7 LRAAIMGAPGSGKGTVSSR   25 (189)
T ss_dssp             CEEEEECCTTSSHHHHHHH
T ss_pred             eeEEEECCCCCCHHHHHHH
Confidence            4688999999999988743

>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=83.34  E-value=0.12  Score=39.57  Aligned_cols=19  Identities=37%  Similarity=0.398  Sum_probs=15.3

Q ss_pred             CccEEEECCCCCCchhHhH
Q 015158           76 GLDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~   94 (412)
                      |..+++.|++|||||+.+-
T Consensus        19 g~vI~L~G~pGSGKTTiAk   37 (195)
T d1x6va3          19 GCTVWLTGLSGAGKTTVSM   37 (195)
T ss_dssp             CEEEEEESSCHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHH
Confidence            4466788999999998764

>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=83.24  E-value=0.23  Score=37.29  Aligned_cols=17  Identities=24%  Similarity=0.302  Sum_probs=13.9

Q ss_pred             ccEEEECCCCCCchhHh
Q 015158           77 LDVIQQAQSGTGKTATF   93 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~   93 (412)
                      .-++++|++|||||+.+
T Consensus        15 ~liil~G~pGsGKST~a   31 (172)
T d1yj5a2          15 EVVVAVGFPGAGKSTFI   31 (172)
T ss_dssp             CEEEEECCTTSSHHHHH
T ss_pred             EEEEEECCCCCCHHHHH
Confidence            35688999999999754

>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=82.87  E-value=0.31  Score=36.78  Aligned_cols=18  Identities=17%  Similarity=0.254  Sum_probs=15.0

Q ss_pred             cEEEECCCCCCchhHhHH
Q 015158           78 DVIQQAQSGTGKTATFCS   95 (412)
Q Consensus        78 ~~lv~~~tGsGKT~~~~~   95 (412)
                      .+++.||+|||||+.+-.
T Consensus         4 rIvl~G~pGSGKtT~a~~   21 (180)
T d1akya1           4 RMVLIGPPGAGKGTQAPN   21 (180)
T ss_dssp             EEEEECCTTSSHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            578899999999987743

>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=82.82  E-value=3.5  Score=35.02  Aligned_cols=36  Identities=8%  Similarity=0.100  Sum_probs=26.2

Q ss_pred             CCCc-EEEeChHHHHHHHHcCCCCCCCceEEEEeCCch
Q 015158          156 SGVH-VVVGTPGRVFDMLRRQSLRPDNIRIFVLDEADE  192 (412)
Q Consensus       156 ~~~~-iii~T~~~l~~~~~~~~~~~~~~~~iiiDE~h~  192 (412)
                      +... |-.||++.+.. +.+.....+.|..|-++|-+.
T Consensus       150 g~~~~I~~tT~~ey~~-~e~d~al~rrF~~v~v~ep~~  186 (387)
T d1qvra2         150 GELRLIGATTLDEYRE-IEKDPALERRFQPVYVDEPTV  186 (387)
T ss_dssp             TCCCEEEEECHHHHHH-HTTCTTTCSCCCCEEECCCCH
T ss_pred             CCcceeeecCHHHHHH-hcccHHHHHhcccccCCCCcH
Confidence            3344 44677777754 677666678899999999985

>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=82.72  E-value=0.27  Score=37.57  Aligned_cols=18  Identities=22%  Similarity=0.231  Sum_probs=14.9

Q ss_pred             ccEEEECCCCCCchhHhH
Q 015158           77 LDVIQQAQSGTGKTATFC   94 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~   94 (412)
                      .-+++.||+|||||+.+-
T Consensus         7 ~iI~i~G~pGSGKsT~a~   24 (194)
T d1qf9a_           7 NVVFVLGGPGSGKGTQCA   24 (194)
T ss_dssp             EEEEEEESTTSSHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHH
Confidence            357889999999998764

>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=82.66  E-value=0.31  Score=37.18  Aligned_cols=17  Identities=24%  Similarity=0.286  Sum_probs=14.5

Q ss_pred             cEEEECCCCCCchhHhH
Q 015158           78 DVIQQAQSGTGKTATFC   94 (412)
Q Consensus        78 ~~lv~~~tGsGKT~~~~   94 (412)
                      .+++.||+|||||+.+-
T Consensus         3 iI~i~GppGSGKsT~a~   19 (194)
T d1teva_           3 VVFVLGGPGAGKGTQCA   19 (194)
T ss_dssp             EEEEECCTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            36889999999998874

>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=82.52  E-value=0.32  Score=37.22  Aligned_cols=18  Identities=17%  Similarity=0.202  Sum_probs=14.7

Q ss_pred             cEEEECCCCCCchhHhHH
Q 015158           78 DVIQQAQSGTGKTATFCS   95 (412)
Q Consensus        78 ~~lv~~~tGsGKT~~~~~   95 (412)
                      -+++.||+|||||+.+-.
T Consensus        10 iI~i~GppGSGKsT~a~~   27 (196)
T d1ukza_          10 VIFVLGGPGAGKGTQCEK   27 (196)
T ss_dssp             EEEEECSTTSSHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            467899999999987643

>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=81.84  E-value=0.5  Score=36.71  Aligned_cols=34  Identities=15%  Similarity=0.154  Sum_probs=21.3

Q ss_pred             ccEEEECC-CCCCchhHhHHHHHHhhccCCCceeEEEE
Q 015158           77 LDVIQQAQ-SGTGKTATFCSGILQQLDYGLVECQALVL  113 (412)
Q Consensus        77 ~~~lv~~~-tGsGKT~~~~~~~~~~~~~~~~~~~~lil  113 (412)
                      ++.+|.+- ||.|||.+.+..+......+   .+++++
T Consensus         2 ~~~~i~gt~~GVGKTtvs~~La~aLa~~G---~rVl~i   36 (224)
T d1byia_           2 KRYFVTGTDTEVGKTVASCALLQAAKAAG---YRTAGY   36 (224)
T ss_dssp             EEEEEEESSTTSCHHHHHHHHHHHHHHTT---CCEEEE
T ss_pred             ceEEEEECCCCccHHHHHHHHHHHHHHCC---CeEEEE
Confidence            45667666 79999987754444333333   467775

>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=81.72  E-value=0.35  Score=36.82  Aligned_cols=15  Identities=27%  Similarity=0.082  Sum_probs=12.4

Q ss_pred             EEECCCCCCchhHhH
Q 015158           80 IQQAQSGTGKTATFC   94 (412)
Q Consensus        80 lv~~~tGsGKT~~~~   94 (412)
                      -|.|++|||||+.+-
T Consensus        26 gI~G~~GSGKSTla~   40 (198)
T d1rz3a_          26 GIDGLSRSGKTTLAN   40 (198)
T ss_dssp             EEEECTTSSHHHHHH
T ss_pred             EEECCCCCCHHHHHH
Confidence            379999999997653

>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=81.54  E-value=0.66  Score=34.11  Aligned_cols=16  Identities=44%  Similarity=0.418  Sum_probs=13.2

Q ss_pred             EEEECCCCCCchhHhH
Q 015158           79 VIQQAQSGTGKTATFC   94 (412)
Q Consensus        79 ~lv~~~tGsGKT~~~~   94 (412)
                      +.+.|+.|||||+..-
T Consensus         5 i~itG~~GSGKTTL~~   20 (170)
T d1np6a_           5 LAFAAWSGTGKTTLLK   20 (170)
T ss_dssp             EEEECCTTSCHHHHHH
T ss_pred             EEEEcCCCCCHHHHHH
Confidence            5789999999997653

>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=81.22  E-value=0.54  Score=39.94  Aligned_cols=23  Identities=17%  Similarity=0.167  Sum_probs=17.2

Q ss_pred             ccEEEECCCCCCchhHhHHHHHHh
Q 015158           77 LDVIQQAQSGTGKTATFCSGILQQ  100 (412)
Q Consensus        77 ~~~lv~~~tGsGKT~~~~~~~~~~  100 (412)
                      +.+++.||+|+|||..+. +++..
T Consensus       155 ~~~~~~g~~~~gk~~~~~-~~~~~  177 (362)
T d1svma_         155 RYWLFKGPIDSGKTTLAA-ALLEL  177 (362)
T ss_dssp             CEEEEECSTTSSHHHHHH-HHHHH
T ss_pred             CeEEEECCCCCCHHHHHH-HHHHH
Confidence            578999999999997653 34433

>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=81.12  E-value=0.41  Score=35.44  Aligned_cols=18  Identities=17%  Similarity=0.219  Sum_probs=14.7

Q ss_pred             cEEEECCCCCCchhHhHH
Q 015158           78 DVIQQAQSGTGKTATFCS   95 (412)
Q Consensus        78 ~~lv~~~tGsGKT~~~~~   95 (412)
                      ++++.|++|+|||+++-.
T Consensus         3 ~IvliG~~G~GKSTig~~   20 (165)
T d2iyva1           3 KAVLVGLPGSGKSTIGRR   20 (165)
T ss_dssp             SEEEECSTTSSHHHHHHH
T ss_pred             cEEEECCCCCCHHHHHHH
Confidence            477889999999987643

>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=80.76  E-value=2.1  Score=33.90  Aligned_cols=23  Identities=26%  Similarity=0.346  Sum_probs=18.1

Q ss_pred             hhhhcCccEEEECCCCCCchhHh
Q 015158           71 VPFCKGLDVIQQAQSGTGKTATF   93 (412)
Q Consensus        71 ~~~~~~~~~lv~~~tGsGKT~~~   93 (412)
                      .....+..++|.|++|+|||.++
T Consensus        18 ~~a~~~~pvlI~Ge~GtGK~~~A   40 (247)
T d1ny5a2          18 KISCAECPVLITGESGVGKEVVA   40 (247)
T ss_dssp             HHTTCCSCEEEECSTTSSHHHHH
T ss_pred             HHhCCCCCEEEECCCCcCHHHHH
Confidence            33445678999999999999765

>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=80.69  E-value=0.77  Score=37.06  Aligned_cols=47  Identities=17%  Similarity=0.165  Sum_probs=33.5

Q ss_pred             CccEEEECCCCCCchhHhHHHHHHhhccCCCceeEEEEcCCHHHHHHHHH
Q 015158           76 GLDVIQQAQSGTGKTATFCSGILQQLDYGLVECQALVLAPTRELAQQIEK  125 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~  125 (412)
                      |+-+.+.+|.|+|||..++..+......+   ..++|+-.-..+..++++
T Consensus        60 g~i~e~~G~~~~GKT~l~l~~~~~~q~~g---~~~vyIDtE~~~~~e~a~  106 (269)
T d1mo6a1          60 GRVIEIYGPESSGKTTVALHAVANAQAAG---GVAAFIDAEHALDPDYAK  106 (269)
T ss_dssp             SSEEEEECSSSSSHHHHHHHHHHHHHHTT---CEEEEEESSCCCCHHHHH
T ss_pred             ceeEEEecCCCcHHHHHHHHHHHHHhcCC---CEEEEEECCccCCHHHHH
Confidence            66788999999999988877766655443   477887765555444443

>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=80.65  E-value=0.36  Score=36.45  Aligned_cols=18  Identities=28%  Similarity=0.401  Sum_probs=15.2

Q ss_pred             CccEEEECCCCCCchhHh
Q 015158           76 GLDVIQQAQSGTGKTATF   93 (412)
Q Consensus        76 ~~~~lv~~~tGsGKT~~~   93 (412)
                      |+-+++.||.|+|||...
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            566789999999999764

>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=80.53  E-value=0.25  Score=40.22  Aligned_cols=15  Identities=27%  Similarity=0.202  Sum_probs=12.5

Q ss_pred             EEEECCCCCCchhHh
Q 015158           79 VIQQAQSGTGKTATF   93 (412)
Q Consensus        79 ~lv~~~tGsGKT~~~   93 (412)
                      +++.||+|+|||.++
T Consensus        49 l~l~GppGtGKT~l~   63 (287)
T d1w5sa2          49 YGSIGRVGIGKTTLA   63 (287)
T ss_dssp             EECTTCCSSSHHHHH
T ss_pred             EEeECCCCCCHHHHH
Confidence            456799999999776

>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=80.23  E-value=0.64  Score=37.57  Aligned_cols=62  Identities=18%  Similarity=0.104  Sum_probs=36.2

Q ss_pred             hhhhhhcCccEEEECCCCCCchhHhHHHHHHhhcc-------CCCceeEEEEcCCHHHHHHHHHHHHHhh
Q 015158           69 GIVPFCKGLDVIQQAQSGTGKTATFCSGILQQLDY-------GLVECQALVLAPTRELAQQIEKVMRALG  131 (412)
Q Consensus        69 a~~~~~~~~~~lv~~~tGsGKT~~~~~~~~~~~~~-------~~~~~~~lil~P~~~L~~q~~~~~~~~~  131 (412)
                      +++-+..|.-+++.|++|+|||..++..++.....       .....+++|+.--. -..++.+++..+.
T Consensus        22 li~G~~pg~~~~i~G~~G~GKS~l~l~la~~ia~g~~~~~~~~~~~~~vl~~~~E~-~~~~~~~Rl~~~~   90 (274)
T d1nlfa_          22 VLPNMVAGTVGALVSPGGAGKSMLALQLAAQIAGGPDLLEVGELPTGPVIYLPAED-PPTAIHHRLHALG   90 (274)
T ss_dssp             EETTEETTSEEEEEESTTSSHHHHHHHHHHHHHTCCCTTCCCCCCCCCEEEEESSS-CHHHHHHHHHHHH
T ss_pred             HhCCccCCcEEEEEeCCCCCHHHHHHHHHHHHHcCCCcccccccCCCceEEEeccc-hHHHHHHHHHHHh
Confidence            34445567788999999999997765544432211       11234577766432 2444555555543